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Merge pull request #18212 from nsoranzo/release_24.0_backport_18197
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[24.0] Backport #18197
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martenson authored May 23, 2024
2 parents 2ddea78 + 9b70b75 commit 1e59ea4
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Showing 35 changed files with 286 additions and 229 deletions.
2 changes: 2 additions & 0 deletions .github/codeql/codeql-config.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
paths-ignore:
- 'lib/galaxy/datatypes/test/*.bcsl.ts'
146 changes: 101 additions & 45 deletions .github/labeler.yml
Original file line number Diff line number Diff line change
@@ -1,73 +1,129 @@
---
area/admin:
- client/src/components/admin/**/*
- doc/source/admin/**/*
- changed-files:
- any-glob-to-any-file:
- client/src/components/admin/**/*
- doc/source/admin/**/*
area/API:
- lib/galaxy/webapps/galaxy/api/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/webapps/galaxy/api/**/*
area/auth:
- lib/galaxy/auth/**/*
- lib/galaxy/authnz/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/auth/**/*
- lib/galaxy/authnz/**/*
area/client:
- client/*
- changed-files:
- any-glob-to-any-file:
- client/*
area/database:
- lib/galaxy/model/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/model/**/*
area/datatypes:
- lib/galaxy/datatypes/**/*
- lib/galaxy/config/sample/datatypes_conf.xml.sample
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/datatypes/**/*
- lib/galaxy/config/sample/datatypes_conf.xml.sample
area/dependencies:
- lib/galaxy/dependencies/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/dependencies/**/*
area/documentation:
- doc/**/*
- changed-files:
- any-glob-to-any-file:
- doc/**/*
area/jobs:
- lib/galaxy/jobs/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/jobs/**/*
area/libraries:
- client/src/components/LibraryFolder/**/*
- lib/galaxy/webapps/galaxy/api/libraries.py
- changed-files:
- any-glob-to-any-file:
- client/src/components/LibraryFolder/**/*
- lib/galaxy/webapps/galaxy/api/libraries.py
area/objectstore:
- lib/galaxy/objectstore/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/objectstore/**/*
area/packaging:
- packages/**/*
- changed-files:
- any-glob-to-any-file:
- packages/**/*
area/reports:
- client/src/reports/**/*
- lib/galaxy/webapps/reports/**/*
- templates/webapps/reports/**/*
- changed-files:
- any-glob-to-any-file:
- client/src/reports/**/*
- lib/galaxy/webapps/reports/**/*
- templates/webapps/reports/**/*
area/scripts:
- scripts/**/*
- changed-files:
- any-glob-to-any-file:
- scripts/**/*
area/security:
- lib/galaxy/security/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/security/**/*
area/testing:
- lib/galaxy_test/**/*
- run_tests.sh
- test/**/*
- test-data/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy_test/**/*
- run_tests.sh
- test/**/*
- test-data/**/*
area/testing/api:
- lib/galaxy_test/api/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy_test/api/**/*
area/testing/integration:
- test/integration/**/*
- test/integration_selenium/**/*
- changed-files:
- any-glob-to-any-file:
- test/integration/**/*
- test/integration_selenium/**/*
area/testing/selenium:
- lib/galaxy/selenium/**/*
- lib/galaxy_test/selenium/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/selenium/**/*
- lib/galaxy_test/selenium/**/*
area/tool-dependencies:
- lib/galaxy/tool_util/deps/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/tool_util/deps/**/*
area/tool-framework:
- lib/galaxy/tools/**/*
- lib/galaxy/tool_util/**/*
- lib/galaxy/webapps/galaxy/api/tools.py
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/tools/**/*
- lib/galaxy/tool_util/**/*
- lib/galaxy/webapps/galaxy/api/tools.py
area/tools:
- tools/**/*
- tool-data/**/*
- changed-files:
- any-glob-to-any-file:
- tools/**/*
- tool-data/**/*
area/toolshed:
- client/src/toolshed/**/*
- lib/galaxy/webapps/galaxy/api/toolshed.py
- lib/toolshed/**/*
- templates/webapps/tool_shed/**/*
- changed-files:
- any-glob-to-any-file:
- client/src/toolshed/**/*
- lib/galaxy/webapps/galaxy/api/toolshed.py
- lib/toolshed/**/*
- templates/webapps/tool_shed/**/*
area/UI-UX:
- all: ["client/src/**/*", "!client/src/api/schema/schema.ts"]
any: ["templates/**/*"]
- changed-files:
- any-glob-to-any-file:
- client/src/**/*
- templates/**/*
- all-globs-to-all-files:
- '!client/src/api/schema/schema.ts'
area/util:
- lib/galaxy/util/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/util/**/*
area/visualizations:
- config/plugins/visualizations/**/*
- changed-files:
- any-glob-to-any-file:
- config/plugins/visualizations/**/*
area/workflows:
- lib/galaxy/workflow/**/*
- changed-files:
- any-glob-to-any-file:
- lib/galaxy/workflow/**/*
12 changes: 6 additions & 6 deletions .github/workflows/api.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -44,28 +44,28 @@ jobs:
run: |
echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
path: 'galaxy root'
- uses: actions/setup-node@v3
- uses: actions/setup-node@v4
with:
node-version: '18.12.1'
cache: 'yarn'
cache-dependency-path: 'galaxy root/client/yarn.lock'
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Get full Python version
id: full-python-version
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache pip dir
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
- name: Cache galaxy venv
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
Expand All @@ -76,7 +76,7 @@ jobs:
with:
flags: api
working-directory: 'galaxy root'
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
if: failure()
with:
name: API test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
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6 changes: 3 additions & 3 deletions .github/workflows/build_client.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@ jobs:
outputs:
commit-id: ${{ steps.client-commit.outputs.commit }}
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
path: 'galaxy root'
- uses: actions/setup-node@v3
- uses: actions/setup-node@v4
with:
node-version: '18.12.1'
cache: 'yarn'
Expand All @@ -25,7 +25,7 @@ jobs:
run: echo "commit=$(git rev-parse HEAD 2>/dev/null)" >> $GITHUB_OUTPUT
working-directory: 'galaxy root'
- name: cache client build
uses: actions/cache@v3
uses: actions/cache@v4
id: cache
with:
key: galaxy-static-${{ steps.client-commit.outputs.commit }}
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2 changes: 1 addition & 1 deletion .github/workflows/build_container_image.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ jobs:
runs-on: ubuntu-latest
if: github.repository_owner == 'galaxyproject'
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
# https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
- name: Set outputs
id: commit
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6 changes: 3 additions & 3 deletions .github/workflows/check_test_class_names.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,12 @@ jobs:
matrix:
python-version: ['3.8']
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache pip dir
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
Expand Down
59 changes: 31 additions & 28 deletions .github/workflows/codeql-analysis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -32,41 +32,44 @@ jobs:
strategy:
fail-fast: false
matrix:
language: ['javascript', 'python']
# CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
language: ['javascript-typescript', 'python']
# CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
# Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support

steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Checkout repository
uses: actions/checkout@v4

# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v2
with:
languages: ${{ matrix.language }}
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v3
with:
languages: ${{ matrix.language }}
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.

# Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
# queries: security-extended,security-and-quality
# Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
# queries: security-extended,security-and-quality

# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
# If this step fails, then you should remove it and run the build manually (see below)
- name: Autobuild
uses: github/codeql-action/autobuild@v2
config-file: ./.github/codeql/codeql-config.yml

# ℹ️ Command-line programs to run using the OS shell.
# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun

# If the Autobuild fails above, remove it and uncomment the following three lines
# modify them (or add more) to build your code if your project
# uses a compiled language
# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
# If this step fails, then you should remove it and run the build manually (see below)
- name: Autobuild
uses: github/codeql-action/autobuild@v3

#- run: |
# make bootstrap
# make release
# ℹ️ Command-line programs to run using the OS shell.
# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun

- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v2
# If the Autobuild fails above, remove it and uncomment the following three lines
# modify them (or add more) to build your code if your project
# uses a compiled language

#- run: |
# make bootstrap
# make release

- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v3
12 changes: 6 additions & 6 deletions .github/workflows/converter_tests.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -28,24 +28,24 @@ jobs:
run: |
echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
path: 'galaxy root'
- uses: actions/setup-node@v3
- uses: actions/setup-node@v4
with:
node-version: '18.12.1'
cache: 'yarn'
cache-dependency-path: 'galaxy root/client/yarn.lock'
- name: Clone galaxyproject/galaxy-test-data
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
repository: galaxyproject/galaxy-test-data
path: galaxy-test-data
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache venv dir
uses: actions/cache@v3
uses: actions/cache@v4
id: pip-cache
with:
path: ~/.cache/pip
Expand All @@ -69,7 +69,7 @@ jobs:
run: |
mapfile -t TOOL_ARRAY < tool_list.txt
planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
if: failure()
with:
name: Converter test results (${{ matrix.python-version }})
Expand Down
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