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Task linked: TASK-8038 Recover opencga-storage-mongodb |
…otationIndexer #TASK-8038
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
| run: | | ||
| STORAGE_FLAG="" | ||
| # Set flag only if variant_storage is NOT 'mongodb' | ||
| if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then |
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| STORAGE_FLAG="" | ||
| # Set flag only if variant_storage is NOT 'mongodb' | ||
| if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then | ||
| STORAGE_FLAG="-Dhadoop=${{ inputs.variant_storage }}" |
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| # Execute Maven command | ||
| mvn -T 2 clean install \ | ||
| $STORAGE_FLAG \ | ||
| -P"${{ inputs.test_profile }}" \ |
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| MODULE=$(basename $MODULE ) | ||
| TAGS=$(echo ${{ inputs.test_profile }} | sed -e 's/run\([^,]*\)Tests/\1/g' | tr ',' '_' | tr '[:upper:]' '[:lower:]' ) | ||
| echo "TESTS_LOG_FILE_NAME=junit_${{ inputs.hadoop }}_${TAGS}_${MODULE}.log.gz" >> $GITHUB_OUTPUT | ||
| echo "TESTS_LOG_FILE_NAME=junit_${{ inputs.variant_storage }}_${TAGS}_${MODULE}.log.gz" >> $GITHUB_OUTPUT |
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| run: | | ||
| STORAGE_FLAG="" | ||
| # Set flag only if variant_storage is NOT 'mongodb' | ||
| if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then |
Check failure
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GitHub Actions should not be vulnerable to script injections High test
| STORAGE_FLAG="" | ||
| # Set flag only if variant_storage is NOT 'mongodb' | ||
| if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then | ||
| STORAGE_FLAG="-Dhadoop=${{ inputs.variant_storage }}" |
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| -Dsurefire.testFailureIgnore=true \ | ||
| -f ${{ (inputs.module == '' || inputs.module == 'all') && '.' || inputs.module }} \ | ||
| $STORAGE_FLAG \ | ||
| -P"${{ inputs.test_profile }}" \ |
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GitHub Actions should not be vulnerable to script injections High test
| $STORAGE_FLAG \ | ||
| -P"${{ inputs.test_profile }}" \ | ||
| -Dcheckstyle.skip \ | ||
| ${{ inputs.mvn_opts }} |& tee >(gzip > ${{ steps.BuildJunitLogFileName.outputs.TESTS_LOG_FILE_NAME }} ) |& grep -a -P '^\[[^\]]*(INFO|WARNING|ERROR)' --colour=never --line-buffered |
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GitHub Actions should not be vulnerable to script injections High test
…amples. #TASK-8038
…cation. #TASK-8038
…e sample queries in MongoDB. #TASK-8038
…StreamVariantMapper pattern. #TASK-8038
…in their name. #TASK-8038
…ve MongoDB filtering. #TASK-8038
…nager instead of StudyConfiguration. #TASK-8038
…" matching Hadoop. #TASK-8038
…, and validate sparse query. #TASK-8038
…ilterTask. #TASK-8038
…erFactory. #TASK-8038
…CF contigs. #TASK-8038
…mpleGenotypeIndexerTask. #TASK-8038
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