diff --git a/.aidigestignore b/.aidigestignore new file mode 100644 index 0000000000000000000000000000000000000000..fba17761e11705190e1ed9ac81732441d10b4578 --- /dev/null +++ b/.aidigestignore @@ -0,0 +1,9 @@ +codebase.md +poetry.lock +public/libs/** +__marimo__ +public/styles/output.css +.venv +cache +**.parquet +.env \ No newline at end of file diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c5b9266244c57f4825b5b0801ab9d051c14bd9a8 --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,58 @@ +FROM ubuntu:24.04 + +ARG DEV_MODE + +ENV DEV_MODE=${DEV_MODE:-false} + +ENV DEBIAN_FRONTEND=noninteractive +ENV PYTHONUNBUFFERED=1 +ENV PYTHONDONTWRITEBYTECODE=1 + +RUN apt update + +RUN apt install -y \ + python3.12 \ + python3.12-dev \ + python3.12-venv \ + python3-pip + +RUN ln -sf /usr/bin/python3 /usr/bin/python && ln -sf /usr/bin/pip3 /usr/bin/pip + +RUN apt install -y \ + curl \ + git \ + git-lfs \ + locales && \ + git lfs install && \ + sed -i 's/# \(en_US.UTF-8 UTF-8\)/\1/' /etc/locale.gen && \ + locale-gen && \ + rm -rf /var/lib/apt/lists/* + +RUN apt update && \ + apt install -y nodejs npm && \ + rm -rf /var/lib/apt/lists/* + +ENV LANG=en_US.UTF-8 \ + LC_ALL=en_US.UTF-8 + +RUN curl -sSL https://install.python-poetry.org | python - && \ + ln -sf ~/.local/bin/poetry /usr/local/bin/poetry + +RUN poetry config virtualenvs.in-project true + +WORKDIR /app + +EXPOSE 80 7860 + +COPY pyproject.toml poetry.lock* ./ + +RUN if [ "$DEV_MODE" = "false" ]; then \ + echo "🏭 Production mode: Clean build without cache"; \ + poetry install --no-root --no-interaction --no-ansi --with data,ml,dev; \ + fi + +COPY . /app + +RUN chmod +x /app/scripts/*.sh || true + +ENTRYPOINT ["/app/scripts/entrypoint.sh"] \ No newline at end of file diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000000000000000000000000000000000000..8d15f75097c642db0a61328d4d91966fa7f4e492 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,119 @@ +{ + "name": "Data Science Web App", + "build": { + "dockerfile": "Dockerfile", + "context": "..", + "args": { + "INSTALL_R": "true", + "INSTALL_OPENCPU": "true", + "DEV_MODE": "true" + } + }, + "mounts": [ + "source=poetry-cache,target=/app/.venv,type=volume" + ], + "forwardPorts": [ + 7860 + ], + "containerEnv": { + "DEV_MODE": "true" + }, + "postCreateCommand": "poetry lock && poetry install --no-interaction --no-ansi --with dev,data,ml,demo", + "postStartCommand": "scripts/entrypoint.sh && mkdir -p ~/.vscode-server/data/Machine", + "customizations": { + "vscode": { + "extensions": [ + "ms-python.python", + "ms-python.vscode-pylance", + "adrianwilczynski.alpine-js-intellisense", + "bradlc.vscode-tailwindcss", + "tamasfe.even-better-toml", + "reditorsupport.r", + "wholroyd.jinja", + "formulahendry.code-runner", + "ms-azuretools.vscode-docker", + "eamodio.gitlens", + "otovo-oss.htmx-tags", + "csstools.postcss", + "dbaeumer.vscode-eslint", + "esbenp.prettier-vscode", + "samuelcolvin.jinjahtml", + "monosans.djlint", + "ms-toolsai.jupyter", + "ms-python.black-formatter", + "naumovs.color-highlight" + ], + "settings": { + "python.defaultInterpreterPath": "/app/.venv/bin/python", + "terminal.integrated.shell.linux": "/bin/bash", + "python.linting.enabled": true, + "python.linting.pylintEnabled": true, + "python.formatting.provider": "black", + "editor.formatOnSave": true, + "editor.defaultFormatter": "esbenp.prettier-vscode", + "[python]": { + "editor.defaultFormatter": "ms-python.python" + }, + "editor.codeActionsOnSave": { + "source.sortImports": "explicit" + }, + "terminal.integrated.defaultProfile.linux": "bash", + "terminal.integrated.profiles.linux": { + "Apache Server": { + "path": "apachectl", + "args": [ + "-DFOREGROUND" + ] + }, + "Uvicorn Server": { + "path": "poetry run uvicorn", + "args": [ + "src.main:app", + "--host", + "0.0.0.0", + "--port", + "7860", + "--reload", + "--reload-include", + "./src/", + "--reload-exclude", + "*.db" + ] + }, + "Edit Demo Marimo Notebook": { + "path": "poetry run marimo", + "args": [ + "edit", + "/app/notebooks/marimo-demo.py", + "--host", + "0.0.0.0", + "--port", + "8080", + "--headless" + ] + }, + "Tailwind CSS": { + "path": "/app/bin/tailwindcss", + "args": [ + "-i", + "/app/public/styles/input.css", + "-o", + "/app/public/styles/output.css", + "--watch=always", + "--poll" + ] + }, + "AI Digest": { + "path": "npx", + "args": [ + "--yes", + "ai-digest" + ] + } + } + } + } + }, + "workspaceMount": "source=${localWorkspaceFolder},target=/app,type=bind,consistency=delegated", + "workspaceFolder": "/app" +} \ No newline at end of file diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000000000000000000000000000000000000..efac44a7c503c5c7a16dcd98edf1b532c00405d6 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,12 @@ +node_modules +.git +*.log +*.tmp +.venv +.git +__pycache__ +__marimo__ +*.pyc +.env +cache +cache/processed_data/ \ No newline at end of file diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000000000000000000000000000000000..909c7e34e95c5e0e549c778f0c9b870ffe105323 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,19 @@ +* text=auto eol=lf + +# Git LFS - Images +*.png filter=lfs diff=lfs merge=lfs -text +*.jpg filter=lfs diff=lfs merge=lfs -text +*.jpeg filter=lfs diff=lfs merge=lfs -text +*.gif filter=lfs diff=lfs merge=lfs -text +*.webp filter=lfs diff=lfs merge=lfs -text +*.svg filter=lfs diff=lfs merge=lfs -text + +# Git LFS - Fonts +*.ttf filter=lfs diff=lfs merge=lfs -text +*.otf filter=lfs diff=lfs merge=lfs -text +*.woff filter=lfs diff=lfs merge=lfs -text +*.woff2 filter=lfs diff=lfs merge=lfs -text + +# Git LFS - Other binary files +*.pdf filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text \ No newline at end of file diff --git a/.github/ISSUE_TEMPLATE/data_donation.yml b/.github/ISSUE_TEMPLATE/data_donation.yml new file mode 100644 index 0000000000000000000000000000000000000000..0ca0fa7fa50648affaed8c434d264d7d66c51d94 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/data_donation.yml @@ -0,0 +1,65 @@ +name: "Data Donation" +description: "Contribute a questionnaire, scale, survey or test to the project." +title: "Data Donation: [Instrument Name]" +labels: ["data-donation", "triage"] +body: + - type: markdown + attributes: + value: | + Thanks for your interest in contributing data! Please fill out the details below. + + - type: input + id: contact + attributes: + label: Contact Email + description: How can we reach you? + placeholder: researcher@university.edu + validations: + required: true + + - type: input + id: instrument_name + attributes: + label: Instrument Name + description: A short, descriptive name for the instrument + placeholder: "e.g., Revised Attitudes Towards Horses Scale (R-ATHS)" + validations: + required: false + + - type: textarea + id: description + attributes: + label: Instrument Description + description: What does this dataset contain? What constructs/scales were measured? + placeholder: | + - Constructs measured: ... + - Target population: ... + - Collection context: ... + validations: + required: true + + - type: input + id: sample_size + attributes: + label: Sample Size + description: Approximate number of participants/observations + placeholder: "N = 500" + validations: + required: false + + - type: textarea + id: publications + attributes: + label: Related Publications + description: Any papers or reports using this data? (Optional) + placeholder: "Author et al. (2023). Title. Journal. https://doi.org/..." + validations: + required: false + + - type: textarea + id: additional + attributes: + label: Additional Information + description: Anything else we should know? + validations: + required: false \ No newline at end of file diff --git a/.github/workflows/push-to-hf-space.yml b/.github/workflows/push-to-hf-space.yml new file mode 100644 index 0000000000000000000000000000000000000000..6f8783728e8655bb514189be27896981b7bb1a03 --- /dev/null +++ b/.github/workflows/push-to-hf-space.yml @@ -0,0 +1,49 @@ +name: Push to Hugging Face Space +on: + push: + branches: [ main ] + workflow_dispatch: + +jobs: + to-hf: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + lfs: true + fetch-depth: 0 + + - name: Prepare staging dir for HF Space + run: | + rm -rf hf_staging + mkdir -p hf_staging + # copy repo contents (excluding Git metadata) + rsync -a --exclude '.git' ./ hf_staging/ + + cd hf_staging + + # 1) Ensure README.md is the HF one (but keep your normal README in GitHub) + if [ -f README_HF.md ]; then + mv -f README_HF.md README.md + fi + + # 2) Promote Dockerfile from .devcontainer to root for HF build + if [ -f .devcontainer/Dockerfile ]; then + cp .devcontainer/Dockerfile ./Dockerfile + fi + + - name: Push to HuggingFace Space + env: + HF_TOKEN: ${{ secrets.HF_TOKEN }} # GitHub repo secret + HF_SPACE: magnolia-psychometrics/synth-net + run: | + cd hf_staging + git init + git lfs install + git config user.email "actions@github.com" + git config user.name "github-actions" + git remote add origin https://huggingface.co/spaces/${HF_SPACE} + git add . + git commit -m "Sync from GitHub (CI)" + # Use token to authenticate + git push --force https://user:${HF_TOKEN}@huggingface.co/spaces/${HF_SPACE} HEAD:main diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..75f3c8e8f7b2ac5f5231183517eb177eb272f002 --- /dev/null +++ b/.gitignore @@ -0,0 +1,215 @@ +cache +bin/tailwindcss +codebase.md +__marimo__ +public/styles/output.css +*:Zone.Identifier +src/data/** + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[codz] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py.cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# UV +# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +#uv.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock +#poetry.toml + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. +# https://pdm-project.org/en/latest/usage/project/#working-with-version-control +#pdm.lock +#pdm.toml +.pdm-python +.pdm-build/ + +# pixi +# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. +#pixi.lock +# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one +# in the .venv directory. It is recommended not to include this directory in version control. +.pixi + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.envrc +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +# Abstra +# Abstra is an AI-powered process automation framework. +# Ignore directories containing user credentials, local state, and settings. +# Learn more at https://abstra.io/docs +.abstra/ + +# Visual Studio Code +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore +# and can be added to the global gitignore or merged into this file. However, if you prefer, +# you could uncomment the following to ignore the entire vscode folder +# .vscode/ + +# Ruff stuff: +.ruff_cache/ + +# PyPI configuration file +.pypirc + +# Cursor +# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to +# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data +# refer to https://docs.cursor.com/context/ignore-files +.cursorignore +.cursorindexingignore + +# Marimo +marimo/_static/ +marimo/_lsp/ +__marimo__/ diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000000000000000000000000000000000000..b29a1ff77464587209460f41de2f22acfeafc3b9 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,42 @@ +{ + "version": "0.2.0", + "configurations": [ + { + "name": "FastAPI: Uvicorn", + "type": "debugpy", + "request": "launch", + "module": "uvicorn", + "args": [ + "src.main:app", + "--host", + "0.0.0.0", + "--port", + "7860", + "--reload", + "--reload-include", + "./src/", + "--reload-exclude", + "*.db" + ], + "jinja": true, + "justMyCode": false, + "console": "integratedTerminal", + }, + { + "name": "Model Server (FastAPI: Uvicorn)", + "type": "debugpy", + "request": "launch", + "module": "uvicorn", + "args": [ + "src.servers.model_server:app", + "--host", + "0.0.0.0", + "--port", + "8001" + ], + "jinja": true, + "justMyCode": false, + "console": "integratedTerminal", + }, + ] +} \ No newline at end of file diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000000000000000000000000000000000000..4fbf1bf2d6ee0ecee8505a63f31fa9ac7078b148 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,52 @@ +{ + "remote.autoForwardPorts": false, + "remote.WSL.useShellEnvironment": true, + "remote.WSL.defaultDistro": "Ubuntu", + "remote.restoreForwardedPorts": true, + "remote.WSL.server.connectThroughLocalhost": false, + "python.analysis.exclude": [ + "**/.cache/**", + "**/site-packages/**", + "**/virtualenvs/**" + ], + "djlint.showInstallError": false, + "python.defaultInterpreterPath": "/app/.venv/bin/python", + "tailwindCSS.experimental.configFile": "./public/styles/input.css", + "tailwindCSS.includeLanguages": { + "html": "html", + "javascript": "javascript", + "css": "css", + "jinja": "html", + "jinja2": "html" + }, + "editor.quickSuggestions": { + "strings": true + }, + "tailwindCSS.emmetCompletions": true, + "editor.formatOnSave": false, + "files.associations": { + "*.jinja": "jinja-html", + "*.jinja2": "jinja-html", + "*.j2": "jinja-html" + }, + "emmet.includeLanguages": { + "jinja-html": "html", + "jinja2": "html", + "django-html": "html" + }, + "[jinja]": { + "editor.defaultFormatter": "monosans.djlint", + "editor.detectIndentation": false, + "editor.tabSize": 2, + "editor.formatOnSave": false + }, + "[jinja-html]": { + "editor.defaultFormatter": "monosans.djlint", + "editor.detectIndentation": false, + "editor.tabSize": 2, + "editor.formatOnSave": false + }, + "djlint.profile": "jinja", + "djlint.useVenv": true, + "alpine-intellisense.settings.languageScopes": "html,jinja-html,django-html", +} \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..c5b9266244c57f4825b5b0801ab9d051c14bd9a8 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,58 @@ +FROM ubuntu:24.04 + +ARG DEV_MODE + +ENV DEV_MODE=${DEV_MODE:-false} + +ENV DEBIAN_FRONTEND=noninteractive +ENV PYTHONUNBUFFERED=1 +ENV PYTHONDONTWRITEBYTECODE=1 + +RUN apt update + +RUN apt install -y \ + python3.12 \ + python3.12-dev \ + python3.12-venv \ + python3-pip + +RUN ln -sf /usr/bin/python3 /usr/bin/python && ln -sf /usr/bin/pip3 /usr/bin/pip + +RUN apt install -y \ + curl \ + git \ + git-lfs \ + locales && \ + git lfs install && \ + sed -i 's/# \(en_US.UTF-8 UTF-8\)/\1/' /etc/locale.gen && \ + locale-gen && \ + rm -rf /var/lib/apt/lists/* + +RUN apt update && \ + apt install -y nodejs npm && \ + rm -rf /var/lib/apt/lists/* + +ENV LANG=en_US.UTF-8 \ + LC_ALL=en_US.UTF-8 + +RUN curl -sSL https://install.python-poetry.org | python - && \ + ln -sf ~/.local/bin/poetry /usr/local/bin/poetry + +RUN poetry config virtualenvs.in-project true + +WORKDIR /app + +EXPOSE 80 7860 + +COPY pyproject.toml poetry.lock* ./ + +RUN if [ "$DEV_MODE" = "false" ]; then \ + echo "🏭 Production mode: Clean build without cache"; \ + poetry install --no-root --no-interaction --no-ansi --with data,ml,dev; \ + fi + +COPY . /app + +RUN chmod +x /app/scripts/*.sh || true + +ENTRYPOINT ["/app/scripts/entrypoint.sh"] \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..4069c559a33b80ef5275b9026c87f2c06b8d8422 --- /dev/null +++ b/LICENSE @@ -0,0 +1,5 @@ +Copyright (c) 2025 magnolia psychometrics GmbH. All rights reserved. + +This software is proprietary and confidential. Unauthorized copying of this file, via any medium is strictly prohibited. + +This repository is provided as a template and is the property of the **magnolia psychometrics GmbH**. For internal use only. diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..caaf10ffa1102afedfb1c29950263b3fc6a5281b --- /dev/null +++ b/README.md @@ -0,0 +1,43 @@ +--- +title: The Synthetic Nomological Net +emoji: 🔍 +colorFrom: purple +colorTo: blue +sdk: docker +suggested_hardware: "cpu-basic" +app_port: 7860 +pinned: true +models: + - "magnolia-psychometrics/surveybot3000" + - "sentence-transformers/all-mpnet-base-v2" +license: mit +--- + +# SynthNet Search + +Mapping over 74,000 scales from more than 31,500 APA PsycTests Questionnaires, Surveys, and Tests. + +## Setup + +This application requires the following environment variables: + +- `MODEL__ITEM_MODEL_PATH`: HuggingFace model respository path +- `MODEL__ITEM_MODEL_ACCESS_TOKEN`: Access token for private HuggingFace model +- `MODEL__SCALE_MODEL_PATH`: HuggingFace model respository path +- `MODEL__SCALE_MODEL_ACCESS_TOKEN`: Access token for private HuggingFace model +- `DATA__DATASET_PATH`: HuggingFace dataset respository path +- `DATA__ENCRYPTION_KEY`: Encryption key for database +- `TRACKING_DB__API_ENDPOINT`: Usage tracking database endpoint +- `TRACKING_DB__ANON_KEY`: Anonymous key for usage tracking database endpoint +- `TRACKING_DB__JWT_TOKEN`: Access token for usage tracking database endpoint + +Configure these in the Space settings under "Repository secrets". + +## Citation +``` +Hommel, B. E., Külpmann, A. I., & Arslan, R. C. (2025). The Synthetic Nomological Net: A search engine to identify conceptual overlap in measures in the behavioral sciences. PsyArXiv. Manuscript in preparation. https://osf.io/preprints/psyarxiv/nfgmv_v1/ +``` + +## About + +This research is part of the [SYNTH research project (#546323839)](https://gepris.dfg.de/gepris/projekt/546323839?language=en), which is conducted as part of the [META-REP Priority Program](https://gepris.dfg.de/gepris/projekt/441890184) aiming to improve the replicability, reproducibility, and generalizability of empirical research in the behavioral sciences. SYNTH contributes to these goals by integrating large language models into current research workflows to reduce burdens on scientists while improving transparency and replicability. \ No newline at end of file diff --git a/notebooks/layouts/marimo-demo.grid.json b/notebooks/layouts/marimo-demo.grid.json new file mode 100644 index 0000000000000000000000000000000000000000..ce765e07d24050dde255f1e7888cfff340cbf3b6 --- /dev/null +++ b/notebooks/layouts/marimo-demo.grid.json @@ -0,0 +1,57 @@ +{ + "type": "grid", + "data": { + "columns": 24, + "rowHeight": 20, + "maxWidth": 300, + "bordered": true, + "cells": [ + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": null + }, + { + "position": [ + 0, + 0, + 24, + 15 + ] + }, + { + "position": [ + 0, + 15, + 24, + 15 + ] + } + ] + } +} \ No newline at end of file diff --git a/notebooks/marimo-demo.py b/notebooks/marimo-demo.py new file mode 100644 index 0000000000000000000000000000000000000000..7ce469f1e7844dba88b9857854306b55db25a8af --- /dev/null +++ b/notebooks/marimo-demo.py @@ -0,0 +1,206 @@ +# /// script +# requires-python = ">=3.12" +# dependencies = [ +# "marimo", +# "matplotlib==3.10.1", +# "numpy==2.2.4", +# ] +# /// + +import marimo + +__generated_with = "0.14.10" +app = marimo.App(css_file="theme.marimo.css", html_head_file="") + + +@app.cell +def _(): + import marimo as mo + return (mo,) + + +@app.cell +def _(mo): + get_applicant_count, set_applicant_count = mo.state(500) + return get_applicant_count, set_applicant_count + + +@app.cell +def _(get_applicant_count, mo, set_applicant_count): + applicant_count = mo.ui.number( + start=1, + step=1, + value=get_applicant_count(), + full_width=True, + label="Number of applicants", + on_change=set_applicant_count, + ) + return (applicant_count,) + + +@app.cell +def _(get_applicant_count, mo): + hire_count = mo.ui.number( + start=1, + stop=get_applicant_count() - 1, + step=1, + value=75, + full_width=True, + label="Hire count", + ) + return (hire_count,) + + +@app.cell +def _(mo): + base_rate = mo.ui.slider( + value=40, start=1, stop=100, step=1, full_width=True, label="Base rate" + ) + return (base_rate,) + + +@app.cell +def _(mo): + validity = mo.ui.slider( + value=0.18, start=0.01, stop=1.00, step=0.01, full_width=True, label="Validity" + ) + return (validity,) + + +@app.cell +def _(applicant_count, base_rate, hire_count, validity): + import requests + + url = "http://localhost:7860/api/v1/demo/r/demo" + params = { + "applicant_count": applicant_count.value, + "hire_count": hire_count.value, + "base_rate": base_rate.value, + "validity": validity.value, + } + headers = {"accept": "application/json"} + + response = requests.post(url, params=params, headers=headers) + + return (response,) + + +@app.cell +def _(response): + import pandas as pd + import plotly.graph_objects as go + from plotly.subplots import make_subplots + + json_data = response.json() + + data = pd.DataFrame( + { + "var": list(json_data.keys()), + "label": [ + "Rightfully hired", + "Incorrectly hired", + "Rightfully rejected", + "Incorrectly rejected", + ], + "value": list(json_data.values()), + } + ) + + data["label_with_value"] = data["label"] + " (" + data["value"].astype(str) + ")" + + fig = make_subplots( + rows=1, + cols=2, + specs=[[{"type": "pie"}, {"type": "pie"}]], + subplot_titles=("Hiring Outcome", "Rejection Outcome"), + horizontal_spacing=0.1, + vertical_spacing=0.15, + ) + + hired_data = data[data["var"].isin(["true_positives", "false_positives"])] + hired_values = hired_data["value"].tolist() + hired_labels = hired_data["label_with_value"].tolist() + + rejected_data = data[data["var"].isin(["true_negatives", "false_negatives"])] + rejected_values = rejected_data["value"].tolist() + rejected_labels = rejected_data["label_with_value"].tolist() + + fig.add_trace( + go.Pie( + values=hired_values, + labels=hired_labels, + hole=0.5, + marker_colors=["#6b71ed", "#403c5d"], + name="Hiring", + legendgroup="hiring", + showlegend=True, + hoverinfo="none", + ), + row=1, + col=1, + ) + + fig.add_trace( + go.Pie( + values=rejected_values, + labels=rejected_labels, + hole=0.5, + marker_colors=["#6b71ed", "#403c5d"], + name="Rejection", + legendgroup="rejection", + showlegend=True, + hoverinfo="none", + ), + row=1, + col=2, + ) + + fig.update_layout( + autosize=True, + margin=dict(l=0, r=0, t=60, b=20), + legend=dict( + orientation="h", + yanchor="top", + y=-0.1, + xanchor="center", + x=0.5, + font=dict(size=12), + ), + title=dict(text=None, x=0.5, font=dict(size=16)), + height=400, + paper_bgcolor="rgba(0,0,0,0)", + plot_bgcolor="rgba(0,0,0,0)", + ) + + fig.update_annotations(font_size=14, y=1.08) + + return (fig,) + + +@app.cell +def _(applicant_count, base_rate, hire_count, mo, validity): + with mo.status.spinner(subtitle="Loading data ...") as _spinner: + mo.vstack([applicant_count, hire_count, base_rate, validity]) + return + + +@app.cell +def _(applicant_count, base_rate, hire_count, mo, validity): + mo.vstack([applicant_count, hire_count, base_rate, validity]) + return + + +@app.cell +def _(fig, mo, response): + if response.status_code == 200: + fig.show( + config={"displayModeBar": False, "staticPlot": True, "responsive": True} + ) + else: + error_msg = mo.md(f"{mo.icon('lucide:ban')} Error in server response") + mo.output.append(error_msg) + return + + +if __name__ == "__main__": + app.run() diff --git a/notebooks/theme.marimo.css b/notebooks/theme.marimo.css new file mode 100644 index 0000000000000000000000000000000000000000..f19e22f2b29168680f7b0d9db0ad24586b773e70 --- /dev/null +++ b/notebooks/theme.marimo.css @@ -0,0 +1,4 @@ +:root { + --background: transparent; + --background-darker: transparent; +} diff --git a/poetry.lock b/poetry.lock new file mode 100644 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0000000000000000000000000000000000000000..268d8603f751dcbefec11b29373ef2c16aca0b2f --- /dev/null +++ b/public/bib/references.bib @@ -0,0 +1,42 @@ +@UNPUBLISHED{HommelArslan2025, + title = "Language models accurately infer correlations between + psychological items and scales from text alone", + author = "Hommel, Bj{\"o}rn E and Arslan, Ruben C", + abstract = "Many behavioural scientists do not agree on core constructs and + how they should be measured. Different literatures measure + related constructs, but the connections are not always obvious to + readers and meta-analysts. Many measures in behavioural science + are based on agreement with survey items. Because these items are + sentences, computerised language models can make connections + between disparate measures and constructs and help researchers + regain an overview over the rapidly growing, fragmented + literature. Our fine-tuned language model, the SurveyBot3000, + accurately predicts the correlations between survey items, the + reliability of aggregated measurement scales, and + intercorrelations between scales from item positions in semantic + vector space. In our pilot study, the out-of-sample accuracy for + item correlations was .71, .89 for reliabilities, and .89 for + scale correlations. In our preregistered validation study using + novel items, the out-of-sample accuracy was slightly reduced to + .59 for item correlations, .84 for reliabilities, and .84 for + scale correlations. The synthetic item correlations showed an + average prediction error of .17, with larger errors for middling + correlations. Predictions exhibited generalizability beyond the + training data and across various domains, with some variability + in accuracy. Our work shows language models can reliably predict + psychometric relationships between survey items, enabling + researchers to evaluate new measures against existing scales, + reduce redundancy in measurement, and work towards a more unified + behavioural science taxonomy.", + journal = "PsyArXiv", + note = "Manuscript submitted for publication", + year = 2025 +} + +@UNPUBLISHED{HommelKuelpmannArslan, + title = "The Synthetic Nomological Net: A search engine to identify conceptual overlap in measures in the behavioral sciences", + author = "Hommel, Bj{\"o}rn E and K{\"u}lpmann, Annika I and Arslan, Ruben C", + journal = "PsyArXiv", + note = "Manuscript in preparation", + year = 2025 +} \ No newline at end of file diff --git a/public/favicon-128x128.png b/public/favicon-128x128.png new file mode 100644 index 0000000000000000000000000000000000000000..0522be1c5b63e9567e31fd9678d553465e60e31f --- /dev/null +++ b/public/favicon-128x128.png @@ -0,0 +1,3 @@ +version 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Calling Alpine.start() more than once can cause problems."),_r=!0,document.body||E("Unable to initialize. Trying to load Alpine before `` is available. Did you forget to add `defer` in Alpine's ` + + + + + + + {% block head %}{% endblock head %} + + + + {% block content %}{% endblock content %} + + + \ No newline at end of file diff --git a/src/templates/components/footer.jinja b/src/templates/components/footer.jinja new file mode 100644 index 0000000000000000000000000000000000000000..c9b0a7bfe2df097d4aa6cf7f98dbc70523fb6cc1 --- /dev/null +++ b/src/templates/components/footer.jinja @@ -0,0 +1,81 @@ +
+
+ + {# Main Footer Content #} +
+ + {# Legal Links #} +
+

Legal

+ +
+ + {# Resources Links #} +
+

Resources

+ +
+ +
+ + {# Bottom Bar with Copyright #} +
+

+ © {{ current_year }} magnolia psychometrics GmbH +

+
+ +
+
\ No newline at end of file diff --git a/src/templates/pages/about/about.jinja b/src/templates/pages/about/about.jinja new file mode 100644 index 0000000000000000000000000000000000000000..463b9c484efdd9ae04a8ceb7faa2107034a6cd51 --- /dev/null +++ b/src/templates/pages/about/about.jinja @@ -0,0 +1,288 @@ +
+
+ + {# Header #} +
+

About the Project

+
+
+ + {# Introduction #} +
+

+ This research is part of the + + SYNTH research project (#546323839) + , which is conducted as part of the + + META-REP Priority Program + + aiming to improve the replicability, reproducibility, and generalizability of empirical research in the behavioral sciences. + SYNTH contributes to these goals by integrating large language models into current research workflows to reduce burdens on + scientists while improving transparency and replicability. +

+
+ + {# Research Team #} +
+

SYNTH Research Team

+ +
+ + {# Björn E. Hommel #} +
+
+
+ Björn E. Hommel +
+
+

Björn E. Hommel

+

Postdoctoral Researcher

+

University of Leipzig

+ + {# Social Media Icons #} + +
+ + {# Ruben C. Arslan #} +
+
+
+ Ruben C. Arslan +
+
+

Ruben C. Arslan

+

Professor, Psychological Research Methods

+

University of Witten

+ + {# Social Media Icons #} + +
+ + {# Annika Külpmann #} +
+
+
+ Ruben C. Arslan +
+
+

Annika Külpmann

+

Doctoral Student

+

University of Witten

+ + {# Social Media Icons #} + +
+ + {# Malte Elson #} +
+
+
+ Malte Elson +
+
+

Malte Elson

+

Professor, Psychology of Digitalisation

+

University of Bern

+ + {# Social Media Icons #} + +
+ + {# Jamie Cummins #} +
+
+
+ Jamie Cummins +
+
+

Jamie Cummins

+

Senior Postdoctoral Researcher

+

University of Bern

+ + {# Social Media Icons #} + +
+ + {# Beth Clarke #} +
+
+
+ Beth Clarke +
+
+

Beth Clarke

+

Postdoctoral Researcher

+

University of Bern

+ + {# Social Media Icons #} + +
+
+ +
+ + {# Correspondence #} +
+

Corresponding Author

+ +
+
+
+ + + + +
+
+

Björn E. Hommel

+

Postdoctoral Researcher

+

Department of Personality Psychology and Psychological Assessment

+

Wilhelm Wundt Institute of Psychology | Leipzig University

+ + bjoern.hommel@uni-leipzig.de + +
+
+
+
+ + {# Acknowledgments #} +
+

Acknowledgements

+

+ We gratefully acknowledge the + + German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) + + for funding this work (#546323839), and the + + American Psychological Association (APA) + + for granting permission to use the + + APA PsycTests Database + for this research. +

+

This web application is maintained by + + magnolia psychometrics GmbH. +

+
+ +
+
\ No newline at end of file diff --git a/src/templates/pages/demo/demo.jinja b/src/templates/pages/demo/demo.jinja new file mode 100644 index 0000000000000000000000000000000000000000..6c34a71015072470e9d889ad267ae1da6cc0be4d --- /dev/null +++ b/src/templates/pages/demo/demo.jinja @@ -0,0 +1,60 @@ +{% extends "base/base.jinja" %} + +{% block content %} + +
+
+ +
+
+
+
+
+

+ Your + Stunning Web App +

+

+ Interactive Data Science with Marimo Notebooks +

+ +
+
+
+ + +
+
+
+
+

Interactive Data Science

+

+ Experience the power of marimo notebooks embedded directly in your web application. + The demo below showcases an interactive sine wave visualization. +

+
+ +
+ +
+
+ +
+ +
+ +{% include "components/footer.jinja" %} + +{% endblock content %} \ No newline at end of file diff --git a/src/templates/pages/donate/donate.jinja b/src/templates/pages/donate/donate.jinja new file mode 100644 index 0000000000000000000000000000000000000000..bfc86eb7b702f2d53d90ca675cff09ee10e2d46b --- /dev/null +++ b/src/templates/pages/donate/donate.jinja @@ -0,0 +1,51 @@ +{# Data Donation Banner - Slim CTA #} + \ No newline at end of file diff --git a/src/templates/pages/faq/faq.jinja b/src/templates/pages/faq/faq.jinja new file mode 100644 index 0000000000000000000000000000000000000000..f763fe35f0376d6eb0abc581df84d971d684561f --- /dev/null +++ b/src/templates/pages/faq/faq.jinja @@ -0,0 +1,239 @@ +
+ {# Subtle background pattern #} +
+
+
+ +
+ + {# Header #} +
+

Instructions

+
+
+ + {# Introduction Text #} +
+

+ This is a search engine designed to help researchers, practitioners, and students discover scales from a database of approximately 30,000 questionnaires, surveys, and tests. +

+

+ Two main modes of operation are currently supported: +

+ + {# Search Mode Cards #} +
+ + {# Item-Based Search Card #} +
+
+
+ + + + + + + + + + + + + + +
+
+

Item-Based Search

+
+
+ +

+ Enter multiple survey items (i.e., statements or questions) to find related instruments. This is the preferred search mode, using a fine-tuned model to predict item-pair correlations (magnolia-psychometrics/surveybot3000) for higher accuracy. +

+
+ + {# Scale-Based Search Card #} +
+
+
+ + + + + +
+
+

Scale-Based Search

+
+
+ +

+ Describe a construct, trait, or scale name to find relevant instruments. This mode uses a general-purpose model and yields results that may be more prone to jingle-jangle fallacies (sentence-transformers/all-mpnet-base-v2). +

+ + +
+ +
+
+ +
+

Motivation

+ +

+ Behavioral science faces a proliferation problem: thousands of psychological measures exist, but researchers often + struggle to determine whether their "new" construct is genuinely novel or merely reinvents existing measures under + different labels. This challenge stems from an inherent asymmetry: Creating new measures is easy and reputationally + rewarding, while systematically comparing them against thousands of existing ones is cumbersome and time-consuming. + Traditional validation methods simply don't scale to the vast landscape of published measures. + This search engine addresses this gap by enabling researchers to quickly identify conceptually similar measures, + helping to reduce redundancy, improve construct clarity, and ultimately make psychological science more cumulative + and efficient. +

+

+ While earlier approaches using latent semantic analysis have shown promise + + (Rosenbusch et al., 2020), this work uses specialized state-of-the-art transformer models and a substantially larger dataset + to better predict the empirical relationships between psychological measures. +

+
+ + {# FAQ Accordion #} +
+

FAQ

+ + {# FAQ Item #} +
+ +
+ What are the data sources for the search engine? +
+
+

+ The data are primarily sourced from the + APA PsycTests Database with permission from the American Psychological Association (APA). + The database includes approximately 30,000 scale representations derived from around 500,000 individual items that were extracted by parsing PDFs using (visual) language models. +

+
+
+ + {# FAQ Item #} +
+ +
+ How trustworthy and accurate are the results? +
+
+

+ Model accuracy: The accuracy of the magnolia-psychometrics/surveybot3000 + model used for item-based search is reported in detail in the sources referenced below (Hommel & Arslan, 2025). + In brief, when predicting scale correlations, the synthetic model estimates converge with empirical correlations from human respondents with an accuracy of r = .83 (95% CI [.81; .85]; manifest). +

+

+ For scale-based search using construct labels, please see Wulff & Mata (2025) on the accuracy of the pre-trained model (sentence-transformers/all-mpnet-base-v2). +

+

+ Data trustworthiness: While we strive for high data quality, please note that the items and scales are extracted automatically from source PDFs. + As such, there may be occasional discrepancies or errors in the extracted text. We recommend verifying any critical information against the original source when possible. + The extraction process involved two models: a visual language model (Qwen/Qwen2.5-VL-7B-Instruct) + to parse the PDF layout and a large language model (Qwen/Qwen3-32B) to interpret and structure the content. + Errors in transcription may occur, especially with complex survey layouts or poor scan quality. Warning codes are provided to flag potential issues (see below). + +

+
+
+ + {# FAQ Item #} +
+ +
+ What are warning codes and what do they mean? +
+
+

+ Warning codes indicate potential data quality issues detected during automated AI-extraction from source PDFs. + While these codes do not necessarily imply errors, they highlight areas that may require additional scrutiny. + Regardless of warning codes, we recommend verifying any critical information against the original source when possible. +

+
+
+ + {# FAQ Item #} +
+ +
+ What does the similarity score mean? +
+
+

+ In item-based search, cosine similarity scores are closely aligned with the correlation coefficients one would expect when + administering two scales to human respondents. In scale-based search, similarity scores reflect semantic relatedness + between the search term and the scale and/or instrument labels in the database. +

+

+ While cosine similarity theoretically ranges from -1 to 1, sentence vectors rarely yield negative scores because their many + abstract linguistic features are predominantly positively correlated. +

+
+
+ + {# FAQ Item #} +
+ +
+ How can I access the full scales and items? Can I download or export search results? +
+
+

+ Unfortunately, due to copyright restrictions, we cannot display individual survey items (statements/questions) directly on the platform. + However, you can follow the DOI link to obtain the items from the original source. To access full instrument details, please: +

+
    +
  • + Click the DOI link in search results to access the original source +
  • +
  • + Contact the instrument authors for permission to use the full measure +
  • +
  • + Check institutional access through your library's APA PsycTests subscription +
  • +
+
+
+ +
+ + {# Contact/Support Notice #} +
+
+ +
+ + + + + + + + + + + +
+
+
+

Found a bug in the app or an error in the data?

+

+ Please let us know by opening an issue in this + GitHub repository + or by contacting us via email. + +

+
+
+
+ +
+
\ No newline at end of file diff --git a/src/templates/pages/index.jinja b/src/templates/pages/index.jinja new file mode 100644 index 0000000000000000000000000000000000000000..46f3c580628360b42c133e466447fe029d00149c --- /dev/null +++ b/src/templates/pages/index.jinja @@ -0,0 +1,125 @@ +{% extends "base/base.jinja" %} + +{% block content %} + +
+ + {# Navigation #} + + + {# Search Section #} + + + {# FAQ Section - Dark Theme #} +
+
+ {% include "pages/faq/faq.jinja" %} +
+
+ + {# Research Section #} +
+
+ {% include "pages/research/research.jinja" %} +
+
+ + {# Data Donation Section #} +
+
+ {% include "pages/donate/donate.jinja" %} +
+
+ + {# About Section #} +
+
+ {% include "pages/about/about.jinja" %} +
+
+ +
+ +{% include "/components/footer.jinja" %} + +{% endblock content %} \ No newline at end of file diff --git a/src/templates/pages/research/research.jinja b/src/templates/pages/research/research.jinja new file mode 100644 index 0000000000000000000000000000000000000000..347672f51e4802e651decf15d5753107afed1e74 --- /dev/null +++ b/src/templates/pages/research/research.jinja @@ -0,0 +1,174 @@ +
+
+ + {# Header #} +
+

Research & Citation

+
+
+ + {# Introduction #} +
+

+ +

+
+ + {# Main App Citation #} +
+

SynthNet Search

+

+ SynthNet Search uses a specialized embedding model to predict the relatedness of survey items and scales. + The database currently includes about 30,000 scale representations obtained from embedding statements from approx. 500,000 items. + It is designed to facilitate the discovery of relevant measures in the behaviorial sciences. +

+

+ For the main application, please cite the following work: +

+ + {# APA Reference - Using Jinja filter #} +
+
+ {{ 'HommelKuelpmannArslan' | cite | safe }} +
+
+ + {# BibTeX with Copy Button #} + +
+ + BibTeX + +
+ +
+
+
+
+ + {# Underlying Model Citation #} +
+

Embedding Model: SurveyBot3000

+ +

+ The conceptual search functionality is powered by a specialized language model trained to predict relationships between psychological items and scales: +

+ + {# APA Reference - Using Jinja filter #} + APA + +
+
+ {{ 'HommelArslan2025' | cite | safe }} +
+
+ + {# BibTeX with Copy Button #} + +
+ + BibTeX + +
+ +
+
+
+
+ + {# Additional Resources #} + + +
+
\ No newline at end of file diff --git a/src/templates/pages/search/partials/_search_results.jinja b/src/templates/pages/search/partials/_search_results.jinja new file mode 100644 index 0000000000000000000000000000000000000000..449f7c5efd3f11e4cfff7417d5dc62abe6dbf633 --- /dev/null +++ b/src/templates/pages/search/partials/_search_results.jinja @@ -0,0 +1,263 @@ +{% set warning_messages = { + "ITEM_COUNT_DEVIATION": "Language model extraction from original PDF resulted in a different item count than reported in the APA PsycTest record.", + "SCALE_COUNT_DEVIATION": "Language model extraction from original PDF resulted in a different scale count than reported in the APA PsycTest record.", + "ITEM_TEXT_DEVIATION": "Language model extraction resulted in item text that may differ from the text contained in the original PDF.", + "KEYING_CORRECTION": "Language model has corrected the keying of one or more items based on the item text in relation to its scale.", +} %} + +
+ + {# Controls Bar #} +
+ + +
+ +
+ [ENTER] + +
+
+
+ + {# Results List #} +
    + {% if search_result %} + {% for result in search_result %} +
  • + + {# Row Header #} +
    +
    +
    +
    {{ "{:.3f}".format(result['max_similarity']).replace("0.", ".") }}
    + +
    +
    +

    {{ result['meta_instrument_name'] }}

    +

    + {% set subscale_count = result['scale_name']|length - 1 %} + {% if subscale_count == 0 %} + No subscales + {% elif subscale_count == 1 %} + 1 subscale + {% else %} + {{ subscale_count }} subscales + {% endif %} +

    +

    + DOI: + + {{ result['meta_doi'] }} + + + + +

    +
    + +
    + + {% if result["warning_codes"] %} +
    + + + + {{ result["warning_count"] }} +
    + {% endif %} + + + + +
    +
    +
    + + {# Expanded Details #} +
    + + {# Scales #} +
    +
    + {% for index in range(result['scale_name'] | length) %} +
    + +
    + {% if index == 0 %} + {{ result['meta_instrument_name'] }} + Global Level + {% else %} + {{ result['scale_name'][index] }} + Subscale Level + {% endif %} +
    + +
    +
    {{ "{:.3f}".format(result['similarity'][index]).replace("0.", ".") }}
    + +
    +
    + {% endfor %} +
    + + {# Warnings #} + {% if result["warning_codes"] %} +
    +
      + {% for code in result["warning_codes"] %} +
    • + + + + {{ warning_messages[code] }} +
    • + {% endfor %} +
    +
    + {% endif %} + +
    +
    +
  • + {% endfor %} + {% else %} +
  • +
    +

    No results found

    +
    +
  • + {% endif %} +
+ + {# Pagination #} + {% set total_pages = (results_count / page_size) | round(0, 'ceil') | int %} + {% set current_display_page = page_index + 1 %} + {% set pages_start = [1, current_display_page - 2] | max %} + {% set pages_end = [total_pages, pages_start + 4] | min %} + {% set pages_start = [1, pages_end - 4] | max %} + +
+
+ {{ "{:,}".format(page_index * page_size + 1) }} to {{ "{:,}".format([results_count, (page_index + 1) * page_size] | min) }} of {{ "{:,}".format(results_count) }} +
+
+ + + {% for page in range(pages_start, pages_end + 1) %} + + {% endfor %} + + +
+
+ + {# Export Button #} + +
\ No newline at end of file diff --git a/src/templates/pages/search/search.jinja b/src/templates/pages/search/search.jinja new file mode 100644 index 0000000000000000000000000000000000000000..a3aca05340a797c93d599fbeabfb35a3571dabef --- /dev/null +++ b/src/templates/pages/search/search.jinja @@ -0,0 +1,619 @@ + + +
+
+ {# #} +
+ SynthNet +
+

+ Mapping over 74,000 scales from more than 31,500 APA PsycTests Questionnaires, Surveys, and Tests. + +

+
+ + {# Main Container #} +
+ + {# Mode Toggle #} +
+
+ + Items + + + + + + Scale + +
+
+ + {# Search Input Group #} +
+ + {# Search Bar #} + + + {# Query Drawer #} +
+ +
+
    + +
+
+
+
+ + {# Hints #} +
+
+ + Press + CTRL + + + V + to paste multiple items, one per line, ending with (R) to indicate reverse scoring. + + Click + + + + + + + to toggle + + reverse scoring for an item. + +
+
+ + {# Disclaimer Checkbox #} +
+ +
+ + {# Submit Form #} +
+ + +
+ + {# Utility Buttons #} +
+ + + +
+ + {# Results #} +
+
+ + {# Loading Skeleton Template #} + + +
+
\ No newline at end of file diff --git a/src/utils/__init__.py b/src/utils/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/src/utils/bibliography.py b/src/utils/bibliography.py new file mode 100644 index 0000000000000000000000000000000000000000..63a2047e047cd406e37732bc295954646b0304bb --- /dev/null +++ b/src/utils/bibliography.py @@ -0,0 +1,123 @@ +import logging +from pathlib import Path +from functools import lru_cache +from typing import Optional +from pybtex.database import parse_file, BibliographyData +from pybtex.plugin import find_plugin + +logger = logging.getLogger(__name__) + +BIB_DIR = Path("public/bib") +STYLE_NAME = "apa7" +OUTPUT_FORMAT = "html" + +@lru_cache(maxsize=1) +def load_bibliography() -> BibliographyData: + + bib_files = list(BIB_DIR.glob("*.bib")) + + if not bib_files: + logger.warning(f"No .bib files found in {BIB_DIR}") + return BibliographyData() + + merged_bib = parse_file(str(bib_files[0])) + logger.info(f"Loaded bibliography from {bib_files[0].name}") + + for bib_file in bib_files[1:]: + try: + bib_data = parse_file(str(bib_file)) + merged_bib.entries.update(bib_data.entries) + logger.info(f"Merged bibliography from {bib_file.name}") + except Exception as e: + logger.error(f"Error parsing {bib_file}: {e}") + + logger.info(f"Total entries loaded: {len(merged_bib.entries)}") + return merged_bib + + +def format_citation( + cite_key: str, + style: str = STYLE_NAME, + output_format: str = OUTPUT_FORMAT +) -> str: + + try: + bibliography = load_bibliography() + + if cite_key not in bibliography.entries: + logger.warning(f"Citation key '{cite_key}' not found in bibliography") + return f"

[Citation not found: {cite_key}]" + + filtered_bib = BibliographyData({cite_key: bibliography.entries[cite_key]}) + + style_plugin = find_plugin('pybtex.style.formatting', style)() + backend = find_plugin('pybtex.backends', output_format)() + + formatted = style_plugin.format_bibliography(filtered_bib) + + for entry in formatted: + return entry.text.render(backend) + + return f"

[Error formatting: {cite_key}]" + + except Exception as e: + logger.error(f"Error formatting citation {cite_key}: {e}") + return f"

[Error: {cite_key}]" + + +def format_bibliography( + cite_keys: Optional[list[str]] = None, + style: str = STYLE_NAME, + output_format: str = OUTPUT_FORMAT +) -> str: + + try: + bibliography = load_bibliography() + + # Filter to requested keys if provided + if cite_keys: + filtered_entries = { + key: bibliography.entries[key] + for key in cite_keys + if key in bibliography.entries + } + + if not filtered_entries: + return "

No valid citation keys provided.

" + + filtered_bib = BibliographyData(filtered_entries) + else: + filtered_bib = bibliography + + style_plugin = find_plugin('pybtex.style.formatting', style)() + backend = find_plugin('pybtex.backends', output_format)() + + formatted = style_plugin.format_bibliography(filtered_bib) + + entries_html = [] + for entry in formatted: + entries_html.append(entry.text.render(backend)) + + return "\n".join(entries_html) + + except Exception as e: + logger.error(f"Error formatting bibliography: {e}") + return f"

[Error formatting bibliography]

" + + +def get_bibtex_entry(cite_key: str) -> Optional[str]: + + try: + bibliography = load_bibliography() + + if cite_key not in bibliography.entries: + logger.warning(f"Citation key '{cite_key}' not found") + return None + + single_entry = BibliographyData({cite_key: bibliography.entries[cite_key]}) + + return single_entry.to_string('bibtex') + + except Exception as e: + logger.error(f"Error getting BibTeX for {cite_key}: {e}") + return None \ No newline at end of file diff --git a/src/utils/logging.py b/src/utils/logging.py new file mode 100644 index 0000000000000000000000000000000000000000..04afca4b3d7dc6f2c84ce00be2ae7e885333b8bb --- /dev/null +++ b/src/utils/logging.py @@ -0,0 +1,33 @@ +import logging +import time +from contextlib import contextmanager +from typing import Optional + + +@contextmanager +def context_logger(operation_name: str, logger: Optional[logging.Logger] = None): + """ + Context manager for logging operation timing. + + Args: + operation_name: Name of the operation being performed + logger: Logger instance to use. If None, uses root logger. + + Example: + with context_logger("Loading search data", logger): + data = load_data() + """ + if logger is None: + logger = logging.getLogger(__name__) + + start_time = time.time() + logger.info(f"Starting {operation_name}...") + + try: + yield + elapsed = time.time() - start_time + logger.info(f"Completed {operation_name} in {elapsed:.3f}s") + except Exception as e: + elapsed = time.time() - start_time + logger.error(f"Failed {operation_name} after {elapsed:.3f}s: {e}") + raise \ No newline at end of file