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Feat: Init Commit and Read Endpoints (#1)
* feat: adds server code * adds generic table read endpt and get table names (wip) * feat: finishes tests, adds github workflows and issue templates * feat: cache get table, renames routes * adds cache for get table * cleanup PR * fixes typo in readme * fix: moves github dir, some small nit fixes * linter fix * RESTful convention routes --------- Co-authored-by: Jon Young <104453205+jtyoung84@users.noreply.github.com>
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Desktop (please complete the following information):**
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- OS: [e.g. iOS]
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- Browser [e.g. chrome, safari]
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- Version [e.g. 22]
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**Smartphone (please complete the following information):**
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- Device: [e.g. iPhone6]
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- OS: [e.g. iOS8.1]
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- Browser [e.g. stock browser, safari]
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- Version [e.g. 22]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/ISSUE_TEMPLATE/user_story.md‎

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---
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name: User story
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about: This template provides a basic structure for user story issues.
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title: ''
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labels: ''
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assignees: ''
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---
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# User story
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As a ..., I want to ..., so I can ...
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*Ideally, this is in the issue title, but if not, you can put it here. If so, delete this section.*
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# Acceptance criteria
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- [ ] This is something that can be verified to show that this user story is satisfied.
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# Sprint Ready Checklist
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- [ ] 1. Acceptance criteria defined
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- [ ] 2. Team understands acceptance criteria
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- [ ] 3. Team has defined solution / steps to satisfy acceptance criteria
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- [ ] 4. Acceptance criteria is verifiable / testable
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- [ ] 5. External / 3rd Party dependencies identified
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- [ ] 6. Ticket is prioritized and sized
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# Notes
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*Add any helpful notes here.*

‎.github/workflows/tag_and_publish.yml‎

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name: Tag and publish
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on:
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push:
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branches:
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- main
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jobs:
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update_badges:
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runs-on: ubuntu-latest
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continue-on-error: true
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defaults:
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run:
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working-directory: ./aind-dataverse-service-server
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steps:
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- uses: actions/checkout@v4
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with:
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ref: ${{ env.DEFAULT_BRANCH }}
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fetch-depth: 0
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token: ${{ secrets.SERVICE_TOKEN }}
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install -e .[dev] --no-cache-dir
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- name: Get Python version and Update README.md
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run: |
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python_version=$(grep "requires-python" pyproject.toml | grep -o ">=[^\"]*")
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python_badge=$(grep '^\!\[Python\]' README.md | sed -n 's/.*\(python-[^)]*\).*/\1/p')
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new_python_badge="python-$python_version-blue?logo=python"
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sed -i "s/$python_badge/$new_python_badge/g" README.md
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- name: Get interrogate values and Update README.md
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run: |
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interrogate_val=$(interrogate . | grep -o 'actual: [0-9]*\.[0-9]*' | awk '{print $2}')
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interrogate_badge=$(grep '^\!\[Interrogate\]' README.md | sed -n 's/.*\(interrogate-[^)]*\).*/\1/p')
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if (( $(echo "$interrogate_val >= 90.00" | bc -l) )); then
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new_interrogate_badge="interrogate-$interrogate_val%25-brightgreen"
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elif (( $(echo "$interrogate_val < 80.00" | bc -l) )); then
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new_interrogate_badge="interrogate-$interrogate_val%25-red"
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else
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new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
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fi
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sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
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- name: Get Coverage values and Update README.md
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run: |
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coverage run -m pytest
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coverage_val=$(coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
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coverage_badge=$(grep '^\!\[Coverage\]' README.md | sed -n 's/.*\(coverage-[^)]*\).*/\1/p')
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if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then
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new_coverage_badge="coverage-$coverage_val%25-brightgreen"
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elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
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new_coverage_badge="coverage-$coverage_val%25-red"
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else
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new_coverage_badge="coverage-$coverage_val%25-yellow"
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fi
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sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
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- name: Commit changes
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uses: EndBug/add-and-commit@v9
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with:
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default_author: github_actions
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message: "ci: update badges [skip actions]"
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add: '["aind-dataverse-service-server/README.md"]'
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bump_version:
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name: Bump version
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needs: update_badges
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runs-on: ubuntu-latest
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outputs:
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new_version: ${{ steps.output_version.outputs.new_version }}
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defaults:
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run:
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working-directory: ./aind-dataverse-service-server
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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ref: ${{ inputs.default_branch }}
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fetch-depth: 0
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token: ${{ secrets.SERVICE_TOKEN }}
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- name: Pull latest changes
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run: git pull origin main
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- name: Compute new version number
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id: tag_version
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uses: mathieudutour/github-tag-action@v6.2
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with:
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github_token: ${{ secrets.SERVICE_TOKEN }}
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release_branches: ${{ inputs.default_branch }}
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default_bump: patch
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dry_run: true # Perform dryrun first to calculate new version
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- name: Get version file name set variables
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run: |
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pkg_name=$(grep -P 'version = \{attr = .*\}' pyproject.toml | grep -oP '\w+.__version__')
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init_file="./src/${pkg_name//.__version__}/__init__.py"
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pkg_version=$(grep -Po '[0-9]+\.[0-9]+\.[0-9]+' "$init_file")
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abs_init_file_path="aind-dataverse-service-server/${init_file}"
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echo "VERSION_FILE=$init_file" >> "$GITHUB_ENV"
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echo "ABS_VERSION_FILE=$abs_init_file_path" >> "$GITHUB_ENV"
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echo "VERSION=${{ steps.tag_version.outputs.new_version }}" >> "$GITHUB_ENV"
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- name: Update version file with new version
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run: |
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grep "__version__" "$VERSION_FILE"
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sed -i --debug --expression="s|__version__.*|__version__ = \"${{ env.VERSION }}\"|" "$VERSION_FILE"
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- name: Set output
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id: output_version
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run: echo "new_version=${{ env.VERSION }}" >> "$GITHUB_OUTPUT"
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- name: Commit changes
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uses: EndBug/add-and-commit@v9
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with:
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default_author: github_actions
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message: "ci: version bump [skip actions]"
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add: ${{ env.ABS_VERSION_FILE }}
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build_client:
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runs-on: ubuntu-latest
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needs: bump_version
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steps:
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- uses: actions/checkout@v4
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with:
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ref: ${{ inputs.default_branch }}
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fetch-depth: 0
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token: ${{ secrets.SERVICE_TOKEN }}
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- name: Pull latest changes
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run: git pull origin main
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- name: Update version
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run: |
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sed -i --debug --expression="s|packageVersion.*|packageVersion\": \"${{ needs.bump_version.outputs.new_version }}\"|" openapirc.json
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sed -i --debug --expression="s|packageVersion.*|packageVersion\": \"${{ needs.bump_version.outputs.new_version }}\"|" openapirc_async.json
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install -e aind-dataverse-service-server --no-cache-dir
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python -m pip install toml
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- name: Generate OpenAPI file
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run: |
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python scripts/generate_openapi.py
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- name: Generate Python Client
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uses: openapi-generators/openapitools-generator-action@v1.5.0
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with:
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generator: python
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generator-tag: v7.13.0
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openapi-file: openapi.json
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config-file: openapirc.json
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- name: Handle files
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run: |
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rm -rf aind-dataverse-service-client
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mv python-client aind-dataverse-service-client
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rm -rf aind-dataverse-service-client/.github
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rm -f aind-dataverse-service-client/.gitignore
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rm -f aind-dataverse-service-client/.gitlab-ci.yml
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rm -f aind-dataverse-service-client/git_push.sh
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rm -f aind-dataverse-service-client/.travis.yml
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- name: Generate Python Async Client
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uses: openapi-generators/openapitools-generator-action@v1.5.0
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with:
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generator: python
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generator-tag: v7.13.0
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openapi-file: openapi.json
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config-file: openapirc_async.json
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- name: Handle async files
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run: |
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rm -rf aind-dataverse-service-async-client
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mv python-client aind-dataverse-service-async-client
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rm -rf aind-dataverse-service-async-client/.github
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rm -f aind-dataverse-service-async-client/.gitignore
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rm -f aind-dataverse-service-async-client/.gitlab-ci.yml
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rm -f aind-dataverse-service-async-client/git_push.sh
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rm -f aind-dataverse-service-async-client/.travis.yml
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- name: Commit changes
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uses: EndBug/add-and-commit@v9
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with:
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default_author: github_actions
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message: "ci: add clients [skip actions]"
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add: '["openapirc.json","aind-dataverse-service-client","openapirc_async.json","aind-dataverse-service-async-client"]'
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update_tag:
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runs-on: ubuntu-latest
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needs: [bump_version, build_client]
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steps:
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- uses: actions/checkout@v4
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- name: Pull latest changes
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run: git pull origin main
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- name: Update tag
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run: |
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git tag v${{ needs.bump_version.outputs.new_version }}
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git push origin v${{ needs.bump_version.outputs.new_version }}
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publish_server:
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runs-on: ubuntu-latest
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needs: [bump_version, update_tag]
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defaults:
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run:
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working-directory: ./aind-dataverse-service-server
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steps:
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- uses: actions/checkout@v4
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- name: Pull latest changes
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run: git pull origin main
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v2
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- name: Login to Github Packages
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uses: docker/login-action@v2
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build image and push to GitHub Container Registry
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uses: docker/build-push-action@v3
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with:
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# relative path to the place where source code with Dockerfile is located
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context: ./aind-dataverse-service-server
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push: true
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tags: |
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ghcr.io/allenneuraldynamics/aind-dataverse-service-server:${{ needs.bump_version.outputs.new_version }}
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ghcr.io/allenneuraldynamics/aind-dataverse-service-server:latest
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publish_client:
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runs-on: ubuntu-latest
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needs: update_tag
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defaults:
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run:
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working-directory: ./aind-dataverse-service-client
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steps:
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- uses: actions/checkout@v4
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- name: Pull latest changes
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run: git pull origin main
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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pip install --upgrade setuptools wheel twine build
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python -m build
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twine check dist/*
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- name: Publish on PyPI
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uses: pypa/gh-action-pypi-publish@release/v1.12
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with:
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packages-dir: ./aind-dataverse-service-client/dist
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password: ${{ secrets.AIND_PYPI_TOKEN }}
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publish_async_client:
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runs-on: ubuntu-latest
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needs: update_tag
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defaults:
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run:
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working-directory: ./aind-dataverse-service-async-client
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steps:
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- uses: actions/checkout@v4
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- name: Pull latest changes
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run: git pull origin main
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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pip install --upgrade setuptools wheel twine build
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python -m build
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twine check dist/*
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- name: Publish on PyPI
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uses: pypa/gh-action-pypi-publish@release/v1.12
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with:
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packages-dir: ./aind-dataverse-service-async-client/dist
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password: ${{ secrets.AIND_PYPI_TOKEN }}

‎.github/workflows/test_server.yml‎

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name: Run tests for server code
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on:
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pull_request:
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branches:
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- main
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paths:
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- aind-dataverse-service-server/**
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jobs:
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tests:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ '3.10', '3.11', '3.12' ]
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defaults:
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run:
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working-directory: ./aind-dataverse-service-server
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install -e .[dev] --no-cache-dir
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- name: Run linter checks
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run: flake8 . && interrogate --verbose .
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- name: Run tests and coverage
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run: coverage run -m pytest && coverage report

‎.gitignore‎

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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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.idea/
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# Abstra
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# Abstra is an AI-powered process automation framework.

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