Fix docker compose deprecation issue (#10939)

* Fix docker package in integration tests
* Update related documentation

.github/workflows/integration-test.yml

@@ -54,7 +54,7 @@ jobs:
       - name: 'Start cbioportal-docker-compose'
         working-directory: ./cbioportal-docker-compose
         run: |
-          docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml up -d
+          docker compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml up -d
       - name: 'Wait for cbioportal to initialize ...'
         id: startup
         uses: nev7n/wait_for_response@v1
@@ -66,7 +66,7 @@ jobs:
       - name: Log cBioPortal Service
         if: ${{ failure() && steps.startup.conclusion == 'failure' }}
         working-directory: ./cbioportal-docker-compose
-        run: docker-compose logs cbioportal
+        run: docker compose logs cbioportal
       - name: 'TEST - Validate and load study_es_0'
         if: steps.startup.conclusion == 'success'
         working-directory: ./cbioportal-docker-compose

docs/Study-Curation-Guide.md

@@ -11,8 +11,8 @@ After having followed the steps in the [Docker Deployment instructions](docker/R
 
 1. Choose another example study from the [datahub](https://github.com/cBioPortal/datahub/tree/master/public). Note the name of the folder which is identical to the study id defined in [meta_study.txt](https://github.com/cBioPortal/datahub/blob/master/public/lgg_ucsf_2014/meta_study.txt#L2).
 2. From the root of the `cbioportal-docker-compose` folder run `DATAHUB_STUDIES=my_study_id ./study/init.sh`. Change `my_study_id` to the study you picked in 1. The study should now be downloaded in `./study/`.
-3. Import the study by running `docker-compose exec cbioportal metaImport.py -u http://cbioportal:8080 -s study/my_study_id/ -o`. Again change `my_study_id` to the study you picked in 1. This should import the study.
-4. Restart the cbioportal instance `docker-compose restart cbioportal` and see if the new study shows up on http://localhost:8080
+3. Import the study by running `docker compose exec cbioportal metaImport.py -u http://cbioportal:8080 -s study/my_study_id/ -o`. Again change `my_study_id` to the study you picked in 1. This should import the study.
+4. Restart the cbioportal instance `docker compose restart cbioportal` and see if the new study shows up on http://localhost:8080
 
 ## Curate a new study
 The cBioPortal team has curated many published studies in formats suitable for import in cBioPortal. These can

docs/deployment/docker/example_commands.md

@@ -5,7 +5,7 @@ Use this command to import a gene panel. Specify the gene panel file by replacin
 gene panel files in `./study` which is mounted inside the container on `/study/.
 
 ```shell
-docker-compose run \
+docker compose run \
     -v <path_to_genepanel_file>:/gene_panels/gene_panel.txt:ro \
     cbioportal \
     bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /gene_panels/gene_panel.txt'
@@ -19,13 +19,13 @@ the study in its associated database. Make sure to replace `<path_to_report_fold
 the absolute path were the html report of the validation will be saved.
 
 ```shell
-docker-compose run \
+docker compose run \
     -v "<path_to_report_folder>:/report" \
     cbioportal \
     metaImport.py -u http://cbioportal:8080 -s /study/name_of_study --html=/report/report.html
 ```
 :warning: after importing a study, remember to restart `cbioportal-container`
-to see the study on the home page. Run `docker-compose restart cbioportal`.
+to see the study on the home page. Run `docker compose restart cbioportal`.
 
 To load data incrementally, specify `-d` instead of `-s` option.
 For more details on incremental data loading, see [this page](./Incremental-Data-Loading.md).
@@ -35,7 +35,7 @@ For more details on incremental data loading, see [this page](./Incremental-Data
 In some setups the data validation step may not have direct access to the web API, for instance when the web API is only accessible to authenticated browser sessions. You can use this command to generate a cached folder of files that the validation script can use instead. Make sure to replace `<path_to_portalinfo>` with the absolute path where the cached folder is going to be generated.
 
 ```shell
-docker-compose run \
+docker compose run \
     -v "<path_to_portalinfo>/portalinfo:/portalinfo" \
     -w /cbioportal/core/src/main/scripts \
     cbioportal \
@@ -45,7 +45,7 @@ docker-compose run \
 Then, grant the validation/loading command access to this folder and tell the script it to use it instead of the API:
 
 ```shell
-docker-compose run \
+docker compose run \
     -v "<path_to_report_folder>:/report" \
     -v "<path_to_portalinfo>/portalinfo:/portalinfo:ro" \
     cbioportal \
@@ -55,7 +55,7 @@ docker-compose run \
 ### Inspecting or adjusting the database ###
 
 ```shell
-docker-compose run cbioportal_database \
+docker compose run cbioportal_database \
     sh -c 'mysql -hcbioportal_database -u"$MYSQL_USER" -p"$MYSQL_PASSWORD" "$MYSQL_DATABASE"'
 ```
 
@@ -64,7 +64,7 @@ docker-compose run cbioportal_database \
 To remove a study, run:
 
 ```shell
-docker-compose run \
+docker compose run \
     cbioportal \
     cbioportalImporter.py -c remove-study -id study_id
 ```

docs/deployment/docker/import_data.md

@@ -14,13 +14,13 @@ To import gene panels for your study, please reference the example commands in [
 These are the commands for importing `study_es_0` gene panels (`data_gene_panel_testpanel1` and `data_gene_panel_testpanel2`):
 
 ```shell
-docker-compose run \
+docker compose run \
     cbioportal \
     bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt'
 ```
 
 ```shell
-docker-compose run \
+docker compose run \
     cbioportal \
     bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt'
 ```
@@ -32,10 +32,10 @@ To import data for your study, please reference the example commands in [this fi
 Command for importing `study_es_0` data:
 
 ```shell
-docker-compose run cbioportal metaImport.py -u http://cbioportal:8080 -s /cbioportal/core/src/test/scripts/test_data/study_es_0 -o
+docker compose run cbioportal metaImport.py -u http://cbioportal:8080 -s /cbioportal/core/src/test/scripts/test_data/study_es_0 -o
 ```
 
-:warning: after importing a study, remember to restart `cbioportal` to see the study on the home page. Run `docker-compose restart cbioportal`.
+:warning: after importing a study, remember to restart `cbioportal` to see the study on the home page. Run `docker compose restart cbioportal`.
 
 You have now imported the test study `study_es_0`. Note that this study is included inside the cbioportal container. The process for adding a study that is outside of the container is similar. Just make sure to add the data files in the `./study` folder. This folder is mounted as `/study/` inside of the container.
 
@@ -57,7 +57,7 @@ Please make sure the seed database was correctly imported.
 Remember to restart the `cbioportal` after data imported.
 
 ```shell
-docker-compose restart cbioportal
+docker compose restart cbioportal
 ```
 
 #### Import GRCh38 data

test/integration/test_integration_test_oncokb_import.sh

@@ -6,9 +6,9 @@ set -e
 run_in_service() {
     service=$1
     shift
-    docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml \
+    docker compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml \
         run --rm \
         "$service" bash -c "$@"
 }
 
-run_in_service cbioportal "cd /cbioportal && ./integration_test_oncokb_import.sh"
+run_in_service cbioportal "cd /cbioportal && ./integration_test_oncokb_import.sh"

test/integration/test_load_study.sh

@@ -6,7 +6,7 @@ set -e
 run_in_service() {
     service=$1
     shift
-    docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml \
+    docker compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml \
         run --rm \
         "$service" bash -c "$@"
 }

test/integration/test_update_oncokb.sh

@@ -5,7 +5,7 @@ set -e
 run_in_service() {
     service=$1
     shift
-    docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml \
+    docker compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml \
         run --rm \
         "$service" bash -c "$@"
 }
@@ -19,4 +19,4 @@ run_in_service cbioportal 'python3 /core/scripts/importer/updateOncokbAnnotation
 
 # Check that mutation annotations have been updated
 # 2 annotations should be changed to "Putative_Driver" (depends on OncoKB version)
-test `run_in_service cbioportal 'mysql -hcbioportal-database -ucbio_user -psomepassword cbioportal -e "SELECT alteration_driver_annotation.DRIVER_FILTER from cbioportal.alteration_driver_annotation inner join genetic_profile on genetic_profile.GENETIC_PROFILE_ID = alteration_driver_annotation.GENETIC_PROFILE_ID inner join cancer_study on cancer_study.CANCER_STUDY_ID = genetic_profile.CANCER_STUDY_ID WHERE cancer_study.CANCER_STUDY_IDENTIFIER = \"study_es_0\";"' | cat | grep -c 'Putative_Driver'` -eq 2
+test `run_in_service cbioportal 'mysql -hcbioportal-database -ucbio_user -psomepassword cbioportal -e "SELECT alteration_driver_annotation.DRIVER_FILTER from cbioportal.alteration_driver_annotation inner join genetic_profile on genetic_profile.GENETIC_PROFILE_ID = alteration_driver_annotation.GENETIC_PROFILE_ID inner join cancer_study on cancer_study.CANCER_STUDY_ID = genetic_profile.CANCER_STUDY_ID WHERE cancer_study.CANCER_STUDY_IDENTIFIER = \"study_es_0\";"' | cat | grep -c 'Putative_Driver'` -eq 2