Official Documentation Needs to Be Updated

[7xuanlu]

I followed https://docs.cbioportal.org/deployment/deploy-without-docker/load-sample-cancer-study/ to import study but running into the database migration issue.

Steps to reproduce:

1. export PORTAL_HOME=<my cbioportal home directory with application.properties>
2. import gene panels like here https://docs.cbioportal.org/deployment/deploy-without-docker/load-sample-cancer-study/#import-gene-panel-for-sample-study
3. validate study https://docs.cbioportal.org/deployment/deploy-without-docker/load-sample-cancer-study/#validating-the-sample-study
4. cd cbioportal-core/src/main/scripts/importer
   It's all working until now
5. ./metaImport.py -s Users/qlu/datahub/public/msk_impact_2017/ -n -o
   After running the command, I got the error message

Expected to find 1 scripts-*.jar, but found 0
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error occurred during data loading step. Please fix the problem and run this again to make sure study is completely loaded.

Then I located the file which print this message, which is envSimple.pl. Doing some testing, I know that perl file expects one core-*.jar to be in /Users/qlu/cbioportal-core/src/main/resources/ . Therefore, I copy core-1.0.5-SNAPSHOT.jar (generated under cbioportal-core/target through maven build) over to /Users/qlu/cbioportal-core/src/main/resources/ .

6. Run ./metaImport.py -s Users/qlu/datahub/public/msk_impact_2017/ -n -o again:

Checked DB schema version: (expected: @db.version@) (found: 2.13.1)
Error, probably due to this version of the portal being out of sync with the database. Run the database migration script located at CBIOPORTAL_SRC/core/src/main/scripts/migrate_db.py before continuing.

7. Run Users/qlu/cbioportal-core/src/main/resources/scripts/migrate_db.py

sql file /Users/qlu/Library/CloudStorage/OneDrive-CarisLifeScience/Documents/cbioportal-core/src/main/resources/db-scripts/migration.sql cannot be found
migrate_db.py --properties-file [portal properties file] --sql [sql migration file]

[meenakshiiyer2531]

Hello,
Can I take up the issue and update the documentation