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mvdbeekmvdbeek
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Merge pull request #20884 from nsoranzo/main_tool_CI_tests
Add main tool CI tests
2 parents dbcf3e3 + 26e6a17 commit 0b743f8

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‎.github/workflows/framework_tools.yaml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ jobs:
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uses: actions/cache@v4
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with:
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path: 'galaxy root/.venv'
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key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-tools
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key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
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- name: Run tests
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run: ./run_tests.sh --coverage --framework-tools
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working-directory: 'galaxy root'
@@ -78,5 +78,5 @@ jobs:
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: Framework test results (${{ matrix.python-version }})
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name: Tool framework test results (${{ matrix.python-version }})
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path: 'galaxy root/run_framework_tests.html'

‎.github/workflows/framework_workflows.yaml‎

Lines changed: 5 additions & 3 deletions
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@@ -5,11 +5,13 @@ on:
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- 'client/**'
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- 'doc/**'
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- 'lib/galaxy_test/selenium/**'
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- 'packages/**'
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pull_request:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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- 'lib/galaxy_test/selenium/**'
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- 'packages/**'
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schedule:
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# Run at midnight UTC every Tuesday
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- cron: '0 0 * * 2'
@@ -66,16 +68,16 @@ jobs:
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uses: actions/cache@v4
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with:
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path: 'galaxy root/.venv'
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key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-workflows
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key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
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- name: Run tests
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run: ./run_tests.sh --coverage --framework-workflows
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working-directory: 'galaxy root'
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- uses: codecov/codecov-action@v3
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with:
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flags: framework
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flags: framework-workflows
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working-directory: 'galaxy root'
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- uses: actions/upload-artifact@v4
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if: failure()
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with:
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name: Framework test results (${{ matrix.python-version }})
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name: Workflow framework test results (${{ matrix.python-version }})
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path: 'galaxy root/run_framework_workflows_tests.html'

‎.github/workflows/main_tools.yaml‎

Lines changed: 75 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,75 @@
1+
name: Main tool tests
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on:
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push:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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- 'lib/galaxy_test/selenium/**'
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- 'packages/**'
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pull_request:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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- 'lib/galaxy_test/selenium/**'
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- 'packages/**'
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env:
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GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
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GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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test:
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name: Test
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.9']
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services:
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postgres:
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image: postgres:17
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env:
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POSTGRES_USER: postgres
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POSTGRES_PASSWORD: postgres
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POSTGRES_DB: postgres
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ports:
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- 5432:5432
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steps:
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- uses: actions/checkout@v4
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with:
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path: 'galaxy root'
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persist-credentials: false
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- name: Read Node.js version
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id: node-version
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run: echo "version=$(cat 'galaxy root/client/.node_version')" >> $GITHUB_OUTPUT
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- uses: actions/setup-node@v4
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with:
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node-version: ${{ steps.node-version.outputs.version }}
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cache: 'yarn'
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cache-dependency-path: 'galaxy root/client/yarn.lock'
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
53+
cache: 'pip'
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cache-dependency-path: 'galaxy root/requirements.txt'
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- name: Get full Python version
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id: full-python-version
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shell: bash
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run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
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- name: Cache galaxy venv
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uses: actions/cache@v4
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with:
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path: 'galaxy root/.venv'
63+
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
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- name: Run tests
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run: ./run_tests.sh --coverage --main_tools
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working-directory: 'galaxy root'
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- uses: codecov/codecov-action@v3
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with:
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flags: main-tools
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working-directory: 'galaxy root'
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- uses: actions/upload-artifact@v4
72+
if: failure()
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with:
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name: Main tool test results (${{ matrix.python-version }})
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path: 'galaxy root/run_framework_tests.html'

‎tools/filters/gff/gff_filter_by_attribute.py‎

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@@ -45,13 +45,16 @@
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"UnaryOp",
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"Invert",
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"Not",
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"UAdd",
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"USub",
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"NotIn",
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"In",
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"Is",
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"IsNot",
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"List",
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"Index",
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"Subscript",
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"Constant",
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"Name",
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]
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‎tools/filters/gff/gff_filter_by_feature_count.py‎

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@@ -48,13 +48,16 @@
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"UnaryOp",
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"Invert",
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"Not",
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"UAdd",
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"USub",
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"NotIn",
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"In",
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"Is",
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"IsNot",
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"List",
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"Index",
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"Subscript",
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"Constant",
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"Name",
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]
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‎tools/filters/gff/gtf_filter_by_attribute_values_list.py‎

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Original file line numberDiff line numberDiff line change
@@ -55,10 +55,11 @@ def gff_filter(gff_file, attribute_name, ids_file, output_file):
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# Filter GFF file using ids.
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with open(output_file, "w") as output, open(gff_file) as ingff:
5757
for line in ingff:
58-
if not line or line.startswith("#"):
58+
if not line.rstrip() or line.startswith("#"):
5959
output.write(line)
6060
continue
6161
fields = line.split("\t")
62+
assert len(fields) == 9, f"Line should have exactly 9 fields: {line}"
6263
attributes = parse_gff_attributes(fields[8])
6364
if attribute_name in attributes and attributes[attribute_name] in ids_dict:
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output.write(line)

‎tools/filters/grep.xml‎

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Original file line numberDiff line numberDiff line change
@@ -76,7 +76,8 @@
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<param name="keep_header" value="true"/>
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<output name="out_file1">
7878
<assert_contents>
79-
<not_has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
79+
<has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
80+
<has_n_lines n="1"></has_n_lines>
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</assert_contents>
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</output>
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</test>

‎tools/phenotype_association/ldtools_wrapper.sh‎

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Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55

66
set -e
77

8-
SCRIPT_DIR=$(dirname $0)
8+
SCRIPT_DIR=$(dirname "$0")
99

1010
## pagetag options
1111
input=
@@ -46,16 +46,7 @@ do
4646
done
4747

4848
## run pagetag
49-
python $SCRIPT_DIR/pagetag.py --rsquare $rsquare --freq $freq "$input" snps.txt neighborhood.txt
50-
if [ $? -ne 0 ]; then
51-
echo "failed: pagetag.py --rsquare $rsquare --freq $freq \"$input\" snps.txt neighborhood.txt"
52-
exit 1
53-
fi
54-
55-
## run sentag
56-
python $SCRIPT_DIR/senatag.py neighborhood.txt snps.txt > "$output"
57-
if [ $? -ne 0 ]; then
58-
echo "failed: senatag.py neighborhood.txt snps.txt"
59-
exit 1
60-
fi
49+
python "$SCRIPT_DIR/pagetag.py" --rsquare $rsquare --freq $freq "$input" snps.txt neighborhood.txt
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51+
## run senatag
52+
python "$SCRIPT_DIR/senatag.py" neighborhood.txt snps.txt > "$output"

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