Import data with Docker has error

[xinxin chen]

Hello,

When I import data with docker, execute this command: docker compose run cbioportal metaImport.py -u http://cbioportal-container:8080 -s /study/lgg_ucsf_2014 -o, it import data successfully, but when I execute: 

docker compose run cbioportal metaImport.py -u http://cbioportal-container:8080 -s /study/study_es_0 -o

show these error messages:

Reading data from:  /study/study_es_0/data_gsva_scores.txt
Recaching...
Finished recaching...
--> profile id:  49
--> profile name:  GSVA scores on oncogenic signatures gene sets
--> genetic alteration type:  GENESET_SCORE
--> total number of samples: 5
--> total number of data lines:  7
07:35:06.692 [main] WARN org.mskcc.cbio.portal.util.ProgressMonitor -- Geneset GO_ACYLGLYCEROL_HOMEOSTASIS not found in DB. Record will be skipped.
07:35:06.694 [main] WARN org.mskcc.cbio.portal.util.ProgressMonitor -- Geneset GO_ANATOMICAL_STRUCTURE_FORMATION_INVOLVED_IN_MORPHOGENESIS not found in DB. Record will be skipped.
07:35:06.696 [main] WARN org.mskcc.cbio.portal.util.ProgressMonitor -- Geneset GO_ANTEROGRADE_AXONAL_TRANSPORT not found in DB. Record will be skipped.
07:35:06.698 [main] WARN org.mskcc.cbio.portal.util.ProgressMonitor -- Geneset GO_APICAL_PROTEIN_LOCALIZATION not found in DB. Record will be skipped.
07:35:06.700 [main] WARN org.mskcc.cbio.portal.util.ProgressMonitor -- Geneset GO_ATP_DEPENDENT_CHROMATIN_REMODELING not found in DB. Record will be skipped.
07:35:06.702 [main] WARN org.mskcc.cbio.portal.util.ProgressMonitor -- Geneset GO_CARBOHYDRATE_CATABOLIC_PROCESS not found in DB. Record will be skipped.
07:35:06.703 [main] WARN org.mskcc.cbio.portal.util.ProgressMonitor -- Geneset GO_CARDIAC_CHAMBER_DEVELOPMENT not found in DB. Record will be skipped.
--> records inserted into `sample_profile` table: 5
--> total number of data entries skipped (see table below):  7
org.mskcc.cbio.portal.dao.DaoException: Something has gone wrong!  I did not save any records to the database!
at org.mskcc.cbio.portal.scripts.ImportTabDelimData.importData(ImportTabDelimData.java:326)
at org.mskcc.cbio.portal.scripts.ImportProfileData.run(ImportProfileData.java:164)
at org.mskcc.cbio.portal.scripts.ConsoleRunnable.runInConsole(ConsoleRunnable.java:145)
at org.mskcc.cbio.portal.scripts.ImportProfileData.main(ImportProfileData.java:189)

Warnings / Errors:
-------------------
0.  Geneset GO_ACYLGLYCEROL_HOMEOSTASIS not found in DB. Record will be skipped.; 1x
1.  Geneset GO_ANATOMICAL_STRUCTURE_FORMATION_INVOLVED_IN_MORPHOGENESIS not found in DB. Record will be skipped.; 1x
2.  Geneset GO_ANTEROGRADE_AXONAL_TRANSPORT not found in DB. Record will be skipped.; 1x
3.  Geneset GO_APICAL_PROTEIN_LOCALIZATION not found in DB. Record will be skipped.; 1x
4.  Geneset GO_ATP_DEPENDENT_CHROMATIN_REMODELING not found in DB. Record will be skipped.; 1x
5.  Geneset GO_CARBOHYDRATE_CATABOLIC_PROCESS not found in DB. Record will be skipped.; 1x
6.  Geneset GO_CARDIAC_CHAMBER_DEVELOPMENT not found in DB. Record will be skipped.; 1x

ABORTED!
java.lang.RuntimeException: org.mskcc.cbio.portal.dao.DaoException: Something has gone wrong!  I did not save any records to the database!
at org.mskcc.cbio.portal.scripts.ImportProfileData.run(ImportProfileData.java:169)
at org.mskcc.cbio.portal.scripts.ConsoleRunnable.runInConsole(ConsoleRunnable.java:145)
at org.mskcc.cbio.portal.scripts.ImportProfileData.main(ImportProfileData.java:189)
Caused by: org.mskcc.cbio.portal.dao.DaoException: Something has gone wrong!  I did not save any records to the database!
at org.mskcc.cbio.portal.scripts.ImportTabDelimData.importData(ImportTabDelimData.java:326)
at org.mskcc.cbio.portal.scripts.ImportProfileData.run(ImportProfileData.java:164)
... 2 more
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error occurred during data loading step. Please fix the problem and run this again to make sure study is completely loaded.
Traceback (most recent call last):
  File "/usr/local/bin/metaImport.py", line 212, in <module>
    cbioportalImporter.main(args)
  File "/core/scripts/importer/cbioportalImporter.py", line 557, in main
    process_directory(jvm_args, study_directory, args.update_generic_assay_entity)
  File "/core/scripts/importer/cbioportalImporter.py", line 394, in process_directory
    import_study_data(jvm_args, meta_filename, data_filename, update_generic_assay_entity, study_meta_dictionary[meta_filename])
  File "/core/scripts/importer/cbioportalImporter.py", line 162, in import_study_data
    run_java(*args)
  File "/core/scripts/importer/cbioportal_common.py", line 1016, in run_java
    raise RuntimeError('Aborting due to error while executing step.')
RuntimeError: Aborting due to error while executing step.

[Ruslan Forostianov]

Hello Xinxin,

Have you imported gene sets prior to importing the study_es_0 study? This study includes GSVA data, which requires gene sets to be loaded beforehand.

Here is the page that shows how to import gene set data in cBioPortal https://docs.cbioportal.org/import-gene-sets/#quick-example

Regards,
Ruslan