first commit

.dockerignore

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+.git
+.gitignore
+LICENSE
+README.md
+deploy/db
+tests
+

.gitattributes

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+deploy/db/data.sql.gz filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/bug-report.md

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+---
+name: Bug Report
+about: Use this to report a new bug
+
+---
+
+### Expected Behavior
+<!--- Tell us what should happen -->
+
+### Current Behavior
+<!--- Tell us what happens instead of the expected behavior -->
+
+### Possible Solution
+<!--- Not obligatory, but suggest a fix/reason for the bug, -->
+
+### Steps to Reproduce
+<!--- Provide a link to a live example, or an unambiguous set of steps to -->
+<!--- reproduce this bug. Include code to reproduce, if relevant -->
+1.
+2.
+3.
+4.
+
+### Context (Environment)
+<!--- How has this issue affected you? What are you trying to accomplish? -->
+<!--- Providing context helps us come up with a solution that is most useful in the real world -->
+
+<!--- Provide a general summary of the issue in the Title above -->

.github/ISSUE_TEMPLATE/feature-request.md

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+---
+name: Feature Request
+about: Suggest an idea for this project
+
+---
+
+### Description
+<!-- What use case are you trying to solve with this feature -->
+
+### Proposed solution
+<!-- A clear and concise description of what you want to happen -->
+
+### Definition of Done
+<!-- How to know this is implemeted. Preferably one short sentence -->

.github/PULL_REQUEST_TEMPLATE.md

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+<!-- Describe the pull request as the first paragraph of this PR. -->
+<!-- Make sure that you have read the "Contributing" guidelines. -->
+
+### What it is about:
+- [ ] Bug fix
+- [ ] Functional change
+- [ ] New feature
+- [ ] Code cleanup
+- [ ] Build system change
+- [ ] Documentation change
+- [ ] Language translation
+<!-- Replace [ ] with [x] to select options. -->
+<!-- Add/Remove items to the list, if necessary. -->
+
+### Pull request long description:
+<!-- Describe your pull request in detail. -->
+
+### Changes made:
+<!-- Enumerate the changes with 1), 2), 3) etc. -->
+<!-- Ensure the test cases are updated if needed. -->
+
+### Related issues:
+<!-- Reference issues with #<issue-num>. -->
+<!-- Write "Fixes #<issue-num>" to notify Github that this PR fixes an issue. -->
+
+### Additional information:
+<!-- Include sample dive log or other relevant information to allow testing the change where feasible. -->
+
+### Release note:
+<!-- Describe if this change needs a release note present in CHANGELOG.md. -->
+<!-- Also, please make sure to add the release note on top of the file CHANGELOG.md. -->
+
+### Documentation change:
+<!-- 
+* If this PR makes changes to user functionality, then the documentation has to be updated too.
+* Briefly outline here what has changed in terms of the user experience (UX).
+-->
+
+<!--
+##################
+##  FINAL NOTE  ##
+##################
+If you are a collaborator,
+please add labels and assign other collaborators for a review.
+
+Delete the commented lines, such as this one, if you want, they are not included in the PR output.
+-->

.github/workflows/testsuite.yml

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+name: "Testsuite"
+
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - 'tests'
+      - 'tests/*'
+
+jobs:
+  testsuite:
+    strategy:
+      max-parallel: 4
+      matrix:
+        # os: [ubuntu-latest, macOS-latest]
+        os: [ubuntu-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    name: Beacon (v2.x) API tests
+
+    steps:
+    - name: Install required tools
+      run: |
+        git clone https://github.com/bats-core/bats-core.git
+        pushd bats-core
+        git checkout v1.1.0
+        sudo ./install.sh /usr/local
+        popd
+        rm -rf bats-core
+        sudo apt-get install curl jq git-lfs
+        sudo -- bash -c -e "echo '127.0.0.1    idp beacon beacon-permissions' >> /etc/hosts"
+    - uses: actions/checkout@master
+    - name: (re)Build docker images
+      run: |
+        pushd deploy
+        docker-compose build beacon
+        popd
+    - name: Bootstrap a Beacon
+      run: |
+        pushd deploy
+        docker-compose up -d db
+        sleep 30
+        docker-compose up -d
+        docker-compose ps
+        sleep 60
+        popd
+    - name: Running testsuite
+      run: bats tests
+    - name: Cleanup
+      run: |
+        pushd deploy
+        docker-compose down -v
+        popd
+
+

.gitignore

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+*~
+.#*
+.DS_Store
+tmp/
+.bak
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+#.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# Grunt
+/ui/grunt
+
+# Tests tmp
+/tests/tmp/
+
+# IntelliJ
+.idea/
+
+# VS Code
+.vscode/
+
+# Custom
+deploy/request.json
+typings/
+deploy/ontologies/*.obo
+deploy/ontologies/*.owl*
+.antlr/

Dockerfile

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+##########################
+## Build env
+##########################
+FROM python:3.10-buster AS BUILD
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update
+#RUN apt-get upgrade -y
+RUN apt-get install -y --no-install-recommends \
+    ca-certificates pkg-config make \
+    libssl-dev libffi-dev libpq-dev
+
+# python packages
+RUN pip install --upgrade pip
+COPY requirements.txt /tmp/requirements.txt
+RUN pip install -r /tmp/requirements.txt
+
+##########################
+## Final image
+##########################
+FROM python:3.10-buster
+
+LABEL maintainer "CRG System Developers"
+LABEL org.label-schema.schema-version="2.0"
+LABEL org.label-schema.vcs-url="https://github.com/EGA-archive/beacon-2.x/"
+
+# Too much ?
+COPY --from=BUILD /usr/local/bin      /usr/local/bin
+COPY --from=BUILD /usr/local/lib      /usr/local/lib
+
+RUN apt-get update && \
+#    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+    nginx \
+    && \
+    rm -rf /var/lib/apt/lists/* /etc/apt/sources.list.d/nginx.list && \
+    apt-get purge -y --auto-remove
+
+COPY deploy/nginx.conf        /beacon/nginx.conf
+COPY deploy/supervisord.conf  /beacon/supervisord.conf
+COPY deploy/entrypoint.sh     /usr/local/bin/entrypoint.sh
+COPY beacon                   /beacon/beacon
+COPY ui                       /beacon/ui
+
+RUN groupadd beacon                              && \
+    useradd -M -g beacon beacon                  && \
+#    mkdir /beacon                                && \
+    mkdir /var/run/beacon                        && \
+    chown -R beacon:beacon /beacon               && \
+#    chmod 400 /beacon/beacon/conf.py             && \
+    chown -R beacon:beacon /var/log/nginx        && \
+    chown -R beacon:beacon /var/lib/nginx        && \
+    chown -R beacon:beacon /etc/nginx            && \
+    chown -R beacon:beacon /var/run/beacon       && \
+    mkdir -p /var/log/supervisord                && \
+    chown -R beacon:beacon /var/log/supervisord  && \
+    chmod +x /usr/local/bin/entrypoint.sh
+
+WORKDIR /beacon
+USER beacon
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]