semvec/pypi-packages huggingface dataset:
cg-maven 0.1.6
Store quality control metrics for cases in Clinical Genomics
Requires Python: >=3.11,<4.0

# Maven
Maven: _"one who is experienced or knowledgeable."_

This repository holds the software interacting with the maven database. Maven is currently a work in progress.

## Aims

The maven database will be used to store quality metrics for cases and their analysis that come through Clinical Genomics.

## Developing Maven

Steps to start developing on Maven locally:
1. Clone the repo
   ```shell
   git clone https://github.com/Clinical-Genomics/maven
   ```
2. Create a working environment 
   - Requires poetry to be installed: https://python-poetry.org/docs/

2a. Create a virtual python environment in the directory
   ```shell
   # Go into the directory
   cd ./maven
   # Create a virtual environment
   python3 -m venv maven
   # Activate the virtual environment
   source venv/bin/activate
   # Install packages
   poetry install
   ```
2b. If you are using pycharm setup a `poetry interpreter`
   - https://www.jetbrains.com/help/pycharm/poetry.html#poetry-pyproject

3. Install a mongodb client locally (for now) follow steps outlined here
    - https://www.mongodb.com/docs/v7.0/tutorial/install-mongodb-on-os-x/#install-mongodb-community-edition
4. Start a mongo server locally that runs the database
   ```shell
      brew services start mongodb-community@7.0
   ```
      - to stop the service when wanted
   ```shell
   brew services stop mongodb-community@7.0
   ```

5. To establish a connection to the database with FastApi and uvicorn run:
```shell
python3 -m uvicorn --reload --app-dir ./api main:app
```
   - If this step worked you should see "Connected to database." in the terminal

6. To view the database in Compass
    - https://www.mongodb.com/products/tools/compass
    - Setup a connection to the localhost
    - Create a new database called "maven"

7. Alternatively to the steps above one can also run maven using docker
   7a. Install docker and start the docker application: https://docs.docker.com/engine/install/ 
      - After step 1
      ```shell
      cd ./maven
      docker compose up
      ```
kineticpdf 0.0.25
Read/Write PDF Text, Forms, and Metadata.
Keywords: python,PDF,PDFForms,extract PDF text,extract PDF Form fields

A 2023+ package for reading text, metadata, and forms from PDFs with the ability to edit metadata and forms data. Based on prior work by pdfrw and pypdf2 updated for PDF forms changes in latter versions. <p>Kinetic PDF is designed to work with Kinetic Forms and Kinetic Email to provide workflows related to processing PDF Forms.