error: difg is not a supported cancer type

[Shixiang Wang (Shawn)]

Hi,

When I test the data import, I found an error and don't know how to fix it.

I followed the documentation and test data import with:

```

docker-compose run -v $PWD/portalInfo:/portalInfo -w /cbioportal/core/src/main/scripts cbioportal ./dumpPortalInfo.pl /portalInfo

docker-compose run -v $PWD/Report/:/report -v $PWD/portalInfo/:/portalInfo:ro cbioportal metaImport.py -p /portalInfo -s study/lgg_ucsf_2014 --html=/report/lgg_ucsf_2014.html

```

The data validation passed with warnings, so I add -o to overwrite it. However, after that, the code report cannot find the cancer type. But it exists in the file portalInfo/cancer-types.json, its content I copied from datahub repository (https://github.com/cBioPortal/datahub/blob/master/.circleci/portalinfo/cancer-types.json).

$ sudo docker-compose run -v $PWD/Report/:/report cbioportal metaImport.py -p /portalInfo -s study/lgg_ucsf_2014 --html=/report/lgg_ucsf_2014.html -o -v
[+] Running 3/0
 ⠿ Container cbioportal-database-container          Running                                                0.0s
 ⠿ Container cbioportal-session-database-container  R...                                                   0.0s
 ⠿ Container cbioportal-session-container           Running                                                0.0s
Starting validation...

DEBUG: -: Reading portal information from /portalInfo/cancer-types.json
DEBUG: -: Reading portal information from /portalInfo/genes.json
DEBUG: -: Reading portal information from /portalInfo/genesets.json
DEBUG: -: Reading portal information from /portalInfo/genesets_version.json
DEBUG: -: Reading portal information from /portalInfo/gene-panels.json
DEBUG: -: Reading portal information from /portalInfo/genesaliases.json

DEBUG: meta_clinical_patient.txt: Starting validation of meta file
INFO: meta_clinical_patient.txt: Validation of meta file complete

DEBUG: meta_clinical_sample.txt: Starting validation of meta file
INFO: meta_clinical_sample.txt: Validation of meta file complete

DEBUG: meta_mutations_extended.txt: Starting validation of meta file
INFO: meta_mutations_extended.txt: Validation of meta file complete

DEBUG: meta_study.txt: Starting validation of meta file
WARNING: meta_study.txt: Unrecognized field in meta file; value encountered: 'short_name'
INFO: meta_study.txt: Validation of meta file complete
INFO: meta_study.txt: No reference genome specified -- using default (hg19)

DEBUG: meta_timeline_specimen.txt: Starting validation of meta file
INFO: meta_timeline_specimen.txt: Validation of meta file complete

DEBUG: meta_timeline_status.txt: Starting validation of meta file
INFO: meta_timeline_status.txt: Validation of meta file complete

DEBUG: meta_timeline_surgery.txt: Starting validation of meta file
INFO: meta_timeline_surgery.txt: Validation of meta file complete

DEBUG: meta_timeline_treatment.txt: Starting validation of meta file
INFO: meta_timeline_treatment.txt: Validation of meta file complete

DEBUG: data_clinical_sample.txt: Starting validation of file
INFO: data_clinical_sample.txt: Validation of file complete
INFO: data_clinical_sample.txt: Read 66 lines. Lines with warning: 0. Lines with error: 0

DEBUG: -: Validating case lists

DEBUG: case_lists/cases_sequenced.txt: Starting validation of meta file
INFO: case_lists/cases_sequenced.txt: Validation of meta file complete

DEBUG: case_lists/cases_all.txt: Starting validation of meta file
INFO: case_lists/cases_all.txt: Validation of meta file complete

INFO: -: Validation of case list folder complete

DEBUG: data_clinical_patient.txt: Starting validation of file
WARNING: data_clinical_patient.txt: Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study.
INFO: data_clinical_patient.txt: Validation of file complete
INFO: data_clinical_patient.txt: Read 28 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_mutations_extended.txt: Starting validation of file
WARNING: data_mutations_extended.txt: line 1: Including the SWISSPROT column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view
INFO: data_mutations_extended.txt: lines [4, 13, 19, (4957 more)]: Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA]; values encountered: ['Silent', 'Intron', '5'Flank', '(4 more)']
WARNING: data_mutations_extended.txt: lines [5, 12, 51, (485 more)]: Gene symbol maps to a single Entrez gene id, but is also associated to other genes as an alias. The system will assume the official gene symbol to be the intended one.; values encountered: ['BDP1', 'DLC1', 'AAK1', '(314 more)']
WARNING: data_mutations_extended.txt: line 827: Gene alias maps to multiple Entrez gene ids (3843/162540), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'IMP5'
WARNING: data_mutations_extended.txt: lines [1022, 1023, 1024, (8 more)]: Gene alias maps to multiple Entrez gene ids (8085/9757), please specify which one you mean or choose a non-ambiguous symbol.; values encountered: ['MLL2', 'MLL4']
WARNING: data_mutations_extended.txt: lines [3141, 3211, 4566, (5 more)]: Gene symbol not known to the cBioPortal instance. This record will not be loaded.; values encountered: ['KIAA1804', 'LOC100653515', 'SMIM43', '(4 more)']
WARNING: data_mutations_extended.txt: line 4563: Gene alias maps to multiple Entrez gene ids (162699/728929), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'TCEB3C'
WARNING: data_mutations_extended.txt: lines [4837, 4838]: Gene alias maps to multiple Entrez gene ids (79888/84803), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'AGPAT9'
WARNING: data_mutations_extended.txt: line 5178: Gene alias maps to multiple Entrez gene ids (1238/51554), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'CCBP2'
WARNING: data_mutations_extended.txt: line 5420: Gene alias maps to multiple Entrez gene ids (1620/57805), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'DBC1'
WARNING: data_mutations_extended.txt: line 5623: Gene alias maps to multiple Entrez gene ids (253725/387680), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'FAM21A'
WARNING: data_mutations_extended.txt: lines [5841, 9369]: Gene alias maps to multiple Entrez gene ids (374977/100527960), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'HEATR8'
WARNING: data_mutations_extended.txt: line 8672: Gene alias maps to multiple Entrez gene ids (738/56912), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'C11ORF2'
WARNING: data_mutations_extended.txt: line 8683: Gene alias maps to multiple Entrez gene ids (348110/100526783), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'C15ORF38'
WARNING: data_mutations_extended.txt: line 9400: Gene alias maps to multiple Entrez gene ids (57585/90861), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'HN1L'
WARNING: data_mutations_extended.txt: lines [9926, 14579]: Gene alias maps to multiple Entrez gene ids (10178/55714), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'ODZ3'
WARNING: data_mutations_extended.txt: line 12196: Gene alias maps to multiple Entrez gene ids (378708/100526739), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'APITD1'
WARNING: data_mutations_extended.txt: line 13759: Gene alias maps to multiple Entrez gene ids (54734/83871), please specify which one you mean or choose a non-ambiguous symbol.; value encountered: 'RAB39'
INFO: data_mutations_extended.txt: Validation of file complete
INFO: data_mutations_extended.txt: Read 15156 lines. Lines with warning: 524. Lines with error: 0

DEBUG: data_timeline_specimen.txt: Starting validation of file
INFO: data_timeline_specimen.txt: Validation of file complete
INFO: data_timeline_specimen.txt: Read 61 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_timeline_status.txt: Starting validation of file
INFO: data_timeline_status.txt: Validation of file complete
INFO: data_timeline_status.txt: Read 42 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_timeline_surgery.txt: Starting validation of file
INFO: data_timeline_surgery.txt: Validation of file complete
INFO: data_timeline_surgery.txt: Read 55 lines. Lines with warning: 0. Lines with error: 0

DEBUG: data_timeline_treatment.txt: Starting validation of file
INFO: data_timeline_treatment.txt: Validation of file complete
INFO: data_timeline_treatment.txt: Read 21 lines. Lines with warning: 0. Lines with error: 0

INFO: -: Validation complete


#######################################################################
Overriding Warnings. Importing study now
#######################################################################

Data loading step using /cbioportal/scripts/target/scripts-4.1.13-dirty-SNAPSHOT.jar

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Checked DB schema version: (expected: 2.12.13) (found: 2.12.13)
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Checking if Cancer study with identifier lgg_ucsf_2014 already exists before removing...
Recaching...
Finished recaching...
Cancer study with identifier lgg_ucsf_2014 does not exist the the database, not removing...
Done.
Total time:  3277 ms

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Recaching...
Finished recaching...

ABORTED!
java.lang.IllegalArgumentException: difg is not a supported cancer type.
at org.mskcc.cbio.portal.util.CancerStudyReader.loadCancerStudy(CancerStudyReader.java:66)
at org.mskcc.cbio.portal.util.CancerStudyReader.loadCancerStudy(CancerStudyReader.java:56)
at org.mskcc.cbio.portal.scripts.ImportCancerStudy.run(ImportCancerStudy.java:57)
at org.mskcc.cbio.portal.scripts.ConsoleRunnable.runInConsole(ConsoleRunnable.java:145)
at org.mskcc.cbio.portal.scripts.ImportCancerStudy.main(ImportCancerStudy.java:93)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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 202, in <module>
    cbioportalImporter.main(args)
  File "/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 533, in main
    process_directory(jvm_args, study_directory, args.update_generic_assay_entity)
  File "/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 345, in process_directory
    import_study(jvm_args, study_meta_filename)
  File "/cbioportal/core/src/main/scripts/importer/cbioportalImporter.py", line 74, in import_study
    run_java(*args)
  File "/cbioportal/core/src/main/scripts/importer/cbioportal_common.py", line 990, in run_java
    raise RuntimeError('Aborting due to error while executing step.')
RuntimeError: Aborting due to error while executing step.

[debr...@mskcc.org]

Hi Shixiang,

 

Thanks for reaching out! Could you clarify which version of cBioPortal and cbioportal-dokcer-compose you are using?

 

Thanks!

Ino

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[Shixiang Wang (Shawn)]

To show docker compose  version here gives the latest commit:

commit 5b396301e4cd34cd02c3fbff3c058cff0a5541a3 (HEAD -> master, origin/master, origin/HEAD)
Merge: 2058305 931dbb0
Date:   Fri Sep 9 14:23:33 2022 -0400

    Merge pull request #19 from cBioPortal/fix-ports-yml

    Fix Ports yml

container information:

$ sudo docker ps
CONTAINER ID        IMAGE                              COMMAND                  CREATED             STATUS
PORTS                    NAMES
40059830cb94        cbioportal/cbioportal:4.1.13       "docker-entrypoint.s…"   11 days ago         Up 11 days
0.0.0.0:8080->8080/tcp   cbioportal-container
8a61120375d3        cbioportal/session-service:0.5.0   "/bin/sh -c 'java ${…"   11 days ago         Up 11 days
                         cbioportal-session-container
e6a56953ba47        mongo:3.7.9                        "docker-entrypoint.s…"   11 days ago         Up 11 days
27017/tcp                cbioportal-session-database-container
0ddfab71bbc8        mysql:5.7                          "docker-entrypoint.s…"   11 days ago         Up 11 days
3306/tcp, 33060/tcp      cbioportal-database-container
a6903c41e8ac        jboss/keycloak:4.8.3.Final         "/opt/jboss/tools/do…"   12 days ago         Up 12 days
0.0.0.0:8180->8080/tcp   cbiokc
3a4f3c5d1878        mysql:5.7                          "docker-entrypoint.s…"   12 days ago         Up 12 days
3306/tcp, 33060/tcp      kcdb

[Shixiang Wang (Shawn)]

Dear Ino,

Any feedback on my reply?

Best,

Shixiang

在2022年9月23日星期五 UTC+8 19:56:59<de Bruijn, Ino/Sloan Kettering Institute> 写道：

[debr...@mskcc.org]

Hi Shixiang,

 

Apologies about the delay

 

It looks like somehow this cancer type doesn’t exist:

 

> java.lang.IllegalArgumentException: difg is not a supported cancer type

 

See also:

 

https://github.com/cBioPortal/datahub/blob/master/public/lgg_ucsf_2014/meta_study.txt#L1

 

It probably means the seed database was not correctly initialized. You can connect to the mysql databse to confirm:

 

docker-compose exec cbioportal-database \

    sh -c 'mysql -hcbioportal-database -u"$MYSQL_USER" -p"$MYSQL_PASSWORD" "$MYSQL_DATABASE"'

 

Once in the mysql prompt you can type:

 

mysql> select * from type_of_cancer where TYPE_OF_CANCER_ID='difg';

 

You should see this:

 

+-------------------+----------------+-----------------+------------+--------+

| TYPE_OF_CANCER_ID | NAME           | DEDICATED_COLOR | SHORT_NAME | PARENT |

+-------------------+----------------+-----------------+------------+--------+

| difg              | Diffuse Glioma | Gray            | DIFG       | brain  |

+-------------------+----------------+-----------------+------------+--------+

 

If you don’t see anything there something probably went wrong with the initialization. I would recommend to delete everything again in that case. That is:

 

docker compose down -v

 

and then remove the repository and clone it again. If that doesn’t work you can also try using the latest development version. That is change:

 

https://github.com/cBioPortal/cbioportal-docker-compose/blob/master/.env#L1

 

to cbioportal/cbioportal:5.1.3

 

Hope that helps!

 

Best wishes,

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