sdk/cwl/arvados_cwl/done.py

   1 def done(self, record, tmpdir, outdir, keepdir):
   2     colname = "Output %s of %s" % (record["output"][0:7], self.name)
   3
   4     # check if collection already exists with same owner, name and content
   5     collection_exists = self.arvrunner.api.collections().list(
   6         filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
   7                  ['portable_data_hash', '=', record["output"]],
   8                  ["name", "=", colname]]
   9     ).execute(num_retries=self.arvrunner.num_retries)
  10
  11     if not collection_exists["items"]:
  12         # Create a collection located in the same project as the
  13         # pipeline with the contents of the output.
  14         # First, get output record.
  15         collections = self.arvrunner.api.collections().list(
  16             limit=1,
  17             filters=[['portable_data_hash', '=', record["output"]]],
  18             select=["manifest_text"]
  19         ).execute(num_retries=self.arvrunner.num_retries)
  20
  21         if not collections["items"]:
  22             raise WorkflowException(
  23                 "Job output '%s' cannot be found on API server" % (
  24                     record["output"]))
  25
  26         # Create new collection in the parent project
  27         # with the output contents.
  28         self.arvrunner.api.collections().create(body={
  29             "owner_uuid": self.arvrunner.project_uuid,
  30             "name": colname,
  31             "portable_data_hash": record["output"],
  32             "manifest_text": collections["items"][0]["manifest_text"]
  33         }, ensure_unique_name=True).execute(
  34             num_retries=self.arvrunner.num_retries)
  35
  36     self.builder.outdir = outdir
  37     self.builder.pathmapper.keepdir = keepdir
  38     return self.collect_outputs("keep:" + record["output"])