Repository: Sage-Bionetworks/schematic (language: python)

Issue:
Fix: remove caching poetry dependencies in CI workfows
## Problem
Relates to: https://sagebionetworks.jira.com/browse/FDS-2439
For some reasons, virtual environment was not created successfully in this step: 
```
      - name: Install Poetry
        run: |
          curl -sSL https://install.python-poetry.org \
            | python3 - --version ${{ env.POETRY_VERSION }};
          poetry config virtualenvs.create true;
          poetry config virtualenvs.in-project true;
```
That caused poetry to show the following error: 
```
The virtual environment found in /home/runner/work/schematic/schematic/.venv seems to be broken.
Recreating virtualenv schematicpy in /home/runner/work/schematic/schematic/.venv
```

I can confirm that the virtual env didn't get created successfully because when I did `poetry env info`, `Path` variable is showing as empty, and `poetry env info --path` didn't work when I ran that on GH remotely. 

Since installing dependencies doesn't take that much time anyway, @BWMac, @jaymedina and I decided to remove the capacity of caching dependencies for now. 

More context can be found [here](https://sagebionetworks.slack.com/archives/C07HLTBS5D2/p1726703103242389)

## Solution 
Remove caching when installing dependencies. 

Note: in the future, if there's a need to utilize cached dependencies, the documentation here: https://python-poetry.org/docs/configuration/#virtualenvsin-project and also looking at these two commit: https://github.com/Sage-Bionetworks/schematic/pull/1507/commits/8339da7edc694f4fe75755e799ee1cbe61f119d2 and https://github.com/Sage-Bionetworks/schematic/pull/1507/commits/7fee9164fe7eaa9cc4fef2cced9677f93b26b17c will be helpful. 



Discussion / hints:

Fix patch:
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
new file mode 100644
index 000000000..482d91a8b
--- /dev/null
+++ b/.github/CODEOWNERS
@@ -0,0 +1,2 @@
+# Global owners of whole repo
+* @andrewelamb @GiaJordan @linglp
\ No newline at end of file
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 58f903f76..12b355dc0 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -17,16 +17,16 @@ jobs:
     steps:
       -
         name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: schematicbot
           password: ${{ secrets.DOCKER_HUB_TOKEN }}
@@ -36,7 +36,7 @@ jobs:
         run: echo "::set-output name=sha_short::$(git rev-parse --short HEAD)"
       -
         name: Build and push (tagged release)
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         if: ${{ github.event_name == 'push' }}
         with:
           platforms: linux/amd64,linux/arm64
@@ -48,7 +48,7 @@ jobs:
             ${{ env.DOCKER_ORG }}/${{ env.DOCKER_REPO }}:commit-${{ steps.vars.outputs.sha_short }}
       -
         name: Build and push (manual release)
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         if: ${{ github.event_name == 'workflow_dispatch' }}
         with:
           platforms: linux/amd64,linux/arm64
diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
index 50596b7db..f1beb3489 100644
--- a/.github/workflows/docker_build.yml
+++ b/.github/workflows/docker_build.yml
@@ -23,13 +23,13 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
           
       - name: Set env variable for version tag
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
 
       - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
@@ -37,7 +37,7 @@ jobs:
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.IMAGE_PATH }}
           tags: |
@@ -46,7 +46,7 @@ jobs:
             type=semver,pattern={{raw}}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v6
         with:
           file: schematic_api/Dockerfile
           push: true
diff --git a/.github/workflows/pdoc.yml b/.github/workflows/pdoc.yml
index 187b5adb1..818bd3a61 100644
--- a/.github/workflows/pdoc.yml
+++ b/.github/workflows/pdoc.yml
@@ -28,21 +28,19 @@ jobs:
     runs-on: ubuntu-latest
     env:
       POETRY_VERSION:  1.3.0
-    strategy:
-      matrix:
-        python-version: ["3.9", "3.10"]
+      PYTHON_VERSION: "3.10"
 
     steps:
       #----------------------------------------------
       #       check-out repo and set-up python     
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+      - name: Set up Python ${{ env.PYTHON_VERSION }}
+        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ env.PYTHON_VERSION }}
       
       #----------------------------------------------
       #          install & configure poetry         
@@ -54,31 +52,21 @@ jobs:
           poetry config virtualenvs.create true; 
           poetry config virtualenvs.in-project true; 
 
-      #----------------------------------------------
-      #       load cached venv if cache exists      
-      #----------------------------------------------
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v3
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-
       #----------------------------------------------
       # install dependencies and root project
       #----------------------------------------------
       - name: Install dependencies and root project
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: poetry install --no-interaction --all-extras
 
       # create documentation
-      - run: poetry add pdoc@13.0.0
+      - run: poetry add pdoc@14.6.0
       - run: poetry show pdoc
-      - run: poetry run pdoc --docformat google -o docs/schematic schematic/manifest schematic/models schematic/schemas schematic/store schematic/utils schematic/visualization
+      - run: poetry run pdoc --docformat google --mermaid -o docs/schematic schematic/manifest schematic/models schematic/schemas schematic/store schematic/utils schematic/visualization
 
-      - uses: actions/upload-pages-artifact@v1
+      - uses: actions/upload-pages-artifact@v3
         with:
           path: docs/schematic
+          name: github-pages
 
   # Deploy the artifact to GitHub pages.
   # This is a separate job so that only actions/deploy-pages has the necessary permissions.
@@ -93,4 +81,4 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     steps:
       - id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index eb2ebafcb..5b85c995f 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -16,10 +16,10 @@ jobs:
       #       check-out repo and set-up python     
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -33,21 +33,10 @@ jobs:
           poetry config virtualenvs.create true;
           poetry config virtualenvs.in-project true;
 
-      #----------------------------------------------
-      #       load cached venv if cache exists      
-      #----------------------------------------------
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-
       #----------------------------------------------
       # install dependencies and root project
       #----------------------------------------------
       - name: Install dependencies and root project
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: poetry install --no-interaction --all-extras
         
       #----------------------------------------------
diff --git a/.github/workflows/scan_repo.yml b/.github/workflows/scan_repo.yml
new file mode 100644
index 000000000..56c7ac35a
--- /dev/null
+++ b/.github/workflows/scan_repo.yml
@@ -0,0 +1,35 @@
+# Modified from mono repo: https://github.com/Sage-Bionetworks/sage-monorepo/blob/main/.github/workflows/scan-repo.yml
+# Also, reference: https://github.com/aquasecurity/trivy-action?tab=readme-ov-file#using-trivy-to-scan-your-git-repo
+name: Scan Git repo
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+  workflow_dispatch: 
+
+jobs:
+  trivy:
+    name: Trivy
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Run Trivy vulnerability scanner in repo mode
+        uses: aquasecurity/trivy-action@master
+        with:
+          # the scan targets the file system.
+          scan-type: 'fs'
+          # it will ignore vulnerabilities without a fix.
+          ignore-unfixed: true
+          format: 'sarif'
+          output: 'trivy-results.sarif'
+          severity: 'CRITICAL,HIGH,MEDIUM,LOW'
+          limit-severities-for-sarif: true
+
+      - name: Upload Trivy scan results to GitHub Security tab
+        uses: github/codeql-action/upload-sarif@v3
+        with:
+          sarif_file: 'trivy-results.sarif'
+          category: Git Repository
diff --git a/.gitignore b/.gitignore
index fa0de2078..6d00e45d3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -146,7 +146,7 @@ dmypy.json
 # End of https://www.toptal.com/developers/gitignore/api/python
 
 # Synapse configuration file
-.synapseConfig
+.synapseConfig*
 
 # Google services authorization credentials file
 credentials.json
diff --git a/README.md b/README.md
index 3d0bf04ca..cf1cd96f6 100644
--- a/README.md
+++ b/README.md
@@ -2,17 +2,28 @@
 [![Build Status](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2FSage-Bionetworks%2Fschematic%2Fbadge%3Fref%3Ddevelop&style=flat)](https://actions-badge.atrox.dev/Sage-Bionetworks/schematic/goto?ref=develop) [![Documentation Status](https://readthedocs.org/projects/sage-schematic/badge/?version=develop)](https://sage-schematic.readthedocs.io/en/develop/?badge=develop) [![PyPI version](https://badge.fury.io/py/schematicpy.svg)](https://badge.fury.io/py/schematicpy)
 
 # Table of contents
+- [Schematic](#schematic)
+- [Table of contents](#table-of-contents)
 - [Introduction](#introduction)
 - [Installation](#installation)
   - [Installation Requirements](#installation-requirements)
-  - [Installation guide for data curator app](#installation-guide-for-data-curator-app)
+  - [Installation guide for Schematic CLI users](#installation-guide-for-schematic-cli-users)
   - [Installation guide for developers/contributors](#installation-guide-for-developerscontributors)
+    - [Development environment setup](#development-environment-setup)
+    - [Development process instruction](#development-process-instruction)
+    - [Example For REST API ](#example-for-rest-api-)
+      - [Use file path of `config.yml` to run API endpoints:](#use-file-path-of-configyml-to-run-api-endpoints)
+      - [Use content of `config.yml` and `schematic_service_account_creds.json`as an environment variable to run API endpoints:](#use-content-of-configyml-and-schematic_service_account_credsjsonas-an-environment-variable-to-run-api-endpoints)
+    - [Example For Schematic on mac/linux ](#example-for-schematic-on-maclinux-)
+    - [Example For Schematic on Windows ](#example-for-schematic-on-windows-)
 - [Other Contribution Guidelines](#other-contribution-guidelines)
-    - [Update readthedocs documentation](#update-readthedocs-documentation)
+  - [Updating readthedocs documentation](#updating-readthedocs-documentation)
+  - [Update toml file and lock file](#update-toml-file-and-lock-file)
+  - [Reporting bugs or feature requests](#reporting-bugs-or-feature-requests)
 - [Command Line Usage](#command-line-usage)
 - [Testing](#testing)
   - [Updating Synapse test resources](#updating-synapse-test-resources)
-- [Code Style](#code-style)
+- [Code style](#code-style)
 - [Contributors](#contributors)
 
 # Introduction
@@ -25,19 +36,32 @@ SCHEMATIC is an acronym for _Schema Engine for Manifest Ingress and Curation_. T
 
 Note: Our credential policy for Google credentials in order to create Google sheet files from Schematic, see tutorial ['HERE'](https://scribehow.com/shared/Get_Credentials_for_Google_Drive_and_Google_Sheets_APIs_to_use_with_schematicpy__yqfcJz_rQVeyTcg0KQCINA). If you plan to use `config.yml`, please ensure that the path of `schematic_service_account_creds.json` is indicated there (see `google_sheets > service_account_creds` section)
 
+## Installation guide for Schematic CLI users
+1. **Verifying Python Version Compatibility**
 
-## Installation guide for data curator app
+To ensure compatibility with Schematic, please follow these steps:
 
-Create and activate a virtual environment within which you can install the package:
+Check your own Python version:
+```
+python3 --version
+```
+
+Check the Supported Python Version: Open the pyproject.toml file in the Schematic repository to find the version of Python that is supported. You can view this file directly on GitHub [here](https://github.com/Sage-Bionetworks/schematic/blob/main/pyproject.toml#L39).
+
+Switching Python Versions: If your current Python version is not supported by Schematic, you can switch to the supported version using tools like [pyenv](https://github.com/pyenv/pyenv?tab=readme-ov-file#switch-between-python-versions). Follow the instructions in the pyenv documentation to install and switch between Python versions easily.
 
+2. **Setting Up the Virtual Environment**
+
+After switching to the version of Python supported by Schematic, please activate a virtual environment within which you can install the package:
 ```
 python3 -m venv .venv
 source .venv/bin/activate
 ```
+Note: Python 3 has built-in support for virtual environments with the venv module, so you no longer need to install virtualenv.
 
-Note: Python 3 has a built-in support for virtual environment [venv](https://docs.python.org/3/library/venv.html#module-venv) so you no longer need to install virtualenv.
+3. **Installing Schematic**
 
-Install and update the package using [pip](https://pip.pypa.io/en/stable/quickstart/):
+Install the package using [pip](https://pip.pypa.io/en/stable/quickstart/):
 
 ```
 python3 -m pip install schematicpy
@@ -68,33 +92,24 @@ poetry shell
 ```
 4. Install the dependencies by doing: 
 ```
-poetry install
+poetry install --all-extras
 ```
 This command will install the dependencies based on what we specify in poetry.lock. If this step is taking a long time, try to go back to step 2 and check your version of poetry. Alternatively, you could also try deleting the lock file and regenerate it by doing `poetry install` (Please note this method should be used as a last resort because this would force other developers to change their development environment)
 
-If you want to install the API you will need to install those dependencies as well:
-
-```
-poetry install --extras "api"
-```
-
-If you want to install the uwsgi:
-
-```
-poetry install --extras "api"
-```
 
 5. Fill in credential files: 
 *Note*: If you won't interact with Synapse, please ignore this section.
 
 There are two main configuration files that need to be edited:
-config.yml
-and [synapseConfig](https://raw.githubusercontent.com/Sage-Bionetworks/synapsePythonClient/v2.3.0-rc/synapseclient/.synapseConfig)
+- config.yml
+- [synapseConfig](https://raw.githubusercontent.com/Sage-Bionetworks/synapsePythonClient/master/synapseclient/.synapseConfig)
 
 <strong>Configure .synapseConfig File</strong>
 
-Download a copy of the ``.synapseConfig`` file, open the file in the
-editor of your choice and edit the `username` and `authtoken` attribute under the `authentication` section 
+Download a copy of the ``.synapseConfig`` file, open the file in the editor of your 
+choice and edit the `username` and `authtoken` attribute under the `authentication` 
+section. **Note:** You must place the file at the root of the project like
+`{project_root}/.synapseConfig` in order for any authenticated tests to work.
 
 *Note*: You could also visit [configparser](https://docs.python.org/3/library/configparser.html#module-configparser>) doc to see the format that `.synapseConfig` must have. For instance:
 >[authentication]<br> username = ABC <br> authtoken = abc
@@ -219,19 +234,6 @@ For new features, bugs, enhancements
 
 *Note*: Make sure you have the latest version of the `develop` branch on your local machine.
 
-## Installation Guide - Docker 
-
-1. Install docker from https://www.docker.com/ . <br>
-2.  Identify docker image of interest from [Schematic DockerHub](https://hub.docker.com/r/sagebionetworks/schematic/tags) <br>
-    Ex `docker pull sagebionetworks/schematic:latest` from the CLI or, run `docker compose up` after cloning the schematic github repo <br>
-    in this case, `sagebionetworks/schematic:latest` is the name of the image chosen
-3. Run Schematic Command with `docker run <flags> <schematic command and args>`. <br>
-<t> - For more information on flags for `docker run` and what they do, visit the [Docker Documentation](https://docs.docker.com/engine/reference/commandline/run/) <br>
-<t> - These example commands assume that you have navigated to the directory you want to run schematic from. To specify your working directory, use `$(pwd)` on MacOS/Linux or `%cd%` on Windows.  <br>
-<t> - If not using the latest image, then the full name should be specified: ie `sagebionetworks/schematic:commit-e611e4a` <br>
-<t> - If using local image created by `docker compose up`, then the docker image name should be changed: i.e. `schematic_schematic` <br>
-<t> - Using the `--name` flag sets the name of the container running locally on your machine <br>
-
 ### Example For REST API <br>
 
 #### Use file path of `config.yml` to run API endpoints: 
@@ -311,7 +313,31 @@ You can **create bug and feature requests** through [Sage Bionetwork's FAIR Data
 - **Provide screenshots of the expected or actual behaviour** where applicable.
 
 # Command Line Usage
-Please visit more documentation [here](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html)
+1. Generate a new manifest as a google sheet
+
+```
+schematic manifest -c /path/to/config.yml get -dt <your data type> -s
+```
+
+2. Grab an existing manifest from synapse 
+
+```
+schematic manifest -c /path/to/config.yml get -dt <your data type> -d <your synapse dataset folder id> -s
+```
+
+3. Validate a manifest
+
+```
+schematic model -c /path/to/config.yml validate -dt <your data type> -mp <your csv manifest path>
+```
+
+4. Submit a manifest as a file
+
+```
+schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse dataset folder id> -vc <your data type> -mrt file_only
+```
+
+Please visit more documentation [here](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html) for more information. 
 
 
 
diff --git a/env.example b/env.example
index afeeda77b..176c22c28 100644
--- a/env.example
+++ b/env.example
@@ -3,4 +3,11 @@ SERVER_PROTOCOL=http://
 SERVER_DOMAIN=localhost
 # port on the host machine
 USE_LISTEN_PORT=81
-SERVICE_ACCOUNT_CREDS='Provide service account creds'
\ No newline at end of file
+SERVICE_ACCOUNT_CREDS='Provide service account creds'
+
+# Integration testing variables (Optional)
+# TRACING_EXPORT_FORMAT=otlp
+# LOGGING_EXPORT_FORMAT=otlp
+# TRACING_SERVICE_NAME=unique-name-testing
+# LOGGING_SERVICE_NAME=unique-name-testing
+# LOGGING_INSTANCE_NAME=unique-name-testing
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 798291b39..b6b193d77 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -35,13 +35,13 @@ dev = ["black", "docutils", "flake8", "ipython", "m2r", "mistune (<2.0.0)", "pyt
 
 [[package]]
 name = "anyio"
-version = "4.3.0"
+version = "4.4.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"},
-    {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"},
+    {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"},
+    {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"},
 ]
 
 [package.dependencies]
@@ -190,6 +190,19 @@ files = [
 [package.dependencies]
 typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
+[[package]]
+name = "asyncio"
+version = "3.4.3"
+description = "reference implementation of PEP 3156"
+optional = false
+python-versions = "*"
+files = [
+    {file = "asyncio-3.4.3-cp33-none-win32.whl", hash = "sha256:b62c9157d36187eca799c378e572c969f0da87cd5fc42ca372d92cdb06e7e1de"},
+    {file = "asyncio-3.4.3-cp33-none-win_amd64.whl", hash = "sha256:c46a87b48213d7464f22d9a497b9eef8c1928b68320a2fa94240f969f6fec08c"},
+    {file = "asyncio-3.4.3-py3-none-any.whl", hash = "sha256:c4d18b22701821de07bd6aea8b53d21449ec0ec5680645e5317062ea21817d2d"},
+    {file = "asyncio-3.4.3.tar.gz", hash = "sha256:83360ff8bc97980e4ff25c964c7bd3923d333d177aa4f7fb736b019f26c7cb41"},
+]
+
 [[package]]
 name = "asyncio-atexit"
 version = "1.0.1"
@@ -206,32 +219,32 @@ test = ["pytest", "uvloop"]
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
+    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
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 [[package]]
@@ -924,13 +972,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -952,13 +1000,13 @@ testing = ["hatch", "pre-commit", "pytest", "tox"]
 
 [[package]]
 name = "executing"
-version = "2.0.1"
+version = "2.1.0"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -966,13 +1014,13 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastjsonschema"
-version = "2.19.1"
+version = "2.20.0"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.extras]
@@ -980,18 +1028,18 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
-version = "3.14.0"
+version = "3.15.4"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
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 typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
@@ -1078,20 +1126,20 @@ files = [
 
 [[package]]
 name = "google-api-core"
-version = "2.19.0"
+version = "2.19.2"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
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 googleapis-common-protos = ">=1.56.2,<2.0.dev0"
 proto-plus = ">=1.22.3,<2.0.0dev"
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 requests = ">=2.18.0,<3.0.0.dev0"
 
 [package.extras]
@@ -1119,13 +1167,13 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.29.0"
+version = "2.34.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1135,7 +1183,7 @@ rsa = ">=3.1.4,<5"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0.dev0)", "requests (>=2.20.0,<3.0.0.dev0)"]
-enterprise-cert = ["cryptography (==36.0.2)", "pyopenssl (==22.0.0)"]
+enterprise-cert = ["cryptography", "pyopenssl"]
 pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
 requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
@@ -1175,17 +1223,17 @@ tool = ["click (>=6.0.0)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.63.0"
+version = "1.65.0"
 description = "Common protobufs used in Google APIs"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
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+protobuf = ">=3.20.2,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<6.0.0.dev0"
 
 [package.extras]
 grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"]
@@ -1351,6 +1399,64 @@ files = [
 docs = ["Sphinx", "furo"]
 test = ["objgraph", "psutil"]
 
+[[package]]
+name = "grpcio"
+version = "1.66.1"
+description = "HTTP/2-based RPC framework"
+optional = true
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.extras]
+protobuf = ["grpcio-tools (>=1.66.1)"]
+
 [[package]]
 name = "h11"
 version = "0.14.0"
@@ -1399,13 +1505,13 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0
 
 [[package]]
 name = "httpx"
-version = "0.27.0"
+version = "0.27.2"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.27.0-py3-none-any.whl", hash = "sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5"},
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 ]
 
 [package.dependencies]
@@ -1420,16 +1526,17 @@ brotli = ["brotli", "brotlicffi"]
 cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "identify"
-version = "2.5.36"
+version = "2.6.0"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.36-py2.py3-none-any.whl", hash = "sha256:37d93f380f4de590500d9dba7db359d0d3da95ffe7f9de1753faa159e71e7dfa"},
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 ]
 
 [package.extras]
@@ -1437,13 +1544,13 @@ license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.8"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -1525,13 +1632,13 @@ tests = ["coverage[toml]", "pytest", "pytest-cov", "pytest-mock"]
 
 [[package]]
 name = "ipykernel"
-version = "6.29.4"
+version = "6.29.5"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1595,21 +1702,21 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.2"
+version = "8.1.5"
 description = "Jupyter interactive widgets"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 comm = ">=0.1.3"
 ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0.10,<3.1.0"
+jupyterlab-widgets = ">=3.0.12,<3.1.0"
 traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.10,<4.1.0"
+widgetsnbextension = ">=4.0.12,<4.1.0"
 
 [package.extras]
 test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
@@ -1749,24 +1856,24 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpointer"
-version = "2.4"
+version = "3.0.0"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+python-versions = ">=3.7"
 files = [
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-    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
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+    {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"},
 ]
 
 [[package]]
 name = "jsonschema"
-version = "4.22.0"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.22.0-py3-none-any.whl", hash = "sha256:ff4cfd6b1367a40e7bc6411caec72effadd3db0bbe5017de188f2d6108335802"},
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+    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [package.dependencies]
@@ -1781,11 +1888,11 @@ rfc3339-validator = {version = "*", optional = true, markers = "extra == \"forma
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rpds-py = ">=0.7.1"
 uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
+webcolors = {version = ">=24.6.0", optional = true, markers = "extra == \"format-nongpl\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
-format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
@@ -1803,13 +1910,13 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter-client"
-version = "8.6.1"
+version = "8.6.2"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-8.6.1-py3-none-any.whl", hash = "sha256:3b7bd22f058434e3b9a7ea4b1500ed47de2713872288c0d511d19926f99b459f"},
-    {file = "jupyter_client-8.6.1.tar.gz", hash = "sha256:e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f"},
+    {file = "jupyter_client-8.6.2-py3-none-any.whl", hash = "sha256:50cbc5c66fd1b8f65ecb66bc490ab73217993632809b6e505687de18e9dea39f"},
+    {file = "jupyter_client-8.6.2.tar.gz", hash = "sha256:2bda14d55ee5ba58552a8c53ae43d215ad9868853489213f37da060ced54d8df"},
 ]
 
 [package.dependencies]
@@ -1822,7 +1929,7 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-core"
@@ -1886,13 +1993,13 @@ jupyter-server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-server"
-version = "2.14.0"
+version = "2.14.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_server-2.14.0-py3-none-any.whl", hash = "sha256:fb6be52c713e80e004fac34b35a0990d6d36ba06fd0a2b2ed82b899143a64210"},
-    {file = "jupyter_server-2.14.0.tar.gz", hash = "sha256:659154cea512083434fd7c93b7fe0897af7a2fd0b9dd4749282b42eaac4ae677"},
+    {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"},
+    {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"},
 ]
 
 [package.dependencies]
@@ -1917,7 +2024,7 @@ traitlets = ">=5.6.0"
 websocket-client = ">=1.7"
 
 [package.extras]
-docs = ["ipykernel", "jinja2", "jupyter-client", "jupyter-server", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi (>=0.8.0)", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
+docs = ["ipykernel", "jinja2", "jupyter-client", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi (>=0.8.0)", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
 test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0,<9)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.7)", "pytest-timeout", "requests"]
 
 [[package]]
@@ -1941,13 +2048,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.1.8"
+version = "4.2.5"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1962,16 +2069,17 @@ jupyter-server = ">=2.4.0,<3"
 jupyterlab-server = ">=2.27.1,<3"
 notebook-shim = ">=0.2"
 packaging = "*"
+setuptools = ">=40.1.0"
 tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""}
 tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.2.0)"]
+dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.3.5)"]
 docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<7.3.0)", "sphinx-copybutton"]
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-upgrade-extension = ["copier (>=8.0,<9.0)", "jinja2-time (<0.3)", "pydantic (<2.0)", "pyyaml-include (<2.0)", "tomli-w (<2.0)"]
+upgrade-extension = ["copier (>=9,<10)", "jinja2-time (<0.3)", "pydantic (<3.0)", "pyyaml-include (<3.0)", "tomli-w (<2.0)"]
 
 [[package]]
 name = "jupyterlab-pygments"
@@ -1986,13 +2094,13 @@ files = [
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.27.1"
+version = "2.27.3"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -2012,13 +2120,13 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.10"
+version = "3.0.13"
 description = "Jupyter interactive widgets for JupyterLab"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
@@ -2069,13 +2177,13 @@ files = [
 
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+version = "1.15.4"
 description = "Small library to dynamically create python functions."
 optional = false
 python-versions = "*"
 files = [
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 [[package]]
@@ -2149,13 +2257,13 @@ files = [
 
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+version = "3.22.0"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
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 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -2163,7 +2271,7 @@ packaging = ">=17.0"
 
 [package.extras]
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 tests = ["pytest", "pytz", "simplejson"]
 
 [[package]]
@@ -2204,44 +2312,44 @@ files = [
 
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 mypy-extensions = ">=1.0.0"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
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+typing-extensions = ">=4.6.0"
 
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
@@ -2372,40 +2480,37 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "nodeenv"
-version = "1.8.0"
+version = "1.9.1"
 description = "Node.js virtual environment builder"
 optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
-    {file = "nodeenv-1.8.0-py2.py3-none-any.whl", hash = "sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec"},
-    {file = "nodeenv-1.8.0.tar.gz", hash = "sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2"},
+    {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"},
+    {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"},
 ]
 
-[package.dependencies]
-setuptools = "*"
-
 [[package]]
 name = "notebook"
-version = "7.1.3"
+version = "7.2.2"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "notebook-7.1.3-py3-none-any.whl", hash = "sha256:919b911e59f41f6e3857ce93c9d93535ba66bb090059712770e5968c07e1004d"},
-    {file = "notebook-7.1.3.tar.gz", hash = "sha256:41fcebff44cf7bb9377180808bcbae066629b55d8c7722f1ebbe75ca44f9cfc1"},
+    {file = "notebook-7.2.2-py3-none-any.whl", hash = "sha256:c89264081f671bc02eec0ed470a627ed791b9156cad9285226b31611d3e9fe1c"},
+    {file = "notebook-7.2.2.tar.gz", hash = "sha256:2ef07d4220421623ad3fe88118d687bc0450055570cdd160814a59cf3a1c516e"},
 ]
 
 [package.dependencies]
 jupyter-server = ">=2.4.0,<3"
-jupyterlab = ">=4.1.1,<4.2"
-jupyterlab-server = ">=2.22.1,<3"
+jupyterlab = ">=4.2.0,<4.3"
+jupyterlab-server = ">=2.27.1,<3"
 notebook-shim = ">=0.2,<0.3"
 tornado = ">=6.2.0"
 
 [package.extras]
 dev = ["hatch", "pre-commit"]
 docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.22.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
+test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
 
 [[package]]
 name = "notebook-shim"
@@ -2505,13 +2610,13 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"]
 
 [[package]]
 name = "openpyxl"
-version = "3.1.2"
+version = "3.1.5"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "openpyxl-3.1.2-py2.py3-none-any.whl", hash = "sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5"},
-    {file = "openpyxl-3.1.2.tar.gz", hash = "sha256:a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184"},
+    {file = "openpyxl-3.1.5-py2.py3-none-any.whl", hash = "sha256:5282c12b107bffeef825f4617dc029afaf41d0ea60823bbb665ef3079dc79de2"},
+    {file = "openpyxl-3.1.5.tar.gz", hash = "sha256:cf0e3cf56142039133628b5acffe8ef0c12bc902d2aadd3e0fe5878dc08d1050"},
 ]
 
 [package.dependencies]
@@ -2547,6 +2652,30 @@ files = [
 backoff = {version = ">=1.10.0,<3.0.0", markers = "python_version >= \"3.7\""}
 opentelemetry-proto = "1.21.0"
 
+[[package]]
+name = "opentelemetry-exporter-otlp-proto-grpc"
+version = "1.21.0"
+description = "OpenTelemetry Collector Protobuf over gRPC Exporter"
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "opentelemetry_exporter_otlp_proto_grpc-1.21.0-py3-none-any.whl", hash = "sha256:ab37c63d6cb58d6506f76d71d07018eb1f561d83e642a8f5aa53dddf306087a4"},
+    {file = "opentelemetry_exporter_otlp_proto_grpc-1.21.0.tar.gz", hash = "sha256:a497c5611245a2d17d9aa1e1cbb7ab567843d53231dcc844a62cea9f0924ffa7"},
+]
+
+[package.dependencies]
+backoff = {version = ">=1.10.0,<3.0.0", markers = "python_version >= \"3.7\""}
+deprecated = ">=1.2.6"
+googleapis-common-protos = ">=1.52,<2.0"
+grpcio = ">=1.0.0,<2.0.0"
+opentelemetry-api = ">=1.15,<2.0"
+opentelemetry-exporter-otlp-proto-common = "1.21.0"
+opentelemetry-proto = "1.21.0"
+opentelemetry-sdk = ">=1.21.0,<1.22.0"
+
+[package.extras]
+test = ["pytest-grpc"]
+
 [[package]]
 name = "opentelemetry-exporter-otlp-proto-http"
 version = "1.21.0"
@@ -2638,13 +2767,13 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "24.0"
+version = "24.1"
 description = "Core utilities for Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5"},
-    {file = "packaging-24.0.tar.gz", hash = "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"},
+    {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"},
+    {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
 ]
 
 [[package]]
@@ -2774,13 +2903,13 @@ files = [
 
 [[package]]
 name = "pdoc"
-version = "12.3.1"
+version = "14.6.0"
 description = "API Documentation for Python Projects"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pdoc-12.3.1-py3-none-any.whl", hash = "sha256:c3f24f31286e634de9c76fa6e67bd5c0c5e74360b41dc91e6b82499831eb52d8"},
-    {file = "pdoc-12.3.1.tar.gz", hash = "sha256:453236f225feddb8a9071428f1982a78d74b9b3da4bc4433aedb64dbd0cc87ab"},
+    {file = "pdoc-14.6.0-py3-none-any.whl", hash = "sha256:36c42c546a317d8e3e8c0b39645f24161374de0c7066ccaae76628d721e49ba5"},
+    {file = "pdoc-14.6.0.tar.gz", hash = "sha256:6e98a24c5e0ca5d188397969cf82581836eaef13f172fc3820047bfe15c61c9a"},
 ]
 
 [package.dependencies]
@@ -2789,7 +2918,7 @@ MarkupSafe = "*"
 pygments = ">=2.12.0"
 
 [package.extras]
-dev = ["black", "hypothesis", "mypy", "pytest", "pytest-cov", "pytest-timeout", "ruff", "tox", "types-pygments"]
+dev = ["hypothesis", "mypy", "pdoc-pyo3-sample-library (==1.0.11)", "pygments (>=2.14.0)", "pytest", "pytest-cov", "pytest-timeout", "ruff", "tox", "types-pygments"]
 
 [[package]]
 name = "pexpect"
@@ -2807,13 +2936,13 @@ ptyprocess = ">=0.5"
 
 [[package]]
 name = "platformdirs"
-version = "4.2.1"
+version = "4.2.2"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "platformdirs-4.2.1-py3-none-any.whl", hash = "sha256:17d5a1161b3fd67b390023cb2d3b026bbd40abde6fdb052dfbd3a29c3ba22ee1"},
-    {file = "platformdirs-4.2.1.tar.gz", hash = "sha256:031cd18d4ec63ec53e82dceaac0417d218a6863f7745dfcc9efe7793b7039bdf"},
+    {file = "platformdirs-4.2.2-py3-none-any.whl", hash = "sha256:2d7a1657e36a80ea911db832a8a6ece5ee53d8de21edd5cc5879af6530b1bfee"},
+    {file = "platformdirs-4.2.2.tar.gz", hash = "sha256:38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3"},
 ]
 
 [package.extras]
@@ -2838,13 +2967,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
-version = "3.7.0"
+version = "3.8.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "pre_commit-3.7.0-py2.py3-none-any.whl", hash = "sha256:5eae9e10c2b5ac51577c3452ec0a490455c45a0533f7960f993a0d01e59decab"},
-    {file = "pre_commit-3.7.0.tar.gz", hash = "sha256:e209d61b8acdcf742404408531f0c37d49d2c734fd7cff2d6076083d191cb060"},
+    {file = "pre_commit-3.8.0-py2.py3-none-any.whl", hash = "sha256:9a90a53bf82fdd8778d58085faf8d83df56e40dfe18f45b19446e26bf1b3a63f"},
+    {file = "pre_commit-3.8.0.tar.gz", hash = "sha256:8bb6494d4a20423842e198980c9ecf9f96607a07ea29549e180eef9ae80fe7af"},
 ]
 
 [package.dependencies]
@@ -2870,13 +2999,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.43"
+version = "3.0.47"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "prompt_toolkit-3.0.43-py3-none-any.whl", hash = "sha256:a11a29cb3bf0a28a387fe5122cdb649816a957cd9261dcedf8c9f1fef33eacf6"},
-    {file = "prompt_toolkit-3.0.43.tar.gz", hash = "sha256:3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d"},
+    {file = "prompt_toolkit-3.0.47-py3-none-any.whl", hash = "sha256:0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10"},
+    {file = "prompt_toolkit-3.0.47.tar.gz", hash = "sha256:1e1b29cb58080b1e69f207c893a1a7bf16d127a5c30c9d17a25a5d77792e5360"},
 ]
 
 [package.dependencies]
@@ -2884,39 +3013,39 @@ wcwidth = "*"
 
 [[package]]
 name = "proto-plus"
-version = "1.23.0"
+version = "1.24.0"
 description = "Beautiful, Pythonic protocol buffers."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "proto-plus-1.23.0.tar.gz", hash = "sha256:89075171ef11988b3fa157f5dbd8b9cf09d65fffee97e29ce403cd8defba19d2"},
-    {file = "proto_plus-1.23.0-py3-none-any.whl", hash = "sha256:a829c79e619e1cf632de091013a4173deed13a55f326ef84f05af6f50ff4c82c"},
+    {file = "proto-plus-1.24.0.tar.gz", hash = "sha256:30b72a5ecafe4406b0d339db35b56c4059064e69227b8c3bda7462397f966445"},
+    {file = "proto_plus-1.24.0-py3-none-any.whl", hash = "sha256:402576830425e5f6ce4c2a6702400ac79897dab0b4343821aa5188b0fab81a12"},
 ]
 
 [package.dependencies]
-protobuf = ">=3.19.0,<5.0.0dev"
+protobuf = ">=3.19.0,<6.0.0dev"
 
 [package.extras]
-testing = ["google-api-core[grpc] (>=1.31.5)"]
+testing = ["google-api-core (>=1.31.5)"]
 
 [[package]]
 name = "protobuf"
-version = "4.25.3"
+version = "4.25.4"
 description = ""
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "protobuf-4.25.3-cp310-abi3-win32.whl", hash = "sha256:d4198877797a83cbfe9bffa3803602bbe1625dc30d8a097365dbc762e5790faa"},
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-    {file = "protobuf-4.25.3-cp37-abi3-macosx_10_9_universal2.whl", hash = "sha256:f1279ab38ecbfae7e456a108c5c0681e4956d5b1090027c1de0f934dfdb4b35c"},
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+    {file = "protobuf-4.25.4-cp310-abi3-win32.whl", hash = "sha256:db9fd45183e1a67722cafa5c1da3e85c6492a5383f127c86c4c4aa4845867dc4"},
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+    {file = "protobuf-4.25.4-cp37-abi3-manylinux2014_x86_64.whl", hash = "sha256:3319e073562e2515c6ddc643eb92ce20809f5d8f10fead3332f71c63be6a7040"},
+    {file = "protobuf-4.25.4-cp38-cp38-win32.whl", hash = "sha256:7e372cbbda66a63ebca18f8ffaa6948455dfecc4e9c1029312f6c2edcd86c4e1"},
+    {file = "protobuf-4.25.4-cp38-cp38-win_amd64.whl", hash = "sha256:051e97ce9fa6067a4546e75cb14f90cf0232dcb3e3d508c448b8d0e4265b61c1"},
+    {file = "protobuf-4.25.4-cp39-cp39-win32.whl", hash = "sha256:90bf6fd378494eb698805bbbe7afe6c5d12c8e17fca817a646cd6a1818c696ca"},
+    {file = "protobuf-4.25.4-cp39-cp39-win_amd64.whl", hash = "sha256:ac79a48d6b99dfed2729ccccee547b34a1d3d63289c71cef056653a846a2240f"},
+    {file = "protobuf-4.25.4-py3-none-any.whl", hash = "sha256:bfbebc1c8e4793cfd58589acfb8a1026be0003e852b9da7db5a4285bde996978"},
+    {file = "protobuf-4.25.4.tar.gz", hash = "sha256:0dc4a62cc4052a036ee2204d26fe4d835c62827c855c8a03f29fe6da146b380d"},
 ]
 
 [[package]]
@@ -2960,13 +3089,13 @@ files = [
 
 [[package]]
 name = "pure-eval"
-version = "0.2.2"
+version = "0.2.3"
 description = "Safely evaluate AST nodes without side effects"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pure_eval-0.2.2-py3-none-any.whl", hash = "sha256:01eaab343580944bc56080ebe0a674b39ec44a945e6d09ba7db3cb8cec289350"},
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+    {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"},
+    {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"},
 ]
 
 [package.extras]
@@ -3032,47 +3161,54 @@ files = [
 
 [[package]]
 name = "pydantic"
-version = "1.10.15"
+version = "1.10.18"
 description = "Data validation and settings management using python type hints"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -3125,6 +3261,23 @@ google-auth-oauthlib = ">=0.7.1"
 [package.extras]
 pandas = ["pandas (>=0.14.0)"]
 
+[[package]]
+name = "pyjwt"
+version = "2.9.0"
+description = "JSON Web Token implementation in Python"
+optional = false
+python-versions = ">=3.8"
+files = [
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+[package.extras]
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+docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"]
+tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
+
 [[package]]
 name = "pylint"
 version = "2.17.7"
@@ -3171,13 +3324,13 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.2"
+version = "3.1.4"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
 files = [
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 ]
 
 [package.extras]
@@ -3185,13 +3338,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "7.4.4"
+version = "8.3.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -3199,11 +3352,29 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
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 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
-tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
+pluggy = ">=1.5,<2"
+tomli = {version = ">=1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+
+[[package]]
+name = "pytest-asyncio"
+version = "0.24.0"
+description = "Pytest support for asyncio"
+optional = false
+python-versions = ">=3.8"
+files = [
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+
+[package.dependencies]
+pytest = ">=8.2,<9"
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+docs = ["sphinx (>=5.3)", "sphinx-rtd-theme (>=1.0)"]
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 [[package]]
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 [package.dependencies]
@@ -3550,101 +3755,101 @@ rpds-py = ">=0.7.0"
 
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 [package.dependencies]
@@ -4038,38 +4247,38 @@ files = [
 
 [[package]]
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+version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
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 python-versions = ">=3.8"
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 ]
 
 [[package]]
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 python-versions = ">=3.9"
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-packaging = ">=21.0"
-Pygments = ">=2.14"
-requests = ">=2.25.0"
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+packaging = ">=23.0"
+Pygments = ">=2.17"
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+snowballstemmer = ">=2.2"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
 sphinxcontrib-htmlhelp = ">=2.0.0"
@@ -4080,8 +4289,8 @@ tomli = {version = ">=2", markers = "python_version < \"3.11\""}
 
 [package.extras]
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 [[package]]
 name = "sphinx-click"
@@ -4101,49 +4310,49 @@ sphinx = ">=2.0"
 
 [[package]]
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+version = "2.0.0"
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 [package.dependencies]
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-typing-extensions = ">=4.2.0"
+greenlet = {version = "!=0.4.17", markers = "python_version < \"3.13\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
+typing-extensions = ">=4.6.0"
 
 [package.extras]
 aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
@@ -4343,13 +4552,13 @@ Jinja2 = ">=2.0"
 
 [[package]]
 name = "synapseclient"
-version = "4.3.1"
+version = "4.4.1"
 description = "A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -4390,13 +4599,13 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "tenacity"
-version = "8.3.0"
+version = "8.5.0"
 description = "Retry code until it succeeds"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -4498,13 +4707,13 @@ files = [
 
 [[package]]
 name = "tomlkit"
-version = "0.12.5"
+version = "0.13.2"
 description = "Style preserving TOML library"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 ]
 
 [[package]]
@@ -4520,33 +4729,33 @@ files = [
 
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+version = "6.4.1"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
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-python-versions = ">= 3.8"
+python-versions = ">=3.8"
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 [[package]]
 name = "tqdm"
-version = "4.66.4"
+version = "4.66.5"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -4575,24 +4784,24 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.9.0.20240316"
+version = "2.9.0.20240906"
 description = "Typing stubs for python-dateutil"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.5.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.12.2"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -4665,13 +4874,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.18"
+version = "1.26.20"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
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 ]
 
 [package.extras]
@@ -4681,12 +4890,12 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "uwsgi"
-version = "2.0.25.1"
+version = "2.0.26"
 description = "The uWSGI server"
 optional = true
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -4707,13 +4916,13 @@ test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.26.1"
+version = "20.26.3"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"},
-    {file = "virtualenv-20.26.1.tar.gz", hash = "sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b"},
+    {file = "virtualenv-20.26.3-py3-none-any.whl", hash = "sha256:8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589"},
+    {file = "virtualenv-20.26.3.tar.gz", hash = "sha256:4c43a2a236279d9ea36a0d76f98d84bd6ca94ac4e0f4a3b9d46d05e10fea542a"},
 ]
 
 [package.dependencies]
@@ -4738,18 +4947,18 @@ files = [
 
 [[package]]
 name = "webcolors"
-version = "1.13"
+version = "24.8.0"
 description = "A library for working with the color formats defined by HTML and CSS."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"},
-    {file = "webcolors-1.13.tar.gz", hash = "sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a"},
+    {file = "webcolors-24.8.0-py3-none-any.whl", hash = "sha256:fc4c3b59358ada164552084a8ebee637c221e4059267d0f8325b3b560f6c7f0a"},
+    {file = "webcolors-24.8.0.tar.gz", hash = "sha256:08b07af286a01bcd30d583a7acadf629583d1f79bfef27dd2c2c5c263817277d"},
 ]
 
 [package.extras]
 docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
-tests = ["pytest", "pytest-cov"]
+tests = ["coverage[toml]"]
 
 [[package]]
 name = "webencodings"
@@ -4797,13 +5006,13 @@ watchdog = ["watchdog (>=2.3)"]
 
 [[package]]
 name = "widgetsnbextension"
-version = "4.0.10"
+version = "4.0.13"
 description = "Jupyter interactive widgets for Jupyter Notebook"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "widgetsnbextension-4.0.10-py3-none-any.whl", hash = "sha256:d37c3724ec32d8c48400a435ecfa7d3e259995201fbefa37163124a9fcb393cc"},
-    {file = "widgetsnbextension-4.0.10.tar.gz", hash = "sha256:64196c5ff3b9a9183a8e699a4227fb0b7002f252c814098e66c4d1cd0644688f"},
+    {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"},
+    {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"},
 ]
 
 [[package]]
@@ -4887,24 +5096,28 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.20.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"},
+    {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [extras]
-api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "flask-opentracing", "jaeger-client", "pyopenssl"]
+api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "flask-opentracing", "jaeger-client", "opentelemetry-exporter-otlp-proto-grpc", "pyopenssl"]
 aws = ["uWSGI"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9.0,<3.11"
-content-hash = "e327e774115908a3edf6c70ff34869b026e560cf9262470b17ebe06359aac06a"
+content-hash = "f814725d68db731c704f4ebcd169ae71e4031f0d939c3ce789145ddcb5f196eb"
diff --git a/pyproject.toml b/pyproject.toml
index 92cf0d962..f7045473c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,7 +54,7 @@ pygsheets = "^2.0.4"
 PyYAML = "^6.0.0"
 rdflib = "^6.0.0"
 setuptools = "^66.0.0"
-synapseclient = "4.3.1"
+synapseclient = "4.4.1"
 tenacity = "^8.0.1"
 toml = "^0.10.2"
 great-expectations = "^0.15.0"
@@ -62,7 +62,7 @@ sphinx-click = "^4.0.0"
 itsdangerous = "^2.0.0"
 openpyxl = "^3.0.9"
 "backports.zoneinfo" = {markers = "python_version < \"3.9\"", version = "^0.2.1"}
-pdoc = "^12.2.0"
+pdoc = "^14.0.0"
 dateparser = "^1.1.4"
 pandarallel = "^1.6.4"
 schematic-db = {version = "0.0.41", extras = ["synapse"]}
@@ -74,19 +74,23 @@ Flask = {version = "2.1.3", optional = true}
 Flask-Cors = {version = "^3.0.10", optional = true}
 uWSGI = {version = "^2.0.21", optional = true}
 Jinja2 = {version = ">2.11.3", optional = true}
+asyncio = "^3.4.3"
 jaeger-client = {version = "^4.8.0", optional = true}
 flask-opentracing = {version="^2.0.0", optional = true}
+PyJWT = "^2.9.0"
+opentelemetry-exporter-otlp-proto-grpc = {version="^1.0.0", optional = true}
 
 [tool.poetry.extras]
-api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "jaeger-client", "flask-opentracing"]
+api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "jaeger-client", "flask-opentracing", "opentelemetry-exporter-otlp-proto-grpc"]
 aws = ["uWSGI"]
 
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.0.0"
+pytest = "^8.0.0"
 pytest-cov = "^4.0.0"
 pytest-mock = "^3.5.1"
 pytest-rerunfailures = "^12.0"
+pytest-asyncio = "^0.24.0"
 flake8 = "^6.0.0"
 python-dotenv = "^0.21.0"
 black = "^23.7.0" #If the version spec of black is changed here, the version specified in .pre-commit-config.yaml should be updated to match
diff --git a/schematic/help.py b/schematic/help.py
index 7bf8c29a0..65c030ac8 100644
--- a/schematic/help.py
+++ b/schematic/help.py
@@ -3,10 +3,10 @@
 #!/usr/bin/env python3
 
 from typing import get_args
+
 from schematic.utils.schema_utils import DisplayLabelType
 from schematic.visualization.tangled_tree import FigureType, TextType
 
-
 DATA_MODEL_LABELS_DICT = {
     "display_label": "use the display name as a label, if it is valid (contains no blacklisted characters) otherwise will default to class_label.",
     "class_label": "default, use standard class or property label.",
@@ -200,6 +200,9 @@
             "project_scope": (
                 "Specify a comma-separated list of projects to search through for cross manifest validation."
             ),
+            "dataset_scope": (
+                "Specify a dataset to validate against for filename validation."
+            ),
             "data_model_labels": DATA_MODEL_LABELS_HELP,
         },
     }
diff --git a/schematic/manifest/generator.py b/schematic/manifest/generator.py
index d7eb16c30..d954506a5 100644
--- a/schematic/manifest/generator.py
+++ b/schematic/manifest/generator.py
@@ -1,38 +1,38 @@
-from collections import OrderedDict
 import json
 import logging
-import networkx as nx
-from openpyxl.styles import Font, Alignment, PatternFill
-from openpyxl import load_workbook
-from openpyxl.utils.dataframe import dataframe_to_rows
 import os
-import pandas as pd
+from collections import OrderedDict
 from pathlib import Path
-import pygsheets as ps
 from tempfile import NamedTemporaryFile
-from typing import Any, Dict, List, Optional, Tuple, Union, BinaryIO, Literal
+from typing import Any, BinaryIO, Dict, List, Literal, Optional, Tuple, Union
 
+import networkx as nx
+import pandas as pd
+import pygsheets as ps
+from openpyxl import load_workbook
+from openpyxl.styles import Alignment, Font, PatternFill
+from openpyxl.utils.dataframe import dataframe_to_rows
+from opentelemetry import trace
+
+from schematic.configuration.configuration import CONFIG
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
-from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_json_schema import DataModelJSONSchema
+from schematic.schemas.data_model_parser import DataModelParser
 
+# TODO: This module should only be aware of the store interface
+# we shouldn't need to expose Synapse functionality explicitly
+from schematic.store.synapse import SynapseStorage
+from schematic.utils.df_utils import load_df, update_df
 from schematic.utils.google_api_utils import (
-    execute_google_api_requests,
     build_service_account_creds,
+    execute_google_api_requests,
+    export_manifest_drive_service,
+)
+from schematic.utils.schema_utils import (
+    DisplayLabelType,
+    extract_component_validation_rules,
 )
-from schematic.utils.df_utils import update_df, load_df
-from schematic.utils.schema_utils import extract_component_validation_rules
 from schematic.utils.validate_utils import rule_in_rule_list
-from schematic.utils.schema_utils import DisplayLabelType
-
-# TODO: This module should only be aware of the store interface
-# we shouldn't need to expose Synapse functionality explicitly
-from schematic.store.synapse import SynapseStorage
-
-from schematic.configuration.configuration import CONFIG
-from schematic.utils.google_api_utils import export_manifest_drive_service
-
-from opentelemetry import trace
 
 logger = logging.getLogger(__name__)
 tracer = trace.get_tracer("Schematic")
@@ -1543,6 +1543,24 @@ def _handle_output_format_logic(
             a pandas dataframe, file path of an excel spreadsheet, or a google sheet URL
         TODO:
             Depreciate sheet URL and add google_sheet as an output_format choice.
+
+        ```mermaid
+        flowchart TD
+            A[Start] --> B{Output Format is 'dataframe'?}
+            B -- Yes --> C[Return DataFrame]
+            B -- No --> D{Output Format is 'excel'?}
+            D -- Yes --> E[Export to Excel]
+            E --> F[Populate Excel]
+            F --> G[Return Excel Path]
+            D -- No --> H{Sheet URL is set?}
+            H -- Yes --> I[Set DataFrame by URL]
+            I --> J[Return Sheet URL]
+            H -- No --> K[Default Return DataFrame]
+            C --> L[End]
+            G --> L
+            J --> L
+            K --> L
+        ```
         """
 
         # if the output type gets set to "dataframe", return a data frame
@@ -1657,6 +1675,33 @@ def create_manifests(
 
         Returns:
             Union[List[str], List[pd.DataFrame]]: a list of Googlesheet URLs, a list of pandas dataframes or excel file paths
+
+        ```mermaid
+        sequenceDiagram
+            participant User
+            participant Function
+            participant DataModelParser
+            participant DataModelGraph
+            participant ManifestGenerator
+            User->>Function: call create_manifests
+            Function->>Function: check dataset_ids and validate inputs
+            Function->>DataModelParser: parse data model
+            DataModelParser-->>Function: return parsed data model
+            Function->>DataModelGraph: generate graph
+            DataModelGraph-->>Function: return graph data model
+            alt data_types == "all manifests"
+                loop for each component
+                    Function->>ManifestGenerator: create manifest for component
+                    ManifestGenerator-->>Function: single manifest
+                end
+            else
+                loop for each data_type
+                    Function->>ManifestGenerator: create single manifest
+                    ManifestGenerator-->>Function: single manifest
+                end
+            end
+            Function-->>User: return manifests based on output_format
+        ```
         """
         if dataset_ids:
             # Check that the number of submitted data_types matches
@@ -1783,6 +1828,44 @@ def get_manifest(
 
         Returns:
             Googlesheet URL, pandas dataframe, or an Excel spreadsheet
+
+        ```mermaid
+        flowchart TD
+            Start[Start] --> DatasetIDCheck{Dataset ID provided?}
+            DatasetIDCheck -- No --> EmptyManifestURL[Get Empty Manifest URL]
+            EmptyManifestURL --> OutputFormatCheck{Output Format is 'excel'?}
+            OutputFormatCheck -- Yes --> ExportToExcel[Export to Excel]
+            OutputFormatCheck -- No --> ReturnManifestURL[Return Manifest URL]
+            DatasetIDCheck -- Yes --> InstantiateSynapseStorage[Instantiate SynapseStorage]
+            InstantiateSynapseStorage --> UpdateManifestFiles[Update Dataset Manifest Files]
+            UpdateManifestFiles --> GetEmptyManifestURL[Get Empty Manifest URL]
+            GetEmptyManifestURL --> ManifestRecordCheck{Manifest Record exists?}
+            ManifestRecordCheck -- Yes --> UpdateDataframe[Update Dataframe]
+            UpdateDataframe --> HandleOutputFormatLogic[Handle Output Format Logic]
+            HandleOutputFormatLogic --> ReturnResult[Return Result]
+            ManifestRecordCheck -- No --> UseAnnotationsCheck{Use Annotations?}
+
+            UseAnnotationsCheck -- No --> CreateDataframe[Create dataframe from empty manifest on Google]
+            CreateDataframe --> ManifestFileBasedCheck1{Manifest file-based?}
+            ManifestFileBasedCheck1 -- Yes --> AddEntityID[Add entityId and filename to manifest df]
+            ManifestFileBasedCheck1 -- No --> UseDataframe[Use dataframe from an empty manifest]
+
+            AddEntityID --> HandleOutputFormatLogic
+            UseDataframe --> HandleOutputFormatLogic
+
+            UseAnnotationsCheck -- Yes --> ManifestFileBasedCheck2{Manifest file-based?}
+            ManifestFileBasedCheck2 -- No --> HandleOutputFormatLogic
+            ManifestFileBasedCheck2 -- Yes --> ProcessAnnotations[Process Annotations]
+            ProcessAnnotations --> AnnotationsEmptyCheck{Annotations Empty?}
+            AnnotationsEmptyCheck -- Yes --> CreateDataframeFromEmpty[Create dataframe from an empty manifest on Google]
+            CreateDataframeFromEmpty --> UpdateDataframeWithAnnotations[Update dataframe]
+            AnnotationsEmptyCheck -- No --> GetManifestWithAnnotations[Get Manifest with Annotations]
+            GetManifestWithAnnotations --> UpdateDataframeWithAnnotations
+            UpdateDataframeWithAnnotations --> HandleOutputFormatLogic
+            ReturnResult --> End[End]
+            ReturnManifestURL --> End
+            ExportToExcel --> End
+        ```
         """
         # Handle case when no dataset ID is provided
         if not dataset_id:
diff --git a/schematic/models/GE_Helpers.py b/schematic/models/GE_Helpers.py
index d73354f31..9eda117a8 100644
--- a/schematic/models/GE_Helpers.py
+++ b/schematic/models/GE_Helpers.py
@@ -1,21 +1,18 @@
-from statistics import mode
-from tabnanny import check
 import logging
 import os
 import re
-import numpy as np
+from statistics import mode
+from tabnanny import check
 
 # allows specifying explicit variable types
-from typing import Any, Dict, Optional, Text, List
-from urllib.parse import urlparse
-from urllib.request import urlopen, OpenerDirector, HTTPDefaultErrorHandler
-from urllib.request import Request
+from typing import Any, Dict, List, Optional, Text
 from urllib import error
-from attr import attr
-
-from ruamel import yaml
+from urllib.parse import urlparse
+from urllib.request import HTTPDefaultErrorHandler, OpenerDirector, Request, urlopen
 
-import great_expectations as ge
+import numpy as np
+from attr import attr
+from great_expectations.core import ExpectationSuite
 from great_expectations.core.expectation_configuration import ExpectationConfiguration
 from great_expectations.data_context import BaseDataContext
 from great_expectations.data_context.types.base import (
@@ -27,18 +24,17 @@
     ExpectationSuiteIdentifier,
 )
 from great_expectations.exceptions.exceptions import GreatExpectationsError
+from ruamel import yaml
 
-
+import great_expectations as ge
 from schematic.models.validate_attribute import GenerateError
 from schematic.schemas.data_model_graph import DataModelGraphExplorer
-
 from schematic.utils.schema_utils import extract_component_validation_rules
-
 from schematic.utils.validate_utils import (
-    rule_in_rule_list,
-    np_array_to_str_list,
     iterable_to_str_list,
+    np_array_to_str_list,
     required_is_only_rule,
+    rule_in_rule_list,
 )
 
 logger = logging.getLogger(__name__)
@@ -147,6 +143,35 @@ def build_context(self):
         # self.context.test_yaml_config(yaml.dump(datasource_config))
         self.context.add_datasource(**datasource_config)
 
+    def add_expectation_suite_if_not_exists(self) -> ExpectationSuite:
+        """
+        Purpose:
+            Add expectation suite if it does not exist
+        Input:
+        Returns:
+            saves expectation suite and identifier to self
+        """
+        self.expectation_suite_name = "Manifest_test_suite"
+        # Get a list of all expectation suites
+        suite_names = self.context.list_expectation_suite_names()
+        # Get a list of all checkpoints
+        all_checkpoints = self.context.list_checkpoints()
+
+        # if the suite exists, delete it
+        if self.expectation_suite_name in suite_names:
+            self.context.delete_expectation_suite(self.expectation_suite_name)
+
+            # also delete all the checkpoints associated with the suite
+            if all_checkpoints:
+                for checkpoint_name in all_checkpoints:
+                    self.context.delete_checkpoint(checkpoint_name)
+
+        self.suite = self.context.add_expectation_suite(
+            expectation_suite_name=self.expectation_suite_name,
+        )
+
+        return self.suite
+
     def build_expectation_suite(
         self,
     ):
@@ -162,10 +187,7 @@ def build_expectation_suite(
         """
 
         # create blank expectation suite
-        self.expectation_suite_name = "Manifest_test_suite"
-        self.suite = self.context.add_expectation_suite(
-            expectation_suite_name=self.expectation_suite_name,
-        )
+        self.suite = self.add_expectation_suite_if_not_exists()
 
         # build expectation configurations for each expectation
         for col in self.manifest.columns:
diff --git a/schematic/models/commands.py b/schematic/models/commands.py
index 2119291b8..fbe31db1b 100644
--- a/schematic/models/commands.py
+++ b/schematic/models/commands.py
@@ -1,26 +1,25 @@
 #!/usr/bin/env python3
 
-from typing import get_args
-from gc import callbacks
 import logging
 import sys
+from gc import callbacks
 from time import perf_counter
+from typing import Optional, get_args
 
 import click
 import click_log
-
 from jsonschema import ValidationError
 
+from schematic.configuration.configuration import CONFIG
+from schematic.exceptions import MissingConfigValueError
+from schematic.help import model_commands
 from schematic.models.metadata import MetadataModel
 from schematic.utils.cli_utils import (
     log_value_from_config,
-    query_dict,
-    parse_syn_ids,
     parse_comma_str_to_list,
+    parse_syn_ids,
+    query_dict,
 )
-from schematic.help import model_commands
-from schematic.exceptions import MissingConfigValueError
-from schematic.configuration.configuration import CONFIG
 from schematic.utils.schema_utils import DisplayLabelType
 
 logger = logging.getLogger("schematic")
@@ -110,6 +109,12 @@ def model(ctx, config):  # use as `schematic model ...`
     callback=parse_syn_ids,
     help=query_dict(model_commands, ("model", "validate", "project_scope")),
 )
+@click.option(
+    "-ds",
+    "--dataset_scope",
+    default=None,
+    help=query_dict(model_commands, ("model", "validate", "dataset_scope")),
+)
 @click.option(
     "--table_manipulation",
     "-tm",
@@ -143,18 +148,19 @@ def model(ctx, config):  # use as `schematic model ...`
 @click.pass_obj
 def submit_manifest(
     ctx,
-    manifest_path,
-    dataset_id,
-    validate_component,
-    manifest_record_type,
-    hide_blanks,
-    restrict_rules,
-    project_scope,
-    table_manipulation,
-    data_model_labels,
-    table_column_names,
-    annotation_keys,
-    file_annotations_upload: bool,
+    manifest_path: str,
+    dataset_id: str,
+    validate_component: Optional[str],
+    manifest_record_type: Optional[str],
+    hide_blanks: Optional[bool],
+    restrict_rules: Optional[bool],
+    project_scope: Optional[list[str]],
+    dataset_scope: Optional[str],
+    table_manipulation: Optional[str],
+    data_model_labels: Optional[str],
+    table_column_names: Optional[str],
+    annotation_keys: Optional[str],
+    file_annotations_upload: Optional[bool],
 ):
     """
     Running CLI with manifest validation (optional) and submission options.
@@ -177,6 +183,7 @@ def submit_manifest(
         restrict_rules=restrict_rules,
         hide_blanks=hide_blanks,
         project_scope=project_scope,
+        dataset_scope=dataset_scope,
         table_manipulation=table_manipulation,
         table_column_names=table_column_names,
         annotation_keys=annotation_keys,
@@ -227,21 +234,29 @@ def submit_manifest(
     callback=parse_syn_ids,
     help=query_dict(model_commands, ("model", "validate", "project_scope")),
 )
+@click.option(
+    "-ds",
+    "--dataset_scope",
+    default=None,
+    help=query_dict(model_commands, ("model", "validate", "dataset_scope")),
+)
 @click.option(
     "--data_model_labels",
     "-dml",
-    is_flag=True,
+    default="class_label",
+    type=click.Choice(list(get_args(DisplayLabelType)), case_sensitive=True),
     help=query_dict(model_commands, ("model", "validate", "data_model_labels")),
 )
 @click.pass_obj
 def validate_manifest(
     ctx,
-    manifest_path,
-    data_type,
-    json_schema,
-    restrict_rules,
-    project_scope,
-    data_model_labels,
+    manifest_path: str,
+    data_type: Optional[list[str]],
+    json_schema: Optional[str],
+    restrict_rules: Optional[bool],
+    project_scope: Optional[list[str]],
+    dataset_scope: Optional[str],
+    data_model_labels: Optional[str],
 ):
     """
     Running CLI for manifest validation.
@@ -276,6 +291,7 @@ def validate_manifest(
         jsonSchema=json_schema,
         restrict_rules=restrict_rules,
         project_scope=project_scope,
+        dataset_scope=dataset_scope,
     )
 
     if not errors:
diff --git a/schematic/models/metadata.py b/schematic/models/metadata.py
index 2747f81d7..582a00168 100644
--- a/schematic/models/metadata.py
+++ b/schematic/models/metadata.py
@@ -1,26 +1,25 @@
-import os
 import logging
-import networkx as nx
+import os
 from os.path import exists
-from jsonschema import ValidationError
 
 # allows specifying explicit variable types
-from typing import Any, Dict, Optional, Text, List
+from typing import Any, Dict, List, Optional, Text
+
+import networkx as nx
+from jsonschema import ValidationError
+from opentelemetry import trace
 
 from schematic.manifest.generator import ManifestGenerator
+from schematic.models.validate_manifest import validate_all
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
-from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_json_schema import DataModelJSONSchema
+from schematic.schemas.data_model_parser import DataModelParser
 
 # TODO: This module should only be aware of the store interface
 # we shouldn't need to expose Synapse functionality explicitly
 from schematic.store.synapse import SynapseStorage
-
 from schematic.utils.df_utils import load_df
 
-from schematic.models.validate_manifest import validate_all
-from opentelemetry import trace
-
 logger = logging.getLogger(__name__)
 
 tracer = trace.get_tracer("Schematic")
@@ -200,6 +199,7 @@ def validateModelManifest(
         restrict_rules: bool = False,
         jsonSchema: Optional[str] = None,
         project_scope: Optional[List] = None,
+        dataset_scope: Optional[str] = None,
         access_token: Optional[str] = None,
     ) -> tuple[list, list]:
         """Check if provided annotations manifest dataframe satisfies all model requirements.
@@ -287,6 +287,7 @@ def validateModelManifest(
             jsonSchema=jsonSchema,
             restrict_rules=restrict_rules,
             project_scope=project_scope,
+            dataset_scope=dataset_scope,
             access_token=access_token,
         )
         return errors, warnings
@@ -332,6 +333,7 @@ def submit_metadata_manifest(  # pylint: disable=too-many-arguments, too-many-lo
         file_annotations_upload: bool = True,
         hide_blanks: bool = False,
         project_scope: Optional[list] = None,
+        dataset_scope: Optional[str] = None,
         table_manipulation: str = "replace",
         table_column_names: str = "class_label",
         annotation_keys: str = "class_label",
@@ -396,6 +398,7 @@ def submit_metadata_manifest(  # pylint: disable=too-many-arguments, too-many-lo
                 rootNode=validate_component,
                 restrict_rules=restrict_rules,
                 project_scope=project_scope,
+                dataset_scope=dataset_scope,
                 access_token=access_token,
             )
 
diff --git a/schematic/models/validate_attribute.py b/schematic/models/validate_attribute.py
index 6ed613bae..e196bbe14 100644
--- a/schematic/models/validate_attribute.py
+++ b/schematic/models/validate_attribute.py
@@ -1,33 +1,31 @@
-import builtins
 import logging
 import re
+from copy import deepcopy
 from time import perf_counter
 
 # allows specifying explicit variable types
-from typing import Any, Optional, Literal, Union
-from urllib import error
+from typing import Any, Literal, Optional, Union
 from urllib.parse import urlparse
-from urllib.request import Request, urlopen
 
 import numpy as np
 import pandas as pd
+import requests
 from jsonschema import ValidationError
+from synapseclient import File
+from synapseclient.core.exceptions import SynapseNoCredentialsError
 
 from schematic.schemas.data_model_graph import DataModelGraphExplorer
-
 from schematic.store.synapse import SynapseStorage
 from schematic.utils.validate_rules_utils import validation_rule_info
 from schematic.utils.validate_utils import (
     comma_separated_list_regex,
-    parse_str_series_to_list,
-    np_array_to_str_list,
+    get_list_robustness,
     iterable_to_str_list,
+    np_array_to_str_list,
+    parse_str_series_to_list,
     rule_in_rule_list,
-    get_list_robustness,
 )
 
-from synapseclient.core.exceptions import SynapseNoCredentialsError
-
 logger = logging.getLogger(__name__)
 
 MessageLevelType = Literal["warning", "error"]
@@ -458,6 +456,52 @@ def generate_no_value_in_manifest_error(
             warnings.append(nv_warnings)
         return errors, warnings
 
+    def generate_filename_error(
+        val_rule: str,
+        attribute_name: str,
+        row_num: str,
+        invalid_entry: Any,
+        error_type: str,
+        dmge: DataModelGraphExplorer,
+    ) -> tuple[list[str], list[str]]:
+        """
+        Purpose:
+            Generate an logging error as well as a stored error message, when
+            a filename error is encountered.
+        Args:
+            val_rule: str, rule as defined in the schema for the component.
+            attribute_name: str, attribute being validated
+            row_num: str, row where the error was detected
+            invalid_entry: str, value that caused the error
+            error_type: str, type of error encountered
+            dmge: DataModelGraphExplorer object
+        Returns:
+            Errors: list[str] Error details for further storage.
+            warnings: list[str] Warning details for further storage.
+        """
+        error_messages = {
+            "mismatched entityId": f"The entityId for file path '{invalid_entry}' on row {row_num}"
+            " does not match the entityId for the file in the file view.",
+            "path does not exist": f"The file path '{invalid_entry}' on row {row_num} does not exist in the file view.",
+            "entityId does not exist": f"The entityId for file path '{invalid_entry}' on row {row_num}"
+            " does not exist in the file view.",
+            "missing entityId": f"The entityId is missing for file path '{invalid_entry}' on row {row_num}.",
+        }
+        error_message = error_messages.get(error_type, None)
+        if not error_message:
+            raise KeyError(f"Unsupported error type provided: '{error_type}'")
+
+        error_list, warning_list = GenerateError.raise_and_store_message(
+            dmge=dmge,
+            val_rule=val_rule,
+            error_row=row_num,
+            error_col=attribute_name,
+            error_message=error_message,
+            error_val=invalid_entry,
+        )
+
+        return error_list, warning_list
+
     def _get_rule_attributes(
         val_rule: str, error_col_name: str, dmge: DataModelGraphExplorer
     ) -> tuple[list, str, MessageLevelType, bool, bool, bool]:
@@ -731,6 +775,31 @@ class ValidateAttribute(object):
     def __init__(self, dmge: DataModelGraphExplorer) -> None:
         self.dmge = dmge
 
+    def _login(
+        self,
+        access_token: Optional[str] = None,
+        project_scope: Optional[list[str]] = None,
+        columns: Optional[list] = None,
+        where_clauses: Optional[list] = None,
+    ):
+        # if the ValidateAttribute object already has a SynapseStorage object, just requery the fileview, if not then login
+        if hasattr(self, "synStore"):
+            if self.synStore.project_scope != project_scope:
+                self.synStore.project_scope = project_scope
+            self.synStore.query_fileview(columns=columns, where_clauses=where_clauses)
+        else:
+            try:
+                self.synStore = SynapseStorage(
+                    access_token=access_token,
+                    project_scope=project_scope,
+                    columns=columns,
+                    where_clauses=where_clauses,
+                )
+            except SynapseNoCredentialsError as e:
+                raise ValueError(
+                    "No Synapse credentials were provided. Credentials must be provided to utilize cross-manfiest validation functionality."
+                ) from e
+
     def get_no_entry(self, entry: str, node_display_name: str) -> bool:
         """Helper function to check if the entry is blank or contains a not applicable type string (and NA is permitted)
         Args:
@@ -770,29 +839,64 @@ def get_entry_has_value(
             node_display_name,
         )
 
+    def _get_target_manifest_dataframes(
+        self,
+        target_component: str,
+        project_scope: Optional[list[str]] = None,
+        access_token: Optional[str] = None,
+    ) -> dict[str, pd.DataFrame]:
+        """Returns target manifest dataframes in the form of a dictionary
+
+        Args:
+            target_component (str): The component to get manifests for
+            project_scope (Optional[list[str]], optional):
+             Projects to limit the scope of cross manifest validation to. Defaults to None.
+            access_token (Optional[str], optional): Asset Store access token. Defaults to None.
+
+        Returns:
+            dict[str, pd.DataFrame]: Keys are synapse ids, values are datframes of the synapse id
+        """
+        manifest_ids, dataset_ids = self.get_target_manifests(
+            target_component, project_scope, access_token
+        )
+        manifests: list[pd.DataFrame] = []
+        for dataset_id in dataset_ids:
+            entity: File = self.synStore.getDatasetManifest(
+                datasetId=dataset_id, downloadFile=True
+            )
+            manifests.append(pd.read_csv(entity.path))
+        return dict(zip(manifest_ids, manifests))
+
     def get_target_manifests(
-        self, target_component: str, project_scope: list[str], access_token: str = None
-    ):
+        self,
+        target_component: str,
+        project_scope: Optional[list[str]],
+        access_token: Optional[str] = None,
+    ) -> tuple[list[str], list[str]]:
+        """Gets a list of synapse ids of mainfests to check against
+
+        Args:
+            target_component (str): Manifet ids are gotten fo this type
+            project_scope (Optional[list[str]]): Projects to limit the scope
+              of cross manifest validation to. Defaults to None.
+            access_token (Optional[str], optional): Synapse access token Defaults to None.
+
+        Returns:
+            tuple[list[str], list[str]]:
+              A list of manifest synapse ids, and their dataset synapse ids
+        """
         t_manifest_search = perf_counter()
         target_manifest_ids = []
         target_dataset_ids = []
 
-        # login
-        try:
-            synStore = SynapseStorage(
-                access_token=access_token, project_scope=project_scope
-            )
-        except SynapseNoCredentialsError as e:
-            raise ValueError(
-                "No Synapse credentials were provided. Credentials must be provided to utilize cross-manfiest validation functionality."
-            ) from e
+        self._login(project_scope=project_scope, access_token=access_token)
 
         # Get list of all projects user has access to
-        projects = synStore.getStorageProjects(project_scope=project_scope)
+        projects = self.synStore.getStorageProjects(project_scope=project_scope)
 
         for project in projects:
             # get all manifests associated with datasets in the projects
-            target_datasets = synStore.getProjectManifests(projectId=project[0])
+            target_datasets = self.synStore.getProjectManifests(projectId=project[0])
 
             # If the manifest includes the target component, include synID in list
             for target_dataset in target_datasets:
@@ -805,7 +909,7 @@ def get_target_manifests(
         logger.debug(
             f"Cross manifest gathering elapsed time {perf_counter()-t_manifest_search}"
         )
-        return synStore, target_manifest_ids, target_dataset_ids
+        return target_manifest_ids, target_dataset_ids
 
     def list_validation(
         self,
@@ -1072,16 +1176,16 @@ def type_validation(
     def url_validation(
         self,
         val_rule: str,
-        manifest_col: str,
+        manifest_col: pd.Series,
     ) -> tuple[list[list[str]], list[list[str]]]:
         """
         Purpose:
             Validate URL's submitted for a particular attribute in a manifest.
             Determine if the URL is valid and contains attributes specified in the
-            schema.
+            schema. Additionally, the server must be reachable to be deemed as valid.
         Input:
             - val_rule: str, Validation rule
-            - manifest_col: pd.core.series.Series, column for a given
+            - manifest_col: pd.Series, column for a given
                 attribute in the manifest
         Output:
             This function will return errors when the user input value
@@ -1099,8 +1203,9 @@ def url_validation(
             )
             if entry_has_value:
                 # Check if a random phrase, string or number was added and
-                # log the appropriate error. Specifically, Raise an error if the value added is not a string or no part
-                # of the string can be parsed as a part of a URL.
+                # log the appropriate error. Specifically, Raise an error if the value
+                # added is not a string or no part of the string can be parsed as a
+                # part of a URL.
                 if not isinstance(url, str) or not (
                     urlparse(url).scheme
                     + urlparse(url).netloc
@@ -1131,10 +1236,13 @@ def url_validation(
                     try:
                         # Check that the URL points to a working webpage
                         # if not log the appropriate error.
-                        request = Request(url)
-                        response = urlopen(request)
                         valid_url = True
-                        response_code = response.getcode()
+                        response = requests.options(url, allow_redirects=True)
+                        logger.debug(
+                            "Validated URL [URL: %s, status_code: %s]",
+                            url,
+                            response.status_code,
+                        )
                     except:
                         valid_url = False
                         url_error = "invalid_url"
@@ -1152,7 +1260,7 @@ def url_validation(
                             errors.append(vr_errors)
                         if vr_warnings:
                             warnings.append(vr_warnings)
-                    if valid_url == True:
+                    if valid_url:
                         # If the URL works, check to see if it contains the proper arguments
                         # as specified in the schema.
                         for arg in url_args:
@@ -1257,19 +1365,19 @@ def _gather_set_warnings_errors(
         val_rule: str,
         source_attribute: str,
         set_validation_store: tuple[
-            dict[str, pd.core.series.Series],
+            dict[str, pd.Series],
             list[str],
-            dict[str, pd.core.series.Series],
+            dict[str, pd.Series],
         ],
-    ) -> tuple[[list[str], list[str]]]:
+    ) -> tuple[list[str], list[str]]:
         """Based on the cross manifest validation rule, and in set rule scope, pass variables to
         _get_cross_errors_warnings
             to log appropriate error or warning.
         Args:
             val_rule, str: Validation Rule
             source_attribute, str: Source manifest column name
-            set_validation_store, tuple[dict[str, pd.core.series.Series], list[string],
-            dict[str, pd.core.series.Series]]:
+            set_validation_store, tuple[dict[str, pd.Series], list[string],
+            dict[str, pd.Series]]:
                 contains the missing_manifest_log, present_manifest_log, and repeat_manifest_log
             dmge: DataModelGraphExplorer Object.
 
@@ -1279,7 +1387,8 @@ def _gather_set_warnings_errors(
             warnings, list[str]: list of warnings to raise, as appropriate, if values in current manifest do
             not pass relevant cross mannifest validation across the target manifest(s)
         """
-        errors, warnings = [], []
+        errors: list[str] = []
+        warnings: list[str] = []
 
         (
             missing_manifest_log,
@@ -1419,18 +1528,13 @@ def _gather_value_warnings_errors(
         self,
         val_rule: str,
         source_attribute: str,
-        value_validation_store: tuple[
-            dict[str, pd.core.series.Series],
-            dict[str, pd.core.series.Series],
-            dict[str, pd.core.series.Series],
-        ],
-    ) -> tuple[[list[str], list[str]]]:
+        value_validation_store: tuple[pd.Series, pd.Series, pd.Series],
+    ) -> tuple[list[str], list[str]]:
         """For value rule scope, find invalid rows and entries, and generate appropriate errors and warnings
         Args:
             val_rule, str: Validation rule
             source_attribute, str: source manifest column name
-            value_validation_store, tuple(dict[str, pd.core.series.Series], dict[str, pd.core.series.Series],
-                dict[str, pd.core.series.Series]):
+            value_validation_store, tuple(pd.Series, pd.Series, pd.Series]):
                 contains missing_values, duplicated_values, and repeat values
         Returns:
             errors, list[str]: list of errors to raise, as appropriate, if values in current manifest do
@@ -1507,20 +1611,20 @@ def _run_validation_across_targets_set(
         self,
         val_rule: str,
         column_names: dict[str, str],
-        manifest_col: pd.core.series.Series,
+        manifest_col: pd.Series,
         target_attribute: str,
-        target_manifest: pd.core.series.Series,
+        target_manifest: pd.DataFrame,
         target_manifest_id: str,
-        missing_manifest_log: dict[str, pd.core.series.Series],
+        missing_manifest_log: dict[str, pd.Series],
         present_manifest_log: list[str],
-        repeat_manifest_log: dict[str, pd.core.series.Series],
+        repeat_manifest_log: dict[str, pd.Series],
         target_attribute_in_manifest_list: list[bool],
         target_manifest_empty: list[bool],
     ) -> tuple[
         tuple[
-            dict[str, pd.core.series.Series],
+            dict[str, pd.Series],
             list[str],
-            dict[str, pd.core.series.Series],
+            dict[str, pd.Series],
         ],
         list[bool],
         list[bool],
@@ -1529,26 +1633,26 @@ def _run_validation_across_targets_set(
         Args:
             val_rule, str: Validation rule
             column_names, dict[str,str]: {stripped_col_name:original_column_name}
-            target_column, pd.core.series.Series: Empty target_column to fill out in this function
-            manifest_col, pd.core.series.Series: Source manifest column
+            target_column, pd.Series: Empty target_column to fill out in this function
+            manifest_col, pd.Series: Source manifest column
             target_attribute, str: current target attribute
-            target_column, pd.core.series.Series: Current target column
-            target_manifest, pd.core.series.Series: Current target manifest
+            target_column, pd.Series: Current target column
+            target_manifest, pd.DataFrame: Current target manifest
             target_manifest_id, str: Current target manifest Synapse ID
-            missing_manifest_log, dict[str, pd.core.series.Series]:
+            missing_manifest_log, dict[str, pd.Series]:
                 Log of manifests with missing values, {synapse_id: index,missing value}, updated.
             present_manifest_log, list[str]
                 Log of present manifests, [synapse_id present manifest], updated.
-            repeat_manifest_log, dict[str, pd.core.series.Series]
+            repeat_manifest_log, dict[str, pd.Series]
                 Log of manifests with repeat values, {synapse_id: index,repeat value}, updated.
 
         Returns:
             tuple(
-            missing_manifest_log, dict[str, pd.core.series.Series]:
+            missing_manifest_log, dict[str, pd.Series]:
                 Log of manifests with missing values, {synapse_id: index,missing value}, updated.
             present_manifest_log, list[str]
                 Log of present manifests, [synapse_id present manifest], updated.
-            repeat_manifest_log, dict[str, pd.core.series.Series]
+            repeat_manifest_log, dict[str, pd.Series]
                 Log of manifests with repeat values, {synapse_id: index,repeat value}, updated.)
             target_attribute_in_manifest, bool: True if the target attribute is in the current manifest.
         """
@@ -1599,11 +1703,11 @@ def _gather_target_columns_value(
         self,
         column_names: dict[str, str],
         target_attribute: str,
-        concatenated_target_column: pd.core.series.Series,
-        target_manifest: pd.core.series.Series,
+        concatenated_target_column: pd.Series,
+        target_manifest: pd.DataFrame,
         target_attribute_in_manifest_list: list[bool],
         target_manifest_empty: list[bool],
-    ) -> tuple[pd.core.series.Series, list[bool], list[bool],]:
+    ) -> tuple[pd.Series, list[bool], list[bool],]:
         """A helper function for creating a concatenating all target attribute columns across all target manifest.
             This function checks if the target attribute is in the current target manifest. If it is, and is the
             first manifest with this column, start recording it, if it has already been recorded from
@@ -1611,11 +1715,11 @@ def _gather_target_columns_value(
         Args:
             column_names, dict: {stripped_col_name:original_column_name}
             target_attribute, str: current target attribute
-            concatenated_target_column, pd.core.series.Series: target column in the process of being built, possibly
+            concatenated_target_column, pd.Series: target column in the process of being built, possibly
                 passed through this function multiple times based on the number of manifests
-            target_manifest, pd.core.series.Series: current target manifest
+            target_manifest, pd.DataFrame: current target manifest
         Returns:
-            concatenated_target_column, pd.core.series.Series: All target columns concatenated into a single column
+            concatenated_target_column, pd.Series: All target columns concatenated into a single column
         """
         # Check if the target_attribute is in the current target manifest.
         target_attribute_in_manifest = False
@@ -1656,20 +1760,20 @@ def _gather_target_columns_value(
 
     def _run_validation_across_targets_value(
         self,
-        manifest_col: pd.core.series.Series,
-        concatenated_target_column: pd.core.series.Series,
-    ) -> tuple[[pd.core.series.Series, pd.core.series.Series, pd.core.series.Series]]:
+        manifest_col: pd.Series,
+        concatenated_target_column: pd.Series,
+    ) -> tuple[pd.Series, pd.Series, pd.Series]:
         """Get missing values, duplicated values and repeat values assesed comapring the source manifest to all
             the values in all target columns.
         Args:
-            manifest_col, pd.core.series.Series: Current source manifest column
-            concatenated_target_column, pd.core.series.Series: All target columns concatenated into a single column
+            manifest_col, pd.Series: Current source manifest column
+            concatenated_target_column, pd.Series: All target columns concatenated into a single column
         Returns:
-            missing_values, pd.core.series.Series: values that are present in the source manifest, but not present
+            missing_values, pd.Series: values that are present in the source manifest, but not present
                 in the target manifest
-            duplicated_values, pd.core.series.Series: values that duplicated in the concatenated target column, and
+            duplicated_values, pd.Series: values that duplicated in the concatenated target column, and
                 also present in the source manifest column
-            repeat_values, pd.core.series.Series: values that are repeated between the manifest column and
+            repeat_values, pd.Series: values that are repeated between the manifest column and
                 concatenated target column
         """
         # Find values that are present in the source manifest, but not present in the target manifest
@@ -1687,12 +1791,10 @@ def _run_validation_across_targets_value(
 
         return missing_values, duplicated_values, repeat_values
 
-    def _get_column_names(
-        self, target_manifest: pd.core.series.Series
-    ) -> dict[str, str]:
+    def _get_column_names(self, target_manifest: pd.DataFrame) -> dict[str, str]:
         """Convert manifest column names into validation rule input format
         Args:
-            target_manifest, pd.core.series.Series: Current target manifest
+            target_manifest, pd.DataFrame: Current target manifest
         Returns:
             column_names, dict[str,str]: {stripped_col_name:original_column_name}
         """
@@ -1714,27 +1816,21 @@ def _get_rule_scope(self, val_rule: str) -> ScopeTypes:
 
     def _run_validation_across_target_manifests(
         self,
-        project_scope: Optional[list[str]],
         rule_scope: ScopeTypes,
-        access_token: str,
         val_rule: str,
-        manifest_col: pd.core.series.Series,
-        target_column: pd.core.series.Series,
+        manifest_col: pd.Series,
+        target_column: pd.Series,
+        access_token: Optional[str] = None,
+        project_scope: Optional[list[str]] = None,
     ) -> tuple[
         float,
         Union[
-            Union[
-                tuple[
-                    dict[str, pd.core.series.Series],
-                    list[str],
-                    dict[str, pd.core.series.Series],
-                ],
-                tuple[
-                    dict[str, pd.core.series.Series],
-                    dict[str, pd.core.series.Series],
-                    dict[str, pd.core.series.Series],
-                ],
+            tuple[
+                dict[str, pd.Series],
+                list[str],
+                dict[str, pd.Series],
             ],
+            tuple[pd.Series, pd.Series, pd.Series],
             bool,
             str,
         ],
@@ -1744,10 +1840,10 @@ def _run_validation_across_target_manifests(
         Args:
             project_scope, Optional[list]: Projects to limit the scope of cross manifest validation to.
             rule_scope, ScopeTypes: The scope of the rule, taken from validation rule
-            access_token, str: Asset Store access token
+            access_token, Optional[str]: Asset Store access token
             val_rule, str: Validation rule.
-            manifest_col, pd.core.series.Series: Source manifest column for a given source component
-            target_column, pd.core.series.Series: Empty target_column to fill out in this function
+            manifest_col, pd.Series: Source manifest column for a given source component
+            target_column, pd.Series: Empty target_column to fill out in this function
         Returns:
             start_time, float: start time in fractional seconds
             valdiation_output:
@@ -1756,9 +1852,9 @@ def _run_validation_across_target_manifests(
                     "values not recorded in targets stored", str, will return a string if targets were found, but there
                         was no data in the target.
                     Union[
-                        tuple[dict[str, pd.core.series.Series], list[str], dict[str, pd.core.series.Series]],
-                        tuple[dict[str, pd.core.series.Series], dict[str, pd.core.series.Series],
-                            dict[str, pd.core.series.Series]]:
+                        tuple[dict[str, pd.Series], list[str], dict[str, pd.Series]],
+                        tuple[dict[str, pd.Series], dict[str, pd.Series],
+                            dict[str, pd.Series]]:
                             validation outputs, exact types depend on scope,
         """
         # Initialize variables
@@ -1777,28 +1873,16 @@ def _run_validation_across_target_manifests(
         [target_component, target_attribute] = val_rule.lower().split(" ")[1].split(".")
         target_column.name = target_attribute
 
-        # Get IDs of manifests with target component
-        (
-            synStore,
-            target_manifest_ids,
-            target_dataset_ids,
-        ) = self.get_target_manifests(target_component, project_scope, access_token)
-
         # Start timer
         start_time = perf_counter()
 
+        manifest_dict = self._get_target_manifest_dataframes(
+            target_component, project_scope, access_token
+        )
+
         # For each target manifest, gather target manifest column and compare to the source manifest column
         # Save relevant data as appropriate for the given scope
-        for target_manifest_id, target_dataset_id in zip(
-            target_manifest_ids, target_dataset_ids
-        ):
-            # Pull manifest from Synapse
-            entity = synStore.getDatasetManifest(
-                datasetId=target_dataset_id, downloadFile=True
-            )
-            # Load manifest
-            target_manifest = pd.read_csv(entity.path)
-
+        for target_manifest_id, target_manifest in manifest_dict.items():
             # Get manifest column names
             column_names = self._get_column_names(target_manifest=target_manifest)
 
@@ -1875,14 +1959,15 @@ def _run_validation_across_target_manifests(
                     concatenated_target_column=target_column,
                 )
                 validation_store = (missing_values, duplicated_values, repeat_values)
+
             return (start_time, validation_store)
 
     def cross_validation(
         self,
         val_rule: str,
-        manifest_col: pd.core.series.Series,
-        project_scope: Optional[list[str]],
-        access_token: str,
+        manifest_col: pd.Series,
+        project_scope: Optional[list[str]] = None,
+        access_token: Optional[str] = None,
     ) -> list[list[str]]:
         """
         Purpose:
@@ -1890,11 +1975,11 @@ def cross_validation(
                 by project scope, if provided).
         Args:
             val_rule, str: Validation rule
-            manifest_col, pd.core.series.Series: column for a given
+            manifest_col, pd.Series: column for a given
                 attribute in the manifest
             project_scope, Optional[list] = None: Projects to limit the scope of cross manifest validation to.
             dmge: DataModelGraphExplorer Object
-            access_token, str: Asset Store access token
+            access_token, Optional[str]: Asset Store access token
         Returns:
             errors, warnings, list[list[str]]: raise warnings and errors as appropriate if values in current manifest do
             no pass relevant cross mannifest validation across the target manifest(s)
@@ -1951,3 +2036,90 @@ def cross_validation(
         logger.debug(f"cross manifest validation time {perf_counter()-start_time}")
 
         return errors, warnings
+
+    def filename_validation(
+        self,
+        val_rule: str,
+        manifest: pd.core.frame.DataFrame,
+        access_token: str,
+        dataset_scope: str,
+        project_scope: Optional[list] = None,
+    ):
+        """
+        Purpose:
+            Validate the filenames in the manifest against the data paths in the fileview.
+        Args:
+            val_rule: str, Validation rule for the component
+            manifest: pd.core.frame.DataFrame, manifest
+            access_token: str, Asset Store access token
+            dataset_scope: str, Dataset with files to validate against
+            project_scope: Optional[list] = None: Projects to limit the scope of cross manifest validation to.
+        Returns:
+            errors: list[str] Error details for further storage.
+            warnings: list[str] Warning details for further storage.
+        """
+
+        if dataset_scope is None:
+            raise ValueError(
+                "A dataset is required to be specified for filename validation"
+            )
+
+        errors = []
+        warnings = []
+
+        where_clauses = []
+
+        dataset_clause = f"parentId='{dataset_scope}'"
+        where_clauses.append(dataset_clause)
+
+        self._login(
+            project_scope=project_scope,
+            access_token=access_token,
+            columns=["id", "path"],
+            where_clauses=where_clauses,
+        )
+
+        fileview = self.synStore.storageFileviewTable.reset_index(drop=True)
+        # filename in dataset?
+        files_in_view = manifest["Filename"].isin(fileview["path"])
+        entity_ids_in_view = manifest["entityId"].isin(fileview["id"])
+        # filenames match with entity IDs in dataset
+        joined_df = manifest.merge(
+            fileview, how="left", left_on="Filename", right_on="path"
+        )
+
+        entity_id_match = joined_df["id"] == joined_df["entityId"]
+
+        # update manifest with types of errors identified
+        manifest_with_errors = deepcopy(manifest)
+        manifest_with_errors["Error"] = pd.NA
+        manifest_with_errors.loc[~entity_id_match, "Error"] = "mismatched entityId"
+        manifest_with_errors.loc[~files_in_view, "Error"] = "path does not exist"
+        manifest_with_errors.loc[
+            ~entity_ids_in_view, "Error"
+        ] = "entityId does not exist"
+        manifest_with_errors.loc[
+            (manifest_with_errors["entityId"].isna())
+            | (manifest_with_errors["entityId"] == ""),
+            "Error",
+        ] = "missing entityId"
+
+        # Generate errors
+        invalid_entries = manifest_with_errors.loc[
+            manifest_with_errors["Error"].notna()
+        ]
+        for index, data in invalid_entries.iterrows():
+            vr_errors, vr_warnings = GenerateError.generate_filename_error(
+                val_rule=val_rule,
+                attribute_name="Filename",
+                # +2 to make consistent with other validation functions
+                row_num=str(index + 2),
+                invalid_entry=data["Filename"],
+                error_type=data["Error"],
+                dmge=self.dmge,
+            )
+            if vr_errors:
+                errors.append(vr_errors)
+            if vr_warnings:
+                warnings.append(vr_warnings)
+        return errors, warnings
diff --git a/schematic/models/validate_manifest.py b/schematic/models/validate_manifest.py
index 686842d20..3b85b1414 100644
--- a/schematic/models/validate_manifest.py
+++ b/schematic/models/validate_manifest.py
@@ -1,35 +1,33 @@
 import json
-from statistics import mode
-from tabnanny import check
-from jsonschema import Draft7Validator, exceptions, ValidationError
 import logging
-
-import numpy as np
 import os
-import pandas as pd
 import re
 import sys
-from time import perf_counter
 from numbers import Number
+from statistics import mode
+from tabnanny import check
+from time import perf_counter
 
 # allows specifying explicit variable types
-from typing import Any, Dict, Optional, Text, List
-from urllib.parse import urlparse
-from urllib.request import urlopen, OpenerDirector, HTTPDefaultErrorHandler
-from urllib.request import Request
+from typing import Any, Dict, List, Optional, Text
 from urllib import error
+from urllib.parse import urlparse
+from urllib.request import HTTPDefaultErrorHandler, OpenerDirector, Request, urlopen
 
-from schematic.models.validate_attribute import ValidateAttribute, GenerateError
+import numpy as np
+import pandas as pd
+from jsonschema import Draft7Validator, ValidationError, exceptions
 
+from schematic.models.GE_Helpers import GreatExpectationsHelpers
+from schematic.models.validate_attribute import GenerateError, ValidateAttribute
 from schematic.schemas.data_model_graph import DataModelGraphExplorer
 from schematic.store.synapse import SynapseStorage
-from schematic.models.GE_Helpers import GreatExpectationsHelpers
+from schematic.utils.schema_utils import extract_component_validation_rules
 from schematic.utils.validate_rules_utils import validation_rule_info
 from schematic.utils.validate_utils import (
-    rule_in_rule_list,
     convert_nan_entries_to_empty_strings,
+    rule_in_rule_list,
 )
-from schematic.utils.schema_utils import extract_component_validation_rules
 
 logger = logging.getLogger(__name__)
 
@@ -107,6 +105,7 @@ def validate_manifest_rules(
         dmge: DataModelGraphExplorer,
         restrict_rules: bool,
         project_scope: list[str],
+        dataset_scope: Optional[str] = None,
         access_token: Optional[str] = None,
     ) -> (pd.core.frame.DataFrame, list[list[str]]):
         """
@@ -153,6 +152,7 @@ def validate_manifest_rules(
             "matchAtLeastOne.*",
             "matchExactlyOne.*",
             "matchNone.*",
+            "filenameExists",
         ]
 
         in_house_rules = [
@@ -166,6 +166,7 @@ def validate_manifest_rules(
             "matchAtLeastOne.*",
             "matchExactlyOne.*",
             "matchNone.*",
+            "filenameExists",
         ]
 
         # initialize error and warning handling lists.
@@ -270,6 +271,14 @@ def validate_manifest_rules(
                         vr_errors, vr_warnings = validation_method(
                             rule, manifest[col], project_scope, access_token
                         )
+                    elif validation_type == "filenameExists":
+                        vr_errors, vr_warnings = validation_method(
+                            rule,
+                            manifest,
+                            access_token,
+                            dataset_scope,
+                            project_scope,
+                        )
                     else:
                         vr_errors, vr_warnings = validation_method(
                             rule,
@@ -347,12 +356,13 @@ def validate_all(
     jsonSchema,
     restrict_rules,
     project_scope: List,
+    dataset_scope: str,
     access_token: str,
 ):
     # Run Validation Rules
     vm = ValidateManifest(errors, manifest, manifestPath, dmge, jsonSchema)
     manifest, vmr_errors, vmr_warnings = vm.validate_manifest_rules(
-        manifest, dmge, restrict_rules, project_scope, access_token
+        manifest, dmge, restrict_rules, project_scope, dataset_scope, access_token
     )
 
     if vmr_errors:
diff --git a/schematic/schemas/data_model_graph.py b/schematic/schemas/data_model_graph.py
index 4aae01a22..64cb59a65 100644
--- a/schematic/schemas/data_model_graph.py
+++ b/schematic/schemas/data_model_graph.py
@@ -1,25 +1,24 @@
 """DataModel Graph"""
 
 import logging
-from typing import Optional, Union, Any
+from typing import Any, Optional, Union
 
-import networkx as nx  # type: ignore
 import graphviz  # type: ignore
+import networkx as nx  # type: ignore
 from opentelemetry import trace
 
 from schematic.schemas.data_model_edges import DataModelEdges
 from schematic.schemas.data_model_nodes import DataModelNodes
 from schematic.schemas.data_model_relationships import DataModelRelationships
-
+from schematic.utils.general import unlist
 from schematic.utils.schema_utils import (
-    get_property_label_from_display_name,
-    get_class_label_from_display_name,
     DisplayLabelType,
     extract_component_validation_rules,
+    get_class_label_from_display_name,
+    get_property_label_from_display_name,
 )
-from schematic.utils.general import unlist
-from schematic.utils.viz_utils import visualize
 from schematic.utils.validate_utils import rule_in_rule_list
+from schematic.utils.viz_utils import visualize
 
 logger = logging.getLogger(__name__)
 
@@ -780,16 +779,26 @@ def get_node_validation_rules(
             node_label: Label of the node for which you need to look up.
             node_display_name: Display name of the node which you want to get the label for.
         Returns:
-            A set of validation rules associated with node, as a list.
+            A set of validation rules associated with node, as a list or a dictionary.
         """
         if not node_label:
-            assert node_display_name is not None
+            if node_display_name is None:
+                raise ValueError(
+                    "Either node_label or node_display_name must be provided."
+                )
+
+            # try search node label using display name
             node_label = self.get_node_label(node_display_name)
 
         if not node_label:
             return []
 
-        node_validation_rules = self.graph.nodes[node_label]["validationRules"]
+        try:
+            node_validation_rules = self.graph.nodes[node_label]["validationRules"]
+        except KeyError as key_error:
+            raise ValueError(
+                f"{node_label} is not in the graph, please provide a proper node label"
+            ) from key_error
 
         return node_validation_rules
 
diff --git a/schematic/store/synapse.py b/schematic/store/synapse.py
index 688bbce4f..7ccb810cf 100644
--- a/schematic/store/synapse.py
+++ b/schematic/store/synapse.py
@@ -1,74 +1,71 @@
 """Synapse storage class"""
 
+import asyncio
 import atexit
-from copy import deepcopy
-from dataclasses import dataclass
 import logging
-import numpy as np
-import pandas as pd
 import os
 import re
 import secrets
 import shutil
-import synapseclient
 import uuid  # used to generate unique names for entities
-
-from tenacity import (
-    retry,
-    stop_after_attempt,
-    wait_chain,
-    wait_fixed,
-    retry_if_exception_type,
-)
+from copy import deepcopy
+from dataclasses import asdict, dataclass
 from time import sleep
 
 # allows specifying explicit variable types
-from typing import Dict, List, Tuple, Sequence, Union, Optional
+from typing import Any, Dict, List, Optional, Sequence, Set, Tuple, Union
 
+import numpy as np
+import pandas as pd
+import synapseclient
+import synapseutils
+from opentelemetry import trace
+from schematic_db.rdb.synapse_database import SynapseDatabase
 from synapseclient import (
-    Synapse,
+    Column,
+    EntityViewSchema,
+    EntityViewType,
     File,
     Folder,
-    Table,
     Schema,
-    EntityViewSchema,
-    EntityViewType,
-    Column,
+    Synapse,
+    Table,
     as_table_columns,
 )
-from synapseclient.entity import File
-from synapseclient.table import CsvFileTable, build_table, Schema
+from synapseclient.api import get_entity_id_bundle2
 from synapseclient.core.exceptions import (
-    SynapseHTTPError,
     SynapseAuthenticationError,
-    SynapseUnmetAccessRestrictions,
     SynapseHTTPError,
+    SynapseUnmetAccessRestrictions,
+)
+from synapseclient.entity import File
+from synapseclient.models.annotations import Annotations
+from synapseclient.table import CsvFileTable, Schema, build_table
+from tenacity import (
+    retry,
+    retry_if_exception_type,
+    stop_after_attempt,
+    wait_chain,
+    wait_fixed,
 )
-import synapseutils
-
-from schematic_db.rdb.synapse_database import SynapseDatabase
 
+from schematic.configuration.configuration import CONFIG
+from schematic.exceptions import AccessCredentialsError
 from schematic.schemas.data_model_graph import DataModelGraphExplorer
-
-from schematic.utils.df_utils import update_df, load_df, col_in_dataframe
-from schematic.utils.validate_utils import comma_separated_list_regex, rule_in_rule_list
+from schematic.store.base import BaseStorage
+from schematic.utils.df_utils import col_in_dataframe, load_df, update_df
 
 # entity_type_mapping, get_dir_size, create_temp_folder, check_synapse_cache_size, and clear_synapse_cache functions are used for AWS deployment
 # Please do not remove these import statements
 from schematic.utils.general import (
-    entity_type_mapping,
-    get_dir_size,
-    create_temp_folder,
     check_synapse_cache_size,
     clear_synapse_cache,
+    create_temp_folder,
+    entity_type_mapping,
+    get_dir_size,
 )
-
 from schematic.utils.schema_utils import get_class_label_from_display_name
-
-from schematic.store.base import BaseStorage
-from schematic.exceptions import AccessCredentialsError
-from schematic.configuration.configuration import CONFIG
-from opentelemetry import trace
+from schematic.utils.validate_utils import comma_separated_list_regex, rule_in_rule_list
 
 logger = logging.getLogger("Synapse storage")
 
@@ -192,12 +189,16 @@ class SynapseStorage(BaseStorage):
     TODO: Need to define the interface and rename and/or refactor some of the methods below.
     """
 
+    @tracer.start_as_current_span("SynapseStorage::__init__")
     def __init__(
         self,
         token: Optional[str] = None,  # optional parameter retrieved from browser cookie
         access_token: Optional[str] = None,
         project_scope: Optional[list] = None,
         synapse_cache_path: Optional[str] = None,
+        perform_query: Optional[bool] = True,
+        columns: Optional[list] = None,
+        where_clauses: Optional[list] = None,
     ) -> None:
         """Initializes a SynapseStorage object.
 
@@ -212,14 +213,18 @@ def __init__(
             synapse_cache_path (Optional[str], optional):
               Location of synapse cache.
               Defaults to None.
+        TODO:
+            Consider necessity of adding "columns" and "where_clauses" params to the constructor. Currently with how `query_fileview` is implemented, these params are not needed at this step but could be useful in the future if the need for more scoped querys expands.
         """
-        self.syn = self.login(synapse_cache_path, token, access_token)
+        self.syn = self.login(synapse_cache_path, access_token)
         self.project_scope = project_scope
         self.storageFileview = CONFIG.synapse_master_fileview_id
         self.manifest = CONFIG.synapse_manifest_basename
         self.root_synapse_cache = self.syn.cache.cache_root_dir
-        self._query_fileview()
+        if perform_query:
+            self.query_fileview(columns=columns, where_clauses=where_clauses)
 
+    @tracer.start_as_current_span("SynapseStorage::_purge_synapse_cache")
     def _purge_synapse_cache(
         self, maximum_storage_allowed_cache_gb: int = 1, minute_buffer: int = 15
     ) -> None:
@@ -251,61 +256,121 @@ def _purge_synapse_cache(
                 # instead of guessing how much space that we left, print out .synapseCache here
                 logger.info(f"the total size of .synapseCache is: {nbytes} bytes")
 
-    @tracer.start_as_current_span("SynapseStorage::_query_fileview")
-    def _query_fileview(self):
+    @tracer.start_as_current_span("SynapseStorage::query_fileview")
+    def query_fileview(
+        self,
+        columns: Optional[list] = None,
+        where_clauses: Optional[list] = None,
+    ) -> None:
+        """
+        Method to query the Synapse FileView and store the results in a pandas DataFrame. The results are stored in the storageFileviewTable attribute.
+        Is called once during initialization of the SynapseStorage object and can be called again later to specify a specific, more limited scope for validation purposes.
+        Args:
+            columns (Optional[list], optional): List of columns to be selected from the table. Defaults behavior is to request all columns.
+            where_clauses (Optional[list], optional): List of where clauses to be used to scope the query. Defaults to None.
+        """
         self._purge_synapse_cache()
-        try:
-            self.storageFileview = CONFIG.synapse_master_fileview_id
-            self.manifest = CONFIG.synapse_manifest_basename
-            if self.project_scope:
-                self.storageFileviewTable = self.syn.tableQuery(
-                    f"SELECT * FROM {self.storageFileview} WHERE projectId IN {tuple(self.project_scope + [''])}"
-                ).asDataFrame()
-            else:
-                # get data in administrative fileview for this pipeline
+
+        self.storageFileview = CONFIG.synapse_master_fileview_id
+        self.manifest = CONFIG.synapse_manifest_basename
+
+        # Initialize to assume that the new fileview query will be different from what may already be stored. Initializes to True because generally one will not have already been performed
+        self.new_query_different = True
+
+        # If a query has already been performed, store the query
+        previous_query_built = hasattr(self, "fileview_query")
+        if previous_query_built:
+            previous_query = self.fileview_query
+
+        # Build a query with the current given parameters and check to see if it is different from the previous
+        self._build_query(columns=columns, where_clauses=where_clauses)
+        if previous_query_built:
+            self.new_query_different = self.fileview_query != previous_query
+
+        # Only perform the query if it is different from the previous query
+        if self.new_query_different:
+            try:
                 self.storageFileviewTable = self.syn.tableQuery(
-                    "SELECT * FROM " + self.storageFileview
+                    query=self.fileview_query,
                 ).asDataFrame()
-        except SynapseHTTPError:
-            raise AccessCredentialsError(self.storageFileview)
+            except SynapseHTTPError as exc:
+                exception_text = str(exc)
+                if "Unknown column path" in exception_text:
+                    raise ValueError(
+                        "The path column has not been added to the fileview. Please make sure that the fileview is up to date. You can add the path column to the fileview by follwing the instructions in the validation rules documentation."
+                    )
+                elif "Unknown column" in exception_text:
+                    missing_column = exception_text.split("Unknown column ")[-1]
+                    raise ValueError(
+                        f"The columns {missing_column} specified in the query do not exist in the fileview. Please make sure that the column names are correct and that all expected columns have been added to the fileview."
+                    )
+                else:
+                    raise AccessCredentialsError(self.storageFileview)
+
+    def _build_query(
+        self, columns: Optional[list] = None, where_clauses: Optional[list] = None
+    ):
+        """
+        Method to build a query for Synapse FileViews
+        Args:
+            columns (Optional[list], optional): List of columns to be selected from the table. Defaults behavior is to request all columns.
+            where_clauses (Optional[list], optional): List of where clauses to be used to scope the query. Defaults to None.
+            self.storageFileview (str): Synapse FileView ID
+            self.project_scope (Optional[list], optional): List of project IDs to be used to scope the query. Defaults to None.
+                Gets added to where_clauses, more included for backwards compatability and as a more user friendly way of subsetting the view in a simple way.
+        """
+        if columns is None:
+            columns = []
+        if where_clauses is None:
+            where_clauses = []
+
+        if self.project_scope:
+            project_scope_clause = f"projectId IN {tuple(self.project_scope + [''])}"
+            where_clauses.append(project_scope_clause)
+
+        if where_clauses:
+            where_clauses = " AND ".join(where_clauses)
+            where_clauses = f"WHERE {where_clauses} ;"
+        else:
+            where_clauses = ";"
+
+        if columns:
+            columns = ",".join(columns)
+        else:
+            columns = "*"
+
+        self.fileview_query = (
+            f"SELECT {columns} FROM {self.storageFileview} {where_clauses}"
+        )
+
+        return
 
     @staticmethod
     def login(
         synapse_cache_path: Optional[str] = None,
-        token: Optional[str] = None,
         access_token: Optional[str] = None,
     ) -> synapseclient.Synapse:
         """Login to Synapse
 
         Args:
-            token (Optional[str], optional): A Synapse token. Defaults to None.
             access_token (Optional[str], optional): A synapse access token. Defaults to None.
             synapse_cache_path (Optional[str]): location of synapse cache
 
         Raises:
-            ValueError: If unable to login with token
             ValueError: If unable to loging with access token
 
         Returns:
             synapseclient.Synapse: A Synapse object that is logged in
         """
         # If no token is provided, try retrieving access token from environment
-        if not token and not access_token:
+        if not access_token:
             access_token = os.getenv("SYNAPSE_ACCESS_TOKEN")
 
         # login using a token
-        if token:
-            syn = synapseclient.Synapse(cache_root_dir=synapse_cache_path)
-            try:
-                syn.login(sessionToken=token, silent=True)
-            except SynapseHTTPError as exc:
-                raise ValueError(
-                    "Please make sure you are logged into synapse.org."
-                ) from exc
-        elif access_token:
+        if access_token:
             try:
                 syn = synapseclient.Synapse(cache_root_dir=synapse_cache_path)
-                syn.default_headers["Authorization"] = f"Bearer {access_token}"
+                syn.login(authToken=access_token, silent=True)
             except SynapseHTTPError as exc:
                 raise ValueError(
                     "No access to resources. Please make sure that your token is correct"
@@ -333,6 +398,22 @@ def wrapper(*args, **kwargs):
 
         return wrapper
 
+    def async_missing_entity_handler(method):
+        """Decorator to handle missing entities in async methods."""
+
+        async def wrapper(*args: Any, **kwargs: Any) -> Any:
+            try:
+                return await method(*args, **kwargs)
+            except SynapseHTTPError as ex:
+                str_message = str(ex).replace("\n", "")
+                if "trash" in str_message or "does not exist" in str_message:
+                    logging.warning(str_message)
+                    return None
+                else:
+                    raise ex
+
+        return wrapper
+
     def getStorageFileviewTable(self):
         """Returns the storageFileviewTable obtained during initialization."""
         return self.storageFileviewTable
@@ -479,30 +560,47 @@ def getFilesInStorageDataset(
         Raises:
             ValueError: Dataset ID not found.
         """
-        # select all files within a given storage dataset folder (top level folder in a Synapse storage project or folder marked with contentType = 'dataset')
+        # select all files within a given storage dataset folder (top level folder in
+        # a Synapse storage project or folder marked with contentType = 'dataset')
         walked_path = synapseutils.walk(
             self.syn, datasetId, includeTypes=["folder", "file"]
         )
 
+        project = self.getDatasetProject(datasetId)
+        project_name = self.syn.get(project, downloadFile=False).name
         file_list = []
 
         # iterate over all results
-        for dirpath, dirname, filenames in walked_path:
+        for dirpath, _, path_filenames in walked_path:
             # iterate over all files in a folder
-            for filename in filenames:
-                if (not "manifest" in filename[0] and not fileNames) or (
-                    fileNames and filename[0] in fileNames
+            for path_filename in path_filenames:
+                if ("manifest" not in path_filename[0] and not fileNames) or (
+                    fileNames and path_filename[0] in fileNames
                 ):
-                    # don't add manifest to list of files unless it is specified in the list of specified fileNames; return all found files
+                    # don't add manifest to list of files unless it is specified in the
+                    # list of specified fileNames; return all found files
                     # except the manifest if no fileNames have been specified
                     # TODO: refactor for clarity/maintainability
 
                     if fullpath:
                         # append directory path to filename
-                        filename = (dirpath[0] + "/" + filename[0], filename[1])
+                        if dirpath[0].startswith(f"{project_name}/"):
+                            path_filename = (
+                                dirpath[0] + "/" + path_filename[0],
+                                path_filename[1],
+                            )
+                        else:
+                            path_filename = (
+                                project_name
+                                + "/"
+                                + dirpath[0]
+                                + "/"
+                                + path_filename[0],
+                                path_filename[1],
+                            )
 
                     # add file name file id tuple, rearranged so that id is first and name follows
-                    file_list.append(filename[::-1])
+                    file_list.append(path_filename[::-1])
 
         return file_list
 
@@ -582,8 +680,8 @@ def getDatasetManifest(
                 manifest_data = ManifestDownload.download_manifest(
                     md, newManifestName=newManifestName, manifest_df=manifest
                 )
-                ## TO DO: revisit how downstream code handle manifest_data. If the downstream code would break when manifest_data is an empty string,
-                ## then we should catch the error here without returning an empty string.
+                # TO DO: revisit how downstream code handle manifest_data. If the downstream code would break when manifest_data is an empty string,
+                # then we should catch the error here without returning an empty string.
                 if not manifest_data:
                     logger.debug(
                         f"No manifest data returned. Please check if you have successfully downloaded manifest: {manifest_syn_id}"
@@ -703,18 +801,49 @@ def fill_in_entity_id_filename(
         # note that if there is an existing manifest and there are files in the dataset
         # the columns Filename and entityId are assumed to be present in manifest schema
         # TODO: use idiomatic panda syntax
-        if dataset_files:
-            new_files = self._get_file_entityIds(
-                dataset_files=dataset_files, only_new_files=True, manifest=manifest
-            )
+        if not dataset_files:
+            manifest = manifest.fillna("")
+            return dataset_files, manifest
 
-            # update manifest so that it contains new dataset files
-            new_files = pd.DataFrame(new_files)
-            manifest = (
-                pd.concat([manifest, new_files], sort=False)
-                .reset_index()
-                .drop("index", axis=1)
-            )
+        all_files = self._get_file_entityIds(
+            dataset_files=dataset_files, only_new_files=False, manifest=manifest
+        )
+        new_files = self._get_file_entityIds(
+            dataset_files=dataset_files, only_new_files=True, manifest=manifest
+        )
+
+        all_files = pd.DataFrame(all_files)
+        new_files = pd.DataFrame(new_files)
+
+        # update manifest so that it contains new dataset files
+        manifest = (
+            pd.concat([manifest, new_files], sort=False)
+            .reset_index()
+            .drop("index", axis=1)
+        )
+
+        # Reindex manifest and new files dataframes according to entityIds to align file paths and metadata
+        manifest_reindex = manifest.set_index("entityId")
+        all_files_reindex = all_files.set_index("entityId")
+        all_files_reindex_like_manifest = all_files_reindex.reindex_like(
+            manifest_reindex
+        )
+
+        # Check if individual file paths in manifest and from synapse match
+        file_paths_match = (
+            manifest_reindex["Filename"] == all_files_reindex_like_manifest["Filename"]
+        )
+
+        # If all the paths do not match, update the manifest with the filepaths from synapse
+        if not file_paths_match.all():
+            manifest_reindex.loc[
+                ~file_paths_match, "Filename"
+            ] = all_files_reindex_like_manifest.loc[~file_paths_match, "Filename"]
+
+            # reformat manifest for further use
+            manifest = manifest_reindex.reset_index()
+            entityIdCol = manifest.pop("entityId")
+            manifest.insert(len(manifest.columns), "entityId", entityIdCol)
 
         manifest = manifest.fillna("")
         return dataset_files, manifest
@@ -1080,6 +1209,7 @@ def move_entities_to_new_project(
             )
         return manifests, manifest_loaded
 
+    @tracer.start_as_current_span("SynapseStorage::get_synapse_table")
     def get_synapse_table(self, synapse_id: str) -> Tuple[pd.DataFrame, CsvFileTable]:
         """Download synapse table as a pd dataframe; return table schema and etags as results too
 
@@ -1092,6 +1222,7 @@ def get_synapse_table(self, synapse_id: str) -> Tuple[pd.DataFrame, CsvFileTable
 
         return df, results
 
+    @tracer.start_as_current_span("SynapseStorage::_get_tables")
     def _get_tables(self, datasetId: str = None, projectId: str = None) -> List[Table]:
         if projectId:
             project = projectId
@@ -1355,10 +1486,147 @@ def upload_manifest_file(
 
         return manifest_synapse_file_id
 
-    @missing_entity_handler
-    def format_row_annotations(
-        self, dmge, row, entityId: str, hideBlanks: bool, annotation_keys: str
-    ):
+    async def get_async_annotation(self, synapse_id: str) -> Dict[str, Any]:
+        """get annotations asynchronously
+
+        Args:
+            synapse_id (str): synapse id of the entity that the annotation belongs
+
+        Returns:
+            Dict[str, Any]: The requested entity bundle matching
+            <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/entitybundle/v2/EntityBundle.html>
+        """
+        return await get_entity_id_bundle2(
+            entity_id=synapse_id,
+            request={"includeAnnotations": True},
+            synapse_client=self.syn,
+        )
+
+    async def store_async_annotation(self, annotation_dict: dict) -> Annotations:
+        """store annotation in an async way
+
+        Args:
+            annotation_dict (dict): annotation in a dictionary format
+
+        Returns:
+            Annotations: The stored annotations.
+        """
+        annotation_data = Annotations.from_dict(
+            synapse_annotations=annotation_dict["annotations"]["annotations"]
+        )
+        annotation_class = Annotations(
+            annotations=annotation_data,
+            etag=annotation_dict["annotations"]["etag"],
+            id=annotation_dict["annotations"]["id"],
+        )
+        return await annotation_class.store_async(synapse_client=self.syn)
+
+    def process_row_annotations(
+        self,
+        dmge: DataModelGraphExplorer,
+        metadata_syn: Dict[str, Any],
+        hide_blanks: bool,
+        csv_list_regex: str,
+        annos: Dict[str, Any],
+        annotation_keys: str,
+    ) -> Dict[str, Any]:
+        """Processes metadata annotations based on the logic below:
+        1. Checks if the hide_blanks flag is True, and if the current annotation value (anno_v) is:
+            An empty or whitespace-only string.
+            A NaN value (if the annotation is a float).
+        if any of the above conditions are met, and hide_blanks is True, the annotation key is not going to be uploaded and skips further processing of that annotation key.
+        if any of the above conditions are met, and hide_blanks is False, assigns an empty string "" as the annotation value for that key.
+
+        2. If the value is a string and matches the pattern defined by csv_list_regex, get validation rule based on "node label" or "node display name".
+        Check if the rule contains "list" as a rule, if it does, split the string by comma and assign the resulting list as the annotation value for that key.
+
+        3. For any other conditions, assigns the original value of anno_v to the annotation key (anno_k).
+
+        4. Returns the updated annotations dictionary.
+
+        Args:
+            dmge (DataModelGraphExplorer): data model graph explorer
+            metadata_syn (dict): metadata used for Synapse storage
+            hideBlanks (bool): if true, does not upload annotation keys with blank values.
+            csv_list_regex (str): Regex to match with comma separated list
+            annos (Dict[str, Any]): dictionary of annotation returned from synapse
+            annotation_keys (str): display_label/class_label
+
+        Returns:
+            Dict[str, Any]: annotations as a dictionary
+
+        ```mermaid
+        flowchart TD
+            A[Start] --> C{Is anno_v empty, whitespace, or NaN?}
+            C -- Yes --> D{Is hide_blanks True?}
+            D -- Yes --> E[Remove this annotation key from the annotation dictionary to be uploaded. Skip further processing]
+            D -- No --> F[Assign empty string to annotation key]
+            C -- No --> G{Is anno_v a string?}
+            G -- No --> H[Assign original value of anno_v to annotation key]
+            G -- Yes --> I{Does anno_v match csv_list_regex?}
+            I -- Yes --> J[Get validation rule of anno_k]
+            J --> K{Does the validation rule contain 'list'}
+            K -- Yes --> L[Split anno_v by commas and assign as list]
+            I -- No --> H
+            K -- No --> H
+        ```
+        """
+        for anno_k, anno_v in metadata_syn.items():
+            # Remove keys with nan or empty string values or string that only contains white space from dict of annotations to be uploaded
+            # if present on current data annotation
+            if hide_blanks and (
+                (isinstance(anno_v, str) and anno_v.strip() == "")
+                or (isinstance(anno_v, float) and np.isnan(anno_v))
+            ):
+                annos["annotations"]["annotations"].pop(anno_k) if anno_k in annos[
+                    "annotations"
+                ]["annotations"].keys() else annos["annotations"]["annotations"]
+                continue
+
+            # Otherwise save annotation as approrpriate
+            if isinstance(anno_v, float) and np.isnan(anno_v):
+                annos["annotations"]["annotations"][anno_k] = ""
+                continue
+
+            # Handle strings that match the csv_list_regex and pass the validation rule
+            if isinstance(anno_v, str) and re.fullmatch(csv_list_regex, anno_v):
+                # Use a dictionary to dynamically choose the argument
+                param = (
+                    {"node_display_name": anno_k}
+                    if annotation_keys == "display_label"
+                    else {"node_label": anno_k}
+                )
+                node_validation_rules = dmge.get_node_validation_rules(**param)
+
+                if rule_in_rule_list("list", node_validation_rules):
+                    annos["annotations"]["annotations"][anno_k] = anno_v.split(",")
+                    continue
+            # default: assign the original value
+            annos["annotations"]["annotations"][anno_k] = anno_v
+
+        return annos
+
+    @async_missing_entity_handler
+    async def format_row_annotations(
+        self,
+        dmge: DataModelGraphExplorer,
+        row: pd.Series,
+        entityId: str,
+        hideBlanks: bool,
+        annotation_keys: str,
+    ) -> Union[None, Dict[str, Any]]:
+        """Format row annotations
+
+        Args:
+            dmge (DataModelGraphExplorer): data moodel graph explorer object
+            row (pd.Series): row of the manifest
+            entityId (str): entity id of the manifest
+            hideBlanks (bool): when true, does not upload annotation keys with blank values. When false, upload Annotation keys with empty string values
+            annotation_keys (str): display_label/class_label
+
+        Returns:
+            Union[None, Dict[str,]]: if entity id is in trash can, return None. Otherwise, return the annotations
+        """
         # prepare metadata for Synapse storage (resolve display name into a name that Synapse annotations support (e.g no spaces, parenthesis)
         # note: the removal of special characters, will apply only to annotation keys; we are not altering the manifest
         # this could create a divergence between manifest column and annotations. this should be ok for most use cases.
@@ -1388,29 +1656,18 @@ def format_row_annotations(
 
             metadataSyn[keySyn] = v
         # set annotation(s) for the various objects/items in a dataset on Synapse
-        annos = self.syn.get_annotations(entityId)
+        annos = await self.get_async_annotation(entityId)
+
         csv_list_regex = comma_separated_list_regex()
-        for anno_k, anno_v in metadataSyn.items():
-            # Remove keys with nan or empty string values from dict of annotations to be uploaded
-            # if present on current data annotation
-            if hideBlanks and (
-                anno_v == "" or (isinstance(anno_v, float) and np.isnan(anno_v))
-            ):
-                annos.pop(anno_k) if anno_k in annos.keys() else annos
-            # Otherwise save annotation as approrpriate
-            else:
-                if isinstance(anno_v, float) and np.isnan(anno_v):
-                    annos[anno_k] = ""
-                elif (
-                    isinstance(anno_v, str)
-                    and re.fullmatch(csv_list_regex, anno_v)
-                    and rule_in_rule_list(
-                        "list", dmge.get_node_validation_rules(anno_k)
-                    )
-                ):
-                    annos[anno_k] = anno_v.split(",")
-                else:
-                    annos[anno_k] = anno_v
+
+        annos = self.process_row_annotations(
+            dmge=dmge,
+            metadata_syn=metadataSyn,
+            hide_blanks=hideBlanks,
+            csv_list_regex=csv_list_regex,
+            annos=annos,
+            annotation_keys=annotation_keys,
+        )
 
         return annos
 
@@ -1610,8 +1867,10 @@ def _add_id_columns_to_manifest(
 
     def _generate_table_name(self, manifest):
         """Helper function to generate a table name for upload to synapse.
+
         Args:
             Manifest loaded as a pd.Dataframe
+
         Returns:
             table_name (str): Name of the table to load
             component_name (str): Name of the manifest component (if applicable)
@@ -1625,37 +1884,6 @@ def _generate_table_name(self, manifest):
             table_name = "synapse_storage_manifest_table"
         return table_name, component_name
 
-    @tracer.start_as_current_span("SynapseStorage::_add_annotations")
-    def _add_annotations(
-        self,
-        dmge,
-        row,
-        entityId: str,
-        hideBlanks: bool,
-        annotation_keys: str,
-    ):
-        """Helper function to format and add annotations to entities in Synapse.
-        Args:
-            dmge: DataModelGraphExplorer object,
-            row: current row of manifest being processed
-            entityId (str): synapseId of entity to add annotations to
-            hideBlanks: Boolean flag that does not upload annotation keys with blank values when true. Uploads Annotation keys with empty string values when false.
-            annotation_keys:  (str) display_label/class_label(default), Determines labeling syle for annotation keys. class_label will format the display
-                name as upper camelcase, and strip blacklisted characters, display_label will strip blacklisted characters including spaces, to retain
-                display label formatting while ensuring the label is formatted properly for Synapse annotations.
-        Returns:
-            Annotations are added to entities in Synapse, no return.
-        """
-        # Format annotations for Synapse
-        annos = self.format_row_annotations(
-            dmge, row, entityId, hideBlanks, annotation_keys
-        )
-
-        if annos:
-            # Store annotations for an entity folder
-            self.syn.set_annotations(annos)
-        return
-
     def _create_entity_id(self, idx, row, manifest, datasetId):
         """Helper function to generate an entityId and add it to the appropriate row in the manifest.
         Args:
@@ -1675,8 +1903,51 @@ def _create_entity_id(self, idx, row, manifest, datasetId):
         manifest.loc[idx, "entityId"] = entityId
         return manifest, entityId
 
+    async def _process_store_annos(self, requests: Set[asyncio.Task]) -> None:
+        """Process annotations and store them on synapse asynchronously
+
+        Args:
+            requests (Set[asyncio.Task]): a set of tasks of formatting annotations created by format_row_annotations function in previous step
+
+        Raises:
+            RuntimeError: raise a run time error if a task failed to complete
+        """
+        while requests:
+            done_tasks, pending_tasks = await asyncio.wait(
+                requests, return_when=asyncio.FIRST_COMPLETED
+            )
+            requests = pending_tasks
+
+            for completed_task in done_tasks:
+                try:
+                    annos = completed_task.result()
+
+                    if isinstance(annos, Annotations):
+                        annos_dict = asdict(annos)
+                        normalized_annos = {k.lower(): v for k, v in annos_dict.items()}
+                        entity_id = normalized_annos["id"]
+                        logger.info(f"Successfully stored annotations for {entity_id}")
+                    else:
+                        # store annotations if they are not None
+                        if annos:
+                            normalized_annos = {
+                                k.lower(): v
+                                for k, v in annos["annotations"]["annotations"].items()
+                            }
+                            entity_id = normalized_annos["entityid"]
+                            logger.info(
+                                f"Obtained and processed annotations for {entity_id} entity"
+                            )
+                            requests.add(
+                                asyncio.create_task(
+                                    self.store_async_annotation(annotation_dict=annos)
+                                )
+                            )
+                except Exception as e:
+                    raise RuntimeError(f"failed with { repr(e) }.") from e
+
     @tracer.start_as_current_span("SynapseStorage::add_annotations_to_entities_files")
-    def add_annotations_to_entities_files(
+    async def add_annotations_to_entities_files(
         self,
         dmge,
         manifest,
@@ -1717,6 +1988,7 @@ def add_annotations_to_entities_files(
             ).drop("entityId_x", axis=1)
 
         # Fill `entityId` for each row if missing and annotate entity as appropriate
+        requests = set()
         for idx, row in manifest.iterrows():
             if not row["entityId"] and (
                 manifest_record_type == "file_and_entities"
@@ -1736,8 +2008,14 @@ def add_annotations_to_entities_files(
 
             # Adding annotations to connected files.
             if entityId:
-                self._add_annotations(dmge, row, entityId, hideBlanks, annotation_keys)
-                logger.info(f"Added annotations to entity: {entityId}")
+                # Format annotations for Synapse
+                annos_task = asyncio.create_task(
+                    self.format_row_annotations(
+                        dmge, row, entityId, hideBlanks, annotation_keys
+                    )
+                )
+                requests.add(annos_task)
+        await self._process_store_annos(requests)
         return manifest
 
     @tracer.start_as_current_span("SynapseStorage::upload_manifest_as_table")
@@ -1791,14 +2069,16 @@ def upload_manifest_as_table(
         )
 
         if file_annotations_upload:
-            manifest = self.add_annotations_to_entities_files(
-                dmge,
-                manifest,
-                manifest_record_type,
-                datasetId,
-                hideBlanks,
-                manifest_synapse_table_id,
-                annotation_keys,
+            manifest = asyncio.run(
+                self.add_annotations_to_entities_files(
+                    dmge,
+                    manifest,
+                    manifest_record_type,
+                    datasetId,
+                    hideBlanks,
+                    manifest_synapse_table_id,
+                    annotation_keys,
+                )
             )
         # Load manifest to synapse as a CSV File
         manifest_synapse_file_id = self.upload_manifest_file(
@@ -1865,13 +2145,15 @@ def upload_manifest_as_csv(
             manifest_synapse_file_id (str): SynID of manifest csv uploaded to synapse.
         """
         if file_annotations_upload:
-            manifest = self.add_annotations_to_entities_files(
-                dmge,
-                manifest,
-                manifest_record_type,
-                datasetId,
-                hideBlanks,
-                annotation_keys=annotation_keys,
+            manifest = asyncio.run(
+                self.add_annotations_to_entities_files(
+                    dmge,
+                    manifest,
+                    manifest_record_type,
+                    datasetId,
+                    hideBlanks,
+                    annotation_keys=annotation_keys,
+                )
             )
 
         # Load manifest to synapse as a CSV File
@@ -1943,14 +2225,16 @@ def upload_manifest_combo(
         )
 
         if file_annotations_upload:
-            manifest = self.add_annotations_to_entities_files(
-                dmge,
-                manifest,
-                manifest_record_type,
-                datasetId,
-                hideBlanks,
-                manifest_synapse_table_id,
-                annotation_keys=annotation_keys,
+            manifest = asyncio.run(
+                self.add_annotations_to_entities_files(
+                    dmge,
+                    manifest,
+                    manifest_record_type,
+                    datasetId,
+                    hideBlanks,
+                    manifest_synapse_table_id,
+                    annotation_keys=annotation_keys,
+                )
             )
 
         # Load manifest to synapse as a CSV File
@@ -2037,9 +2321,9 @@ def associateMetadataWithFiles(
         # Upload manifest to synapse based on user input (manifest_record_type)
         if manifest_record_type == "file_only":
             manifest_synapse_file_id = self.upload_manifest_as_csv(
-                dmge,
-                manifest,
-                metadataManifestPath,
+                dmge=dmge,
+                manifest=manifest,
+                metadataManifestPath=metadataManifestPath,
                 datasetId=datasetId,
                 restrict=restrict_manifest,
                 hideBlanks=hideBlanks,
@@ -2050,9 +2334,9 @@ def associateMetadataWithFiles(
             )
         elif manifest_record_type == "table_and_file":
             manifest_synapse_file_id = self.upload_manifest_as_table(
-                dmge,
-                manifest,
-                metadataManifestPath,
+                dmge=dmge,
+                manifest=manifest,
+                metadataManifestPath=metadataManifestPath,
                 datasetId=datasetId,
                 table_name=table_name,
                 component_name=component_name,
@@ -2066,9 +2350,9 @@ def associateMetadataWithFiles(
             )
         elif manifest_record_type == "file_and_entities":
             manifest_synapse_file_id = self.upload_manifest_as_csv(
-                dmge,
-                manifest,
-                metadataManifestPath,
+                dmge=dmge,
+                manifest=manifest,
+                metadataManifestPath=metadataManifestPath,
                 datasetId=datasetId,
                 restrict=restrict_manifest,
                 hideBlanks=hideBlanks,
@@ -2079,9 +2363,9 @@ def associateMetadataWithFiles(
             )
         elif manifest_record_type == "table_file_and_entities":
             manifest_synapse_file_id = self.upload_manifest_combo(
-                dmge,
-                manifest,
-                metadataManifestPath,
+                dmge=dmge,
+                manifest=manifest,
+                metadataManifestPath=metadataManifestPath,
                 datasetId=datasetId,
                 table_name=table_name,
                 component_name=component_name,
@@ -2263,6 +2547,7 @@ def checkIfinAssetView(self, syn_id) -> str:
         else:
             return False
 
+    @tracer.start_as_current_span("SynapseStorage::getDatasetProject")
     @retry(
         stop=stop_after_attempt(5),
         wait=wait_chain(
@@ -2294,7 +2579,7 @@ def getDatasetProject(self, datasetId: str) -> str:
         # re-query if no datasets found
         if dataset_row.empty:
             sleep(5)
-            self._query_fileview()
+            self.query_fileview()
             # Subset main file view
             dataset_index = self.storageFileviewTable["id"] == datasetId
             dataset_row = self.storageFileviewTable[dataset_index]
@@ -2400,6 +2685,7 @@ def __init__(
         self.existingTableId = existingTableId
         self.restrict = restrict
 
+    @tracer.start_as_current_span("TableOperations::createTable")
     def createTable(
         self,
         columnTypeDict: dict = None,
@@ -2468,6 +2754,7 @@ def createTable(
             table = self.synStore.syn.store(table, isRestricted=self.restrict)
             return table.schema.id
 
+    @tracer.start_as_current_span("TableOperations::replaceTable")
     def replaceTable(
         self,
         specifySchema: bool = True,
@@ -2562,6 +2849,7 @@ def replaceTable(
         existing_table.drop(columns=["ROW_ID", "ROW_VERSION"], inplace=True)
         return self.existingTableId
 
+    @tracer.start_as_current_span("TableOperations::_get_auth_token")
     def _get_auth_token(
         self,
     ):
@@ -2605,6 +2893,7 @@ def _get_auth_token(
 
         return authtoken
 
+    @tracer.start_as_current_span("TableOperations::upsertTable")
     def upsertTable(self, dmge: DataModelGraphExplorer):
         """
         Method to upsert rows from a new manifest into an existing table on synapse
@@ -2645,6 +2934,7 @@ def upsertTable(self, dmge: DataModelGraphExplorer):
 
         return self.existingTableId
 
+    @tracer.start_as_current_span("TableOperations::_update_table_uuid_column")
     def _update_table_uuid_column(
         self,
         dmge: DataModelGraphExplorer,
@@ -2710,6 +3000,7 @@ def _update_table_uuid_column(
 
         return
 
+    @tracer.start_as_current_span("TableOperations::updateTable")
     def updateTable(
         self,
         update_col: str = "Id",
@@ -2876,6 +3167,8 @@ def _fix_int_columns(self):
         for col in int_columns:
             # Coercing to string because NaN is a floating point value
             # and cannot exist alongside integers in a column
-            to_int_fn = lambda x: "" if np.isnan(x) else str(int(x))
+            def to_int_fn(x):
+                return "" if np.isnan(x) else str(int(x))
+
             self.table[col] = self.table[col].apply(to_int_fn)
         return self.table
diff --git a/schematic/utils/validate_rules_utils.py b/schematic/utils/validate_rules_utils.py
index e5192ce8a..5da5510ab 100644
--- a/schematic/utils/validate_rules_utils.py
+++ b/schematic/utils/validate_rules_utils.py
@@ -1,10 +1,10 @@
 """validate rules utils"""
 
 import logging
-from typing import TypedDict, Optional, Literal
-from typing_extensions import assert_never
-from jsonschema import ValidationError
+from typing import Literal, Optional, TypedDict
 
+from jsonschema import ValidationError
+from typing_extensions import assert_never
 
 logger = logging.getLogger(__name__)
 
@@ -149,6 +149,13 @@ def validation_rule_info() -> dict[str, Rule]:
             "default_message_level": None,
             "fixed_arg": None,
         },
+        "filenameExists": {
+            "arguments": (1, 1),
+            "type": "filename_validation",
+            "complementary_rules": None,
+            "default_message_level": "error",
+            "fixed_arg": None,
+        },
     }
 
 
diff --git a/schematic/visualization/tangled_tree.py b/schematic/visualization/tangled_tree.py
index 59ba62139..95eac7e75 100644
--- a/schematic/visualization/tangled_tree.py
+++ b/schematic/visualization/tangled_tree.py
@@ -3,24 +3,24 @@
 # pylint: disable=logging-fstring-interpolation
 # pylint: disable=too-many-lines
 
-from io import StringIO
+import ast
 import json
 import logging
 import os
+from io import StringIO
 from os import path
-from typing import Optional, Literal, TypedDict, Union
-from typing_extensions import assert_never
+from typing import Literal, Optional, TypedDict, Union
 
 import networkx as nx  # type: ignore
-from networkx.classes.reportviews import NodeView, EdgeDataView  # type: ignore
 import pandas as pd
+from networkx.classes.reportviews import EdgeDataView, NodeView  # type: ignore
+from typing_extensions import assert_never
 
-from schematic.visualization.attributes_explorer import AttributesExplorer
-from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
+from schematic.schemas.data_model_parser import DataModelParser
 from schematic.utils.io_utils import load_json
 from schematic.utils.schema_utils import DisplayLabelType
-
+from schematic.visualization.attributes_explorer import AttributesExplorer
 
 logger = logging.getLogger(__name__)
 
@@ -258,11 +258,16 @@ def _get_ca_alias(self, conditional_requirements: list[str]) -> dict[str, str]:
                 value: attribute
         """
         ca_alias: dict[str, str] = {}
+        extracted_conditional_requirements = []
+        for conditional_requirement in conditional_requirements:
+            extracted_conditional_requirements.extend(
+                ast.literal_eval(node_or_string=conditional_requirement)
+            )
 
         # clean up conditional requirements
         conditional_requirements = [
             self._remove_unwanted_characters_from_conditional_statement(req)
-            for req in conditional_requirements
+            for req in extracted_conditional_requirements
         ]
 
         for req in conditional_requirements:
diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml
index 15a3540d1..8689a8ae2 100644
--- a/schematic_api/api/openapi/api.yaml
+++ b/schematic_api/api/openapi/api.yaml
@@ -15,7 +15,7 @@ components:
       type: http
       scheme: bearer
       bearerFormat: JWT
-      x-bearerInfoFunc: schematic_api.api.security_controller_.info_from_bearerAuth
+      x-bearerInfoFunc: schematic_api.api.security_controller.info_from_bearer_auth
 
 # TO DO: refactor query parameters and remove access_token
 paths:
@@ -303,6 +303,14 @@ paths:
           description: List, a subset of the projects contained within the asset view that are relevant for the current operation. Speeds up some operations that interact with Synapse. Relevant for validating manifests involving cross-manifest validation, but optional.
           example: ['syn23643250', 'syn47218127', 'syn47218347']
           required: false
+        - in: query
+          name: dataset_scope
+          schema:
+            type: string
+            nullable: true
+          description: Specify a dataset to validate against for filename validation.
+          example: 'syn61682648'
+          required: false
 
       operationId: schematic_api.api.routes.validate_manifest_route
       responses:
@@ -459,6 +467,14 @@ paths:
           description: List, a subset of the projects contained within the asset view that are relevant for the current operation. Speeds up some operations that interact with Synapse.
           example: ['syn23643250', 'syn47218127', 'syn47218347']
           required: false
+        - in: query
+          name: dataset_scope
+          schema:
+            type: string
+            nullable: true
+          description: Specify a dataset to validate against for filename validation.
+          example: 'syn61682648'
+          required: false
       operationId: schematic_api.api.routes.submit_manifest_route
       responses:
         "200":
diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py
index ae73428eb..e977e480d 100644
--- a/schematic_api/api/routes.py
+++ b/schematic_api/api/routes.py
@@ -1,4 +1,3 @@
-import json
 import logging
 import os
 import pathlib
@@ -8,12 +7,10 @@
 import time
 import urllib.request
 from functools import wraps
-from json.decoder import JSONDecodeError
-from typing import Any, List, Optional
+from typing import List, Tuple
 
 import connexion
 import pandas as pd
-from connexion.decorators.uri_parsing import Swagger2URIParser
 from flask import current_app as app
 from flask import request, send_from_directory
 from flask_cors import cross_origin
@@ -28,14 +25,6 @@
     Span,
 )
 from opentelemetry.sdk.trace.sampling import ALWAYS_OFF
-from synapseclient.core.exceptions import (
-    SynapseAuthenticationError,
-    SynapseHTTPError,
-    SynapseNoCredentialsError,
-    SynapseTimeoutError,
-    SynapseUnmetAccessRestrictions,
-)
-from werkzeug.debug import DebuggedApplication
 
 from schematic.configuration.configuration import CONFIG
 from schematic.manifest.generator import ManifestGenerator
@@ -54,8 +43,10 @@
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.DEBUG)
 
+tracing_service_name = os.environ.get("TRACING_SERVICE_NAME", "schematic-api")
+
 trace.set_tracer_provider(
-    TracerProvider(resource=Resource(attributes={SERVICE_NAME: "schematic-api"}))
+    TracerProvider(resource=Resource(attributes={SERVICE_NAME: tracing_service_name}))
 )
 
 
@@ -410,6 +401,7 @@ def validate_manifest_route(
     json_str=None,
     asset_view=None,
     project_scope=None,
+    dataset_scope=None,
 ):
     # Access token now stored in request header
     access_token = get_access_token()
@@ -450,6 +442,7 @@ def validate_manifest_route(
         restrict_rules=restrict_rules,
         project_scope=project_scope,
         access_token=access_token,
+        dataset_scope=dataset_scope,
     )
 
     res_dict = {"errors": errors, "warnings": warnings}
@@ -457,7 +450,7 @@ def validate_manifest_route(
     return res_dict
 
 
-#####profile validate manifest route function
+# profile validate manifest route function
 @trace_function_params()
 def submit_manifest_route(
     schema_url,
@@ -469,6 +462,7 @@ def submit_manifest_route(
     data_type=None,
     hide_blanks=False,
     project_scope=None,
+    dataset_scope=None,
     table_column_names=None,
     annotation_keys=None,
     file_annotations_upload: bool = True,
@@ -526,6 +520,7 @@ def submit_manifest_route(
         hide_blanks=hide_blanks,
         table_manipulation=table_manipulation,
         project_scope=project_scope,
+        dataset_scope=dataset_scope,
         table_column_names=table_column_names,
         annotation_keys=annotation_keys,
         file_annotations_upload=file_annotations_upload,
@@ -596,7 +591,9 @@ def get_storage_projects_datasets(asset_view, project_id):
     return sorted_dataset_lst
 
 
-def get_files_storage_dataset(asset_view, dataset_id, full_path, file_names=None):
+def get_files_storage_dataset(
+    asset_view: str, dataset_id: str, full_path: bool, file_names: List[str] = None
+) -> List[Tuple[str, str]]:
     # Access token now stored in request header
     access_token = get_access_token()
 
diff --git a/schematic_api/api/security_controller.py b/schematic_api/api/security_controller.py
new file mode 100644
index 000000000..5b881576d
--- /dev/null
+++ b/schematic_api/api/security_controller.py
@@ -0,0 +1,48 @@
+import logging
+from typing import Dict, Union
+
+from jwt import PyJWKClient, decode
+from jwt.exceptions import PyJWTError
+from synapseclient import Synapse
+
+from schematic.configuration.configuration import CONFIG
+
+logger = logging.getLogger(__name__)
+
+syn = Synapse(
+    configPath=CONFIG.synapse_configuration_path,
+    cache_client=False,
+    skip_checks=True,
+)
+jwks_client = PyJWKClient(
+    uri=syn.authEndpoint + "/oauth2/jwks", headers=syn._generate_headers()
+)
+
+
+def info_from_bearer_auth(token: str) -> Dict[str, Union[str, int]]:
+    """
+    Authenticate user using bearer token. The token claims are decoded and returned.
+
+    Example from:
+    <https://pyjwt.readthedocs.io/en/stable/usage.html#retrieve-rsa-signing-keys-from-a-jwks-endpoint>
+
+    Args:
+        token (str): Bearer token.
+
+    Returns:
+        dict: Decoded token information.
+    """
+    try:
+        signing_key = jwks_client.get_signing_key_from_jwt(token)
+        data = decode(
+            jwt=token,
+            key=signing_key.key,
+            algorithms=[signing_key.algorithm_name],
+            options={"verify_aud": False},
+        )
+
+        return data
+    except PyJWTError:
+        logger.exception("Error decoding authentication token")
+        # When the return type is None the web framework will return a 401 OAuthResponseProblem exception
+        return None
diff --git a/schematic_api/api/security_controller_.py b/schematic_api/api/security_controller_.py
deleted file mode 100644
index fbde596bb..000000000
--- a/schematic_api/api/security_controller_.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from typing import List
-
-
-def info_from_bearerAuth(token):
-    """
-    Check and retrieve authentication information from custom bearer token.
-    Returned value will be passed in 'token_info' parameter of your operation function, if there is one.
-    'sub' or 'uid' will be set in 'user' parameter of your operation function, if there is one.
-    :param token Token provided by Authorization header
-    :type token: str
-    :return: Decoded token information or None if token is invalid
-    :rtype: dict | None
-    """
-    return {"uid": "user_id"}
diff --git a/sonar-project.properties b/sonar-project.properties
new file mode 100644
index 000000000..6aeb19c1c
--- /dev/null
+++ b/sonar-project.properties
@@ -0,0 +1,5 @@
+sonar.projectKey=Sage-Bionetworks_schematic
+sonar.organization=sage-bionetworks
+sonar.python.coverage.reportPaths=coverage.xml
+sonar.sources=schematic
+sonar.tests=tests


Test patch:
diff --git a/.github/workflows/api_test.yml b/.github/workflows/api_test.yml
index 354cbe3ba..0dea21710 100644
--- a/.github/workflows/api_test.yml
+++ b/.github/workflows/api_test.yml
@@ -27,10 +27,10 @@ jobs:
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -43,21 +43,11 @@ jobs:
             | python3 - --version ${{ env.POETRY_VERSION }};
           poetry config virtualenvs.create true;
           poetry config virtualenvs.in-project true;
-      #----------------------------------------------
-      #       load cached venv if cache exists
-      #----------------------------------------------
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-
+          
       #----------------------------------------------
       # install dependencies and root project
       #----------------------------------------------
       - name: Install dependencies and root project
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: poetry install --no-interaction --all-extras
 
       #----------------------------------------------
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0b1a152ef..3fb546bbe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -7,7 +7,7 @@ name: Test schematic
 
 on:
   push:
-    branches: ['main']
+    branches: ['main', 'develop']
   pull_request:
     branches: ['*']
   workflow_dispatch:  # Allow manually triggering the workflow
@@ -25,7 +25,7 @@ concurrency:
   cancel-in-progress: true
 jobs:
   test:
-    runs-on: ubuntu-22.04-4core-16GBRAM-150GBSSD
+    runs-on: ubuntu-latest
     env:
       POETRY_VERSION:  1.3.0
     strategy:
@@ -39,13 +39,25 @@ jobs:
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
+      #----------------------------------------------
+      #       verify runner environment
+      #----------------------------------------------
+      # - name: Print runner environment information
+      #   run: |
+      #     echo "Running on runner: $RUNNER_NAME"
+      #     echo "Runner OS: $RUNNER_OS"
+      #     echo "Runner OS version: $RUNNER_OS_VERSION"
+      #     echo "Runner architecture: $RUNNER_ARCH"
+      #     echo "Total memory: $(free -h)"
+      #     echo "CPU info: $(lscpu)"
+
       #----------------------------------------------
       #          install & configure poetry
       #----------------------------------------------
@@ -55,23 +67,12 @@ jobs:
             | python3 - --version ${{ env.POETRY_VERSION }};
           poetry config virtualenvs.create true;
           poetry config virtualenvs.in-project true;
-      #----------------------------------------------
-      #       load cached venv if cache exists
-      #----------------------------------------------
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
 
       #----------------------------------------------
       # install dependencies and root project
       #----------------------------------------------
       - name: Install dependencies and root project
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: poetry install --no-interaction --all-extras
-
       #----------------------------------------------
       #             perform linting
       #----------------------------------------------
@@ -113,21 +114,76 @@ jobs:
           poetry run pylint schematic/visualization/* schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py schematic/utils/*.py schematic/schemas/*.py
 
       #----------------------------------------------
-      #              run test suite
+      #              run unit test suite
+      #----------------------------------------------
+      - name: Run unit tests
+        env:
+          SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
+          SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
+        run: >
+          poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov 
+          --cov-report=xml:coverage.xml --cov=schematic/ --reruns 4 -n 8 tests/unit;
+
+      #----------------------------------------------
+      #              run integration test suite
       #----------------------------------------------
-      - name: Run tests
+      - name: Run integration tests
+        if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) }}
         env:
           SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
           SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
         run: >
-          source .venv/bin/activate;
-          pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/
-          -m "not (google_credentials_needed or schematic_api or table_operations)" --reruns 2 -n auto
+          poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/
+          -m "not (rule_benchmark)" --reruns 4 -n 8 --ignore=tests/unit
+
 
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: pytest-results-${{ matrix.python-version }}
           path: htmlcov
         # Use always() to always run this step to publish test results when there are test failures
+        if: ${{ always() && contains(fromJSON('["3.10"]'), matrix.python-version) }}
+      - name: Upload XML coverage report
+        id: upload_coverage_report
+        uses: actions/upload-artifact@v4
+        # Only upload a single python version to pass along to sonarcloud
+        if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) && always() }}
+        with:
+          name: coverage-report
+          path: coverage.xml
+
+  sonarcloud:
+    needs: [test]
+    if: ${{ always() && !cancelled()}}
+    name: SonarCloud
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Check coverage-report artifact existence
+        id: check_coverage_report
+        uses: LIT-Protocol/artifact-exists-action@v0
+        with:
+          name: "coverage-report"
+      - name: Download coverage report
+        uses: actions/download-artifact@v4
+        if: steps.check_coverage_report.outputs.exists == 'true'
+        with:
+          name: coverage-report
+      - name: Check coverage.xml file existence
+        id: check_coverage_xml
+        uses: andstor/file-existence-action@v3
+        with:
+          files: "coverage.xml"
+        # This is a workaround described in https://community.sonarsource.com/t/sonar-on-github-actions-with-python-coverage-source-issue/36057
+      - name: Override Coverage Source Path for Sonar
+        if: steps.check_coverage_xml.outputs.files_exists == 'true'
+        run: sed -i "s/<source>\/home\/runner\/work\/schematic\/schematic\/schematic<\/source>/<source>\/github\/workspace\/schematic<\/source>/g" coverage.xml
+      - name: SonarCloud Scan
+        uses: SonarSource/sonarcloud-github-action@master
         if: ${{ always() }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 000000000..982e6ef86
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,6 @@
+[pytest]
+python_files = test_*.py
+asyncio_mode = auto
+asyncio_default_fixture_loop_scope = session
+log_cli = False
+log_cli_level = INFO
\ No newline at end of file
diff --git a/tests/conftest.py b/tests/conftest.py
index 62c2cb3e3..e6382ed40 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,19 +1,34 @@
 """Fixtures and helpers for use across all tests"""
-import os
+import configparser
 import logging
+import os
+import shutil
 import sys
-from typing import Generator
+from typing import Callable, Generator, Set
 
-import shutil
 import pytest
 from dotenv import load_dotenv
-
-from schematic.schemas.data_model_parser import DataModelParser
+from opentelemetry import trace
+from opentelemetry._logs import set_logger_provider
+from opentelemetry.exporter.otlp.proto.grpc._log_exporter import OTLPLogExporter
+from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter
+from opentelemetry.sdk._logs import LoggerProvider, LoggingHandler
+from opentelemetry.sdk._logs.export import BatchLogRecordProcessor
+from opentelemetry.sdk.resources import SERVICE_NAME, Resource
+from opentelemetry.sdk.trace import TracerProvider
+from opentelemetry.sdk.trace.export import BatchSpanProcessor
+from opentelemetry.sdk.trace.sampling import ALWAYS_OFF
+from pytest_asyncio import is_async_test
+
+from schematic.configuration.configuration import CONFIG, Configuration
+from schematic.models.metadata import MetadataModel
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
-
-from schematic.configuration.configuration import CONFIG
-from schematic.utils.df_utils import load_df
+from schematic.schemas.data_model_parser import DataModelParser
 from schematic.store.synapse import SynapseStorage
+from schematic.utils.df_utils import load_df
+from tests.utils import CleanupAction, CleanupItem
+
+tracer = trace.get_tracer("Schematic-Tests")
 
 load_dotenv()
 
@@ -117,14 +132,8 @@ def config():
 
 
 @pytest.fixture(scope="session")
-def synapse_store(request):
-    access_token = os.getenv("SYNAPSE_ACCESS_TOKEN")
-    if access_token:
-        synapse_store = SynapseStorage(access_token=access_token)
-    else:
-        synapse_store = SynapseStorage()
-
-    yield synapse_store
+def synapse_store():
+    yield SynapseStorage()
 
 
 # These fixtures make copies of existing test manifests.
@@ -149,3 +158,126 @@ def temporary_file_copy(request, helpers: Helpers) -> Generator[str, None, None]
     # Teardown
     if os.path.exists(temp_csv_path):
         os.remove(temp_csv_path)
+
+
+@pytest.fixture(name="dmge", scope="function")
+def DMGE(helpers: Helpers) -> DataModelGraphExplorer:
+    """Fixture to instantiate a DataModelGraphExplorer object."""
+    dmge = helpers.get_data_model_graph_explorer(path="example.model.jsonld")
+    return dmge
+
+
+@pytest.fixture(scope="class")
+def syn_token(config: Configuration):
+    synapse_config_path = config.synapse_configuration_path
+    config_parser = configparser.ConfigParser()
+    config_parser.read(synapse_config_path)
+    # try using synapse access token
+    if "SYNAPSE_ACCESS_TOKEN" in os.environ:
+        token = os.environ["SYNAPSE_ACCESS_TOKEN"]
+    else:
+        token = config_parser["authentication"]["authtoken"]
+    return token
+
+
+def metadata_model(helpers, data_model_labels):
+    metadata_model = MetadataModel(
+        inputMModelLocation=helpers.get_data_path("example.model.jsonld"),
+        data_model_labels=data_model_labels,
+        inputMModelLocationType="local",
+    )
+
+    return metadata_model
+
+
+@pytest.fixture(scope="function")
+def schedule_for_cleanup(
+    request, synapse_store: SynapseStorage
+) -> Callable[[CleanupItem], None]:
+    """Returns a closure that takes an item that should be scheduled for cleanup."""
+
+    items: Set[CleanupItem] = set()
+
+    def _append_cleanup(item: CleanupItem):
+        print(f"Added {item} to cleanup list")
+        items.add(item)
+
+    def cleanup_scheduled_items() -> None:
+        for item in items:
+            print(f"Cleaning up {item}")
+            try:
+                if item.action == CleanupAction.DELETE:
+                    if item.synapse_id:
+                        synapse_store.syn.delete(obj=item.synapse_id)
+                    elif item.name and item.parent_id:
+                        synapse_id = synapse_store.syn.findEntityId(
+                            name=item.name, parent=item.parent_id
+                        )
+                        if synapse_id:
+                            synapse_store.syn.delete(obj=synapse_id)
+                    else:
+                        logger.error(f"Invalid cleanup item {item}")
+                else:
+                    logger.error(f"Invalid cleanup action {item.action}")
+            except Exception as ex:
+                logger.exception(f"Failed to delete {item}")
+
+    request.addfinalizer(cleanup_scheduled_items)
+
+    return _append_cleanup
+
+
+active_span_processors = []
+
+
+@pytest.fixture(scope="session", autouse=True)
+def set_up_tracing() -> None:
+    """Set up tracing for the API."""
+    tracing_export = os.environ.get("TRACING_EXPORT_FORMAT", None)
+    tracing_service_name = os.environ.get("TRACING_SERVICE_NAME", "schematic-tests")
+    if tracing_export == "otlp":
+        trace.set_tracer_provider(
+            TracerProvider(
+                resource=Resource(attributes={SERVICE_NAME: tracing_service_name})
+            )
+        )
+        processor = BatchSpanProcessor(OTLPSpanExporter())
+        active_span_processors.append(processor)
+        trace.get_tracer_provider().add_span_processor(processor)
+    else:
+        trace.set_tracer_provider(TracerProvider(sampler=ALWAYS_OFF))
+
+
+@pytest.fixture(autouse=True, scope="function")
+def wrap_with_otel(request):
+    """Start a new OTEL Span for each test function."""
+    with tracer.start_as_current_span(request.node.name):
+        try:
+            yield
+        finally:
+            for processor in active_span_processors:
+                processor.force_flush()
+
+
+@pytest.fixture(scope="session", autouse=True)
+def set_up_logging() -> None:
+    """Set up logging to export to OTLP."""
+    logging_export = os.environ.get("LOGGING_EXPORT_FORMAT", None)
+    logging_service_name = os.environ.get("LOGGING_SERVICE_NAME", "schematic-tests")
+    logging_instance_name = os.environ.get("LOGGING_INSTANCE_NAME", "local")
+    if logging_export == "otlp":
+        resource = Resource.create(
+            {
+                "service.name": logging_service_name,
+                "service.instance.id": logging_instance_name,
+            }
+        )
+
+        logger_provider = LoggerProvider(resource=resource)
+        set_logger_provider(logger_provider=logger_provider)
+
+        # TODO: Add support for secure connections
+        exporter = OTLPLogExporter(insecure=True)
+        logger_provider.add_log_record_processor(BatchLogRecordProcessor(exporter))
+        handler = LoggingHandler(level=logging.NOTSET, logger_provider=logger_provider)
+        logging.getLogger().addHandler(handler)
diff --git a/tests/data/example.model.csv b/tests/data/example.model.csv
index a99a404f1..a85cf8cbf 100644
--- a/tests/data/example.model.csv
+++ b/tests/data/example.model.csv
@@ -12,7 +12,7 @@ Biospecimen,,,"Sample ID, Patient ID, Tissue Status, Component",,FALSE,DataType,
 Sample ID,,,,,TRUE,DataProperty,,,
 Tissue Status,,"Healthy, Malignant",,,TRUE,DataProperty,,,
 Bulk RNA-seq Assay,,,"Filename, Sample ID, File Format, Component",,FALSE,DataType,Biospecimen,,
-Filename,,,,,TRUE,DataProperty,,,
+Filename,,,,,TRUE,DataProperty,,,#MockFilename filenameExists^^
 File Format,,"FASTQ, BAM, CRAM, CSV/TSV",,,TRUE,DataProperty,,,
 BAM,,,Genome Build,,FALSE,ValidValue,,,
 CRAM,,,"Genome Build, Genome FASTA",,FALSE,ValidValue,,,
@@ -51,4 +51,5 @@ Check Date,,,,,TRUE,DataProperty,,,date
 Check NA,,,,,TRUE,DataProperty,,,int::IsNA
 MockRDB,,,"Component, MockRDB_id, SourceManifest",,FALSE,DataType,,,
 MockRDB_id,,,,,TRUE,DataProperty,,,int
-SourceManifest,,,,,TRUE,DataProperty,,,
\ No newline at end of file
+SourceManifest,,,,,TRUE,DataProperty,,,
+MockFilename,,,"Component, Filename",,FALSE,DataType,,,
diff --git a/tests/data/example.model.jsonld b/tests/data/example.model.jsonld
index 44cea61d5..3f13b188e 100644
--- a/tests/data/example.model.jsonld
+++ b/tests/data/example.model.jsonld
@@ -614,7 +614,9 @@
             },
             "sms:displayName": "Filename",
             "sms:required": "sms:true",
-            "sms:validationRules": []
+            "sms:validationRules": {
+                "MockFilename": "filenameExists"
+            }
         },
         {
             "@id": "bts:FileFormat",
@@ -1719,6 +1721,31 @@
             "sms:displayName": "SourceManifest",
             "sms:required": "sms:true",
             "sms:validationRules": []
+        },
+        {
+            "@id": "bts:MockFilename",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "MockFilename",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:DataType"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "MockFilename",
+            "sms:required": "sms:false",
+            "sms:requiresDependency": [
+                {
+                    "@id": "bts:Component"
+                },
+                {
+                    "@id": "bts:Filename"
+                }
+            ],
+            "sms:validationRules": []
         }
     ],
     "@id": "http://schema.biothings.io/#0.1"
diff --git a/tests/data/mock_manifests/BulkRNAseq_component_based_required_rule_test.manifest.csv b/tests/data/mock_manifests/BulkRNAseq_component_based_required_rule_test.manifest.csv
index d0cd7a01c..9818cb966 100644
--- a/tests/data/mock_manifests/BulkRNAseq_component_based_required_rule_test.manifest.csv
+++ b/tests/data/mock_manifests/BulkRNAseq_component_based_required_rule_test.manifest.csv
@@ -1,4 +1,4 @@
 Filename,Sample ID,File Format,Component,Genome Build,Genome FASTA
-test/file/name.png,fake_id,BAM,BulkRNA-seqAssay,GRCh37,
-test/file/name_2.png,fake_id_2,CRAM,BulkRNA-seqAssay,GRCh38,
-test/file/name_3.png,fake_id_3,,BulkRNA-seqAssay,,
\ No newline at end of file
+schematic - main/test/file/name.png,fake_id,BAM,BulkRNA-seqAssay,GRCh37,
+schematic - main/test/file/name_2.png,fake_id_2,CRAM,BulkRNA-seqAssay,GRCh38,
+schematic - main/test/file/name_3.png,fake_id_3,,BulkRNA-seqAssay,,
diff --git a/tests/data/mock_manifests/InvalidFilenameManifest.csv b/tests/data/mock_manifests/InvalidFilenameManifest.csv
new file mode 100644
index 000000000..bc2619e55
--- /dev/null
+++ b/tests/data/mock_manifests/InvalidFilenameManifest.csv
@@ -0,0 +1,7 @@
+Component,Filename,entityId
+MockFilename,schematic - main/MockFilenameComponent/txt1.txt,syn61682653
+MockFilename,schematic - main/MockFilenameComponent/txt2.txt,syn61682660
+MockFilename,schematic - main/MockFilenameComponent/txt3.txt,syn61682653
+MockFilename,schematic - main/MockFilenameComponent/this_file_does_not_exist.txt,syn61682653
+MockFilename,schematic - main/MockFilenameComponent/txt4.txt,syn6168265
+MockFilename,schematic - main/MockFilenameComponent/txt6.txt,
diff --git a/tests/data/mock_manifests/ValidFilenameManifest.csv b/tests/data/mock_manifests/ValidFilenameManifest.csv
new file mode 100644
index 000000000..de1b7a448
--- /dev/null
+++ b/tests/data/mock_manifests/ValidFilenameManifest.csv
@@ -0,0 +1,5 @@
+Component,Sample ID,Filename,Id,entityId
+MockFilename,1.0,schematic - main/TestSubmitMockFilename/txt1.txt,3c4c384b-5c49-4a7c-90a6-43f03a5ddbdc,syn62822369
+MockFilename,2.0,schematic - main/TestSubmitMockFilename/txt2.txt,3b45f5f3-408f-47ff-945e-9badf0a43195,syn62822368
+MockFilename,3.0,schematic - main/TestSubmitMockFilename/txt3.txt,2bbc898f-2651-4af3-834a-10c506de0fbd,syn62822366
+MockFilename,4.0,schematic - main/TestSubmitMockFilename/txt4.txt,5a2d3816-436e-458f-9887-cb8355518e23,syn62822364
diff --git a/tests/data/mock_manifests/filepath_submission_test_manifest.csv b/tests/data/mock_manifests/filepath_submission_test_manifest.csv
new file mode 100644
index 000000000..3b1a349fc
--- /dev/null
+++ b/tests/data/mock_manifests/filepath_submission_test_manifest.csv
@@ -0,0 +1,3 @@
+Filename,Sample ID,File Format,Component,Genome Build,Genome FASTA,Id,entityId
+schematic - main/Test Filename Upload/txt1.txt,1.0,,BulkRNA-seqAssay,,,01ded8fc-0915-4959-85ab-64e9644c8787,syn62276954
+schematic - main/Test Filename Upload/txt2.txt,2.0,,BulkRNA-seqAssay,,,fd122bb5-3353-4c94-b1f5-0bb93a3e9fc9,syn62276956
diff --git a/tests/data/mock_manifests/filepath_submission_test_manifest_sampleidx10.csv b/tests/data/mock_manifests/filepath_submission_test_manifest_sampleidx10.csv
new file mode 100644
index 000000000..082170549
--- /dev/null
+++ b/tests/data/mock_manifests/filepath_submission_test_manifest_sampleidx10.csv
@@ -0,0 +1,3 @@
+Filename,Sample ID,File Format,Component,Genome Build,Genome FASTA,Id,entityId
+schematic - main/Test Filename Upload/txt1.txt,10.0,,BulkRNA-seqAssay,,,01ded8fc-0915-4959-85ab-64e9644c8787,syn62276954
+schematic - main/Test Filename Upload/txt2.txt,20.0,,BulkRNA-seqAssay,,,fd122bb5-3353-4c94-b1f5-0bb93a3e9fc9,syn62276956
diff --git a/tests/data/mock_manifests/test_BulkRNAseq.csv b/tests/data/mock_manifests/test_BulkRNAseq.csv
index facfa3f6a..3dfddf90d 100644
--- a/tests/data/mock_manifests/test_BulkRNAseq.csv
+++ b/tests/data/mock_manifests/test_BulkRNAseq.csv
@@ -1,3 +1,3 @@
 Filename,Sample ID,File Format,Component,Genome Build,Genome FASTA
-TestRNA-seqDataset1/TestRNA-seq-dummy-dataset.rtf,ABCD,BAM,BulkRNA-seqAssay,GRCh38,
-TestRNA-seqDataset1/TestRNA-seq-dummy-dataset2.rtf,EFGH,CRAM,BulkRNA-seqAssay,GRCm39,
+schematic - main/TestRNA-seqDataset1/TestRNA-seq-dummy-dataset.rtf,ABCD,BAM,BulkRNA-seqAssay,GRCh38,
+schematic - main/TestRNA-seqDataset1/TestRNA-seq-dummy-dataset2.rtf,EFGH,CRAM,BulkRNA-seqAssay,GRCm39,
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/integration/test_metadata_model.py b/tests/integration/test_metadata_model.py
new file mode 100644
index 000000000..6aa15bf18
--- /dev/null
+++ b/tests/integration/test_metadata_model.py
@@ -0,0 +1,261 @@
+"""
+This script contains a test suite for verifying the submission and annotation of
+file-based manifests using the `TestMetadataModel` class to communicate with Synapse
+and verify the expected behavior of uploading annotation manifest CSVs using the
+metadata model.
+
+It utilizes the `pytest` framework along with `pytest-mock` to mock and spy on methods
+of the `SynapseStorage` class, which is responsible for handling file uploads and
+annotations in Synapse.
+"""
+
+import logging
+import pytest
+import tempfile
+
+from contextlib import nullcontext as does_not_raise
+
+from pytest_mock import MockerFixture
+from schematic.store.synapse import SynapseStorage
+from tests.conftest import metadata_model
+
+logging.basicConfig(level=logging.DEBUG)
+logger = logging.getLogger(__name__)
+
+
+class TestMetadataModel:
+    # Define the test cases as a class attribute
+    test_cases = [
+        # Test 1: Check that a valid manifest can be submitted, and corresponding entities annotated from it
+        (
+            "mock_manifests/filepath_submission_test_manifest.csv",
+            "syn62276880",
+            None,
+            "syn62280543",
+            "syn53011753",
+            None,
+        ),
+        # Test 2: Change the Sample ID annotation from the previous test to ensure the manifest file is getting updated
+        (
+            "mock_manifests/filepath_submission_test_manifest_sampleidx10.csv",
+            "syn62276880",
+            None,
+            "syn62280543",
+            "syn53011753",
+            None,
+        ),
+        # Test 3: Test manifest file upload with validation based on the MockFilename component and given dataset_scope
+        (
+            "mock_manifests/ValidFilenameManifest.csv",
+            "syn62822337",
+            "MockFilename",
+            "syn62822975",
+            "syn63192751",
+            "syn62822337",
+        ),
+    ]
+
+    def validate_manifest_annotations(
+        self,
+        manifest_annotations,
+        manifest_entity_type,
+        expected_entity_id,
+        manifest_file_contents=None,
+    ):
+        """
+        Validates that the annotations on a manifest entity (file or table) were correctly updated
+        by comparing the annotations on the manifest entity with the contents of the manifest file itself,
+        and ensuring the eTag annotation is not empty.
+
+        This method is wrapped by ``_submit_and_verify_manifest()``
+
+        Arguments:
+            manifest_annotations (pd.DataFrame): manifest annotations
+            manifest_entity_type (str): type of manifest (file or table)
+            expected_entity_id (str): expected entity ID of the manifest
+            manifest_file_contents (pd.DataFrame): manifest file contents
+
+        Returns:
+            None
+        """
+        # Check that the eTag annotation is not empty
+        assert len(manifest_annotations["eTag"][0]) > 0
+
+        # Check that entityId is expected
+        assert manifest_annotations["entityId"][0] == expected_entity_id
+
+        # For manifest files only: Check that all other annotations from the manifest match the annotations in the manifest file itself
+        if manifest_entity_type.lower() != "file":
+            return
+        for annotation in manifest_annotations.keys():
+            if annotation in ["eTag", "entityId"]:
+                continue
+            else:
+                assert (
+                    manifest_annotations[annotation][0]
+                    == manifest_file_contents[annotation].unique()
+                )
+
+    @pytest.mark.parametrize(
+        "manifest_path, dataset_id, validate_component, expected_manifest_id, "
+        "expected_table_id, dataset_scope",
+        test_cases,
+    )
+    def test_submit_filebased_manifest_file_and_entities(
+        self,
+        helpers,
+        manifest_path,
+        dataset_id,
+        validate_component,
+        expected_manifest_id,
+        expected_table_id,
+        dataset_scope,
+        mocker: MockerFixture,
+        synapse_store,
+    ):
+        self._submit_and_verify_manifest(
+            helpers=helpers,
+            mocker=mocker,
+            synapse_store=synapse_store,
+            manifest_path=manifest_path,
+            dataset_id=dataset_id,
+            expected_manifest_id=expected_manifest_id,
+            expected_table_id=expected_table_id,
+            manifest_record_type="file_and_entities",
+            validate_component=validate_component,
+            dataset_scope=dataset_scope,
+        )
+
+    @pytest.mark.parametrize(
+        "manifest_path, dataset_id, validate_component, expected_manifest_id, "
+        "expected_table_id, dataset_scope",
+        test_cases,
+    )
+    def test_submit_filebased_manifest_table_and_file(
+        self,
+        helpers,
+        manifest_path,
+        dataset_id,
+        validate_component,
+        expected_manifest_id,
+        expected_table_id,
+        dataset_scope,
+        mocker: MockerFixture,
+        synapse_store,
+    ):
+        self._submit_and_verify_manifest(
+            helpers=helpers,
+            mocker=mocker,
+            synapse_store=synapse_store,
+            manifest_path=manifest_path,
+            dataset_id=dataset_id,
+            expected_manifest_id=expected_manifest_id,
+            expected_table_id=expected_table_id,
+            manifest_record_type="table_and_file",
+            validate_component=validate_component,
+            dataset_scope=dataset_scope,
+        )
+
+    def _submit_and_verify_manifest(
+        self,
+        helpers,
+        mocker,
+        synapse_store,
+        manifest_path,
+        dataset_id,
+        expected_manifest_id,
+        expected_table_id,
+        manifest_record_type,
+        validate_component=None,
+        dataset_scope=None,
+    ):
+        # Spies
+        spy_upload_file_as_csv = mocker.spy(SynapseStorage, "upload_manifest_as_csv")
+        spy_upload_file_as_table = mocker.spy(
+            SynapseStorage, "upload_manifest_as_table"
+        )
+        spy_upload_file_combo = mocker.spy(SynapseStorage, "upload_manifest_combo")
+        spy_add_annotations = mocker.spy(
+            SynapseStorage, "add_annotations_to_entities_files"
+        )
+
+        # GIVEN a metadata model object using class labels
+        meta_data_model = metadata_model(helpers, "class_label")
+
+        # AND a filebased test manifest
+        load_args = {"dtype": "string"}
+        manifest = helpers.get_data_frame(
+            manifest_path, preserve_raw_input=True, **load_args
+        )
+        manifest_full_path = helpers.get_data_path(manifest_path)
+
+        # WHEN the manifest is submitted and files are annotated
+        # THEN submission should complete without error
+
+        with does_not_raise():
+            manifest_id = meta_data_model.submit_metadata_manifest(
+                manifest_path=manifest_full_path,
+                dataset_id=dataset_id,
+                manifest_record_type=manifest_record_type,
+                restrict_rules=False,
+                file_annotations_upload=True,
+                hide_blanks=False,
+                validate_component=validate_component,
+                dataset_scope=dataset_scope,
+            )
+
+        # AND the files should be annotated
+        spy_add_annotations.assert_called_once()
+
+        # AND the annotations on the entities should have the correct metadata
+        for index, row in manifest.iterrows():
+            entityId = row["entityId"]
+            expected_sample_id = row["Sample ID"]
+            annos = synapse_store.syn.get_annotations(entityId)
+            sample_id = annos["SampleID"][0]
+            assert str(sample_id) == str(expected_sample_id)
+
+        # AND the annotations on the manifest file itself are correct
+        manifest_file_annotations = synapse_store.syn.get_annotations(
+            expected_manifest_id
+        )
+        self.validate_manifest_annotations(
+            manifest_annotations=manifest_file_annotations,
+            manifest_entity_type="file",
+            expected_entity_id=expected_manifest_id,
+            manifest_file_contents=manifest,
+        )
+
+        if manifest_record_type == "table_and_file":
+            with tempfile.TemporaryDirectory() as download_dir:
+                manifest_table = synapse_store.syn.tableQuery(
+                    f"select * from {expected_table_id}", downloadLocation=download_dir
+                ).asDataFrame()
+
+                # AND the columns in the manifest table should reflect the ones in the file
+                table_columns = manifest_table.columns
+                manifest_columns = [col.replace(" ", "") for col in manifest.columns]
+                assert set(table_columns) == set(manifest_columns)
+
+                # AND the annotations on the manifest table itself are correct
+                manifest_table_annotations = synapse_store.syn.get_annotations(
+                    expected_table_id
+                )
+                self.validate_manifest_annotations(
+                    manifest_annotations=manifest_table_annotations,
+                    manifest_entity_type="table",
+                    expected_entity_id=expected_table_id,
+                )
+
+        # AND the manifest should be submitted to the correct place
+        assert manifest_id == expected_manifest_id
+
+        # AND the correct upload methods were called for the given record type
+        if manifest_record_type == "file_and_entities":
+            spy_upload_file_as_csv.assert_called_once()
+            spy_upload_file_as_table.assert_not_called()
+            spy_upload_file_combo.assert_not_called()
+        elif manifest_record_type == "table_and_file":
+            spy_upload_file_as_table.assert_called_once()
+            spy_upload_file_as_csv.assert_not_called()
+            spy_upload_file_combo.assert_not_called()
diff --git a/tests/integration/test_security_controller.py b/tests/integration/test_security_controller.py
new file mode 100644
index 000000000..43a4748a4
--- /dev/null
+++ b/tests/integration/test_security_controller.py
@@ -0,0 +1,59 @@
+import jwt
+from cryptography.hazmat.backends import default_backend
+from cryptography.hazmat.primitives.asymmetric import rsa
+from pytest import LogCaptureFixture
+
+from schematic_api.api.security_controller import info_from_bearer_auth
+
+
+class TestSecurityController:
+    def test_valid_synapse_token(self, syn_token: str) -> None:
+        # GIVEN a valid synapse token
+        assert syn_token is not None
+
+        # WHEN the token is decoded
+        decoded_token = info_from_bearer_auth(syn_token)
+
+        # THEN the decoded claims are a dictionary
+        assert isinstance(decoded_token, dict)
+        assert "sub" in decoded_token
+        assert decoded_token["sub"] is not None
+        assert "token_type" in decoded_token
+        assert decoded_token["token_type"] is not None
+
+    def test_invalid_synapse_signing_key(self, caplog: LogCaptureFixture) -> None:
+        # GIVEN an invalid synapse token
+        private_key = rsa.generate_private_key(
+            public_exponent=65537, key_size=2048, backend=default_backend()
+        )
+
+        random_token = jwt.encode(
+            payload={"sub": "random"}, key=private_key, algorithm="RS256"
+        )
+
+        # WHEN the token is decoded
+        decoded_token = info_from_bearer_auth(random_token)
+
+        # THEN nothing is returned
+        assert decoded_token is None
+
+        # AND an error is logged
+        assert (
+            "jwt.exceptions.PyJWKClientError: Unable to find a signing key that matches:"
+            in caplog.text
+        )
+
+    def test_invalid_synapse_token_not_enough_parts(
+        self, caplog: LogCaptureFixture
+    ) -> None:
+        # GIVEN an invalid synapse token
+        random_token = "invalid token"
+
+        # WHEN the token is decoded
+        decoded_token = info_from_bearer_auth(random_token)
+
+        # THEN nothing is returned
+        assert decoded_token is None
+
+        # AND an error is logged
+        assert "jwt.exceptions.DecodeError: Not enough segments" in caplog.text
diff --git a/tests/integration/test_store_synapse.py b/tests/integration/test_store_synapse.py
new file mode 100644
index 000000000..0bf23c1b1
--- /dev/null
+++ b/tests/integration/test_store_synapse.py
@@ -0,0 +1,128 @@
+from unittest.mock import MagicMock
+
+import numpy as np
+import pytest
+
+from schematic.schemas.data_model_graph import DataModelGraphExplorer
+from schematic.store.synapse import SynapseStorage
+from schematic.utils.validate_utils import comma_separated_list_regex
+from tests.conftest import Helpers
+
+
+class TestStoreSynapse:
+    @pytest.mark.parametrize("hideBlanks", [True, False])
+    @pytest.mark.parametrize(
+        "label_options",
+        ["display_label", "class_label"],
+        ids=["display_label", "class_label"],
+    )
+    def test_process_row_annotations_hide_blanks(
+        self,
+        dmge: DataModelGraphExplorer,
+        synapse_store: SynapseStorage,
+        hideBlanks: bool,
+        label_options: str,
+    ) -> None:
+        """ensure that blank values are not added to the annotations dictionary if hideBlanks is True"""
+
+        metadata_syn_with_blanks = {
+            "PatientID": "value1",
+            "Sex": "value2",
+            "Diagnosis": "",  # Blank value (empty string)
+            "FamilyHistory": 3,  # Non-string value
+            "YearofBirth": np.nan,  # Blank value (NaN)
+            "CancerType": "   ",  # Blank value (whitespace string)
+        }
+        annos = {
+            "annotations": {
+                "annotations": {
+                    "PatientID": "old_value1",
+                    "Sex": "old_value2",
+                    "Diagnosis": "old_value3",
+                    "FamilyHistory": "old_value4",
+                    "YearofBirth": "old_value5",
+                    "CancerType": "old_value6",
+                }
+            }
+        }
+        comma_separated_list = comma_separated_list_regex()
+        processed_annos = synapse_store.process_row_annotations(
+            dmge=dmge,
+            metadata_syn=metadata_syn_with_blanks,
+            csv_list_regex=comma_separated_list,
+            hide_blanks=hideBlanks,
+            annos=annos,
+            annotation_keys=label_options,
+        )
+        processed_annos = processed_annos["annotations"]["annotations"]
+
+        # make sure that empty keys are removed if hideBlanks is True
+        if hideBlanks:
+            assert (
+                "Diagnosis"
+                and "YearofBirth"
+                and "CancerType" not in processed_annos.keys()
+            )
+        else:
+            # make sure that empty keys are added if hideBlanks is False
+            # make sure that nan values are converted to empty strings
+            assert processed_annos["Diagnosis"] == ""
+            assert processed_annos["YearofBirth"] == ""
+            assert processed_annos["CancerType"] == "   "
+
+        # make sure that annotations already in the dictionary are not overwritten
+        assert processed_annos["PatientID"] == "value1"
+        assert processed_annos["Sex"] == "value2"
+        assert processed_annos["FamilyHistory"] == 3
+
+    @pytest.mark.parametrize(
+        "label_options",
+        ["display_label", "class_label"],
+        ids=["display_label", "class_label"],
+    )
+    @pytest.mark.parametrize("hideBlanks", [True, False])
+    def test_process_row_annotations_get_validation(
+        self,
+        dmge: DataModelGraphExplorer,
+        synapse_store: SynapseStorage,
+        hideBlanks: bool,
+        label_options: str,
+    ) -> None:
+        """ensure that get_node_validation_rules is called with the correct arguments"""
+        comma_separated_list = comma_separated_list_regex()
+        metadata_syn = {
+            "FamilyHistory": "value1,value2,value3",
+        }
+        annos = {"annotations": {"annotations": {"FamilyHistory": "old_value"}}}
+
+        dmge.get_node_validation_rules = MagicMock()
+
+        # pretend that "FamilyHistory" has a list of validation rules
+        dmge.get_node_validation_rules.return_value = ["list", "regex"]
+
+        processed_annos = synapse_store.process_row_annotations(
+            dmge=dmge,
+            metadata_syn=metadata_syn,
+            csv_list_regex=comma_separated_list,
+            hide_blanks=hideBlanks,
+            annos=annos,
+            annotation_keys=label_options,
+        )
+
+        if label_options == "display_label":
+            # get_node_validation_rules was called with node_display_name
+            dmge.get_node_validation_rules.assert_any_call(
+                node_display_name="FamilyHistory"
+            )
+            dmge.get_node_validation_rules.assert_any_call(
+                node_display_name="FamilyHistory"
+            )
+        else:
+            # get_node_validation_rules was called with node_label
+            dmge.get_node_validation_rules.assert_any_call(node_label="FamilyHistory")
+        # ensure that the value is split into a list
+        assert processed_annos["annotations"]["annotations"]["FamilyHistory"] == [
+            "value1",
+            "value2",
+            "value3",
+        ]
diff --git a/tests/integration/test_validate_attribute.py b/tests/integration/test_validate_attribute.py
new file mode 100644
index 000000000..b6d3b74b1
--- /dev/null
+++ b/tests/integration/test_validate_attribute.py
@@ -0,0 +1,88 @@
+import pandas as pd
+
+from schematic.models.validate_attribute import ValidateAttribute
+from schematic.schemas.data_model_graph import DataModelGraphExplorer
+
+CHECK_URL_NODE_NAME = "Check URL"
+VALIDATION_RULE_URL = "url"
+
+
+class TestValidateAttribute:
+    """Integration tests for the ValidateAttribute class."""
+
+    def test_url_validation_valid_url(self, dmge: DataModelGraphExplorer) -> None:
+        # GIVEN a valid URL:
+        url = "https://github.com/Sage-Bionetworks/schematic"
+
+        # AND a pd.core.series.Series that contains this URL
+        content = pd.Series(data=[url], name=CHECK_URL_NODE_NAME)
+
+        # AND a validation attribute
+        validator = ValidateAttribute(dmge=dmge)
+
+        # WHEN the URL is validated
+        result = validator.url_validation(
+            val_rule=VALIDATION_RULE_URL, manifest_col=content
+        )
+
+        # THEN the result should pass validation
+        assert result == ([], [])
+
+    def test_url_validation_valid_doi(self, dmge: DataModelGraphExplorer) -> None:
+        # GIVEN a valid URL:
+        url = "https://doi.org/10.1158/0008-5472.can-23-0128"
+
+        # AND a pd.core.series.Series that contains this URL
+        content = pd.Series(data=[url], name=CHECK_URL_NODE_NAME)
+
+        # AND a validation attribute
+        validator = ValidateAttribute(dmge=dmge)
+
+        # WHEN the URL is validated
+        result = validator.url_validation(
+            val_rule=VALIDATION_RULE_URL, manifest_col=content
+        )
+
+        # THEN the result should pass validation
+        assert result == ([], [])
+
+    def test_url_validation_invalid_url(self, dmge: DataModelGraphExplorer) -> None:
+        # GIVEN an invalid URL:
+        url = "http://googlef.com/"
+
+        # AND a pd.core.series.Series that contains this URL
+        content = pd.Series(data=[url], name=CHECK_URL_NODE_NAME)
+
+        # AND a validation attribute
+        validator = ValidateAttribute(dmge=dmge)
+
+        # WHEN the URL is validated
+        result = validator.url_validation(
+            val_rule=VALIDATION_RULE_URL, manifest_col=content
+        )
+
+        # THEN the result should not pass validation
+        assert result == (
+            [
+                [
+                    "2",
+                    "Check URL",
+                    "For the attribute 'Check URL', on row 2, the URL provided (http://googlef.com/) does not conform to the standards of a URL. Please make sure you are entering a real, working URL as required by the Schema.",
+                    "http://googlef.com/",
+                ]
+            ],
+            [],
+        )
+
+    def test__get_target_manifest_dataframes(
+        self, dmge: DataModelGraphExplorer
+    ) -> None:
+        """
+        This test checks that the method successfully returns manifests from Synapse
+
+        """
+        validator = ValidateAttribute(dmge=dmge)
+        manifests = validator._get_target_manifest_dataframes(  # pylint:disable= protected-access
+            "patient", project_scope=["syn54126707"]
+        )
+        assert list(manifests.keys()) == ["syn54126997", "syn54127001"]
diff --git a/tests/test_api.py b/tests/test_api.py
index 97183186f..08e0bd4a6 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -1,37 +1,36 @@
-import configparser
 import json
 import logging
 import os
 import re
-import time
 from math import ceil
 from time import perf_counter
+from typing import Dict, Generator, List, Tuple, Union
 
-import numpy as np
+import flask
 import pandas as pd  # third party library import
 import pytest
+from flask.testing import FlaskClient
 
 from schematic.configuration.configuration import Configuration
-from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
-from schematic.schemas.data_model_relationships import DataModelRelationships
-
+from schematic.schemas.data_model_parser import DataModelParser
 from schematic_api.api import create_app
 
-
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+BENCHMARK_DATA_MODEL_JSON_LD = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.single_rule.model.jsonld"
+DATA_MODEL_JSON_LD = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld"
+
 
-## TO DO: Clean up url and use a global variable SERVER_URL
 @pytest.fixture(scope="class")
-def app():
+def app() -> flask.Flask:
     app = create_app()
-    yield app
+    return app
 
 
 @pytest.fixture(scope="class")
-def client(app):
+def client(app: flask.Flask) -> Generator[FlaskClient, None, None]:
     app.config["SCHEMATIC_CONFIG"] = None
 
     with app.test_client() as client:
@@ -39,62 +38,70 @@ def client(app):
 
 
 @pytest.fixture(scope="class")
-def test_manifest_csv(helpers):
+def valid_test_manifest_csv(helpers) -> str:
     test_manifest_path = helpers.get_data_path("mock_manifests/Valid_Test_Manifest.csv")
-    yield test_manifest_path
+    return test_manifest_path
+
+
+@pytest.fixture(scope="class")
+def valid_filename_manifest_csv(helpers) -> str:
+    test_manifest_path = helpers.get_data_path(
+        "mock_manifests/ValidFilenameManifest.csv"
+    )
+    return test_manifest_path
 
 
 @pytest.fixture(scope="class")
-def test_manifest_submit(helpers):
+def invalid_filename_manifest_csv(helpers) -> str:
+    test_manifest_path = helpers.get_data_path(
+        "mock_manifests/InvalidFilenameManifest.csv"
+    )
+    return test_manifest_path
+
+
+@pytest.fixture(scope="class")
+def test_manifest_submit(helpers) -> str:
     test_manifest_path = helpers.get_data_path(
         "mock_manifests/example_biospecimen_test.csv"
     )
-    yield test_manifest_path
+    return test_manifest_path
 
 
 @pytest.fixture(scope="class")
-def test_invalid_manifest(helpers):
+def test_invalid_manifest(helpers) -> pd.DataFrame:
     test_invalid_manifest = helpers.get_data_frame(
         "mock_manifests/Invalid_Test_Manifest.csv", preserve_raw_input=False
     )
-    yield test_invalid_manifest
+    return test_invalid_manifest
 
 
 @pytest.fixture(scope="class")
-def test_upsert_manifest_csv(helpers):
+def test_upsert_manifest_csv(helpers) -> str:
     test_upsert_manifest_path = helpers.get_data_path(
         "mock_manifests/rdb_table_manifest.csv"
     )
-    yield test_upsert_manifest_path
+    return test_upsert_manifest_path
 
 
 @pytest.fixture(scope="class")
-def test_manifest_json(helpers):
+def test_manifest_json(helpers) -> str:
     test_manifest_path = helpers.get_data_path(
         "mock_manifests/Example.Patient.manifest.json"
     )
-    yield test_manifest_path
-
-
-@pytest.fixture(scope="class")
-def data_model_jsonld():
-    data_model_jsonld = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld"
-    yield data_model_jsonld
+    return test_manifest_path
 
 
 @pytest.fixture(scope="class")
-def benchmark_data_model_jsonld():
-    benchmark_data_model_jsonld = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.single_rule.model.jsonld"
-    yield benchmark_data_model_jsonld
+def patient_manifest_json_str() -> str:
+    return '[{"Patient ID": 123, "Sex": "Female", "Year of Birth": "", "Diagnosis": "Healthy", "Component": "Patient", "Cancer Type": "Breast", "Family History": "Breast, Lung"}]'
 
 
-def get_MockComponent_attribute():
+def get_MockComponent_attribute() -> Generator[str, None, None]:
     """
     Yield all of the mock conponent attributes one at a time
     TODO: pull in jsonld from fixture
     """
-    schema_url = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.single_rule.model.jsonld"
-    data_model_parser = DataModelParser(path_to_data_model=schema_url)
+    data_model_parser = DataModelParser(path_to_data_model=BENCHMARK_DATA_MODEL_JSON_LD)
     # Parse Model
     parsed_data_model = data_model_parser.parse_model()
 
@@ -113,34 +120,23 @@ def get_MockComponent_attribute():
         yield MockComponent_attribute
 
 
-@pytest.fixture(scope="class")
-def syn_token(config: Configuration):
-    synapse_config_path = config.synapse_configuration_path
-    config_parser = configparser.ConfigParser()
-    config_parser.read(synapse_config_path)
-    # try using synapse access token
-    if "SYNAPSE_ACCESS_TOKEN" in os.environ:
-        token = os.environ["SYNAPSE_ACCESS_TOKEN"]
-    else:
-        token = config_parser["authentication"]["authtoken"]
-    yield token
-
-
 @pytest.fixture
-def request_headers(syn_token):
+def request_headers(syn_token: str) -> Dict[str, str]:
     headers = {"Authorization": "Bearer " + syn_token}
-    yield headers
+    return headers
 
 
 @pytest.fixture
-def request_invalid_headers():
+def request_invalid_headers() -> Dict[str, str]:
     headers = {"Authorization": "Bearer invalid headers"}
-    yield headers
+    return headers
 
 
 @pytest.mark.schematic_api
 class TestSynapseStorage:
-    def test_invalid_authentication(self, client, request_invalid_headers):
+    def test_invalid_authentication(
+        self, client: FlaskClient, request_invalid_headers: Dict[str, str]
+    ) -> None:
         response = client.get(
             "http://localhost:3001/v1/storage/assets/tables",
             query_string={"asset_view": "syn23643253", "return_type": "csv"},
@@ -148,7 +144,9 @@ def test_invalid_authentication(self, client, request_invalid_headers):
         )
         assert response.status_code == 401
 
-    def test_insufficent_auth(self, client, request_headers):
+    def test_insufficent_auth(
+        self, client: FlaskClient, request_headers: Dict[str, str]
+    ) -> None:
         response = client.get(
             "http://localhost:3001/v1/storage/assets/tables",
             query_string={"asset_view": "syn23643252", "return_type": "csv"},
@@ -158,7 +156,9 @@ def test_insufficent_auth(self, client, request_headers):
 
     @pytest.mark.synapse_credentials_needed
     @pytest.mark.parametrize("return_type", ["json", "csv"])
-    def test_get_storage_assets_tables(self, client, return_type, request_headers):
+    def test_get_storage_assets_tables(
+        self, client: FlaskClient, return_type, request_headers: Dict[str, str]
+    ):
         params = {"asset_view": "syn23643253", "return_type": return_type}
 
         response = client.get(
@@ -186,7 +186,13 @@ def test_get_storage_assets_tables(self, client, return_type, request_headers):
     @pytest.mark.synapse_credentials_needed
     @pytest.mark.parametrize("full_path", [True, False])
     @pytest.mark.parametrize("file_names", [None, "Sample_A.txt"])
-    def test_get_dataset_files(self, full_path, file_names, request_headers, client):
+    def test_get_dataset_files(
+        self,
+        full_path: bool,
+        file_names: Union[str, None],
+        request_headers: Dict[str, str],
+        client: FlaskClient,
+    ) -> None:
         params = {
             "asset_view": "syn23643253",
             "dataset_id": "syn23643250",
@@ -203,17 +209,19 @@ def test_get_dataset_files(self, full_path, file_names, request_headers, client)
         )
 
         assert response.status_code == 200
-        response_dt = json.loads(response.data)
+        response_dt: List[Tuple[str, str]] = json.loads(response.data)
 
         # would show full file path .txt in result
         if full_path:
             if file_names:
                 assert (
                     ["syn23643255", "schematic - main/DataTypeX/Sample_A.txt"]
+                    in response_dt
                     and [
                         "syn24226530",
                         "schematic - main/TestDatasets/TestDataset-Annotations/Sample_A.txt",
                     ]
+                    in response_dt
                     and [
                         "syn25057024",
                         "schematic - main/TestDatasets/TestDataset-Annotations-v2/Sample_A.txt",
@@ -228,23 +236,25 @@ def test_get_dataset_files(self, full_path, file_names, request_headers, client)
         else:
             if file_names:
                 assert (
-                    ["syn23643255", "Sample_A.txt"]
-                    and ["syn24226530", "Sample_A.txt"]
+                    ["syn23643255", "Sample_A.txt"] in response_dt
+                    and ["syn24226530", "Sample_A.txt"] in response_dt
                     and ["syn25057024", "Sample_A.txt"] in response_dt
                 )
-                assert ["syn23643256", "Sample_C.txt"] and [
+                assert ["syn23643256", "Sample_C.txt"] not in response_dt and [
                     "syn24226531",
                     "Sample_B.txt",
                 ] not in response_dt
             else:
                 assert (
-                    ["syn23643256", "Sample_C.txt"]
-                    and ["syn24226530", "Sample_A.txt"]
+                    ["syn23643256", "Sample_C.txt"] in response_dt
+                    and ["syn24226530", "Sample_A.txt"] in response_dt
                     and ["syn24226531", "Sample_B.txt"] in response_dt
                 )
 
     @pytest.mark.synapse_credentials_needed
-    def test_get_storage_project_dataset(self, request_headers, client):
+    def test_get_storage_project_dataset(
+        self, request_headers: Dict[str, str], client: FlaskClient
+    ) -> None:
         params = {"asset_view": "syn23643253", "project_id": "syn26251192"}
 
         response = client.get(
@@ -257,7 +267,9 @@ def test_get_storage_project_dataset(self, request_headers, client):
         assert ["syn26251193", "Issue522"] in response_dt
 
     @pytest.mark.synapse_credentials_needed
-    def test_get_storage_project_manifests(self, request_headers, client):
+    def test_get_storage_project_manifests(
+        self, request_headers: Dict[str, str], client: FlaskClient
+    ) -> None:
         params = {"asset_view": "syn23643253", "project_id": "syn30988314"}
 
         response = client.get(
@@ -269,7 +281,9 @@ def test_get_storage_project_manifests(self, request_headers, client):
         assert response.status_code == 200
 
     @pytest.mark.synapse_credentials_needed
-    def test_get_storage_projects(self, request_headers, client):
+    def test_get_storage_projects(
+        self, request_headers: Dict[str, str], client: FlaskClient
+    ) -> None:
         params = {"asset_view": "syn23643253"}
 
         response = client.get(
@@ -282,7 +296,9 @@ def test_get_storage_projects(self, request_headers, client):
 
     @pytest.mark.synapse_credentials_needed
     @pytest.mark.parametrize("entity_id", ["syn34640850", "syn23643253", "syn24992754"])
-    def test_get_entity_type(self, request_headers, client, entity_id):
+    def test_get_entity_type(
+        self, request_headers: Dict[str, str], client: FlaskClient, entity_id: str
+    ) -> None:
         params = {"asset_view": "syn23643253", "entity_id": entity_id}
         response = client.get(
             "http://localhost:3001/v1/storage/entity/type",
@@ -301,7 +317,9 @@ def test_get_entity_type(self, request_headers, client, entity_id):
 
     @pytest.mark.synapse_credentials_needed
     @pytest.mark.parametrize("entity_id", ["syn30988314", "syn27221721"])
-    def test_if_in_assetview(self, request_headers, client, entity_id):
+    def test_if_in_assetview(
+        self, request_headers: Dict[str, str], client: FlaskClient, entity_id: str
+    ) -> None:
         params = {"asset_view": "syn23643253", "entity_id": entity_id}
         response = client.get(
             "http://localhost:3001/v1/storage/if_in_asset_view",
@@ -320,9 +338,9 @@ def test_if_in_assetview(self, request_headers, client, entity_id):
 @pytest.mark.schematic_api
 class TestMetadataModelOperation:
     @pytest.mark.parametrize("as_graph", [True, False])
-    def test_component_requirement(self, client, data_model_jsonld, as_graph):
+    def test_component_requirement(self, client: FlaskClient, as_graph: bool) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "source_component": "BulkRNA-seqAssay",
             "as_graph": as_graph,
         }
@@ -347,7 +365,9 @@ def test_component_requirement(self, client, data_model_jsonld, as_graph):
 @pytest.mark.schematic_api
 class TestUtilsOperation:
     @pytest.mark.parametrize("strict_camel_case", [True, False])
-    def test_get_property_label_from_display_name(self, client, strict_camel_case):
+    def test_get_property_label_from_display_name(
+        self, client: FlaskClient, strict_camel_case: bool
+    ) -> None:
         params = {
             "display_name": "mocular entity",
             "strict_camel_case": strict_camel_case,
@@ -369,8 +389,8 @@ def test_get_property_label_from_display_name(self, client, strict_camel_case):
 
 @pytest.mark.schematic_api
 class TestDataModelGraphExplorerOperation:
-    def test_get_schema(self, client, data_model_jsonld):
-        params = {"schema_url": data_model_jsonld, "data_model_labels": "class_label"}
+    def test_get_schema(self, client: FlaskClient) -> None:
+        params = {"schema_url": DATA_MODEL_JSON_LD, "data_model_labels": "class_label"}
         response = client.get(
             "http://localhost:3001/v1/schemas/get/schema", query_string=params
         )
@@ -383,9 +403,9 @@ def test_get_schema(self, client, data_model_jsonld):
         if os.path.exists(response_dt):
             os.remove(response_dt)
 
-    def test_if_node_required(test, client, data_model_jsonld):
+    def test_if_node_required(test, client: FlaskClient) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "node_display_name": "FamilyHistory",
             "data_model_labels": "class_label",
         }
@@ -397,9 +417,9 @@ def test_if_node_required(test, client, data_model_jsonld):
         assert response.status_code == 200
         assert response_dta == True
 
-    def test_get_node_validation_rules(test, client, data_model_jsonld):
+    def test_get_node_validation_rules(test, client: FlaskClient) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "node_display_name": "CheckRegexList",
         }
         response = client.get(
@@ -411,9 +431,9 @@ def test_get_node_validation_rules(test, client, data_model_jsonld):
         assert "list" in response_dta
         assert "regex match [a-f]" in response_dta
 
-    def test_get_nodes_display_names(test, client, data_model_jsonld):
+    def test_get_nodes_display_names(test, client: FlaskClient) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "node_list": ["FamilyHistory", "Biospecimen"],
         }
         response = client.get(
@@ -427,8 +447,8 @@ def test_get_nodes_display_names(test, client, data_model_jsonld):
     @pytest.mark.parametrize(
         "relationship", ["parentOf", "requiresDependency", "rangeValue", "domainValue"]
     )
-    def test_get_subgraph_by_edge(self, client, data_model_jsonld, relationship):
-        params = {"schema_url": data_model_jsonld, "relationship": relationship}
+    def test_get_subgraph_by_edge(self, client: FlaskClient, relationship: str) -> None:
+        params = {"schema_url": DATA_MODEL_JSON_LD, "relationship": relationship}
 
         response = client.get(
             "http://localhost:3001/v1/schemas/get/graph_by_edge_type",
@@ -439,10 +459,10 @@ def test_get_subgraph_by_edge(self, client, data_model_jsonld, relationship):
     @pytest.mark.parametrize("return_display_names", [True, False])
     @pytest.mark.parametrize("node_label", ["FamilyHistory", "TissueStatus"])
     def test_get_node_range(
-        self, client, data_model_jsonld, return_display_names, node_label
-    ):
+        self, client: FlaskClient, return_display_names: bool, node_label: str
+    ) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "return_display_names": return_display_names,
             "node_label": node_label,
         }
@@ -466,17 +486,16 @@ def test_get_node_range(
     @pytest.mark.parametrize("source_node", ["Patient", "Biospecimen"])
     def test_node_dependencies(
         self,
-        client,
-        data_model_jsonld,
-        source_node,
-        return_display_names,
-        return_schema_ordered,
-    ):
+        client: FlaskClient,
+        source_node: str,
+        return_display_names: Union[bool, None],
+        return_schema_ordered: Union[bool, None],
+    ) -> None:
         return_display_names = True
         return_schema_ordered = False
 
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "source_node": source_node,
             "return_display_names": return_display_names,
             "return_schema_ordered": return_schema_ordered,
@@ -519,7 +538,7 @@ def test_node_dependencies(
 
 @pytest.mark.schematic_api
 class TestManifestOperation:
-    def ifExcelExists(self, response, file_name):
+    def ifExcelExists(self, response, file_name) -> None:
         # return one excel file
         d = response.headers["content-disposition"]
         fname = re.findall("filename=(.+)", d)[0]
@@ -543,13 +562,12 @@ def ifPandasDataframe(self, response_dt):
     )
     def test_generate_existing_manifest(
         self,
-        client,
-        data_model_jsonld,
-        data_type,
-        output_format,
-        caplog,
-        request_headers,
-    ):
+        client: FlaskClient,
+        data_type: str,
+        output_format: str,
+        caplog: pytest.LogCaptureFixture,
+        request_headers: Dict[str, str],
+    ) -> None:
         # set dataset
         if data_type == "Patient":
             dataset_id = ["syn51730545"]  # Mock Patient Manifest folder on synapse
@@ -561,7 +579,7 @@ def test_generate_existing_manifest(
             dataset_id = None  # if "all manifests", dataset id is None
 
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "asset_view": "syn23643253",
             "title": "Example",
             "data_type": data_type,
@@ -627,15 +645,14 @@ def test_generate_existing_manifest(
     )
     def test_generate_new_manifest(
         self,
-        caplog,
-        client,
-        data_model_jsonld,
-        data_type,
-        output_format,
-        request_headers,
-    ):
+        caplog: pytest.LogCaptureFixture,
+        client: FlaskClient,
+        data_type: str,
+        output_format: str,
+        request_headers: Dict[str, str],
+    ) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "asset_view": "syn23643253",
             "title": "Example",
             "data_type": data_type,
@@ -731,10 +748,10 @@ def test_generate_new_manifest(
         ],
     )
     def test_generate_manifest_file_based_annotations(
-        self, client, use_annotations, expected, data_model_jsonld
-    ):
+        self, client: FlaskClient, use_annotations: bool, expected: list[str]
+    ) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": "BulkRNA-seqAssay",
             "dataset_id": "syn25614635",
             "asset_view": "syn51707141",
@@ -763,9 +780,9 @@ def test_generate_manifest_file_based_annotations(
 
         # make sure Filename, entityId, and component get filled with correct value
         assert google_sheet_df["Filename"].to_list() == [
-            "TestDataset-Annotations-v3/Sample_A.txt",
-            "TestDataset-Annotations-v3/Sample_B.txt",
-            "TestDataset-Annotations-v3/Sample_C.txt",
+            "schematic - main/TestDataset-Annotations-v3/Sample_A.txt",
+            "schematic - main/TestDataset-Annotations-v3/Sample_B.txt",
+            "schematic - main/TestDataset-Annotations-v3/Sample_C.txt",
         ]
         assert google_sheet_df["entityId"].to_list() == [
             "syn25614636",
@@ -781,10 +798,10 @@ def test_generate_manifest_file_based_annotations(
     # test case: generate a manifest with annotations when use_annotations is set to True for a component that is not file-based
     # the dataset folder does not contain an existing manifest
     def test_generate_manifest_not_file_based_with_annotations(
-        self, client, data_model_jsonld
-    ):
+        self, client: FlaskClient
+    ) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": "Patient",
             "dataset_id": "syn25614635",
             "asset_view": "syn51707141",
@@ -816,9 +833,9 @@ def test_generate_manifest_not_file_based_with_annotations(
             ]
         )
 
-    def test_generate_manifest_data_type_not_found(self, client, data_model_jsonld):
+    def test_generate_manifest_data_type_not_found(self, client: FlaskClient) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": "wrong data type",
             "use_annotations": False,
         }
@@ -829,13 +846,15 @@ def test_generate_manifest_data_type_not_found(self, client, data_model_jsonld):
         assert response.status_code == 500
         assert "LookupError" in str(response.data)
 
-    def test_populate_manifest(self, client, data_model_jsonld, test_manifest_csv):
+    def test_populate_manifest(
+        self, client: FlaskClient, valid_test_manifest_csv: str
+    ) -> None:
         # test manifest
-        test_manifest_data = open(test_manifest_csv, "rb")
+        test_manifest_data = open(valid_test_manifest_csv, "rb")
 
         params = {
             "data_type": "MockComponent",
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "title": "Example",
             "csv_file": test_manifest_data,
         }
@@ -851,64 +870,89 @@ def test_populate_manifest(self, client, data_model_jsonld, test_manifest_csv):
         assert isinstance(response_dt[0], str)
         assert response_dt[0].startswith("https://docs.google.com/")
 
-    @pytest.mark.parametrize("restrict_rules", [False, True, None])
     @pytest.mark.parametrize(
-        "json_str",
+        "json_str_fixture, test_manifest_fixture, data_type, update_headers, project_scope, dataset_scope",
         [
-            None,
-            '[{"Patient ID": 123, "Sex": "Female", "Year of Birth": "", "Diagnosis": "Healthy", "Component": "Patient", "Cancer Type": "Breast", "Family History": "Breast, Lung"}]',
+            (
+                None,
+                "valid_test_manifest_csv",
+                "MockComponent",
+                True,
+                "syn54126707",
+                None,
+            ),
+            ("patient_manifest_json_str", None, "Patient", False, None, None),
+            (
+                None,
+                "invalid_filename_manifest_csv",
+                "MockFilename",
+                True,
+                "syn23643250",
+                "syn61682648",
+            ),
         ],
     )
+    @pytest.mark.parametrize("restrict_rules", [True, False, None])
     def test_validate_manifest(
         self,
-        data_model_jsonld,
-        client,
-        json_str,
-        restrict_rules,
-        test_manifest_csv,
-        request_headers,
-    ):
-        params = {"schema_url": data_model_jsonld, "restrict_rules": restrict_rules}
+        client: FlaskClient,
+        json_str_fixture: Union[str, None],
+        test_manifest_fixture: Union[str, None],
+        data_type: str,
+        update_headers: bool,
+        project_scope: Union[str, None],
+        dataset_scope: Union[str, None],
+        restrict_rules: Union[bool, None],
+        request_headers: Dict[str, str],
+        request: pytest.FixtureRequest,
+    ) -> None:
+        # GIVEN a set of test prameters
+        params = {
+            "schema_url": DATA_MODEL_JSON_LD,
+            "asset_view": "syn23643253",
+            "restrict_rules": restrict_rules,
+            "project_scope": project_scope,
+            "dataset_scope": dataset_scope,
+            "data_type": data_type,
+        }
 
-        if json_str:
-            params["json_str"] = json_str
-            params["data_type"] = "Patient"
-            response = client.post(
-                "http://localhost:3001/v1/model/validate", query_string=params
-            )
-            response_dt = json.loads(response.data)
-            assert response.status_code == 200
+        # AND a test manifest as a json string
+        params["json_str"] = (
+            request.getfixturevalue(json_str_fixture) if json_str_fixture else None
+        )
 
-        else:
-            params["data_type"] = "MockComponent"
+        # OR a test manifest as a file
+        data = None
+        if test_manifest_fixture:
+            test_manifest_path = request.getfixturevalue(test_manifest_fixture)
+            data = {"file_name": (open(test_manifest_path, "rb"), "test.csv")}
 
+        # AND the appropriate headers for the test
+        if update_headers:
             request_headers.update(
                 {"Content-Type": "multipart/form-data", "Accept": "application/json"}
             )
 
-            # test uploading a csv file
-            response_csv = client.post(
-                "http://localhost:3001/v1/model/validate",
-                query_string=params,
-                data={"file_name": (open(test_manifest_csv, "rb"), "test.csv")},
-                headers=request_headers,
-            )
-            response_dt = json.loads(response_csv.data)
-            assert response_csv.status_code == 200
+        # WHEN the manifest is validated
+        response = client.post(
+            "http://localhost:3001/v1/model/validate",
+            query_string=params,
+            data=data,
+            headers=request_headers,
+        )
 
-            # test uploading a json file
-            # change data type to patient since the testing json manifest is using Patient component
-            # WILL DEPRECATE uploading a json file for validation
-            # params["data_type"] = "Patient"
-            # response_json =  client.post('http://localhost:3001/v1/model/validate', query_string=params, data={"file_name": (open(test_manifest_json, 'rb'), "test.json")}, headers=headers)
-            # response_dt = json.loads(response_json.data)
-            # assert response_json.status_code == 200
+        # THEN the request should be successful
+        assert response.status_code == 200
 
+        # AND the response should contain the expected error and warning lists
+        response_dt = json.loads(response.data)
         assert "errors" in response_dt.keys()
         assert "warnings" in response_dt.keys()
 
     @pytest.mark.synapse_credentials_needed
-    def test_get_datatype_manifest(self, client, request_headers):
+    def test_get_datatype_manifest(
+        self, client: FlaskClient, request_headers: Dict[str, str]
+    ) -> None:
         params = {"asset_view": "syn23643253", "manifest_id": "syn27600110"}
 
         response = client.get(
@@ -944,14 +988,14 @@ def test_get_datatype_manifest(self, client, request_headers):
     def test_manifest_download(
         self,
         config: Configuration,
-        client,
-        request_headers,
-        manifest_id,
-        new_manifest_name,
-        as_json,
-        expected_component,
-        expected_file_name,
-    ):
+        client: FlaskClient,
+        request_headers: Dict[str, str],
+        manifest_id: str,
+        new_manifest_name: str,
+        as_json: Union[bool, None],
+        expected_component: str,
+        expected_file_name: str,
+    ) -> None:
         params = {
             "manifest_id": manifest_id,
             "new_manifest_name": new_manifest_name,
@@ -1006,7 +1050,9 @@ def test_manifest_download(
 
     @pytest.mark.synapse_credentials_needed
     # test downloading a manifest with access restriction and see if the correct error message got raised
-    def test_download_access_restricted_manifest(self, client, request_headers):
+    def test_download_access_restricted_manifest(
+        self, client: FlaskClient, request_headers: Dict[str, str]
+    ) -> None:
         params = {"manifest_id": "syn29862078"}
 
         response = client.get(
@@ -1023,8 +1069,12 @@ def test_download_access_restricted_manifest(self, client, request_headers):
     @pytest.mark.parametrize("as_json", [None, True, False])
     @pytest.mark.parametrize("new_manifest_name", [None, "Test"])
     def test_dataset_manifest_download(
-        self, client, as_json, request_headers, new_manifest_name
-    ):
+        self,
+        client: FlaskClient,
+        as_json: Union[bool, None],
+        request_headers: Dict[str, str],
+        new_manifest_name: Union[str, None],
+    ) -> None:
         params = {
             "asset_view": "syn28559058",
             "dataset_id": "syn28268700",
@@ -1056,11 +1106,14 @@ def test_dataset_manifest_download(
     @pytest.mark.synapse_credentials_needed
     @pytest.mark.submission
     def test_submit_manifest_table_and_file_replace(
-        self, client, request_headers, data_model_jsonld, test_manifest_submit
-    ):
+        self,
+        client: FlaskClient,
+        request_headers: Dict[str, str],
+        test_manifest_submit: str,
+    ) -> None:
         """Testing submit manifest in a csv format as a table and a file. Only replace the table"""
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": "Biospecimen",
             "restrict_rules": False,
             "hide_blanks": False,
@@ -1086,22 +1139,21 @@ def test_submit_manifest_table_and_file_replace(
         "data_type, manifest_path_fixture",
         [
             ("Biospecimen", "test_manifest_submit"),
-            ("MockComponent", "test_manifest_csv"),
+            ("MockComponent", "valid_test_manifest_csv"),
         ],
     )
     def test_submit_manifest_file_only_replace(
         self,
         helpers,
-        client,
-        request_headers,
-        data_model_jsonld,
-        data_type,
-        manifest_path_fixture,
-        request,
-    ):
+        client: FlaskClient,
+        request_headers: Dict[str, str],
+        data_type: str,
+        manifest_path_fixture: str,
+        request: pytest.FixtureRequest,
+    ) -> None:
         """Testing submit manifest in a csv format as a file"""
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": data_type,
             "restrict_rules": False,
             "manifest_record_type": "file_only",
@@ -1144,12 +1196,12 @@ def test_submit_manifest_file_only_replace(
     @pytest.mark.synapse_credentials_needed
     @pytest.mark.submission
     def test_submit_manifest_json_str_replace(
-        self, client, request_headers, data_model_jsonld
-    ):
+        self, client: FlaskClient, request_headers: Dict[str, str]
+    ) -> None:
         """Submit json str as a file"""
         json_str = '[{"Sample ID": 123, "Patient ID": 1,"Tissue Status": "Healthy","Component": "Biospecimen"}]'
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": "Biospecimen",
             "json_str": json_str,
             "restrict_rules": False,
@@ -1172,10 +1224,13 @@ def test_submit_manifest_json_str_replace(
     @pytest.mark.synapse_credentials_needed
     @pytest.mark.submission
     def test_submit_manifest_w_file_and_entities(
-        self, client, request_headers, data_model_jsonld, test_manifest_submit
-    ):
+        self,
+        client: FlaskClient,
+        request_headers: Dict[str, str],
+        test_manifest_submit: str,
+    ) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": "Biospecimen",
             "restrict_rules": False,
             "manifest_record_type": "file_and_entities",
@@ -1200,13 +1255,12 @@ def test_submit_manifest_w_file_and_entities(
     @pytest.mark.submission
     def test_submit_manifest_table_and_file_upsert(
         self,
-        client,
-        request_headers,
-        data_model_jsonld,
-        test_upsert_manifest_csv,
-    ):
+        client: FlaskClient,
+        request_headers: Dict[str, str],
+        test_upsert_manifest_csv: str,
+    ) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "data_type": "MockRDB",
             "restrict_rules": False,
             "manifest_record_type": "table_and_file",
@@ -1214,7 +1268,8 @@ def test_submit_manifest_table_and_file_upsert(
             "dataset_id": "syn51514551",
             "table_manipulation": "upsert",
             "data_model_labels": "class_label",
-            "table_column_names": "display_name",  # have to set table_column_names to display_name to ensure upsert feature works
+            # have to set table_column_names to display_name to ensure upsert feature works
+            "table_column_names": "display_name",
         }
 
         # test uploading a csv file
@@ -1226,11 +1281,44 @@ def test_submit_manifest_table_and_file_upsert(
         )
         assert response_csv.status_code == 200
 
+    @pytest.mark.synapse_credentials_needed
+    @pytest.mark.submission
+    def test_submit_and_validate_filebased_manifest(
+        self,
+        client: FlaskClient,
+        request_headers: Dict[str, str],
+        valid_filename_manifest_csv: str,
+    ) -> None:
+        # GIVEN the appropriate upload parameters
+        params = {
+            "schema_url": DATA_MODEL_JSON_LD,
+            "data_type": "MockFilename",
+            "restrict_rules": False,
+            "manifest_record_type": "file_and_entities",
+            "asset_view": "syn23643253",
+            "dataset_id": "syn62822337",
+            "project_scope": "syn23643250",
+            "dataset_scope": "syn62822337",
+            "data_model_labels": "class_label",
+            "table_column_names": "class_label",
+        }
+
+        # WHEN a filebased manifest is validated with the filenameExists rule and uploaded
+        response_csv = client.post(
+            "http://localhost:3001/v1/model/submit",
+            query_string=params,
+            data={"file_name": (open(valid_filename_manifest_csv, "rb"), "test.csv")},
+            headers=request_headers,
+        )
+
+        # THEN the validation and submission should be successful
+        assert response_csv.status_code == 200
+
 
 @pytest.mark.schematic_api
 class TestSchemaVisualization:
-    def test_visualize_attributes(self, client, data_model_jsonld):
-        params = {"schema_url": data_model_jsonld}
+    def test_visualize_attributes(self, client: FlaskClient) -> None:
+        params = {"schema_url": DATA_MODEL_JSON_LD}
 
         response = client.get(
             "http://localhost:3001/v1/visualize/attributes", query_string=params
@@ -1240,10 +1328,10 @@ def test_visualize_attributes(self, client, data_model_jsonld):
 
     @pytest.mark.parametrize("figure_type", ["component", "dependency"])
     def test_visualize_tangled_tree_layers(
-        self, client, figure_type, data_model_jsonld
-    ):
+        self, client: FlaskClient, figure_type: str
+    ) -> None:
         # TODO: Determine a 2nd data model to use for this test, test both models sequentially, add checks for content of response
-        params = {"schema_url": data_model_jsonld, "figure_type": figure_type}
+        params = {"schema_url": DATA_MODEL_JSON_LD, "figure_type": figure_type}
 
         response = client.get(
             "http://localhost:3001/v1/visualize/tangled_tree/layers",
@@ -1252,6 +1340,94 @@ def test_visualize_tangled_tree_layers(
 
         assert response.status_code == 200
 
+        response_data = json.loads(response.data)
+
+        if figure_type == "component":
+            assert len(response_data) == 3
+            expected_data = [
+                {
+                    "id": "Patient",
+                    "parents": [],
+                    "direct_children": ["Biospecimen"],
+                    "children": ["Biospecimen", "BulkRNA-seqAssay"],
+                },
+                {
+                    "id": "Biospecimen",
+                    "parents": ["Patient"],
+                    "direct_children": ["BulkRNA-seqAssay"],
+                    "children": ["BulkRNA-seqAssay"],
+                },
+                {
+                    "id": "BulkRNA-seqAssay",
+                    "parents": ["Biospecimen"],
+                    "direct_children": [],
+                    "children": [],
+                },
+            ]
+            for data_list in response_data:
+                for data_point in data_list:
+                    assert any(
+                        data_point["id"] == expected["id"]
+                        and data_point["parents"] == expected["parents"]
+                        and data_point["direct_children"] == expected["direct_children"]
+                        and set(data_point["children"]) == set(expected["children"])
+                        for expected in expected_data
+                    )
+        elif figure_type == "dependency":
+            assert len(response_data) == 3
+            expected_data = [
+                {
+                    "id": "BulkRNA-seqAssay",
+                    "parents": [],
+                    "direct_children": ["SampleID", "Filename", "FileFormat"],
+                    "children": [],
+                },
+                {
+                    "id": "SampleID",
+                    "parents": ["BulkRNA-seqAssay"],
+                    "direct_children": [],
+                    "children": [],
+                },
+                {
+                    "id": "FileFormat",
+                    "parents": ["BulkRNA-seqAssay"],
+                    "direct_children": [
+                        "GenomeBuild",
+                        "GenomeBuild",
+                        "GenomeBuild",
+                        "GenomeFASTA",
+                    ],
+                    "children": [],
+                },
+                {
+                    "id": "Filename",
+                    "parents": ["BulkRNA-seqAssay"],
+                    "direct_children": [],
+                    "children": [],
+                },
+                {
+                    "id": "GenomeBuild",
+                    "parents": ["FileFormat", "FileFormat", "FileFormat"],
+                    "direct_children": [],
+                    "children": [],
+                },
+                {
+                    "id": "GenomeFASTA",
+                    "parents": ["FileFormat"],
+                    "direct_children": [],
+                    "children": [],
+                },
+            ]
+            for data_list in response_data:
+                for data_point in data_list:
+                    assert any(
+                        data_point["id"] == expected["id"]
+                        and data_point["parents"] == expected["parents"]
+                        and data_point["direct_children"] == expected["direct_children"]
+                        and set(data_point["children"]) == set(expected["children"])
+                        for expected in expected_data
+                    )
+
     @pytest.mark.parametrize(
         "component, response_text",
         [
@@ -1260,10 +1436,10 @@ def test_visualize_tangled_tree_layers(
         ],
     )
     def test_visualize_component(
-        self, client, data_model_jsonld, component, response_text
-    ):
+        self, client: FlaskClient, component: str, response_text: str
+    ) -> None:
         params = {
-            "schema_url": data_model_jsonld,
+            "schema_url": DATA_MODEL_JSON_LD,
             "component": component,
             "include_index": False,
             "data_model_labels": "class_label",
@@ -1288,11 +1464,10 @@ class TestValidationBenchmark:
     def test_validation_performance(
         self,
         helpers,
-        benchmark_data_model_jsonld,
-        client,
-        test_invalid_manifest,
-        MockComponent_attribute,
-    ):
+        client: FlaskClient,
+        test_invalid_manifest: pd.DataFrame,
+        MockComponent_attribute: Generator[str, None, None],
+    ) -> None:
         """
         Test to benchamrk performance of validation rules on large manifests
         Test loads the invalid_test_manifest.csv and isolates one attribute at a time
@@ -1309,7 +1484,7 @@ def test_validation_performance(
 
         # Set paramters for endpoint
         params = {
-            "schema_url": benchmark_data_model_jsonld,
+            "schema_url": BENCHMARK_DATA_MODEL_JSON_LD,
             "data_type": "MockComponent",
         }
         headers = {"Content-Type": "multipart/form-data", "Accept": "application/json"}
@@ -1356,7 +1531,7 @@ def test_validation_performance(
 
         # Log and check time and ensure successful response
         logger.warning(
-            f"validation endpiont response time {round(response_time,2)} seconds."
+            f"validation endpoint response time {round(response_time,2)} seconds."
         )
         assert response.status_code == 200
         assert response_time < 5.00
diff --git a/tests/test_ge_helpers.py b/tests/test_ge_helpers.py
new file mode 100644
index 000000000..6e0b3e01c
--- /dev/null
+++ b/tests/test_ge_helpers.py
@@ -0,0 +1,72 @@
+from typing import Generator
+from unittest.mock import MagicMock
+
+import pandas as pd
+import pytest
+
+from schematic.models.GE_Helpers import GreatExpectationsHelpers
+from tests.conftest import Helpers
+
+
+@pytest.fixture(scope="class")
+def mock_ge_helpers(
+    helpers: Helpers,
+) -> Generator[GreatExpectationsHelpers, None, None]:
+    """Fixture for creating a GreatExpectationsHelpers object"""
+    dmge = helpers.get_data_model_graph_explorer(path="example.model.jsonld")
+    unimplemented_expectations = ["url"]
+    test_manifest_path = helpers.get_data_path("mock_manifests/Valid_Test_Manifest.csv")
+    manifest = helpers.get_data_frame(test_manifest_path)
+
+    ge_helpers = GreatExpectationsHelpers(
+        dmge=dmge,
+        unimplemented_expectations=unimplemented_expectations,
+        manifest=manifest,
+        manifestPath=test_manifest_path,
+    )
+    yield ge_helpers
+
+
+class TestGreatExpectationsHelpers:
+    def test_add_expectation_suite_if_not_exists_does_not_exist(
+        self, mock_ge_helpers: Generator[GreatExpectationsHelpers, None, None]
+    ) -> None:
+        """test add_expectation_suite_if_not_exists method when the expectation suite does not exists"""
+        # mock context provided by ge_helpers
+        mock_ge_helpers.context = MagicMock()
+        mock_ge_helpers.context.list_expectation_suite_names.return_value = []
+
+        # Call the method
+        result = mock_ge_helpers.add_expectation_suite_if_not_exists()
+
+        # Make sure the method of creating expectation suites if it doesn't exist
+        mock_ge_helpers.context.list_expectation_suite_names.assert_called_once()
+        mock_ge_helpers.context.add_expectation_suite.assert_called_once_with(
+            expectation_suite_name="Manifest_test_suite"
+        )
+
+    def test_add_expectation_suite_if_not_exists_does_exist(
+        self, mock_ge_helpers: Generator[GreatExpectationsHelpers, None, None]
+    ) -> None:
+        """test add_expectation_suite_if_not_exists method when the expectation suite does exists"""
+        # mock context provided by ge_helpers
+        mock_ge_helpers.context = MagicMock()
+        mock_ge_helpers.context.list_expectation_suite_names.return_value = [
+            "Manifest_test_suite"
+        ]
+        mock_ge_helpers.context.list_checkpoints.return_value = ["test_checkpoint"]
+
+        # Call the method
+        result = mock_ge_helpers.add_expectation_suite_if_not_exists()
+
+        # Make sure the method of deleting suites gets called
+        mock_ge_helpers.context.list_expectation_suite_names.assert_called_once()
+        mock_ge_helpers.context.delete_expectation_suite.assert_called_once_with(
+            "Manifest_test_suite"
+        )
+        mock_ge_helpers.context.add_expectation_suite.assert_called_once_with(
+            expectation_suite_name="Manifest_test_suite"
+        )
+        mock_ge_helpers.context.delete_checkpoint.assert_called_once_with(
+            "test_checkpoint"
+        )
diff --git a/tests/test_manifest.py b/tests/test_manifest.py
index c34148dab..06bd7b168 100644
--- a/tests/test_manifest.py
+++ b/tests/test_manifest.py
@@ -1,16 +1,16 @@
+import logging
 import os
 import shutil
-import logging
-import pytest
+from unittest.mock import MagicMock, Mock, patch
+
 import pandas as pd
-from unittest.mock import Mock
-from unittest.mock import patch
-from unittest.mock import MagicMock
+import pytest
+
+from schematic.configuration.configuration import Configuration
 from schematic.manifest.generator import ManifestGenerator
-from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
 from schematic.schemas.data_model_json_schema import DataModelJSONSchema
-from schematic.configuration.configuration import Configuration
+from schematic.schemas.data_model_parser import DataModelParser
 from schematic.utils.google_api_utils import execute_google_api_requests
 from schematic_api.api import create_app
 
@@ -213,9 +213,9 @@ def test_get_manifest_first_time(self, manifest):
 
         # Confirm contents of Filename column
         assert output["Filename"].tolist() == [
-            "TestDataset-Annotations-v3/Sample_A.txt",
-            "TestDataset-Annotations-v3/Sample_B.txt",
-            "TestDataset-Annotations-v3/Sample_C.txt",
+            "schematic - main/TestDataset-Annotations-v3/Sample_A.txt",
+            "schematic - main/TestDataset-Annotations-v3/Sample_B.txt",
+            "schematic - main/TestDataset-Annotations-v3/Sample_C.txt",
         ]
 
         # Test dimensions of data frame
@@ -763,22 +763,52 @@ def test_create_manifests(
             assert all_results == expected_result
 
     @pytest.mark.parametrize(
-        "component,datasetId",
-        [("Biospecimen", "syn61260107"), ("BulkRNA-seqAssay", "syn61374924")],
+        "component,datasetId,expected_file_based,expected_rows,expected_files",
+        [
+            ("Biospecimen", "syn61260107", False, 4, None),
+            (
+                "BulkRNA-seqAssay",
+                "syn61374924",
+                True,
+                4,
+                pd.Series(
+                    [
+                        "schematic - main/BulkRNASeq and files/txt1.txt",
+                        "schematic - main/BulkRNASeq and files/txt2.txt",
+                        "schematic - main/BulkRNASeq and files/txt4.txt",
+                        "schematic - main/BulkRNASeq and files/txt3.txt",
+                    ],
+                    name="Filename",
+                ),
+            ),
+        ],
         ids=["Record based", "File based"],
     )
-    def test_get_manifest_with_files(self, helpers, component, datasetId):
+    def test_get_manifest_with_files(
+        self,
+        helpers,
+        component,
+        datasetId,
+        expected_file_based,
+        expected_rows,
+        expected_files,
+    ):
         """
-        Test to ensure that when generating a record based manifset that has files in the dataset that the files are not added to the manifest as well
+        Test to ensure that
+            when generating a record based manifset that has files in the dataset that the files are not added to the manifest as well
+            when generating a file based manifest from a dataset thathas had files added that the files are added correctly
         """
+        # GIVEN the example data model
         path_to_data_model = helpers.get_data_path("example.model.jsonld")
 
+        # AND a graph data model
         graph_data_model = generate_graph_data_model(
             helpers,
             path_to_data_model=path_to_data_model,
             data_model_labels="class_label",
         )
 
+        # AND a manifest generator
         generator = ManifestGenerator(
             path_to_data_model=path_to_data_model,
             graph=graph_data_model,
@@ -786,16 +816,24 @@ def test_get_manifest_with_files(self, helpers, component, datasetId):
             use_annotations=True,
         )
 
+        # WHEN a manifest is generated for the appropriate dataset as a dataframe
         manifest = generator.get_manifest(
             dataset_id=datasetId, output_format="dataframe"
         )
 
-        filename_in_manifest_columns = "Filename" in manifest.columns
+        # AND it is determined if the manifest is filebased
+        is_file_based = "Filename" in manifest.columns
+
+        # AND the number of rows are checked
         n_rows = manifest.shape[0]
 
-        if component == "Biospecimen":
-            assert not filename_in_manifest_columns
-            assert n_rows == 4
-        elif component == "BulkRNA-seqAssay":
-            assert filename_in_manifest_columns
-            assert n_rows == 3
+        # THEN the manifest should have the expected number of rows
+        assert n_rows == expected_rows
+
+        # AND the manifest should be filebased or not as expected
+        assert is_file_based == expected_file_based
+
+        # AND if the manifest is file based
+        if expected_file_based:
+            # THEN the manifest should have the expected files
+            assert manifest["Filename"].equals(expected_files)
diff --git a/tests/test_metadata.py b/tests/test_metadata.py
index bf0c4d97b..fca1d3db5 100644
--- a/tests/test_metadata.py
+++ b/tests/test_metadata.py
@@ -2,8 +2,8 @@
 
 import logging
 import os
-from typing import Optional, Generator
 from pathlib import Path
+from typing import Generator, Optional
 from unittest.mock import patch
 
 import pytest
diff --git a/tests/test_schemas.py b/tests/test_schemas.py
index f80449b18..409c653b0 100644
--- a/tests/test_schemas.py
+++ b/tests/test_schemas.py
@@ -1,46 +1,40 @@
-from copy import deepcopy
 import json
 import logging
+import os
+import random
+from copy import deepcopy
+
 import networkx as nx
 import numpy as np
-import os
 import pandas as pd
 import pytest
-import random
-from typing import Optional
 
 from schematic.schemas.data_model_edges import DataModelEdges
-from schematic.schemas.data_model_nodes import DataModelNodes
-from schematic.schemas.data_model_relationships import DataModelRelationships
-
-from schematic.utils.df_utils import load_df
-from schematic.utils.schema_utils import (
-    get_label_from_display_name,
-    get_attribute_display_name_from_label,
-    convert_bool_to_str,
-    parse_validation_rules,
-    DisplayLabelType,
-    get_json_schema_log_file_path,
-)
-from schematic.utils.io_utils import load_json
-
-from schematic.schemas.data_model_graph import DataModelGraph
-from schematic.schemas.data_model_nodes import DataModelNodes
-from schematic.schemas.data_model_edges import DataModelEdges
-from schematic.schemas.data_model_graph import DataModelGraphExplorer
-from schematic.schemas.data_model_relationships import DataModelRelationships
+from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
+from schematic.schemas.data_model_json_schema import DataModelJSONSchema
 from schematic.schemas.data_model_jsonld import (
-    DataModelJsonLD,
-    convert_graph_to_jsonld,
     BaseTemplate,
-    PropertyTemplate,
     ClassTemplate,
+    DataModelJsonLD,
+    PropertyTemplate,
+    convert_graph_to_jsonld,
 )
-from schematic.schemas.data_model_json_schema import DataModelJSONSchema
+from schematic.schemas.data_model_nodes import DataModelNodes
 from schematic.schemas.data_model_parser import (
-    DataModelParser,
     DataModelCSVParser,
     DataModelJSONLDParser,
+    DataModelParser,
+)
+from schematic.schemas.data_model_relationships import DataModelRelationships
+from schematic.utils.df_utils import load_df
+from schematic.utils.io_utils import load_json
+from schematic.utils.schema_utils import (
+    DisplayLabelType,
+    convert_bool_to_str,
+    get_attribute_display_name_from_label,
+    get_json_schema_log_file_path,
+    get_label_from_display_name,
+    parse_validation_rules,
 )
 
 logging.basicConfig(level=logging.DEBUG)
@@ -621,9 +615,6 @@ def test_get_node_range(self):
     def test_get_node_required(self):
         return
 
-    def test_get_node_validation_rules(self):
-        return
-
     def test_get_subgraph_by_edge_type(self):
         return
 
@@ -898,12 +889,24 @@ def test_run_rel_functions(self, helpers, data_model, rel_func, test_dn, test_bo
                     if "::" in rule[0]:
                         assert parsed_vrs[ind] == rule[0].split("::")
                     elif "^^" in rule[0]:
+                        component_with_specific_rules = []
                         component_rule_sets = rule[0].split("^^")
                         components = [
                             cr.split(" ")[0].replace("#", "")
                             for cr in component_rule_sets
                         ]
-                        assert components == [k for k in parsed_vrs[0].keys()]
+                        if "" in components:
+                            components.remove("")
+                        for parsed_rule in parsed_vrs:
+                            if isinstance(parsed_rule, dict):
+                                for k in parsed_rule.keys():
+                                    component_with_specific_rules.append(k)
+                        assert all(
+                            [
+                                component in component_with_specific_rules
+                                for component in components
+                            ]
+                        )
                     else:
                         assert parsed_vrs[ind] == rule
             elif DATA_MODEL_DICT[data_model] == "JSONLD":
diff --git a/tests/test_store.py b/tests/test_store.py
index 5ac61f3d0..f79761b28 100644
--- a/tests/test_store.py
+++ b/tests/test_store.py
@@ -2,28 +2,34 @@
 
 from __future__ import annotations
 
+import asyncio
 import logging
 import math
 import os
-from time import sleep
-from typing import Generator, Any
-from unittest.mock import patch
 import shutil
+import tempfile
+import uuid
+from contextlib import nullcontext as does_not_raise
+from typing import Any, Callable, Generator
+from unittest.mock import AsyncMock, MagicMock, patch
 
 import pandas as pd
 import pytest
+from pandas.testing import assert_frame_equal
 from synapseclient import EntityViewSchema, Folder
+from synapseclient.core.exceptions import SynapseHTTPError
 from synapseclient.entity import File
-from pandas.testing import assert_frame_equal
+from synapseclient.models import Annotations
+from synapseclient.models import Folder as FolderModel
 
-from schematic.configuration.configuration import Configuration
+from schematic.configuration.configuration import CONFIG, Configuration
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
 from schematic.schemas.data_model_parser import DataModelParser
-from tests.conftest import Helpers
-
 from schematic.store.base import BaseStorage
 from schematic.store.synapse import DatasetFileView, ManifestDownload, SynapseStorage
 from schematic.utils.general import check_synapse_cache_size
+from tests.conftest import Helpers
+from tests.utils import CleanupItem
 
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
@@ -71,14 +77,18 @@ def projectId(synapse_store, helpers):
 
 
 @pytest.fixture
-def datasetId(synapse_store, projectId, helpers):
+def datasetId(
+    synapse_store: SynapseStorage, projectId: str, helpers, schedule_for_cleanup
+):
     dataset = Folder(
-        name="Table Test  Dataset " + helpers.get_python_version(),
+        name="Table Test Dataset "
+        + helpers.get_python_version()
+        + f" integration_test_{str(uuid.uuid4()).replace('-', '_')}",
         parent=projectId,
     )
 
     datasetId = synapse_store.syn.store(dataset).id
-    sleep(5)
+    schedule_for_cleanup(CleanupItem(synapse_id=datasetId))
     yield datasetId
 
 
@@ -114,6 +124,11 @@ def dmge(
     yield dmge
 
 
+@pytest.fixture(scope="module")
+def synapse_store_special_scope():
+    yield SynapseStorage(perform_query=False)
+
+
 def raise_final_error(retry_state):
     return retry_state.outcome.result()
 
@@ -152,6 +167,130 @@ def test_login(self) -> None:
         assert synapse_client.cache.cache_root_dir == "test_cache_dir"
         shutil.rmtree("test_cache_dir")
 
+    @pytest.mark.parametrize(
+        "project_scope,columns,where_clauses,expected,expected_new_query",
+        [
+            (None, None, None, "SELECT * FROM syn23643253 ;", True),
+            (
+                ["syn23643250"],
+                None,
+                None,
+                "SELECT * FROM syn23643253 WHERE projectId IN ('syn23643250', '') ;",
+                True,
+            ),
+            (
+                None,
+                None,
+                ["projectId IN ('syn23643250')"],
+                "SELECT * FROM syn23643253 WHERE projectId IN ('syn23643250') ;",
+                True,
+            ),
+            (
+                ["syn23643250"],
+                ["name", "id", "path"],
+                None,
+                "SELECT name,id,path FROM syn23643253 WHERE projectId IN ('syn23643250', '') ;",
+                True,
+            ),
+            (
+                None,
+                ["name", "id", "path"],
+                ["parentId='syn61682648'", "type='file'"],
+                "SELECT name,id,path FROM syn23643253 WHERE parentId='syn61682648' AND type='file' ;",
+                True,
+            ),
+            (
+                ["syn23643250"],
+                None,
+                ["parentId='syn61682648'", "type='file'"],
+                "SELECT * FROM syn23643253 WHERE parentId='syn61682648' AND type='file' AND projectId IN ('syn23643250', '') ;",
+                True,
+            ),
+            (
+                ["syn23643250"],
+                ["name", "id", "path"],
+                ["parentId='syn61682648'", "type='file'"],
+                "SELECT name,id,path FROM syn23643253 WHERE parentId='syn61682648' AND type='file' AND projectId IN ('syn23643250', '') ;",
+                True,
+            ),
+            (
+                ["syn23643250"],
+                ["name", "id", "path"],
+                ["parentId='syn61682648'", "type='file'"],
+                "SELECT name,id,path FROM syn23643253 WHERE parentId='syn61682648' AND type='file' AND projectId IN ('syn23643250', '') ;",
+                False,
+            ),
+        ],
+    )
+    def test_view_query(
+        self,
+        synapse_store_special_scope: SynapseStorage,
+        project_scope: list,
+        columns: list,
+        where_clauses: list,
+        expected: str,
+        expected_new_query: bool,
+    ) -> None:
+        # GIVEN a the correct fileview
+        assert synapse_store_special_scope.storageFileview == "syn23643253"
+
+        # AND the approrpiate project scope
+        synapse_store_special_scope.project_scope = project_scope
+
+        # WHEN the query is built and run
+        # THEN it should complete without raising an exception
+        with does_not_raise():
+            synapse_store_special_scope.query_fileview(columns, where_clauses)
+            # AND the query string should be as expected
+            assert synapse_store_special_scope.fileview_query == expected
+            # AND query should have recieved a non-empty table
+            assert synapse_store_special_scope.storageFileviewTable.empty is False
+            # AND the query should be new if expected
+            assert synapse_store_special_scope.new_query_different == expected_new_query
+
+    @pytest.mark.parametrize(
+        "asset_view,columns,message",
+        [
+            (
+                "syn62339865",
+                ["path"],
+                r"The path column has not been added to the fileview. .*",
+            ),
+            (
+                "syn62340177",
+                ["id"],
+                r"The columns id specified in the query do not exist in the fileview. .*",
+            ),
+        ],
+    )
+    def test_view_query_exception(
+        self,
+        asset_view: str,
+        columns: list[str],
+        message: str,
+    ) -> None:
+        # GIVEN a project scope
+        project_scope = ["syn23643250"]
+
+        # AND a test configuration
+        TEST_CONFIG = Configuration()
+        with patch(
+            "schematic.store.synapse.CONFIG", return_value=TEST_CONFIG
+        ) as mock_config:
+            # AND the appropriate test file view
+            mock_config.synapse_master_fileview_id = asset_view
+            # AND a real path to the synapse config file
+            mock_config.synapse_configuration_path = CONFIG.synapse_configuration_path
+            # AND a unique synapse storage object that uses the values modified in the test config
+            synapse_store = SynapseStorage(perform_query=False)
+            # AND the given project scope
+            synapse_store.project_scope = project_scope
+
+            # WHEN the query is built and run
+            # THEN it should raise a ValueError with the appropriate message
+            with pytest.raises(ValueError, match=message):
+                synapse_store.query_fileview(columns)
+
     def test_getFileAnnotations(self, synapse_store: SynapseStorage) -> None:
         expected_dict = {
             "author": "bruno, milen, sujay",
@@ -267,7 +406,7 @@ def test_getDatasetAnnotations(self, dataset_id, synapse_store, force_batch):
         expected_df = pd.DataFrame.from_records(
             [
                 {
-                    "Filename": "TestDataset-Annotations-v3/Sample_A.txt",
+                    "Filename": "schematic - main/TestDataset-Annotations-v3/Sample_A.txt",
                     "author": "bruno, milen, sujay",
                     "impact": "42.9",
                     "confidence": "high",
@@ -277,13 +416,13 @@ def test_getDatasetAnnotations(self, dataset_id, synapse_store, force_batch):
                     "IsImportantText": "TRUE",
                 },
                 {
-                    "Filename": "TestDataset-Annotations-v3/Sample_B.txt",
+                    "Filename": "schematic - main/TestDataset-Annotations-v3/Sample_B.txt",
                     "confidence": "low",
                     "FileFormat": "csv",
                     "date": "2020-02-01",
                 },
                 {
-                    "Filename": "TestDataset-Annotations-v3/Sample_C.txt",
+                    "Filename": "schematic - main/TestDataset-Annotations-v3/Sample_C.txt",
                     "FileFormat": "fastq",
                     "IsImportantBool": "False",
                     "IsImportantText": "FALSE",
@@ -318,8 +457,11 @@ def test_getDatasetProject(self, dataset_id, synapse_store):
             (
                 True,
                 [
-                    ("syn126", "parent_folder/test_file"),
-                    ("syn125", "parent_folder/test_folder/test_file_2"),
+                    ("syn126", "schematic - main/parent_folder/test_file"),
+                    (
+                        "syn125",
+                        "schematic - main/parent_folder/test_folder/test_file_2",
+                    ),
                 ],
             ),
             (False, [("syn126", "test_file"), ("syn125", "test_file_2")]),
@@ -333,16 +475,26 @@ def test_getFilesInStorageDataset(self, synapse_store, full_path, expected):
                 [("test_file", "syn126")],
             ),
             (
-                (os.path.join("parent_folder", "test_folder"), "syn124"),
+                (
+                    os.path.join("schematic - main", "parent_folder", "test_folder"),
+                    "syn124",
+                ),
                 [],
                 [("test_file_2", "syn125")],
             ),
         ]
-        with patch("synapseutils.walk_functions._help_walk", return_value=mock_return):
+        with patch(
+            "synapseutils.walk_functions._help_walk", return_value=mock_return
+        ) as mock_walk_patch, patch(
+            "schematic.store.synapse.SynapseStorage.getDatasetProject",
+            return_value="syn23643250",
+        ) as mock_project_id_patch, patch(
+            "synapseclient.entity.Entity.__getattr__", return_value="schematic - main"
+        ) as mock_project_name_patch:
             file_list = synapse_store.getFilesInStorageDataset(
                 datasetId="syn_mock", fileNames=None, fullpath=full_path
             )
-            assert file_list == expected
+        assert file_list == expected
 
     @pytest.mark.parametrize("downloadFile", [True, False])
     def test_getDatasetManifest(self, synapse_store, downloadFile):
@@ -360,42 +512,67 @@ def test_getDatasetManifest(self, synapse_store, downloadFile):
             assert manifest_data == "syn51204513"
 
     @pytest.mark.parametrize(
-        "existing_manifest_df",
+        "existing_manifest_df,fill_in_return_value,expected_df",
         [
-            pd.DataFrame(),
-            pd.DataFrame(
-                {
-                    "Filename": ["existing_mock_file_path"],
-                    "entityId": ["existing_mock_entity_id"],
-                }
+            (
+                pd.DataFrame(),
+                [
+                    {
+                        "Filename": ["new_mock_file_path"],
+                        "entityId": ["new_mock_entity_id"],
+                    },
+                    {
+                        "Filename": ["new_mock_file_path"],
+                        "entityId": ["new_mock_entity_id"],
+                    },
+                ],
+                pd.DataFrame(
+                    {
+                        "Filename": ["new_mock_file_path"],
+                        "entityId": ["new_mock_entity_id"],
+                    }
+                ),
+            ),
+            (
+                pd.DataFrame(
+                    {
+                        "Filename": ["existing_mock_file_path"],
+                        "entityId": ["existing_mock_entity_id"],
+                    }
+                ),
+                [
+                    {
+                        "Filename": ["existing_mock_file_path", "new_mock_file_path"],
+                        "entityId": ["existing_mock_entity_id", "new_mock_entity_id"],
+                    },
+                    {
+                        "Filename": ["new_mock_file_path"],
+                        "entityId": ["new_mock_entity_id"],
+                    },
+                ],
+                pd.DataFrame(
+                    {
+                        "Filename": ["existing_mock_file_path", "new_mock_file_path"],
+                        "entityId": ["existing_mock_entity_id", "new_mock_entity_id"],
+                    }
+                ),
             ),
         ],
     )
-    def test_fill_in_entity_id_filename(self, synapse_store, existing_manifest_df):
+    def test_fill_in_entity_id_filename(
+        self, synapse_store, existing_manifest_df, fill_in_return_value, expected_df
+    ):
         with patch(
             "schematic.store.synapse.SynapseStorage.getFilesInStorageDataset",
             return_value=["syn123", "syn124", "syn125"],
         ) as mock_get_file_storage, patch(
             "schematic.store.synapse.SynapseStorage._get_file_entityIds",
-            return_value={
-                "Filename": ["mock_file_path"],
-                "entityId": ["mock_entity_id"],
-            },
+            side_effect=fill_in_return_value,
         ) as mock_get_file_entity_id:
             dataset_files, new_manifest = synapse_store.fill_in_entity_id_filename(
                 datasetId="test_syn_id", manifest=existing_manifest_df
             )
-            if not existing_manifest_df.empty:
-                expected_df = pd.DataFrame(
-                    {
-                        "Filename": ["existing_mock_file_path", "mock_file_path"],
-                        "entityId": ["existing_mock_entity_id", "mock_entity_id"],
-                    }
-                )
-            else:
-                expected_df = pd.DataFrame(
-                    {"Filename": ["mock_file_path"], "entityId": ["mock_entity_id"]}
-                )
+
             assert_frame_equal(new_manifest, expected_df)
             assert dataset_files == ["syn123", "syn124", "syn125"]
 
@@ -448,6 +625,47 @@ def test_add_entity_id_and_filename_without_component_col(self, synapse_store):
             )
             assert_frame_equal(manifest_to_return, expected_df)
 
+    @pytest.mark.parametrize(
+        "hideBlanks, annotation_keys",
+        [
+            (True, "display_label"),
+            (False, "display_label"),
+            (True, "class_label"),
+            (False, "class_label"),
+        ],
+    )
+    async def test_format_row_annotations_entity_id_trash_can(
+        self,
+        caplog: pytest.LogCaptureFixture,
+        dmge: DataModelGraph,
+        synapse_store: SynapseStorage,
+        hideBlanks: bool,
+        annotation_keys: str,
+    ) -> None:
+        """make sure that missing_entity_handler gets triggered when entity is in the trash can"""
+        with patch(
+            "schematic.store.synapse.SynapseStorage.get_async_annotation",
+            side_effect=SynapseHTTPError("entity syn123 is in the trash can"),
+            new_callable=AsyncMock,
+        ):
+            mock_row_dict = {
+                "Component": "MockComponent",
+                "Mock_id": 1,
+                "Id": "Mock_id",
+                "entityId": "mock_syn_id",
+            }
+            mock_row = pd.Series(mock_row_dict)
+            with caplog.at_level(logging.WARNING):
+                formatted_annotations = await synapse_store.format_row_annotations(
+                    dmge,
+                    mock_row,
+                    entityId="mock_syn_id",
+                    hideBlanks=hideBlanks,
+                    annotation_keys=annotation_keys,
+                )
+                assert "entity syn123 is in the trash can" in caplog.text
+                assert formatted_annotations == None
+
     def test_get_files_metadata_from_dataset(self, synapse_store):
         patch_get_children = [
             ("syn123", "parent_folder/test_A.txt"),
@@ -478,6 +696,228 @@ def test_get_files_metadata_from_dataset(self, synapse_store):
                     "entityId": ["syn123", "syn456"],
                 }
 
+    async def test_get_async_annotation(self, synapse_store: SynapseStorage) -> None:
+        """test get annotation async function"""
+        mock_syn_id = "syn1234"
+
+        with patch(
+            "schematic.store.synapse.get_entity_id_bundle2",
+            new_callable=AsyncMock,
+            return_value="mock",
+        ) as mock_get_entity_id_bundle2:
+            mock_get_entity_id_bundle2.return_value = "mock"
+            result = await synapse_store.get_async_annotation(synapse_id=mock_syn_id)
+
+            mock_get_entity_id_bundle2.assert_called_once_with(
+                entity_id=mock_syn_id,
+                request={"includeAnnotations": True},
+                synapse_client=synapse_store.syn,
+            )
+            assert result == "mock"
+
+    async def test_store_async_annotation(self, synapse_store: SynapseStorage) -> None:
+        """test store annotations async function"""
+        annos_dict = {
+            "annotations": {
+                "id": "mock_syn_id",
+                "etag": "mock etag",
+                "annotations": {
+                    "Id": {"type": "STRING", "value": ["mock value"]},
+                    "EntityId": {"type": "STRING", "value": ["mock_syn_id"]},
+                    "SampleID": {"type": "STRING", "value": [""]},
+                    "Component": {"type": "STRING", "value": ["mock value"]},
+                },
+            },
+            "FileFormat": "mock format",
+            "Component": "mock component",
+            "Id": "mock_string",
+            "EntityId": "mock_id",
+        }
+        expected_dict = Annotations(
+            annotations={
+                "Id": ["mock_string"],
+                "EntityId": ["mock_syn_id"],
+                "SampleID": [""],
+                "Component": ["mock value"],
+                "FileFormat": ["mock_format"],
+            },
+            etag="mock etag",
+            id="mock syn_id",
+        )
+
+        with patch(
+            "schematic.store.synapse.Annotations.store_async",
+            new_callable=AsyncMock,
+            return_value=expected_dict,
+        ) as mock_store_async:
+            result = await synapse_store.store_async_annotation(annos_dict)
+
+            mock_store_async.assert_called_once_with(synapse_client=synapse_store.syn)
+            assert result == expected_dict
+            assert isinstance(result, Annotations)
+
+    async def test_process_store_annos_failure(
+        self, synapse_store: SynapseStorage
+    ) -> None:
+        """test _process_store_annos function when there's an error either getting or storing annotations"""
+
+        async def mock_failure_coro():
+            raise ValueError("sample error")
+
+        # create tasks that will fail
+        tasks = set()
+        tasks.add(asyncio.create_task(mock_failure_coro()))
+
+        synapse_store._process_store_annos
+        # make sure error message can be raised
+        with pytest.raises(RuntimeError, match="failed with"):
+            await synapse_store._process_store_annos(tasks)
+
+    async def test_process_store_annos_success_store(
+        self, synapse_store: SynapseStorage
+    ) -> None:
+        """test _process_store_annos function and make sure that annotations can be stored after successfully getting annotations."""
+        # mock annotation obtained after async_store
+        stored_annos = Annotations(
+            annotations={
+                "Id": ["mock_string"],
+                "EntityId": ["mock_syn_id"],
+                "SampleID": [""],
+                "Component": ["mock value"],
+                "FileFormat": ["mock_format"],
+            },
+            etag="mock etag",
+            id="mock_syn_id",
+        )
+
+        async def mock_success_coro():
+            return stored_annos
+
+        with patch(
+            "schematic.store.synapse.SynapseStorage.store_async_annotation",
+            new_callable=AsyncMock,
+        ) as mock_store_async1:
+            tasks = set()
+            tasks.add(asyncio.create_task(mock_success_coro()))
+            await synapse_store._process_store_annos(tasks)
+            # make sure that the if statement is working
+            mock_store_async1.assert_not_called()
+
+    async def test_process_store_annos_success_get(
+        self, synapse_store: SynapseStorage
+    ) -> None:
+        """test _process_store_annos function and make sure that task of storing annotations can be triggered"""
+        # mock annotation obtained after get_async
+        mock_annos_dict = {
+            "annotations": {
+                "id": "mock_syn_id",
+                "etag": "mock etag",
+                "annotations": {
+                    "Id": {"type": "STRING", "value": ["mock value"]},
+                    "EntityId": {"type": "STRING", "value": ["mock_syn_id"]},
+                    "SampleID": {"type": "STRING", "value": [""]},
+                    "Component": {"type": "STRING", "value": ["mock value"]},
+                },
+            },
+            "FileFormat": "mock format",
+            "Component": "mock component",
+            "Id": "mock_string",
+            "EntityId": "mock_id",
+        }
+
+        mock_stored_annos = Annotations(
+            annotations={
+                "Id": ["mock_string"],
+                "EntityId": ["mock_syn_id"],
+            },
+            etag="mock etag",
+            id="mock_syn_id",
+        )
+
+        async def mock_success_coro():
+            return mock_annos_dict
+
+        # make sure that the else statement is working
+        new_tasks = set()
+        with patch(
+            "schematic.store.synapse.SynapseStorage.store_async_annotation",
+            new_callable=AsyncMock,
+            return_value=mock_stored_annos,
+        ) as mock_store_async2:
+            new_tasks.add(asyncio.create_task(mock_success_coro()))
+            await synapse_store._process_store_annos(new_tasks)
+            mock_store_async2.assert_called_once()
+
+    async def test_process_store_annos_success_get_entity_id_variants(
+        self, synapse_store: SynapseStorage
+    ) -> None:
+        "mock annotations obtained after gettinng annotations have different annotations and formatting"
+        annotations_variants = [
+            {"EntityId": ["mock_syn_id"], "Id": ["mock_string"]},
+            {"entityId": ["mock_syn_id"], "id": ["mock_string"]},
+            {"entityid": ["mock_syn_id"], "id": ["mock_string"]},
+            {"ENTITYID": ["mock_syn_id"], "ID": ["mock_string"]},
+        ]
+        for anno_variant in annotations_variants:
+            mock_annos_dict = {
+                "annotations": {
+                    "id": "mock_syn_id",
+                    "etag": "mock etag",
+                    "annotations": {
+                        "Id": {"type": "STRING", "value": ["mock value"]},
+                        "EntityId": {"type": "STRING", "value": ["mock_syn_id"]},
+                        "SampleID": {"type": "STRING", "value": [""]},
+                        "Component": {"type": "STRING", "value": ["mock value"]},
+                    },
+                },
+                "FileFormat": "mock format",
+                "Component": "mock component",
+                **anno_variant,
+            }
+            mock_stored_annos = Annotations(
+                annotations={
+                    **anno_variant,
+                    "SampleID": [""],
+                    "Component": ["mock value"],
+                    "FileFormat": ["mock_format"],
+                },
+                etag="mock etag",
+                id="mock syn_id",
+            )
+
+            async def mock_success_coro() -> dict[str, Any]:
+                return mock_annos_dict
+
+            # make sure that the else statement is working
+            new_tasks = set()
+            with patch(
+                "schematic.store.synapse.SynapseStorage.store_async_annotation",
+                new_callable=AsyncMock,
+                return_value=mock_stored_annos,
+            ) as mock_store_async2:
+                new_tasks.add(asyncio.create_task(mock_success_coro()))
+                await synapse_store._process_store_annos(new_tasks)
+                mock_store_async2.assert_called_once()
+
+    async def test_process_store_annos_get_annos_empty(
+        self, synapse_store: SynapseStorage
+    ) -> None:
+        """ "test _process_store_annos function and make sure that task of storing annotations wont be triggered when annotations are empty"""
+
+        # make sure that the else statement is working
+        # and that the task of storing annotations is not triggered when annotations are empty
+        async def mock_success_coro() -> None:
+            return None
+
+        with patch(
+            "schematic.store.synapse.SynapseStorage.store_async_annotation",
+            new_callable=AsyncMock,
+        ) as mock_store_async:
+            new_tasks = set()
+            new_tasks.add(asyncio.create_task(mock_success_coro()))
+            await synapse_store._process_store_annos(new_tasks)
+            mock_store_async.assert_not_called()
+
 
 class TestDatasetFileView:
     def test_init(self, dataset_id, dataset_fileview, synapse_store):
@@ -557,51 +997,62 @@ class TestTableOperations:
         ["display_label", "class_label"],
         ids=["aks_display_label", "aks_class_label"],
     )
-    def test_createTable(
+    async def test_create_table(
         self,
-        helpers,
-        synapse_store,
-        config: Configuration,
-        projectId,
-        datasetId,
-        table_column_names,
-        annotation_keys,
+        helpers: Helpers,
+        synapse_store: SynapseStorage,
+        projectId: str,
+        datasetId: str,
+        table_column_names: str,
+        annotation_keys: str,
         dmge: DataModelGraphExplorer,
-    ):
+        schedule_for_cleanup: Callable[[CleanupItem], None],
+    ) -> None:
+        # GIVEN a table to create
         table_manipulation = None
+        table_name = f"followup_synapse_storage_manifest_table_integration_test_{str(uuid.uuid4()).replace('-', '_')}"
+        schedule_for_cleanup(CleanupItem(name=table_name, parent_id=projectId))
 
-        # Check if FollowUp table exists if so delete
-        existing_tables = synapse_store.get_table_info(projectId=projectId)
-
-        table_name = "followup_synapse_storage_manifest_table"
+        # AND a manifest to associate metadata with files
+        manifest_path = "mock_manifests/table_manifest.csv"
 
-        if table_name in existing_tables.keys():
-            synapse_store.syn.delete(existing_tables[table_name])
-            sleep(10)
-            # assert no table
-            assert (
-                table_name
-                not in synapse_store.get_table_info(projectId=projectId).keys()
+        # AND a copy of all the folders in the manifest. Added to the dataset directory for easy cleanup
+        manifest = helpers.get_data_frame(manifest_path)
+        for index, row in manifest.iterrows():
+            folder_id = row["entityId"]
+            folder_copy = FolderModel(id=folder_id).copy(
+                parent_id=datasetId, synapse_client=synapse_store.syn
+            )
+            schedule_for_cleanup(CleanupItem(synapse_id=folder_copy.id))
+            manifest.at[index, "entityId"] = folder_copy.id
+
+        with patch.object(
+            synapse_store, "_generate_table_name", return_value=(table_name, "followup")
+        ), patch.object(
+            synapse_store, "getDatasetProject", return_value=projectId
+        ), tempfile.NamedTemporaryFile(
+            delete=True, suffix=".csv"
+        ) as tmp_file:
+            # Write the DF to a temporary file to prevent modifying the original
+            manifest.to_csv(tmp_file.name, index=False)
+
+            # WHEN I associate metadata with files
+            manifest_id = synapse_store.associateMetadataWithFiles(
+                dmge=dmge,
+                metadataManifestPath=tmp_file.name,
+                datasetId=datasetId,
+                manifest_record_type="table_and_file",
+                hideBlanks=True,
+                restrict_manifest=False,
+                table_manipulation=table_manipulation,
+                table_column_names=table_column_names,
+                annotation_keys=annotation_keys,
             )
+            schedule_for_cleanup(CleanupItem(synapse_id=manifest_id))
 
-        # associate metadata with files
-        manifest_path = "mock_manifests/table_manifest.csv"
-        # updating file view on synapse takes a long time
-        manifestId = synapse_store.associateMetadataWithFiles(
-            dmge=dmge,
-            metadataManifestPath=helpers.get_data_path(manifest_path),
-            datasetId=datasetId,
-            manifest_record_type="table_and_file",
-            hideBlanks=True,
-            restrict_manifest=False,
-            table_manipulation=table_manipulation,
-            table_column_names=table_column_names,
-            annotation_keys=annotation_keys,
-        )
+        # THEN the table should exist
         existing_tables = synapse_store.get_table_info(projectId=projectId)
 
-        # clean Up
-        synapse_store.syn.delete(manifestId)
         # assert table exists
         assert table_name in existing_tables.keys()
 
@@ -615,142 +1066,166 @@ def test_createTable(
         ["display_label", "class_label"],
         ids=["aks_display_label", "aks_class_label"],
     )
-    def test_replaceTable(
+    async def test_replace_table(
         self,
-        helpers,
-        synapse_store,
-        config: Configuration,
-        projectId,
-        datasetId,
-        table_column_names,
-        annotation_keys,
+        helpers: Helpers,
+        synapse_store: SynapseStorage,
+        projectId: str,
+        datasetId: str,
+        table_column_names: str,
+        annotation_keys: str,
         dmge: DataModelGraphExplorer,
-    ):
+        schedule_for_cleanup: Callable[[str], None],
+    ) -> None:
         table_manipulation = "replace"
 
-        table_name = "followup_synapse_storage_manifest_table"
+        table_name = f"followup_synapse_storage_manifest_table_integration_test_{str(uuid.uuid4()).replace('-', '_')}"
+        schedule_for_cleanup(CleanupItem(name=table_name, parent_id=projectId))
         manifest_path = "mock_manifests/table_manifest.csv"
         replacement_manifest_path = "mock_manifests/table_manifest_replacement.csv"
         column_of_interest = "DaystoFollowUp"
 
+        # AND a copy of all the folders in the manifest. Added to the dataset directory for easy cleanup
+        manifest = helpers.get_data_frame(manifest_path)
+        replacement_manifest = helpers.get_data_frame(replacement_manifest_path)
+        for index, row in manifest.iterrows():
+            folder_id = row["entityId"]
+            folder_copy = FolderModel(id=folder_id).copy(
+                parent_id=datasetId, synapse_client=synapse_store.syn
+            )
+            schedule_for_cleanup(CleanupItem(synapse_id=folder_copy.id))
+            manifest.at[index, "entityId"] = folder_copy.id
+            replacement_manifest.at[index, "entityId"] = folder_copy.id
+
         # Check if FollowUp table exists if so delete
         existing_tables = synapse_store.get_table_info(projectId=projectId)
 
-        if table_name in existing_tables.keys():
-            synapse_store.syn.delete(existing_tables[table_name])
-            sleep(10)
-            # assert no table
-            assert (
-                table_name
-                not in synapse_store.get_table_info(projectId=projectId).keys()
+        with patch.object(
+            synapse_store, "_generate_table_name", return_value=(table_name, "followup")
+        ), patch.object(
+            synapse_store, "getDatasetProject", return_value=projectId
+        ), tempfile.NamedTemporaryFile(
+            delete=True, suffix=".csv"
+        ) as tmp_file:
+            # Write the DF to a temporary file to prevent modifying the original
+            manifest.to_csv(tmp_file.name, index=False)
+
+            # updating file view on synapse takes a long time
+            manifest_id = synapse_store.associateMetadataWithFiles(
+                dmge=dmge,
+                metadataManifestPath=tmp_file.name,
+                datasetId=datasetId,
+                manifest_record_type="table_and_file",
+                hideBlanks=True,
+                restrict_manifest=False,
+                table_manipulation=table_manipulation,
+                table_column_names=table_column_names,
+                annotation_keys=annotation_keys,
             )
-
-        # updating file view on synapse takes a long time
-        manifestId = synapse_store.associateMetadataWithFiles(
-            dmge=dmge,
-            metadataManifestPath=helpers.get_data_path(manifest_path),
-            datasetId=datasetId,
-            manifest_record_type="table_and_file",
-            hideBlanks=True,
-            restrict_manifest=False,
-            table_manipulation=table_manipulation,
-            table_column_names=table_column_names,
-            annotation_keys=annotation_keys,
-        )
+            schedule_for_cleanup(CleanupItem(synapse_id=manifest_id))
         existing_tables = synapse_store.get_table_info(projectId=projectId)
 
         # Query table for DaystoFollowUp column
-        tableId = existing_tables[table_name]
-        daysToFollowUp = (
-            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {tableId}")
+        table_id = existing_tables[table_name]
+        days_to_follow_up = (
+            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {table_id}")
             .asDataFrame()
             .squeeze()
         )
 
         # assert Days to FollowUp == 73
-        assert (daysToFollowUp == 73).all()
-
-        # Associate replacement manifest with files
-        manifestId = synapse_store.associateMetadataWithFiles(
-            dmge=dmge,
-            metadataManifestPath=helpers.get_data_path(replacement_manifest_path),
-            datasetId=datasetId,
-            manifest_record_type="table_and_file",
-            hideBlanks=True,
-            restrict_manifest=False,
-            table_manipulation=table_manipulation,
-            table_column_names=table_column_names,
-            annotation_keys=annotation_keys,
-        )
+        assert (days_to_follow_up == 73).all()
+
+        with patch.object(
+            synapse_store, "_generate_table_name", return_value=(table_name, "followup")
+        ), patch.object(
+            synapse_store, "getDatasetProject", return_value=projectId
+        ), tempfile.NamedTemporaryFile(
+            delete=True, suffix=".csv"
+        ) as tmp_file:
+            # Write the DF to a temporary file to prevent modifying the original
+            replacement_manifest.to_csv(tmp_file.name, index=False)
+
+            # Associate replacement manifest with files
+            manifest_id = synapse_store.associateMetadataWithFiles(
+                dmge=dmge,
+                metadataManifestPath=tmp_file.name,
+                datasetId=datasetId,
+                manifest_record_type="table_and_file",
+                hideBlanks=True,
+                restrict_manifest=False,
+                table_manipulation=table_manipulation,
+                table_column_names=table_column_names,
+                annotation_keys=annotation_keys,
+            )
+            schedule_for_cleanup(CleanupItem(synapse_id=manifest_id))
         existing_tables = synapse_store.get_table_info(projectId=projectId)
 
         # Query table for DaystoFollowUp column
-        tableId = existing_tables[table_name]
-        daysToFollowUp = (
-            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {tableId}")
+        table_id = existing_tables[table_name]
+        days_to_follow_up = (
+            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {table_id}")
             .asDataFrame()
             .squeeze()
         )
 
         # assert Days to FollowUp == 89 now and not 73
-        assert (daysToFollowUp == 89).all()
-        # delete table
-        synapse_store.syn.delete(tableId)
+        assert (days_to_follow_up == 89).all()
 
     @pytest.mark.parametrize(
         "annotation_keys",
         ["display_label", "class_label"],
         ids=["aks_display_label", "aks_class_label"],
     )
-    def test_upsertTable(
+    async def test_upsert_table(
         self,
-        helpers,
-        synapse_store,
-        config: Configuration,
-        projectId,
-        datasetId,
-        annotation_keys,
+        helpers: Helpers,
+        synapse_store: SynapseStorage,
+        projectId: str,
+        datasetId: str,
+        annotation_keys: str,
         dmge: DataModelGraphExplorer,
+        schedule_for_cleanup: Callable[[str], None],
     ):
         table_manipulation = "upsert"
 
-        table_name = "MockRDB_synapse_storage_manifest_table".lower()
+        table_name = f"MockRDB_synapse_storage_manifest_table_integration_test_{str(uuid.uuid4()).replace('-', '_')}".lower()
+        schedule_for_cleanup(CleanupItem(name=table_name, parent_id=projectId))
         manifest_path = "mock_manifests/rdb_table_manifest.csv"
         replacement_manifest_path = "mock_manifests/rdb_table_manifest_upsert.csv"
         column_of_interest = "MockRDB_id,SourceManifest"
 
-        # Check if FollowUp table exists if so delete
-        existing_tables = synapse_store.get_table_info(projectId=projectId)
-
-        if table_name in existing_tables.keys():
-            synapse_store.syn.delete(existing_tables[table_name])
-            sleep(10)
-            # assert no table
-            assert (
-                table_name
-                not in synapse_store.get_table_info(projectId=projectId).keys()
+        with patch.object(
+            synapse_store, "_generate_table_name", return_value=(table_name, "mockrdb")
+        ), patch.object(
+            synapse_store, "getDatasetProject", return_value=projectId
+        ), tempfile.NamedTemporaryFile(
+            delete=True, suffix=".csv"
+        ) as tmp_file:
+            # Copy to a temporary file to prevent modifying the original
+            shutil.copyfile(helpers.get_data_path(manifest_path), tmp_file.name)
+
+            # updating file view on synapse takes a long time
+            manifest_id = synapse_store.associateMetadataWithFiles(
+                dmge=dmge,
+                metadataManifestPath=tmp_file.name,
+                datasetId=datasetId,
+                manifest_record_type="table_and_file",
+                hideBlanks=True,
+                restrict_manifest=False,
+                table_manipulation=table_manipulation,
+                table_column_names="display_name",
+                annotation_keys=annotation_keys,
             )
-
-        # updating file view on synapse takes a long time
-        manifestId = synapse_store.associateMetadataWithFiles(
-            dmge=dmge,
-            metadataManifestPath=helpers.get_data_path(manifest_path),
-            datasetId=datasetId,
-            manifest_record_type="table_and_file",
-            hideBlanks=True,
-            restrict_manifest=False,
-            table_manipulation=table_manipulation,
-            table_column_names="display_name",
-            annotation_keys=annotation_keys,
-        )
+            schedule_for_cleanup(CleanupItem(synapse_id=manifest_id))
         existing_tables = synapse_store.get_table_info(projectId=projectId)
 
         # set primary key annotation for uploaded table
-        tableId = existing_tables[table_name]
+        table_id = existing_tables[table_name]
 
         # Query table for DaystoFollowUp column
         table_query = (
-            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {tableId}")
+            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {table_id}")
             .asDataFrame()
             .squeeze()
         )
@@ -760,24 +1235,37 @@ def test_upsertTable(
         assert table_query.MockRDB_id.size == 4
         assert table_query["SourceManifest"][3] == "Manifest1"
 
-        # Associate new manifest with files
-        manifestId = synapse_store.associateMetadataWithFiles(
-            dmge=dmge,
-            metadataManifestPath=helpers.get_data_path(replacement_manifest_path),
-            datasetId=datasetId,
-            manifest_record_type="table_and_file",
-            hideBlanks=True,
-            restrict_manifest=False,
-            table_manipulation=table_manipulation,
-            table_column_names="display_name",
-            annotation_keys=annotation_keys,
-        )
+        with patch.object(
+            synapse_store, "_generate_table_name", return_value=(table_name, "mockrdb")
+        ), patch.object(
+            synapse_store, "getDatasetProject", return_value=projectId
+        ), tempfile.NamedTemporaryFile(
+            delete=True, suffix=".csv"
+        ) as tmp_file:
+            # Copy to a temporary file to prevent modifying the original
+            shutil.copyfile(
+                helpers.get_data_path(replacement_manifest_path), tmp_file.name
+            )
+
+            # Associate new manifest with files
+            manifest_id = synapse_store.associateMetadataWithFiles(
+                dmge=dmge,
+                metadataManifestPath=tmp_file.name,
+                datasetId=datasetId,
+                manifest_record_type="table_and_file",
+                hideBlanks=True,
+                restrict_manifest=False,
+                table_manipulation=table_manipulation,
+                table_column_names="display_name",
+                annotation_keys=annotation_keys,
+            )
+            schedule_for_cleanup(CleanupItem(synapse_id=manifest_id))
         existing_tables = synapse_store.get_table_info(projectId=projectId)
 
         # Query table for DaystoFollowUp column
-        tableId = existing_tables[table_name]
+        table_id = existing_tables[table_name]
         table_query = (
-            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {tableId}")
+            synapse_store.syn.tableQuery(f"SELECT {column_of_interest} FROM {table_id}")
             .asDataFrame()
             .squeeze()
         )
@@ -786,8 +1274,6 @@ def test_upsertTable(
         assert table_query.MockRDB_id.max() == 8
         assert table_query.MockRDB_id.size == 8
         assert table_query["SourceManifest"][3] == "Manifest2"
-        # delete table
-        synapse_store.syn.delete(tableId)
 
 
 class TestDownloadManifest:
@@ -931,7 +1417,7 @@ class TestManifestUpload:
             ),
         ],
     )
-    def test_add_annotations_to_entities_files(
+    async def test_add_annotations_to_entities_files(
         self,
         synapse_store: SynapseStorage,
         dmge: DataModelGraphExplorer,
@@ -951,27 +1437,49 @@ def test_add_annotations_to_entities_files(
             expected_filenames (list(str)): expected list of file names
             expected_entity_ids (list(str)): expected list of entity ids
         """
+
+        async def mock_format_row_annos():
+            return
+
+        async def mock_process_store_annos(requests):
+            return
+
         with patch(
             "schematic.store.synapse.SynapseStorage.getFilesInStorageDataset",
             return_value=files_in_dataset,
         ):
-            manifest_df = pd.DataFrame(original_manifest)
+            with patch(
+                "schematic.store.synapse.SynapseStorage.format_row_annotations",
+                return_value=mock_format_row_annos,
+                new_callable=AsyncMock,
+            ) as mock_format_row:
+                with patch(
+                    "schematic.store.synapse.SynapseStorage._process_store_annos",
+                    return_value=mock_process_store_annos,
+                    new_callable=AsyncMock,
+                ) as mock_process_store:
+                    manifest_df = pd.DataFrame(original_manifest)
+
+                    new_df = await synapse_store.add_annotations_to_entities_files(
+                        dmge,
+                        manifest_df,
+                        manifest_record_type="entity",
+                        datasetId="mock id",
+                        hideBlanks=True,
+                    )
 
-            new_df = synapse_store.add_annotations_to_entities_files(
-                dmge,
-                manifest_df,
-                manifest_record_type="entity",
-                datasetId="mock id",
-                hideBlanks=True,
-            )
-            file_names_lst = new_df["Filename"].tolist()
-            entity_ids_lst = new_df["entityId"].tolist()
+                    file_names_lst = new_df["Filename"].tolist()
+                    entity_ids_lst = new_df["entityId"].tolist()
 
-            # test entityId and Id columns get added
-            assert "entityId" in new_df.columns
-            assert "Id" in new_df.columns
-            assert file_names_lst == expected_filenames
-            assert entity_ids_lst == expected_entity_ids
+                    # test entityId and Id columns get added
+                    assert "entityId" in new_df.columns
+                    assert "Id" in new_df.columns
+                    assert file_names_lst == expected_filenames
+                    assert entity_ids_lst == expected_entity_ids
+
+                    # make sure async function gets called as expected
+                    assert mock_format_row.call_count == len(expected_entity_ids)
+                    assert mock_process_store.call_count == 1
 
     @pytest.mark.parametrize(
         "mock_manifest_file_path",
@@ -1055,9 +1563,14 @@ def test_upload_manifest_as_csv(
         hide_blanks: bool,
         restrict: bool,
     ) -> None:
+        async def mock_add_annotations_to_entities_files():
+            return
+
         with (
             patch(
-                "schematic.store.synapse.SynapseStorage.add_annotations_to_entities_files"
+                "schematic.store.synapse.SynapseStorage.add_annotations_to_entities_files",
+                return_value=mock_add_annotations_to_entities_files,
+                new_callable=AsyncMock,
             ) as add_anno_mock,
             patch(
                 "schematic.store.synapse.SynapseStorage.upload_manifest_file",
@@ -1105,13 +1618,19 @@ def test_upload_manifest_as_table(
         manifest_record_type: str,
     ) -> None:
         mock_df = pd.DataFrame()
+
+        async def mock_add_annotations_to_entities_files():
+            return
+
         with (
             patch(
                 "schematic.store.synapse.SynapseStorage.uploadDB",
                 return_value=["mock_table_id", mock_df, "mock_table_manifest"],
             ) as update_db_mock,
             patch(
-                "schematic.store.synapse.SynapseStorage.add_annotations_to_entities_files"
+                "schematic.store.synapse.SynapseStorage.add_annotations_to_entities_files",
+                return_value=mock_add_annotations_to_entities_files,
+                new_callable=AsyncMock,
             ) as add_anno_mock,
             patch(
                 "schematic.store.synapse.SynapseStorage.upload_manifest_file",
@@ -1165,13 +1684,19 @@ def test_upload_manifest_combo(
         mock_df = pd.DataFrame()
         manifest_path = helpers.get_data_path("mock_manifests/test_BulkRNAseq.csv")
         manifest_df = helpers.get_data_frame(manifest_path)
+
+        async def mock_add_annotations_to_entities_files():
+            return
+
         with (
             patch(
                 "schematic.store.synapse.SynapseStorage.uploadDB",
                 return_value=["mock_table_id", mock_df, "mock_table_manifest"],
             ) as update_db_mock,
             patch(
-                "schematic.store.synapse.SynapseStorage.add_annotations_to_entities_files"
+                "schematic.store.synapse.SynapseStorage.add_annotations_to_entities_files",
+                return_value=mock_add_annotations_to_entities_files,
+                new_callable=AsyncMock,
             ) as add_anno_mock,
             patch(
                 "schematic.store.synapse.SynapseStorage.upload_manifest_file",
diff --git a/tests/test_validation.py b/tests/test_validation.py
index 9ea47b973..cdd6766c0 100644
--- a/tests/test_validation.py
+++ b/tests/test_validation.py
@@ -1,33 +1,20 @@
-import os
 import logging
+import os
 import re
-import networkx as nx
-import jsonschema
+
 import pytest
-from pathlib import Path
-import itertools
 
-from schematic.models.validate_attribute import ValidateAttribute, GenerateError
-from schematic.models.validate_manifest import ValidateManifest
 from schematic.models.metadata import MetadataModel
-from schematic.store.synapse import SynapseStorage
-
-from schematic.schemas.data_model_parser import DataModelParser
+from schematic.models.validate_attribute import GenerateError, ValidateAttribute
+from schematic.models.validate_manifest import ValidateManifest
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
 from schematic.schemas.data_model_json_schema import DataModelJSONSchema
-
 from schematic.utils.validate_rules_utils import validation_rule_info
 
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 
-@pytest.fixture(name="dmge")
-def DMGE(helpers):
-    dmge = helpers.get_data_model_graph_explorer(path="example.model.jsonld")
-    yield dmge
-
-
 def get_metadataModel(helpers, model_name: str):
     metadataModel = MetadataModel(
         inputMModelLocation=helpers.get_data_path(model_name),
@@ -692,6 +679,87 @@ def test_in_house_validation(self, helpers, dmge):
             in warnings
         )
 
+    def test_filename_manifest(self, helpers, dmge):
+        metadataModel = get_metadataModel(helpers, model_name="example.model.jsonld")
+
+        manifestPath = helpers.get_data_path(
+            "mock_manifests/InvalidFilenameManifest.csv"
+        )
+        rootNode = "MockFilename"
+
+        errors, warnings = metadataModel.validateModelManifest(
+            manifestPath=manifestPath,
+            rootNode=rootNode,
+            project_scope=["syn23643250"],
+            dataset_scope="syn61682648",
+        )
+        # Check errors
+        assert (
+            GenerateError.generate_filename_error(
+                val_rule="filenameExists syn61682648",
+                attribute_name="Filename",
+                row_num="4",
+                invalid_entry="schematic - main/MockFilenameComponent/txt3.txt",
+                error_type="mismatched entityId",
+                dmge=dmge,
+            )[0]
+            in errors
+        )
+
+        assert (
+            GenerateError.generate_filename_error(
+                val_rule="filenameExists syn61682648",
+                attribute_name="Filename",
+                row_num="5",
+                invalid_entry="schematic - main/MockFilenameComponent/this_file_does_not_exist.txt",
+                error_type="path does not exist",
+                dmge=dmge,
+            )[0]
+            in errors
+        )
+
+        assert (
+            GenerateError.generate_filename_error(
+                val_rule="filenameExists syn61682648",
+                attribute_name="Filename",
+                row_num="6",
+                invalid_entry="schematic - main/MockFilenameComponent/txt4.txt",
+                error_type="entityId does not exist",
+                dmge=dmge,
+            )[0]
+            in errors
+        )
+
+        assert (
+            GenerateError.generate_filename_error(
+                val_rule="filenameExists syn61682648",
+                attribute_name="Filename",
+                row_num="7",
+                invalid_entry="schematic - main/MockFilenameComponent/txt6.txt",
+                error_type="missing entityId",
+                dmge=dmge,
+            )[0]
+            in errors
+        )
+
+        assert len(errors) == 4
+        assert len(warnings) == 0
+
+    def test_filename_manifest_exception(self, helpers, dmge):
+        metadataModel = get_metadataModel(helpers, model_name="example.model.jsonld")
+
+        manifestPath = helpers.get_data_path(
+            "mock_manifests/InvalidFilenameManifest.csv"
+        )
+        rootNode = "MockFilename"
+
+        with pytest.raises(ValueError):
+            errors, warnings = metadataModel.validateModelManifest(
+                manifestPath=manifestPath,
+                rootNode=rootNode,
+                project_scope=["syn23643250"],
+            )
+
     def test_missing_column(self, helpers, dmge: DataModelGraph):
         """Test that a manifest missing a column returns the proper error."""
         model_name = "example.model.csv"
@@ -1031,3 +1099,26 @@ def test_rule_combinations(
             restrict_rules=False,
             project_scope=None,
         )
+
+
+class TestValidateAttributeObject:
+    def test_login(self, dmge: DataModelGraphExplorer) -> None:
+        """
+        Tests that sequential logins update the view query as necessary
+        """
+        validate_attribute = ValidateAttribute(dmge)
+        validate_attribute._login()
+
+        assert (
+            validate_attribute.synStore.fileview_query == "SELECT * FROM syn23643253 ;"
+        )
+
+        validate_attribute._login(
+            project_scope=["syn23643250"],
+            columns=["name", "id", "path"],
+            where_clauses=["parentId='syn61682648'", "type='file'"],
+        )
+        assert (
+            validate_attribute.synStore.fileview_query
+            == "SELECT name,id,path FROM syn23643253 WHERE parentId='syn61682648' AND type='file' AND projectId IN ('syn23643250', '') ;"
+        )
diff --git a/tests/test_viz.py b/tests/test_viz.py
index f40aca332..b94d79688 100644
--- a/tests/test_viz.py
+++ b/tests/test_viz.py
@@ -1,9 +1,9 @@
-from io import StringIO
 import json
-import os
-import pandas as pd
 import logging
+import os
+from io import StringIO
 
+import pandas as pd
 import pytest
 
 from schematic.visualization.attributes_explorer import AttributesExplorer
@@ -124,6 +124,31 @@ def test_text(self, helpers, tangled_tree):
         assert actual_patient_text == expected_patient_text
         assert actual_Biospecimen_text == expected_Biospecimen_text
 
+    @pytest.mark.parametrize(
+        "conditional_requirements, expected",
+        [
+            # Test case 1: Multiple file formats
+            (
+                [
+                    "['File Format is \"BAM\"', 'File Format is \"CRAM\"', 'File Format is \"CSV/TSV\"']"
+                ],
+                {"BAM": "FileFormat", "CRAM": "FileFormat", "CSV/TSV": "FileFormat"},
+            ),
+            # Test case 2: Single file format
+            (["['File Format is \"CRAM\"']"], {"CRAM": "FileFormat"}),
+            # Test case 3: with "OR" keyword
+            (
+                ['[\'File Format is "BAM" OR "CRAM" OR "CSV/TSV"\']'],
+                {"BAM": "File Format", "CRAM": "File Format", "CSV/TSV": "File Format"},
+            ),
+        ],
+    )
+    def test_get_ca_alias(
+        self, helpers, tangled_tree, conditional_requirements, expected
+    ):
+        ca_alias = tangled_tree._get_ca_alias(conditional_requirements)
+        assert ca_alias == expected
+
     def test_layers(self, helpers, tangled_tree):
         layers_str = tangled_tree.get_tangled_tree_layers(save_file=False)[0]
 
diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/unit/test_data_model_graph.py b/tests/unit/test_data_model_graph.py
new file mode 100644
index 000000000..27b55b6cf
--- /dev/null
+++ b/tests/unit/test_data_model_graph.py
@@ -0,0 +1,86 @@
+from typing import Optional, Union
+
+import pytest
+
+from tests.conftest import Helpers
+
+DATA_MODEL_DICT = {"example.model.csv": "CSV", "example.model.jsonld": "JSONLD"}
+
+
+class TestDataModelGraphExplorer:
+    @pytest.mark.parametrize(
+        "data_model", list(DATA_MODEL_DICT.keys()), ids=list(DATA_MODEL_DICT.values())
+    )
+    @pytest.mark.parametrize(
+        "node_label, node_display_name, expected_validation_rule",
+        [
+            # Test case 1: node label is provided
+            (
+                "PatientID",
+                None,
+                {"Biospecimen": "unique error", "Patient": "unique warning"},
+            ),
+            (
+                "CheckRegexListStrict",
+                None,
+                ["list strict", "regex match [a-f]"],
+            ),
+            # Test case 2: node label is not provided and display label is not part of the schema
+            (
+                None,
+                "invalid display label",
+                [],
+            ),
+            # Test case 3: node label is not provided but a valid display label is provided
+            (
+                None,
+                "Patient ID",
+                {"Biospecimen": "unique error", "Patient": "unique warning"},
+            ),
+        ],
+    )
+    def test_get_node_validation_rules_valid(
+        self,
+        helpers: Helpers,
+        data_model: str,
+        node_label: Optional[str],
+        node_display_name: Optional[str],
+        expected_validation_rule: Union[list[str], dict[str, str]],
+    ):
+        DMGE = helpers.get_data_model_graph_explorer(path=data_model)
+
+        node_validation_rules = DMGE.get_node_validation_rules(
+            node_label=node_label, node_display_name=node_display_name
+        )
+        assert node_validation_rules == expected_validation_rule
+
+    @pytest.mark.parametrize(
+        "data_model", list(DATA_MODEL_DICT.keys()), ids=list(DATA_MODEL_DICT.values())
+    )
+    @pytest.mark.parametrize(
+        "node_label, node_display_name",
+        [
+            # Test case 1: node label and node display name are not provided
+            (
+                None,
+                None,
+            ),
+            # Test case 2: node label is not valid and display name is not provided
+            (
+                "invalid node",
+                None,
+            ),
+        ],
+    )
+    def test_get_node_validation_rules_invalid(
+        self,
+        helpers,
+        data_model,
+        node_label,
+        node_display_name,
+    ):
+        DMGE = helpers.get_data_model_graph_explorer(path=data_model)
+        with pytest.raises(ValueError):
+            DMGE.get_node_validation_rules(
+                node_label=node_label, node_display_name=node_display_name
+            )
diff --git a/tests/unit/test_validate_attribute.py b/tests/unit/test_validate_attribute.py
new file mode 100644
index 000000000..d782fab12
--- /dev/null
+++ b/tests/unit/test_validate_attribute.py
@@ -0,0 +1,1576 @@
+"""Unit testing for the ValidateAttribute class"""
+
+from typing import Generator
+from unittest.mock import Mock, patch
+
+import numpy as np
+import pytest
+from pandas import DataFrame, Series, concat
+
+import schematic.models.validate_attribute
+from schematic.models.validate_attribute import GenerateError, ValidateAttribute
+from schematic.schemas.data_model_graph import DataModelGraphExplorer
+
+# pylint: disable=protected-access
+# pylint: disable=too-many-public-methods
+# pylint: disable=too-many-arguments
+
+MATCH_ATLEAST_ONE_SET_RULES = [
+    "matchAtLeastOne Patient.PatientID set error",
+    "matchAtLeastOne Patient.PatientID set warning",
+]
+MATCH_EXACTLY_ONE_SET_RULES = [
+    "matchExactlyOne Patient.PatientID set error",
+    "matchExactlyOne Patient.PatientID set warning",
+]
+MATCH_NONE_SET_RULES = [
+    "matchNone Patient.PatientID set error",
+    "matchNone Patient.PatientID set warning",
+]
+ALL_SET_RULES = (
+    MATCH_ATLEAST_ONE_SET_RULES + MATCH_EXACTLY_ONE_SET_RULES + MATCH_NONE_SET_RULES
+)
+MATCH_ATLEAST_ONE_VALUE_RULES = [
+    "matchAtLeastOne Patient.PatientID value error",
+    "matchAtLeastOne Patient.PatientID value warning",
+]
+MATCH_EXACTLY_ONE_VALUE_RULES = [
+    "matchExactlyOne Patient.PatientID value error",
+    "matchExactlyOne Patient.PatientID value warning",
+]
+MATCH_NONE_VALUE_RULES = [
+    "matchNone Patient.PatientID value error",
+    "matchNone Patient.PatientID value warning",
+]
+ALL_VALUE_RULES = (
+    MATCH_ATLEAST_ONE_VALUE_RULES
+    + MATCH_EXACTLY_ONE_VALUE_RULES
+    + MATCH_NONE_VALUE_RULES
+)
+EXACTLY_ATLEAST_PASSING_SERIES = [
+    Series(["A", "B", "C"], index=[0, 1, 2], name="PatientID"),
+    Series(["A", "B", "C", "C"], index=[0, 1, 2, 3], name="PatientID"),
+    Series(["A", "B", "C", "A", "B", "C"], index=[0, 1, 2, 3, 4, 5], name="PatientID"),
+    Series(["A", "B"], index=[0, 1], name="PatientID"),
+    Series([], name="PatientID"),
+]
+
+TEST_DF1 = DataFrame(
+    {
+        "PatientID": ["A", "B", "C"],
+        "component": ["comp1", "comp1", "comp1"],
+        "id": ["id1", "id2", "id3"],
+        "entityid": ["x", "x", "x"],
+    }
+)
+
+TEST_DF2 = DataFrame(
+    {
+        "PatientID": ["D", "E", "F"],
+        "component": ["comp1", "comp1", "comp1"],
+        "id": ["id1", "id2", "id3"],
+        "entityid": ["x", "x", "x"],
+    }
+)
+
+TEST_DF_MISSING_VALS = DataFrame(
+    {
+        "PatientID": [np.isnan, ""],
+        "component": ["comp1", "comp1"],
+        "id": ["id1", "id2"],
+        "entityid": ["x", "x"],
+    }
+)
+
+TEST_DF_MISSING_PATIENT = DataFrame(
+    {
+        "component": ["comp1", "comp1"],
+        "id": ["id1", "id2"],
+        "entityid": ["x", "x"],
+    }
+)
+
+TEST_DF_EMPTY_COLS = DataFrame(
+    {
+        "PatientID": [],
+        "component": [],
+        "id": [],
+        "entityid": [],
+    }
+)
+
+TEST_DF_FILEVIEW = DataFrame(
+    {
+        "id": ["syn1", "syn2", "syn3"],
+        "path": ["test1.txt", "test2.txt", "test3.txt"],
+    }
+)
+
+TEST_MANIFEST_GOOD = DataFrame(
+    {
+        "Component": ["Mockfilename", "Mockfilename", "Mockfilename"],
+        "Filename": ["test1.txt", "test2.txt", "test3.txt"],
+        "entityId": ["syn1", "syn2", "syn3"],
+    }
+)
+
+TEST_MANIFEST_MISSING_ENTITY_ID = DataFrame(
+    {
+        "Component": ["Mockfilename", "Mockfilename", "Mockfilename"],
+        "Filename": ["test1.txt", "test2.txt", "test3.txt"],
+        "entityId": ["syn1", "syn2", ""],
+    }
+)
+
+TEST_MANIFEST_FILENAME_NOT_IN_VIEW = DataFrame(
+    {
+        "Component": ["Mockfilename", "Mockfilename", "Mockfilename"],
+        "Filename": ["test1.txt", "test2.txt", "test_bad.txt"],
+        "entityId": ["syn1", "syn2", "syn3"],
+    }
+)
+
+TEST_MANIFEST_ENTITY_ID_NOT_IN_VIEW = DataFrame(
+    {
+        "Component": ["Mockfilename", "Mockfilename", "Mockfilename"],
+        "Filename": ["test1.txt", "test2.txt", "test3.txt"],
+        "entityId": ["syn1", "syn2", "syn_bad"],
+    }
+)
+
+TEST_MANIFEST_ENTITY_ID_MISMATCH = DataFrame(
+    {
+        "Component": ["Mockfilename", "Mockfilename", "Mockfilename"],
+        "Filename": ["test1.txt", "test2.txt", "test3.txt"],
+        "entityId": ["syn1", "syn2", "syn2"],
+    }
+)
+
+
+@pytest.fixture(name="va_obj")
+def fixture_va_obj(
+    dmge: DataModelGraphExplorer,
+) -> Generator[ValidateAttribute, None, None]:
+    """Yield a ValidateAttribute object"""
+    yield ValidateAttribute(dmge)
+
+
+@pytest.fixture(name="cross_val_df1")
+def fixture_cross_val_df1() -> Generator[DataFrame, None, None]:
+    """Yields a dataframe"""
+    df = DataFrame(
+        {
+            "PatientID": ["A", "B", "C"],
+            "component": ["comp1", "comp1", "comp1"],
+            "id": ["id1", "id2", "id3"],
+            "entityid": ["x", "x", "x"],
+        }
+    )
+    yield df
+
+
+@pytest.fixture(name="cross_val_df2")
+def fixture_cross_val_df2(cross_val_df1: DataFrame) -> Generator[DataFrame, None, None]:
+    """Yields dataframe df1 with an extra row"""
+    df = concat(
+        [
+            cross_val_df1,
+            DataFrame(
+                {
+                    "PatientID": ["D"],
+                    "component": ["comp1"],
+                    "id": ["id4"],
+                    "entityid": ["x"],
+                }
+            ),
+        ]
+    )
+    yield df
+
+
+@pytest.fixture(name="cross_val_df3")
+def fixture_cross_val_df3() -> Generator[DataFrame, None, None]:
+    """Yields empty dataframe"""
+    df = DataFrame(
+        {
+            "PatientID": [],
+            "component": [],
+            "id": [],
+            "entityid": [],
+        }
+    )
+    yield df
+
+
+@pytest.fixture(name="cross_val_col_names")
+def fixture_cross_val_col_names() -> Generator[dict[str, str], None, None]:
+    """
+    Yields:
+        Generator[dict[str, str], None, None]: A dicitonary of column names
+          keys are the label, and values are the display name
+    """
+    column_names = {
+        "patientid": "PatientID",
+        "component": "component",
+        "id": "id",
+        "entityid": "entityid",
+    }
+    yield column_names
+
+
+class TestGenerateError:
+    """Unit tests for the GenerateError class"""
+
+    val_rule = "filenameExists syn123456"
+    attribute_name = "Filename"
+    row_num = "2"
+    invalid_entry = "test_file.txt"
+
+    @pytest.mark.parametrize(
+        "error_type, expected_message",
+        [
+            (
+                "mismatched entityId",
+                "The entityId for file path 'test_file.txt' on row 2 does not match the entityId for the file in the file view.",
+            ),
+            (
+                "path does not exist",
+                "The file path 'test_file.txt' on row 2 does not exist in the file view.",
+            ),
+            (
+                "entityId does not exist",
+                "The entityId for file path 'test_file.txt' on row 2 does not exist in the file view.",
+            ),
+            (
+                "missing entityId",
+                "The entityId is missing for file path 'test_file.txt' on row 2.",
+            ),
+        ],
+        ids=[
+            "mismatched entityId",
+            "path does not exist",
+            "entityId does not exist",
+            "missing entityId",
+        ],
+    )
+    def test_generate_filename_error(
+        self, dmge: DataModelGraphExplorer, error_type: str, expected_message: str
+    ):
+        with patch.object(
+            GenerateError,
+            "raise_and_store_message",
+            return_value=(
+                [
+                    self.row_num,
+                    self.attribute_name,
+                    expected_message,
+                    self.invalid_entry,
+                ],
+                [],
+            ),
+        ) as mock_raise_and_store:
+            error_list, _ = GenerateError.generate_filename_error(
+                val_rule=self.val_rule,
+                attribute_name=self.attribute_name,
+                row_num=self.row_num,
+                invalid_entry=self.invalid_entry,
+                error_type=error_type,
+                dmge=dmge,
+            )
+        mock_raise_and_store.assert_called_once_with(
+            dmge=dmge,
+            val_rule=self.val_rule,
+            error_row=self.row_num,
+            error_col=self.attribute_name,
+            error_message=expected_message,
+            error_val=self.invalid_entry,
+        )
+
+        assert len(error_list) == 4
+        assert error_list[2] == expected_message
+
+    def test_generate_filename_error_unsupported_error_type(
+        self, dmge: DataModelGraphExplorer
+    ):
+        with pytest.raises(
+            KeyError, match="Unsupported error type provided: 'unsupported error type'"
+        ) as exc_info:
+            GenerateError.generate_filename_error(
+                dmge=dmge,
+                val_rule=self.val_rule,
+                attribute_name=self.attribute_name,
+                row_num=self.row_num,
+                invalid_entry=self.invalid_entry,
+                error_type="unsupported error type",
+            )
+
+
+class TestValidateAttributeObject:
+    """Testing for ValidateAttribute class with all Synapse calls mocked"""
+
+    ##################
+    # cross_validation
+    ##################
+
+    @pytest.mark.parametrize("series", EXACTLY_ATLEAST_PASSING_SERIES)
+    @pytest.mark.parametrize("rule", MATCH_ATLEAST_ONE_SET_RULES)
+    def test_cross_validation_match_atleast_one_set_rules_passing(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        series: Series,
+        rule: str,
+    ):
+        """
+        Tests for ValidateAttribute.cross_validation using matchAtLeastOne rule
+        These tests pass with no errors or warnings
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            assert va_obj.cross_validation(rule, series) == ([], [])
+
+    @pytest.mark.parametrize("series", EXACTLY_ATLEAST_PASSING_SERIES)
+    @pytest.mark.parametrize("rule", MATCH_EXACTLY_ONE_SET_RULES)
+    def test_cross_validation_match_exactly_one_set_rules_passing(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        series: Series,
+        rule: str,
+    ):
+        """
+        Tests for ValidateAttribute.cross_validation using matchExactlyOne rule
+        These tests pass with no errors or warnings
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            assert va_obj.cross_validation(rule, series) == ([], [])
+
+    @pytest.mark.parametrize(
+        "series",
+        [
+            Series(["A", "B", "C", "D"], index=[0, 1, 2, 3], name="PatientID"),
+            Series([np.nan], index=[0], name="PatientID"),
+            Series([""], index=[0], name="PatientID"),
+            Series([1], index=[0], name="PatientID"),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_ATLEAST_ONE_SET_RULES)
+    def test_cross_validation_match_atleast_one_set_rules_errors(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        series: Series,
+        rule: str,
+    ):
+        """
+        Tests for ValidateAttribute.cross_validation using matchAtLeastOne rule
+        These tests fail with either one error or warning depending on the rule
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            errors, warnings = va_obj.cross_validation(rule, series)
+            if rule.endswith("error"):
+                assert warnings == []
+                assert len(errors) == 1
+            else:
+                assert len(warnings) == 1
+                assert errors == []
+
+    @pytest.mark.parametrize(
+        "series",
+        [
+            Series(["A", "B", "C"], index=[0, 1, 2], name="PatientID"),
+            Series(["A", "B", "C", "C"], index=[0, 1, 2, 3], name="PatientID"),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_EXACTLY_ONE_SET_RULES)
+    def test_cross_validation_match_exactly_one_set_rules_errors(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        series: Series,
+        rule: str,
+    ):
+        """
+        Tests for ValidateAttribute.cross_validation using matchExactlyOne rule
+        These tests fail with either one error or warning depending on the rule
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1, "syn2": cross_val_df1},
+        ):
+            errors, warnings = va_obj.cross_validation(rule, series)
+            if rule.endswith("error"):
+                assert warnings == []
+                assert len(errors) == 1
+            else:
+                assert len(warnings) == 1
+                assert errors == []
+
+    @pytest.mark.parametrize(
+        "series",
+        [
+            Series(["D"], index=[0], name="PatientID"),
+            Series(["D", "D"], index=[0, 1], name="PatientID"),
+            Series([np.nan], index=[0], name="PatientID"),
+            Series([""], index=[0], name="PatientID"),
+            Series([1], index=[0], name="PatientID"),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_NONE_SET_RULES)
+    def test_cross_validation_match_none_set_rules_passing(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        series: Series,
+        rule: str,
+    ):
+        """
+        Tests for cross manifest validation for matchNone set rules
+        These tests pass with no errors or warnings
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            assert va_obj.cross_validation(rule, series) == ([], [])
+
+    @pytest.mark.parametrize(
+        "series",
+        [
+            Series(["A", "B", "C"], index=[0, 1, 2], name="PatientID"),
+            Series(["A", "B", "C", "D"], index=[0, 1, 2, 3], name="PatientID"),
+            Series(["A", "B"], index=[0, 1], name="PatientID"),
+            Series(["A"], index=[0], name="PatientID"),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_NONE_SET_RULES)
+    def test_cross_validation_match_none_set_rules_errors(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        series: Series,
+        rule: str,
+    ):
+        """
+        Tests for cross manifest validation for matchNone set rules
+        These tests fail with either one error or warning depending on the rule
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            errors, warnings = va_obj.cross_validation(rule, series)
+            if rule.endswith("error"):
+                assert warnings == []
+                assert len(errors) == 1
+            else:
+                assert len(warnings) == 1
+                assert errors == []
+
+    @pytest.mark.parametrize("rule", MATCH_ATLEAST_ONE_VALUE_RULES)
+    @pytest.mark.parametrize(
+        "tested_column",
+        [
+            ([]),
+            (["A"]),
+            (["A", "A"]),
+            (["A", "B"]),
+            (["A", "B", "C"]),
+            (["A", "B", "C", "C"]),
+        ],
+    )
+    def test_cross_validation_value_match_atleast_one_rules_passing(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: list,
+    ):
+        """
+        Tests ValidateAttribute.cross_validation
+        These tests show what columns pass for matchAtLeastOne
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            assert va_obj.cross_validation(rule, Series(tested_column)) == ([], [])
+
+    @pytest.mark.parametrize("rule", MATCH_ATLEAST_ONE_VALUE_RULES)
+    @pytest.mark.parametrize(
+        "tested_column",
+        [
+            Series(["D"], index=[0], name="PatientID"),
+            Series(["D", "D"], index=[0, 1], name="PatientID"),
+            Series(["D", "F"], index=[0, 1], name="PatientID"),
+            Series([np.nan], index=[0], name="PatientID"),
+            Series([1], index=[0], name="PatientID"),
+        ],
+    )
+    def test_cross_validation_value_match_atleast_one_rules_errors(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: Series,
+    ):
+        """
+        Tests ValidateAttribute.cross_validation
+        These tests show what columns fail for matchAtLeastOne
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            errors, warnings = va_obj.cross_validation(rule, tested_column)
+            if rule.endswith("error"):
+                assert len(errors) == 1
+                assert warnings == []
+            else:
+                assert errors == []
+                assert len(warnings) == 1
+
+    @pytest.mark.parametrize("rule", MATCH_EXACTLY_ONE_VALUE_RULES)
+    @pytest.mark.parametrize(
+        "tested_column",
+        [
+            ([]),
+            (["A"]),
+            (["A", "A"]),
+            (["A", "B"]),
+            (["A", "B", "C"]),
+            (["A", "B", "C", "C"]),
+        ],
+    )
+    def test_cross_validation_match_exactly_one_value_rules_passing(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: list,
+    ):
+        """
+        Tests ValidateAttribute.cross_validation
+        These tests show what columns pass for matchExactlyOne
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            assert va_obj.cross_validation(rule, Series(tested_column)) == ([], [])
+
+    @pytest.mark.parametrize("rule", MATCH_EXACTLY_ONE_VALUE_RULES)
+    @pytest.mark.parametrize(
+        "tested_column",
+        [
+            Series(["D"], index=[0], name="PatientID"),
+            Series(["D", "D"], index=[0, 1], name="PatientID"),
+            Series(["D", "F"], index=[0, 1], name="PatientID"),
+            Series([1], index=[0], name="PatientID"),
+        ],
+    )
+    def test_cross_validation_value_match_exactly_one_rules_errors(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: Series,
+    ):
+        """
+        Tests ValidateAttribute.cross_validation
+        These tests show what columns fail for matchExactlyOne
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            errors, warnings = va_obj.cross_validation(rule, tested_column)
+            if rule.endswith("error"):
+                assert len(errors) == 1
+                assert warnings == []
+            else:
+                assert errors == []
+                assert len(warnings) == 1
+
+    @pytest.mark.parametrize("rule", MATCH_NONE_VALUE_RULES)
+    @pytest.mark.parametrize(
+        "tested_column",
+        [([]), (["D"]), (["D", "D"]), (["D", "F"]), ([1]), ([np.nan])],
+    )
+    def test_cross_validation_match_none_value_rules_passing(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: list,
+    ):
+        """
+        Tests ValidateAttribute.cross_validation
+        These tests show what columns pass for matchNone
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            assert va_obj.cross_validation(rule, Series(tested_column)) == ([], [])
+
+    @pytest.mark.parametrize("rule", MATCH_NONE_VALUE_RULES)
+    @pytest.mark.parametrize(
+        "tested_column",
+        [
+            Series(["A"], index=[0], name="PatientID"),
+            Series(["A", "B"], index=[0, 1], name="PatientID"),
+            Series(["A", "A"], index=[0, 1], name="PatientID"),
+        ],
+    )
+    def test_cross_validation_value_match_none_rules_errors(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: Series,
+    ):
+        """
+        Tests ValidateAttribute.cross_validation
+        These tests show what columns fail for matchNone
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            errors, warnings = va_obj.cross_validation(rule, tested_column)
+            if rule.endswith("error"):
+                assert len(errors) == 1
+                assert warnings == []
+            else:
+                assert errors == []
+                assert len(warnings) == 1
+
+    @pytest.mark.parametrize(
+        "manifest, expected_errors, expected_warnings, generates_error",
+        [
+            (TEST_MANIFEST_GOOD, [], [], False),
+            (
+                TEST_MANIFEST_MISSING_ENTITY_ID,
+                [
+                    [
+                        "4",
+                        "Filename",
+                        "The entityId for file path 'test3.txt' on row 4 does not exist in the file view.",
+                        "test3.txt",
+                    ]
+                ],
+                [],
+                True,
+            ),
+            (
+                TEST_MANIFEST_FILENAME_NOT_IN_VIEW,
+                [
+                    [
+                        "4",
+                        "Filename",
+                        "The file path 'test_bad.txt' on row 4 does not exist in the file view.",
+                        "test_bad.txt",
+                    ]
+                ],
+                [],
+                True,
+            ),
+            (
+                TEST_MANIFEST_ENTITY_ID_NOT_IN_VIEW,
+                [
+                    [
+                        "4",
+                        "Filename",
+                        "The entityId for file path 'test3.txt' on row 4 does not exist in the file view.",
+                        "test3.txt",
+                    ]
+                ],
+                [],
+                True,
+            ),
+            (
+                TEST_MANIFEST_ENTITY_ID_MISMATCH,
+                [
+                    [
+                        "4",
+                        "Filename",
+                        "The entityId for file path 'test3.txt' on row 4 does not match "
+                        "the entityId for the file in the file view.",
+                        "test3.txt",
+                    ]
+                ],
+                [],
+                True,
+            ),
+        ],
+        ids=[
+            "valid_manifest",
+            "missing_entity_id",
+            "bad_filename",
+            "bad_entity_id",
+            "entity_id_mismatch",
+        ],
+    )
+    def test_filename_validation(
+        self,
+        va_obj: ValidateAttribute,
+        manifest: DataFrame,
+        expected_errors: list,
+        expected_warnings: list,
+        generates_error: bool,
+    ):
+        mock_synapse_storage = Mock()
+        mock_synapse_storage.storageFileviewTable = TEST_DF_FILEVIEW
+        va_obj.synStore = mock_synapse_storage
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_login",
+        ), patch.object(
+            mock_synapse_storage, "reset_index", return_value=TEST_DF_FILEVIEW
+        ), patch.object(
+            schematic.models.validate_attribute.GenerateError,
+            "generate_filename_error",
+            return_value=(
+                expected_errors if len(expected_errors) < 1 else expected_errors[0],
+                expected_warnings,
+            ),
+        ) as mock_generate_filename_error:
+            actual_errors, actual_warnings = va_obj.filename_validation(
+                val_rule="filenameExists syn61682648",
+                manifest=manifest,
+                access_token="test_access_token",
+                dataset_scope="syn1",
+            )
+            mock_generate_filename_error.assert_called_once() if generates_error else mock_generate_filename_error.assert_not_called()
+            assert (actual_errors, actual_warnings) == (
+                expected_errors,
+                expected_warnings,
+            )
+
+    def test_filename_validation_null_dataset_scope(self, va_obj: ValidateAttribute):
+        with pytest.raises(
+            ValueError,
+            match="A dataset is required to be specified for filename validation",
+        ):
+            va_obj.filename_validation(
+                val_rule="filenameExists syn61682648",
+                manifest=TEST_MANIFEST_GOOD,
+                access_token="test_access_token",
+                dataset_scope=None,
+            )
+
+    #########################################
+    # _run_validation_across_target_manifests
+    #########################################
+
+    @pytest.mark.parametrize("input_column", [(Series([])), (Series(["A"]))])
+    @pytest.mark.parametrize("rule", ALL_SET_RULES)
+    @pytest.mark.parametrize(
+        "target_manifests", [({"syn1": TEST_DF_MISSING_PATIENT}), ({})]
+    )
+    def test__run_validation_across_target_manifests_return_false(
+        self,
+        va_obj: ValidateAttribute,
+        input_column: Series,
+        rule: str,
+        target_manifests: dict[str, DataFrame],
+    ) -> None:
+        """
+        Tests for ValidateAttribute._run_validation_across_target_manifests that return False
+        These tests show that when no target manifests are found to check against, or the target
+        manifest is missing the target column, False is returned
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value=target_manifests,
+        ):
+            _, result = va_obj._run_validation_across_target_manifests(
+                rule_scope="value",
+                val_rule=rule,
+                manifest_col=input_column,
+                target_column=Series([]),
+            )
+            assert result is False
+
+    @pytest.mark.parametrize("input_column", [(Series([])), (Series(["A"]))])
+    @pytest.mark.parametrize("rule", ALL_SET_RULES)
+    def test__run_validation_across_target_manifests_return_msg(
+        self, va_obj: ValidateAttribute, input_column: Series, rule: str
+    ) -> None:
+        """
+        Tests for ValidateAttribute._run_validation_across_target_manifests that return a string
+        These tests show that if at least one target manifest does'nt have
+
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": TEST_DF1, "syn2": TEST_DF_EMPTY_COLS},
+        ):
+            _, result = va_obj._run_validation_across_target_manifests(
+                rule_scope="value",
+                val_rule=rule,
+                manifest_col=input_column,
+                target_column=Series([]),
+            )
+            assert result == "values not recorded in targets stored"
+
+    @pytest.mark.parametrize("rule", ALL_VALUE_RULES)
+    def test__run_validation_across_target_manifests_value_scope(
+        self, va_obj: ValidateAttribute, cross_val_df1: DataFrame, rule: str
+    ) -> None:
+        """Tests for ValidateAttribute._run_validation_across_target_manifests with value rule"""
+
+        # This tests when an empty column is validated there are no missing values to be returned
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            _, validation_output = va_obj._run_validation_across_target_manifests(
+                rule_scope="value",
+                val_rule=rule,
+                manifest_col=Series([]),
+                target_column=Series([]),
+            )
+            assert isinstance(validation_output, tuple)
+            assert isinstance(validation_output[0], Series)
+            assert validation_output[0].empty
+            assert isinstance(validation_output[1], Series)
+            assert validation_output[1].empty
+            assert isinstance(validation_output[2], Series)
+            assert validation_output[2].empty
+
+    @pytest.mark.parametrize(
+        "input_column, missing_ids, present_ids, repeat_ids",
+        [
+            ([], [], ["syn1"], []),
+            (["A"], [], ["syn1"], []),
+            (["A", "A"], [], ["syn1"], []),
+            (["A", "B", "C"], [], ["syn1"], []),
+            (["D"], ["syn1"], [], []),
+            (["D", "D"], ["syn1"], [], []),
+            (["D", "E"], ["syn1"], [], []),
+            ([1], ["syn1"], [], []),
+        ],
+    )
+    @pytest.mark.parametrize(
+        "rule", MATCH_ATLEAST_ONE_SET_RULES + MATCH_EXACTLY_ONE_SET_RULES
+    )
+    def test__run_validation_across_target_manifests_match_atleast_exactly_with_one_target(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        input_column: list,
+        missing_ids: list[str],
+        present_ids: list[str],
+        repeat_ids: list[str],
+        rule: str,
+    ) -> None:
+        """
+        Tests for ValidateAttribute._run_validation_across_target_manifests
+          using matchAtleastOne set and matchExactlyOne rule.
+        This shows that these rules behave the same.
+        If all values in the column match the target manifest, the manifest id gets added
+          to the present ids list.
+        Otherwise the maniferst id gets added to the missing ids list
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            _, validation_output = va_obj._run_validation_across_target_manifests(
+                rule_scope="set",
+                val_rule=rule,
+                manifest_col=Series(input_column),
+                target_column=Series([]),
+            )
+            assert isinstance(validation_output, tuple)
+            assert list(validation_output[0].keys()) == missing_ids
+            assert validation_output[1] == present_ids
+            assert list(validation_output[2].keys()) == repeat_ids
+
+    @pytest.mark.parametrize(
+        "input_column, missing_ids, present_ids, repeat_ids",
+        [
+            ([], [], ["syn1", "syn2"], []),
+            (["A"], [], ["syn1", "syn2"], []),
+            (["D"], ["syn1", "syn2"], [], []),
+        ],
+    )
+    @pytest.mark.parametrize(
+        "rule", MATCH_ATLEAST_ONE_SET_RULES + MATCH_EXACTLY_ONE_SET_RULES
+    )
+    def test__run_validation_across_target_manifests_match_atleast_exactly_with_two_targets(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        input_column: list,
+        missing_ids: list[str],
+        present_ids: list[str],
+        repeat_ids: list[str],
+        rule: str,
+    ) -> None:
+        """
+        Tests for ValidateAttribute._run_validation_across_target_manifests
+          using matchAtleastOne set and matchExactlyOne rule.
+        This shows these rules behave the same.
+        This also shows that when thare are multiple target mnaifests they both get added to
+          either the present of missing manifest ids
+        """
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1, "syn2": cross_val_df1},
+        ):
+            _, validation_output = va_obj._run_validation_across_target_manifests(
+                rule_scope="set",
+                val_rule=rule,
+                manifest_col=Series(input_column),
+                target_column=Series([]),
+            )
+            assert isinstance(validation_output, tuple)
+            assert list(validation_output[0].keys()) == missing_ids
+            assert validation_output[1] == present_ids
+            assert list(validation_output[2].keys()) == repeat_ids
+
+    @pytest.mark.parametrize(
+        "input_column, missing_ids, present_ids, repeat_ids",
+        [
+            ([], [], [], []),
+            (["D"], [], [], []),
+            (["D", "D"], [], [], []),
+            (["D", "E"], [], [], []),
+            ([1], [], [], []),
+            (["A"], [], [], ["syn1"]),
+            (["A", "A"], [], [], ["syn1"]),
+            (["A", "B", "C"], [], [], ["syn1"]),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_NONE_SET_RULES)
+    def test__run_validation_across_target_manifests_set_rules_match_none_with_one_target(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        input_column: list,
+        missing_ids: list[str],
+        present_ids: list[str],
+        repeat_ids: list[str],
+        rule: str,
+    ) -> None:
+        """
+        Tests for ValidateAttribute._run_validation_across_target_manifests
+          using matchNone set rule
+        When there are nt matching values, no id get added
+        When there are mathcing values the id gets added to the repeat ids
+        """
+
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1},
+        ):
+            _, validation_output = va_obj._run_validation_across_target_manifests(
+                rule_scope="set",
+                val_rule=rule,
+                manifest_col=Series(input_column),
+                target_column=Series([]),
+            )
+            assert isinstance(validation_output, tuple)
+            assert list(validation_output[0].keys()) == missing_ids
+            assert validation_output[1] == present_ids
+            assert list(validation_output[2].keys()) == repeat_ids
+
+    @pytest.mark.parametrize(
+        "input_column, missing_ids, present_ids, repeat_ids",
+        [
+            ([], [], [], []),
+            (["D"], [], [], []),
+            (["D", "D"], [], [], []),
+            (["D", "E"], [], [], []),
+            ([1], [], [], []),
+            (["A"], [], [], ["syn1", "syn2"]),
+            (["A", "A"], [], [], ["syn1", "syn2"]),
+            (["A", "B", "C"], [], [], ["syn1", "syn2"]),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_NONE_SET_RULES)
+    def test__run_validation_across_target_manifests_set_rules_match_none_with_two_targets(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_df1: DataFrame,
+        input_column: list,
+        missing_ids: list[str],
+        present_ids: list[str],
+        repeat_ids: list[str],
+        rule: str,
+    ) -> None:
+        """
+        Tests for ValidateAttribute._run_validation_across_target_manifests
+          using matchNone set rule
+        When there are nt matching values, no id get added
+        When there are mathcing values the id gets added to the repeat ids
+        """
+
+        with patch.object(
+            schematic.models.validate_attribute.ValidateAttribute,
+            "_get_target_manifest_dataframes",
+            return_value={"syn1": cross_val_df1, "syn2": cross_val_df1},
+        ):
+            _, validation_output = va_obj._run_validation_across_target_manifests(
+                rule_scope="set",
+                val_rule=rule,
+                manifest_col=Series(input_column),
+                target_column=Series([]),
+            )
+            assert isinstance(validation_output, tuple)
+            assert list(validation_output[0].keys()) == missing_ids
+            assert validation_output[1] == present_ids
+            assert list(validation_output[2].keys()) == repeat_ids
+
+    ######################################
+    # _run_validation_across_targets_value
+    ######################################
+
+    @pytest.mark.parametrize(
+        "tested_column, target_column, missing, duplicated, repeat",
+        [
+            (["A", "B", "C"], ["A", "B", "C"], [], [], ["A", "B", "C"]),
+            (["A", "B", "C", "C"], ["A", "B", "C"], [], [], ["A", "B", "C", "C"]),
+            (["A", "B"], ["A", "B", "C"], [], [], ["A", "B"]),
+            (["C"], ["C", "C"], [], ["C"], ["C"]),
+            (["C"], ["C", "C", "C"], [], ["C"], ["C"]),
+            (["A", "B", "C", "D"], ["A", "B", "C"], ["D"], [], ["A", "B", "C"]),
+            (
+                ["A", "B", "C", "D", "D"],
+                ["A", "B", "C"],
+                ["D", "D"],
+                [],
+                ["A", "B", "C"],
+            ),
+            (["D"], ["A", "B", "C"], ["D"], [], []),
+        ],
+    )
+    def test__run_validation_across_targets_value(
+        self,
+        va_obj: ValidateAttribute,
+        tested_column: list,
+        target_column: list,
+        missing: list,
+        duplicated: list,
+        repeat: list,
+    ) -> None:
+        """
+        Tests for ValidateAttribute._run_validation_across_targets_value
+        These tests show:
+        To get repeat values, a value must appear in both the tested and target column
+        To get duplicated values, a value must appear more than once in the target column
+        To get missing values, a value must appear in the tested column, but not the target column
+
+        """
+        validation_output = va_obj._run_validation_across_targets_value(
+            manifest_col=Series(tested_column),
+            concatenated_target_column=Series(target_column),
+        )
+        assert validation_output[0].to_list() == missing
+        assert validation_output[1].to_list() == duplicated
+        assert validation_output[2].to_list() == repeat
+
+    ####################################
+    # _run_validation_across_targets_set
+    ####################################
+
+    @pytest.mark.parametrize("tested_column", [(), ("A"), ("A", "A"), ("A", "B")])
+    @pytest.mark.parametrize(
+        "rule", MATCH_ATLEAST_ONE_SET_RULES + MATCH_EXACTLY_ONE_SET_RULES
+    )
+    @pytest.mark.parametrize(
+        "target_id, present_log_input, present_log_expected",
+        [
+            ("syn1", [], ["syn1"]),
+            ("syn2", ["syn1"], ["syn1", "syn2"]),
+            ("syn3", ["syn1"], ["syn1", "syn3"]),
+        ],
+    )
+    def test__run_validation_across_targets_set_match_exactly_atleaset_one_no_missing_values(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_col_names: dict[str, str],
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: list,
+        target_id: str,
+        present_log_input: list[str],
+        present_log_expected: list[str],
+    ) -> None:
+        """
+        This test shows that for matchAtLeastOne and matchExactlyOne rules that as long as all
+          values in the tested column are in the target manifest, only the present manifest list
+          is updated
+
+        """
+        output, bool_list1, bool_list2 = va_obj._run_validation_across_targets_set(
+            val_rule=rule,
+            column_names=cross_val_col_names,
+            manifest_col=Series(tested_column),
+            target_attribute="patientid",
+            target_manifest=cross_val_df1,
+            target_manifest_id=target_id,
+            missing_manifest_log={},
+            present_manifest_log=present_log_input.copy(),
+            repeat_manifest_log={},
+            target_attribute_in_manifest_list=[],
+            target_manifest_empty=[],
+        )
+        assert output[0] == {}
+        assert output[1] == present_log_expected
+        assert output[2] == {}
+        assert bool_list1 == [True]
+        assert bool_list2 == [False]
+
+    @pytest.mark.parametrize(
+        "rule", MATCH_ATLEAST_ONE_SET_RULES + MATCH_EXACTLY_ONE_SET_RULES
+    )
+    @pytest.mark.parametrize(
+        "tested_column, target_id, present_log_input, present_log_expected",
+        [
+            (["D"], "syn1", [], []),
+            (["D", "D"], "syn2", [], []),
+            (["D", "F"], "syn3", [], []),
+        ],
+    )
+    def test__run_validation_across_targets_set_match_exactly_atleaset_one_missing_values(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_col_names: dict[str, str],
+        cross_val_df1: DataFrame,
+        rule: str,
+        tested_column: list,
+        target_id: str,
+        present_log_input: list[str],
+        present_log_expected: list[str],
+    ) -> None:
+        """
+        This test shows that for matchAtLeastOne and matchExactlyOne rules,
+          that missing values get added
+        """
+        output, bool_list1, bool_list2 = va_obj._run_validation_across_targets_set(
+            val_rule=rule,
+            column_names=cross_val_col_names,
+            manifest_col=Series(tested_column),
+            target_attribute="patientid",
+            target_manifest=cross_val_df1,
+            target_manifest_id=target_id,
+            missing_manifest_log={},
+            present_manifest_log=present_log_input.copy(),
+            repeat_manifest_log={},
+            target_attribute_in_manifest_list=[],
+            target_manifest_empty=[],
+        )
+        assert output[0][target_id].to_list() == tested_column
+        assert output[1] == present_log_expected
+        assert output[2] == {}
+        assert bool_list1 == [True]
+        assert bool_list2 == [False]
+
+    def test__run_validation_across_targets_set_match_none(
+        self,
+        va_obj: ValidateAttribute,
+        cross_val_col_names: dict[str, str],
+        cross_val_df1: DataFrame,
+    ) -> None:
+        """Tests for ValidateAttribute._run_validation_across_targets_set for matchAtLeastOne"""
+
+        output, bool_list1, bool_list2 = va_obj._run_validation_across_targets_set(
+            val_rule="matchNone, Patient.PatientID, set",
+            column_names=cross_val_col_names,
+            manifest_col=Series(["A", "B", "C"]),
+            target_attribute="patientid",
+            target_manifest=cross_val_df1,
+            target_manifest_id="syn1",
+            missing_manifest_log={},
+            present_manifest_log=[],
+            repeat_manifest_log={},
+            target_attribute_in_manifest_list=[],
+            target_manifest_empty=[],
+        )
+        assert output[0] == {}
+        assert output[1] == []
+        assert list(output[2].keys()) == ["syn1"]
+        assert output[2]["syn1"].to_list() == ["A", "B", "C"]
+        assert bool_list1 == [True]
+        assert bool_list2 == [False]
+
+        output, bool_list1, bool_list2 = va_obj._run_validation_across_targets_set(
+            val_rule="matchNone, Patient.PatientID, set",
+            column_names=cross_val_col_names,
+            manifest_col=Series(["A"]),
+            target_attribute="patientid",
+            target_manifest=cross_val_df1,
+            target_manifest_id="syn2",
+            missing_manifest_log={},
+            present_manifest_log=[],
+            repeat_manifest_log={"syn1": Series(["A", "B", "C"])},
+            target_attribute_in_manifest_list=[],
+            target_manifest_empty=[],
+        )
+        assert output[0] == {}
+        assert output[1] == []
+        assert list(output[2].keys()) == ["syn1", "syn2"]
+        assert output[2]["syn1"].to_list() == ["A", "B", "C"]
+        assert output[2]["syn2"].to_list() == ["A"]
+        assert bool_list1 == [True]
+        assert bool_list2 == [False]
+
+    ###############################
+    # _gather_value_warnings_errors
+    ###############################
+
+    @pytest.mark.parametrize(
+        "rule, missing, duplicated, repeat",
+        [
+            ("matchAtLeastOne Patient.PatientID value error", [], [], []),
+            ("matchAtLeastOne Patient.PatientID value error", [], ["A"], []),
+            ("matchAtLeastOne Patient.PatientID value error", [], ["A", "A"], []),
+            ("matchAtLeastOne Patient.PatientID value error", [], ["A", "B", "C"], []),
+            ("matchExactlyOne Patient.PatientID value error", [], [], []),
+            ("matchNone Patient.PatientID value error", [], [], []),
+        ],
+    )
+    def test__gather_value_warnings_errors_passing(
+        self,
+        va_obj: ValidateAttribute,
+        rule: str,
+        missing: list,
+        duplicated: list,
+        repeat: list,
+    ) -> None:
+        """
+        Tests for ValidateAttribute._gather_value_warnings_errors
+        For matchAtLeastOne to pass there must be no mssing values
+        For matchExactlyOne there must be no missing or duplicated values
+        For matchNone there must be no repeat values
+        """
+        assert va_obj._gather_value_warnings_errors(
+            val_rule=rule,
+            source_attribute="PatientID",
+            value_validation_store=(
+                Series(missing),
+                Series(duplicated),
+                Series(repeat),
+            ),
+        ) == ([], [])
+
+    @pytest.mark.parametrize(
+        "rule, missing, duplicated, repeat",
+        [
+            ("matchAtLeastOne Patient.PatientID value error", ["A"], [], []),
+            ("matchAtLeastOne Patient.PatientID value warning", ["A"], [], []),
+            ("matchExactlyOne Patient.PatientID value error", ["A"], [], []),
+            ("matchExactlyOne Patient.PatientID value warning", ["A"], [], []),
+            ("matchExactlyOne Patient.PatientID value error", [], ["B"], []),
+            ("matchExactlyOne Patient.PatientID value warning", [], ["B"], []),
+            ("matchNonePatient.PatientID value error", [], [], ["A"]),
+            ("matchNone Patient.PatientID value warning", [], [], ["A"]),
+        ],
+    )
+    def test__gather_value_warnings_errors_with_errors(
+        self,
+        va_obj: ValidateAttribute,
+        rule: str,
+        missing: list,
+        duplicated: list,
+        repeat: list,
+    ) -> None:
+        """Tests for ValidateAttribute._gather_value_warnings_errors"""
+
+        errors, warnings = va_obj._gather_value_warnings_errors(
+            val_rule=rule,
+            source_attribute="PatientID",
+            value_validation_store=(
+                Series(missing, name="PatientID"),
+                Series(duplicated, name="PatientID"),
+                Series(repeat, name="PatientID"),
+            ),
+        )
+        if rule.endswith("error"):
+            assert warnings == []
+            assert len(errors) == 1
+        else:
+            assert len(warnings) == 1
+            assert errors == []
+
+    #############################
+    # _gather_set_warnings_errors
+    #############################
+
+    @pytest.mark.parametrize(
+        "validation_tuple",
+        [
+            (({}, [], {})),
+            (({}, ["syn1"], {})),
+            (({"syn1": Series(["A"])}, ["syn1"], {"syn2": Series(["B"])})),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_EXACTLY_ONE_SET_RULES)
+    def test__gather_set_warnings_errors_match_atleast_one_passes(
+        self,
+        va_obj: ValidateAttribute,
+        validation_tuple: tuple[dict[str, Series], list[str], dict[str, Series]],
+        rule: str,
+    ) -> None:
+        """Tests for ValidateAttribute._gather_set_warnings_errors for matchAtLeastOne"""
+
+        assert va_obj._gather_set_warnings_errors(
+            val_rule=rule,
+            source_attribute="PatientID",
+            set_validation_store=validation_tuple,
+        ) == ([], [])
+
+    def test__gather_set_warnings_errors_match_atleast_one_errors(
+        self, va_obj: ValidateAttribute
+    ) -> None:
+        """Tests for ValidateAttribute._gather_set_warnings_errors for matchAtLeastOne"""
+
+        errors, warnings = va_obj._gather_set_warnings_errors(
+            val_rule="matchAtLeastOne Patient.PatientID set error",
+            source_attribute="PatientID",
+            set_validation_store=({"syn1": Series(["A"])}, [], {}),
+        )
+        assert len(warnings) == 0
+        assert len(errors) == 1
+        assert errors[0][0] == ["2"]
+        assert errors[0][1] == "PatientID"
+        assert errors[0][2] == (
+            "Value(s) ['A'] from row(s) ['2'] of the attribute PatientID in the source "
+            "manifest are missing. Manifest(s) ['syn1'] are missing the value(s)."
+        )
+        assert errors[0][3] == ["A"]
+
+    @pytest.mark.parametrize(
+        "validation_tuple",
+        [
+            (({}, [], {})),
+            (({}, ["syn1"], {})),
+            ({"syn1": Series(["A"])}, ["syn1"], {"syn2": Series(["B"])}),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_EXACTLY_ONE_SET_RULES)
+    def test__gather_set_warnings_errors_match_exactly_one_passes(
+        self,
+        va_obj: ValidateAttribute,
+        validation_tuple: tuple[dict[str, Series], list[str], dict[str, Series]],
+        rule: str,
+    ) -> None:
+        """Tests for ValidateAttribute._gather_set_warnings_errors for matchExactlyOne"""
+        assert va_obj._gather_set_warnings_errors(
+            val_rule=rule,
+            source_attribute="PatientID",
+            set_validation_store=validation_tuple,
+        ) == ([], [])
+
+    @pytest.mark.parametrize(
+        "input_store, expected_list",
+        [
+            (
+                ({}, ["syn1", "syn2"], {}),
+                [
+                    [
+                        None,
+                        "PatientID",
+                        (
+                            "All values from attribute PatientID in the source manifest are "
+                            "present in 2 manifests instead of only 1. Manifests ['syn1', 'syn2'] "
+                            "match the values in the source attribute."
+                        ),
+                        None,
+                    ]
+                ],
+            ),
+            (
+                ({}, ["syn1", "syn2", "syn3"], {}),
+                [
+                    [
+                        None,
+                        "PatientID",
+                        (
+                            "All values from attribute PatientID in the source manifest are "
+                            "present in 3 manifests instead of only 1. Manifests "
+                            "['syn1', 'syn2', 'syn3'] match the values in the source attribute."
+                        ),
+                        None,
+                    ]
+                ],
+            ),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_EXACTLY_ONE_SET_RULES)
+    def test__gather_set_warnings_errors_match_exactly_one_errors(
+        self,
+        va_obj: ValidateAttribute,
+        input_store: tuple[dict[str, Series], list[str], dict[str, Series]],
+        expected_list: list[str],
+        rule: str,
+    ) -> None:
+        """Tests for ValidateAttribute._gather_set_warnings_errors for matchExactlyOne"""
+
+        errors, warnings = va_obj._gather_set_warnings_errors(
+            val_rule=rule,
+            source_attribute="PatientID",
+            set_validation_store=input_store,
+        )
+        if rule.endswith("error"):
+            assert warnings == []
+            assert errors == expected_list
+        else:
+            assert warnings == expected_list
+            assert errors == []
+
+    @pytest.mark.parametrize(
+        "validation_tuple", [(({}, [], {})), (({"syn1": Series(["A"])}, ["syn1"], {}))]
+    )
+    @pytest.mark.parametrize("rule", MATCH_NONE_SET_RULES)
+    def test__gather_set_warnings_errors_match_none_passes(
+        self,
+        va_obj: ValidateAttribute,
+        validation_tuple: tuple[dict[str, Series], list[str], dict[str, Series]],
+        rule: str,
+    ) -> None:
+        """Tests for ValidateAttribute._gather_set_warnings_errors for matchNone"""
+
+        assert va_obj._gather_set_warnings_errors(
+            val_rule=rule,
+            source_attribute="PatientID",
+            set_validation_store=validation_tuple,
+        ) == ([], [])
+
+    @pytest.mark.parametrize(
+        "input_store, expected_list",
+        [
+            (
+                ({}, [], {"syn1": Series(["A"])}),
+                [
+                    [
+                        ["2"],
+                        "PatientID",
+                        (
+                            "Value(s) ['A'] from row(s) ['2'] for the attribute PatientID "
+                            "in the source manifest are not unique. "
+                            "Manifest(s) ['syn1'] contain duplicate values."
+                        ),
+                        ["A"],
+                    ]
+                ],
+            ),
+            (
+                ({"x": Series(["A"])}, ["x"], {"syn1": Series(["A"])}),
+                [
+                    [
+                        ["2"],
+                        "PatientID",
+                        (
+                            "Value(s) ['A'] from row(s) ['2'] for the attribute PatientID "
+                            "in the source manifest are not unique. "
+                            "Manifest(s) ['syn1'] contain duplicate values."
+                        ),
+                        ["A"],
+                    ]
+                ],
+            ),
+            (
+                ({}, [], {"syn2": Series(["B"])}),
+                [
+                    [
+                        ["2"],
+                        "PatientID",
+                        (
+                            "Value(s) ['B'] from row(s) ['2'] for the attribute PatientID "
+                            "in the source manifest are not unique. "
+                            "Manifest(s) ['syn2'] contain duplicate values."
+                        ),
+                        ["B"],
+                    ]
+                ],
+            ),
+        ],
+    )
+    @pytest.mark.parametrize("rule", MATCH_NONE_SET_RULES)
+    def test__gather_set_warnings_errors_match_none_errors(
+        self,
+        va_obj: ValidateAttribute,
+        input_store: tuple[dict[str, Series], list[str], dict[str, Series]],
+        expected_list: list[str],
+        rule: str,
+    ) -> None:
+        """
+        Tests for ValidateAttribute._gather_set_warnings_errors for matchNone
+        This test shows that only the repeat_manifest_log matters
+        NOTE: when the repeat repeat_manifest_log is longer than one the order
+        of the values and synapse ids in the msg are inconsistent, making that
+        case hard to test
+        """
+
+        errors, warnings = va_obj._gather_set_warnings_errors(
+            val_rule=rule,
+            source_attribute="PatientID",
+            set_validation_store=input_store,
+        )
+        if rule.endswith("error"):
+            assert warnings == []
+            assert errors == expected_list
+        else:
+            assert warnings == expected_list
+            assert errors == []
+
+    ###################
+    # _get_column_names
+    ###################
+
+    @pytest.mark.parametrize(
+        "input_dict, expected_dict",
+        [
+            ({}, {}),
+            ({"col1": []}, {"col1": "col1"}),
+            ({"COL 1": []}, {"col1": "COL 1"}),
+            ({"ColId": []}, {"colid": "ColId"}),
+            ({"ColID": []}, {"colid": "ColID"}),
+            (
+                {"col1": [], "col2": []},
+                {
+                    "col1": "col1",
+                    "col2": "col2",
+                },
+            ),
+        ],
+    )
+    def test__get_column_names(
+        self,
+        va_obj: ValidateAttribute,
+        input_dict: dict[str, list],
+        expected_dict: dict[str, str],
+    ) -> None:
+        """Tests for ValidateAttribute._get_column_names"""
+        assert va_obj._get_column_names(DataFrame(input_dict)) == expected_dict
diff --git a/tests/utils.py b/tests/utils.py
new file mode 100644
index 000000000..ecaaf2450
--- /dev/null
+++ b/tests/utils.py
@@ -0,0 +1,34 @@
+"""Catch all utility functions and classes used in the tests."""
+from dataclasses import dataclass
+from enum import Enum
+from typing import Optional
+
+
+class CleanupAction(str, Enum):
+    """Actions that can be performed on a cleanup item."""
+
+    DELETE = "delete"
+
+    def __str__(self) -> str:
+        # See https://peps.python.org/pep-0663/
+        return self.value
+
+
+@dataclass(frozen=True)
+class CleanupItem:
+    """Simple class used to create a test finalizer and cleanup resources after test execution.
+
+    synapse_id or (name and parent_id) must be provided.
+
+    Attributes:
+        synapse_id (str): The Synapse ID of the resource to cleanup.
+        name (str): The name of the resource to cleanup.
+        parent_id (str): The parent ID of the resource to cleanup.
+        action (CleanupAction): The action to perform on the resource.
+
+    """
+
+    synapse_id: Optional[str] = None
+    name: Optional[str] = None
+    parent_id: Optional[str] = None
+    action: CleanupAction = CleanupAction.DELETE