Merge branch 'main' into task5-workflow

.github/workflows/github_test.yml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: GitHub Unit Testing
+run-name: Unit Testing on ${{ github.event_name }}
+
+on:
+  push:
+    branches: [ "development" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install flake8 pytest wheel
+    - name: Install text2term
+      run: |
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        cd test
+        python -m unittest simple_tests

.github/workflows/upload_pypi.yml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Upload PyPI
+run-name: Upload ${{ github.event.release.tag_name }} to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install flake8 twine sdist wheel build
+    - name: Install text2term
+      run: |
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Build dist/
+      run: |
+        python -m build --sdist --wheel --no-isolation --outdir dist/ .
+    - name: Upload to pypi
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/upload_testpypi.yml

@@ -0,0 +1,47 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Upload Test PyPI
+run-name: Upload ${{ github.event.release.tag_name }} to Test PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install flake8 twine sdist wheel build
+    - name: Install text2term
+      run: |
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Build dist/
+      run: |
+        python -m build --sdist --wheel --no-isolation --outdir dist/ .
+    - name: Upload to pypi
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

.gitignore

@@ -84,6 +84,13 @@ ipython_config.py
 # pyenv
 .python-version
 
+# For PyPi upload
+make-pypi.sh
+.pypirc
+
+# Cache should not be uploaded
+cache/
+
 # 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
@@ -130,5 +137,4 @@ dmypy.json
 
 # Other
 .idea
-.DS_Store
-test/*
+.DS_Store

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: requirements.txt

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 ccb-hms
+Copyright (c) 2022 Center for Computational Biomedicine, Harvard Medical School
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README-UI.md

@@ -0,0 +1,90 @@
+# ontology-mapper-ui
+The following information pertains to the text2term UI, which is written [here](https://github.com/ccb-hms/ontology-mapper-ui) and runs online [here](https://text2term.hms.harvard.edu/). It supports fewer features than the base package does, but provides a user interface for non-programmers.
+
+### Running Locally via Node + Python
+
+##### Requirements
+
+-   Node >= 16.0.0
+-   npm >= 8.0.0
+-   Python >= 3.9.0
+-   pip >= 21.0.0
+-   text2term >= 4.1.2
+
+**\*** These are the versions I have that work; while I know Python 3.9 or higher is necessary, the others may not strictly require the listed versions.
+
+**\*\*** If you are running this locally on Google Chrome, you will likely run into issues with CORS (Cross-Origin Requests) that I have been unable to completely resolve. I would recommend using a different browser, using the Docker method, or finding some way to disable CORS on Chrome while running this.
+
+#### Instructions
+
+##### Initial Setup
+
+When first cloned, run the command:
+
+
+```
+npm install
+```
+
+to install all necessary packages for the React frontend.
+
+Next, go into the `flask-api` folder (perhaps by running `cd flask-api`) and run
+
+```
+pip install -r requirements-flask.txt
+```
+
+to install necessary packages for the Flask api.
+
+##### Running
+
+To run, make sure you are in the root of the repository and run, in two separate command line instances, the command
+
+```
+npm start
+```
+
+to start the front-end, which can be seen at `localhost:3000`, and the command
+
+```
+npm run flask-api
+```
+
+to start the back-end, which can be interacted with at `localhost:5000`.
+
+### Running Locally via Docker
+
+#### Requirements
+
+-   Docker
+
+#### Instructions
+
+##### Initial Setup
+
+Before running, make sure you have the latest version of the repository built by running the command
+
+```
+docker-compose build
+```
+
+Docker should build two images:
+
+-   `ontology-mapper-api`: the Flask backend API
+-   `ontology-mapper-client`: the React frontend
+
+##### Running
+
+To run the website, run the command:
+
+```
+docker-compose up
+```
+
+Docker should build two containers corresponding to the two images.
+
+In a browser, navigate to `localhost:8602` to see the front-end.
+
+### Acknowledgements
+
+Initial setup of React and Flask and Dockerization aided by an [article series](https://blog.miguelgrinberg.com/post/how-to-dockerize-a-react-flask-project) by Miguel Grinberg.