-
Notifications
You must be signed in to change notification settings - Fork 104
Conversation
halender
commented
Nov 27, 2025
Contributor
Task linked: TASK-8038 Recover opencga-storage-mongodb
@j-coll
j-coll
changed the title
(削除) TASK-8038 (削除ここまで)
(追記) TASK-8038 - Recover opencga-storage-mongodb (追記ここまで)
Dec 2, 2025
...otationIndexer #TASK-8038
@j-coll
j-coll
force-pushed
the
TASK-8038
branch
from
February 10, 2026 16:13
9cf7745 to
e26f671
Compare
run: |
STORAGE_FLAG=""
# Set flag only if variant_storage is NOT 'mongodb'
if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
STORAGE_FLAG=""
# Set flag only if variant_storage is NOT 'mongodb'
if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then
STORAGE_FLAG="-Dhadoop=${{ inputs.variant_storage }}"
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
# Execute Maven command
mvn -T 2 clean install \
$STORAGE_FLAG \
-P"${{ inputs.test_profile }}" \
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
MODULE=$(basename $MODULE )
TAGS=$(echo ${{ inputs.test_profile }} | sed -e 's/run\([^,]*\)Tests/1円/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" >> $GITHUB_OUTPUT
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
run: |
STORAGE_FLAG=""
# Set flag only if variant_storage is NOT 'mongodb'
if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
STORAGE_FLAG=""
# Set flag only if variant_storage is NOT 'mongodb'
if [ "${{ inputs.variant_storage }}" != "mongodb" ]; then
STORAGE_FLAG="-Dhadoop=${{ inputs.variant_storage }}"
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
-Dsurefire.testFailureIgnore=true \
-f ${{ (inputs.module == '' || inputs.module == 'all') && '.' || inputs.module }} \
$STORAGE_FLAG \
-P"${{ inputs.test_profile }}" \
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
$STORAGE_FLAG \
-P"${{ 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
Check failure
Code scanning / SonarCloud
GitHub Actions should not be vulnerable to script injections High test
Change this workflow to not use user-controlled data directly in a run block. See more on SonarQube Cloud
...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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.