getzlab / dalmatian

dalmatian is a collection of high-level companion functions for Firecloud and FISS.
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configuration error #19

Closed jkobject closed 5 years ago

jkobject commented 5 years ago

when I submit new jobs any change to the configuration json results in the same error for all workspaces and pipelines

User provided a full method configuration, which did not match the configuration already present on the workspace
Either upload the provided configuration, or use a different reference type to fetch the online version
---------------------------------------------------------------------------
ConfigNotUnique                           Traceback (most recent call last)
<ipython-input-21-2e080c5450d6> in <module>()
      1 samtofastq['samtofastq_workflow.samtofastq.input_bam_cram']= 'this.WES_bam'
----> 2 refwm.create_submission(samtofastq, samplesetname,'sample_set',expression='this.samples')

~/anaconda2/envs/py36/lib/python3.6/site-packages/dalmatian/wmanager.py in create_submission(self, config, entity, etype, expression, use_callcache)
   1430                     print("User provided a full method configuration, which did not match the configuration already present on the workspace", file=sys.stderr)
   1431                     print("Either upload the provided configuration, or use a different reference type to fetch the online version", file=sys.stderr)
-> 1432                     raise ConfigNotUnique("Provided configuration did not match live version {}/{}".format(cfg['namespace'], cfg['name']))
   1433             except ConfigNotFound:
   1434                 self.update_config(config)

ConfigNotUnique: 'Provided configuration did not match live version broadinstitute_gtex/samtofastq_v1-0_BETA_cfg'
agraubert commented 5 years ago

This is a safety check. You gave a full method configuration to wm.create_submission, but the configuration didn't match the version present live on firecloud. Dalmatian can't tell which version should take precedence over the other. You can avoid this in one of two ways:

jkobject commented 5 years ago

OK thanks!