-
Notifications
You must be signed in to change notification settings - Fork 120
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #2075 from cBioPortal/fix_ci
Fix validation tests in CI
- Loading branch information
Showing
5 changed files
with
103 additions
and
78 deletions.
There are no files selected for viewing
This file contains 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
This file contains 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
This file contains 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,9 @@ | ||
| requests==2.27.1 | ||
| Jinja2==3.1.4 | ||
| mysqlclient==1.3.13 | ||
| Jinja2==3.0.3 | ||
| mysqlclient==2.1.0 | ||
| docker==3.5.0 | ||
| urllib3==1.26.19 | ||
| gitpython==3.1.41 | ||
| PyYAML==5.4 | ||
| gitpython==3.1.18 | ||
| PyYAML==6.0.1 | ||
| markupsafe==2.0.1 | ||
| dsnparse==0.1.15 |
This file contains 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,31 @@ | ||
| #!/usr/bin/env bash | ||
| # This script runs validation on all public studies. | ||
|
|
||
| STUDIES_DIR="public/" | ||
| STUDIES_DIRS=("public/" "crdc/gdc/") | ||
| GIT_REMOTE_URL="[email protected]:cbioportal/datahub.git" | ||
| test_reports_location="$HOME/test-reports" | ||
|
|
||
| git remote add upstream [email protected]:cbioportal/datahub.git | ||
| git remote add upstream "$GIT_REMOTE_URL" | ||
| git fetch upstream master | ||
|
|
||
| git lfs pull -I "public" | ||
|
|
||
| num_studies=${#list_of_study_dirs[@]} | ||
|
|
||
| test_reports_location="$HOME/test-reports" | ||
| validation_command="$HOME/cbioportal-core/scripts/importer/./validateStudies.py -d $HOME/repo/public/ -p $HOME/repo/.circleci/portalinfo -html $test_reports_location" | ||
| echo $'\nExecuting: '; echo $validation_command | ||
| if sh -c "$validation_command" ; then | ||
| echo "Tests passed successfully" | ||
| exit 0 | ||
| else | ||
| echo "Errors found" | ||
| # move errors to ERRORS/ folder: | ||
| erred_studies=`grep -rnlz $test_reports_location -e 'Validation status.*Failed' ` | ||
| mv $erred_studies $test_reports_location/ERRORS | ||
| exit 1 | ||
| fi | ||
| for STUDIES_DIR in "${STUDIES_DIRS[@]}"; do | ||
| git lfs pull -I "STUDIES_DIR" | ||
| validation_command="$HOME/cbioportal-core/scripts/importer/./validateStudies.py -d $HOME/repo/$STUDIES_DIR -p $HOME/repo/.circleci/portalinfo -html $test_reports_location" | ||
| echo $'\nExecuting: '; echo $validation_command | ||
| if sh -c "$validation_command" ; then | ||
| echo "Tests passed successfully for $STUDIES_DIR" | ||
| EXIT_STATUS=0 | ||
| else | ||
| echo "Errors found" | ||
| # move errors to ERRORS/ folder: | ||
| erred_studies=$(grep -rnlz "$test_reports_location" -e 'Failed') | ||
| if [ -n "$erred_studies" ]; then | ||
| mv $erred_studies $test_reports_location/ERRORS | ||
| EXIT_STATUS=1 | ||
| fi | ||
| fi | ||
| done | ||
|
|
||
| exit "$EXIT_STATUS" |
This file contains 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,68 +1,76 @@ | ||
| #!/usr/bin/env bash | ||
| # This script detects the studies that were changed and triggers the validation accordingly | ||
|
|
||
| STUDIES_DIR="public/" | ||
| STUDIES_DIRS=("public/" "crdc/gdc/") | ||
| REPO_DIR="$HOME/repo/" | ||
| TEST_REPORTS_LOCATION="$HOME/test-reports" | ||
| ERRORS_DIR="$TEST_REPORTS_LOCATION/ERRORS" | ||
| LOG_DIR="$TEST_REPORTS_LOCATION/logs" | ||
| VALIDATION_SCRIPT="$HOME/cbioportal-core/scripts/importer/validateStudies.py" | ||
| GIT_REMOTE_URL="[email protected]:cbioportal/datahub.git" | ||
| MAX_THREADS=7 | ||
|
|
||
| git remote add upstream [email protected]:cbioportal/datahub.git | ||
| git remote add upstream "$GIT_REMOTE_URL" | ||
| git fetch upstream master | ||
|
|
||
| files_changing=`git diff --name-only --diff-filter=ACMRU upstream/master` | ||
| mkdir -p "$LOG_DIR" | ||
|
|
||
| files_changing=$(git diff --name-only --diff-filter=ACMRU upstream/master) | ||
| list_of_study_dirs=() | ||
|
|
||
| for file_changing in $files_changing | ||
| do | ||
| #echo "file > [$file_changing]" | ||
| for file_changing in $files_changing; do | ||
| # if file is part of studies_dir, store its directory path (except case_lists) | ||
| if [[ $file_changing = *$STUDIES_DIR* ]] && [[ $file_changing != *".htm"* ]]; then | ||
| echo "study file changing > [$file_changing]" | ||
| dir_name=`dirname $file_changing` | ||
| # match case_list*, caselist* as a case list dir (actually only case_lists is valid, | ||
| # but this is up to validation script to flag): | ||
| if [[ $dir_name != *"/case_list"* ]] && [[ $dir_name != *"/caselist"* ]] && [[ $dir_name != *"/archived_files"* ]] && [[ $dir_name != *"/gene_sets"* ]] && [[ $dir_name != *"/normals"* ]]; then | ||
| echo "study dir > [$dir_name]" | ||
| else | ||
| # get parent dir: | ||
| dir_name=`dirname $dir_name` | ||
| echo "study dir > [$dir_name]" | ||
| fi | ||
| found_in_list=`echo ${list_of_study_dirs[@]} | grep $dir_name` | ||
| if [[ $found_in_list = "" ]]; then | ||
| echo "adding to list..." | ||
| list_of_study_dirs+=($dir_name) | ||
| echo "downloading files from git lfs..." | ||
| git lfs pull -I "$dir_name/*" | ||
| git lfs pull -I "$dir_name/case_lists/*" | ||
| for STUDIES_DIR in "${STUDIES_DIRS[@]}"; do | ||
| if [[ $file_changing = *$STUDIES_DIR* ]] && [[ $file_changing != *".htm"* ]]; then | ||
| echo "study file changing > [$file_changing]" | ||
| dir_name=$(dirname $file_changing) | ||
| # match case_list*, caselist* as a case list dir (actually only case_lists is valid, | ||
| # but this is up to validation script to flag): | ||
| if [[ $dir_name != *"/case_list"* ]] && [[ $dir_name != *"/caselist"* ]] && [[ $dir_name != *"/archived_files"* ]] && [[ $dir_name != *"/gene_sets"* ]] && [[ $dir_name != *"/normals"* ]] && [[ $dir_name != *"/validation_reports"* ]]; then | ||
| echo "study dir > [$dir_name]" | ||
| else | ||
| # get parent dir: | ||
| dir_name=`dirname $dir_name` | ||
| echo "study dir > [$dir_name]" | ||
| fi | ||
| if [[ ! " ${list_of_study_dirs[@]} " =~ " $dir_name " ]]; then | ||
| echo "adding to list..." | ||
| list_of_study_dirs+=("$dir_name") | ||
| echo "downloading files from git lfs..." | ||
| git lfs pull -I "$dir_name/*" | ||
| git lfs pull -I "$dir_name/case_lists/*" | ||
| fi | ||
| fi | ||
| fi | ||
| done | ||
| done | ||
| num_studies=${#list_of_study_dirs[@]} | ||
| if [[ $num_studies > 0 ]]; then | ||
| echo $'\n====List of studies:====\n' | ||
| list_csv=`echo ${list_of_study_dirs[@]} | tr ' ' ','` | ||
| echo $list_csv | ||
| list_csv=$(printf "%s," "${list_of_study_dirs[@]}" | sed 's/,$//') | ||
| echo "$list_csv" | ||
|
|
||
| test_reports_location="$HOME/test-reports" | ||
| mkdir -p "$ERRORS_DIR" | ||
| validation_command="" | ||
| num=0 | ||
| max_threads=7 | ||
| break_num=$(($num_studies / $max_threads + 1)) | ||
| break_num=$((num_studies / MAX_THREADS + 1)) | ||
| for study in ${list_csv//,/ } | ||
| do | ||
| # append sleep command between commands | ||
| ((num=num+1)) | ||
| mod=$(($num % $break_num)) | ||
| log_file="$LOG_DIR/$(basename $study).log" | ||
| # if [ $mod = 0 ] ; then | ||
| # validation_command="${validation_command} && sleep $((num*2))" | ||
| # fi | ||
| # append the first study | ||
| if [ "$validation_command" = "" ] ; then | ||
| validation_command="($HOME/cbioportal-core/src/main/resources/scripts/importer/./validateStudies.py -d $HOME/repo/ -l $study -p $HOME/repo/.circleci/portalinfo -html $test_reports_location/$study" | ||
| if [[ -z "$validation_command" ]] ; then | ||
| validation_command="($VALIDATION_SCRIPT -d $REPO_DIR -l $study -p $REPO_DIR/.circleci/portalinfo -html $TEST_REPORTS_LOCATION/$study > $log_file 2>&1" | ||
| else | ||
| # run each validation individually in the background | ||
| if [ $mod = 0 ] ; then | ||
| validation_command="${validation_command}) & ($HOME/cbioportal-core/src/main/resources/scripts/importer/./validateStudies.py -d $HOME/repo/ -l $study -p $HOME/repo/.circleci/portalinfo -html $test_reports_location/$study" | ||
| validation_command="${validation_command}) & ($VALIDATION_SCRIPT -d $REPO_DIR -l $study -p $REPO_DIR/.circleci/portalinfo -html $TEST_REPORTS_LOCATION/$study > $log_file 2>&1" | ||
| else | ||
| validation_command="${validation_command} ; $HOME/cbioportal-core/src/main/resources/scripts/importer/./validateStudies.py -d $HOME/repo/ -l $study -p $HOME/repo/.circleci/portalinfo -html $test_reports_location/$study" | ||
| validation_command="${validation_command} ; $VALIDATION_SCRIPT -d $REPO_DIR -l $study -p $REPO_DIR/.circleci/portalinfo -html $TEST_REPORTS_LOCATION/$study > $log_file 2>&1" | ||
| fi | ||
| fi | ||
| done | ||
|
|
@@ -73,25 +81,36 @@ if [[ $num_studies > 0 ]]; then | |
| while true; do | ||
| wait -n || { | ||
| code="$?" | ||
| echo "waiting for all processes to finish ...................." | ||
| echo -e "waiting for all processes to finish...\n\n" | ||
| # exit only when all processes finished | ||
| if ([[ $code = "127" ]] && exit 0) ; then | ||
| if (( code = 127 )); then | ||
| break | ||
| fi | ||
| } | ||
| done; | ||
|
|
||
| done | ||
|
|
||
| for log in "$LOG_DIR"/*.log; do | ||
| if [[ -f "$log" ]]; then | ||
| cat "$log" | ||
| echo -e "\n----------------------------------------------------\n" | ||
| fi | ||
| done | ||
|
|
||
| # Remove the log directory | ||
| if [[ -d "$LOG_DIR" ]]; then | ||
| rm -rf "$LOG_DIR" | ||
| fi | ||
|
|
||
| # find all studies with error | ||
| erred_studies=`grep -rnlz $test_reports_location -e 'Validation status.*Failed' ` | ||
| if [[ $? -eq 0 ]]; then | ||
| erred_studies=$(grep -rl "$TEST_REPORTS_LOCATION" -e 'Failed') | ||
| if [[ $? -eq 0 ]] && [[ -n "$erred_studies" ]]; then | ||
| echo $'\n====List of error studies:====\n' | ||
| echo $erred_studies | ||
| mv $erred_studies $test_reports_location/ERRORS | ||
| echo "$erred_studies" | ||
| echo "$erred_studies" | xargs -I {} mv {} "$ERRORS_DIR" | ||
| exit 1 | ||
| else | ||
| echo "All tests passed successfully" | ||
| exit 0 | ||
| echo "No error studies found." | ||
| fi | ||
| else | ||
| echo "No studies were changed" | ||
| fi | ||
| fi | ||