from collections import deque
def done(self, record, tmpdir, outdir, keepdir):
- colname = "Output %s of %s" % (record["output"][0:7], self.name)
+ cols = [
+ ("output", "Output %s of %s" % (record["output"][0:7], self.name), record["output"]),
+ ("log", "Log of %s" % (record["uuid"]), record["log"])
+ ]
- # check if collection already exists with same owner, name and content
- collection_exists = self.arvrunner.api.collections().list(
- filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
- ['portable_data_hash', '=', record["output"]],
- ["name", "=", colname]]
- ).execute(num_retries=self.arvrunner.num_retries)
-
- if not collection_exists["items"]:
- # Create a collection located in the same project as the
- # pipeline with the contents of the output.
- # First, get output record.
- collections = self.arvrunner.api.collections().list(
- limit=1,
- filters=[['portable_data_hash', '=', record["output"]]],
- select=["manifest_text"]
+ for coltype, colname, colpdh in cols:
+ # check if collection already exists with same owner, name and content
+ collection_exists = self.arvrunner.api.collections().list(
+ filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
+ ['portable_data_hash', '=', colpdh],
+ ["name", "=", colname]]
).execute(num_retries=self.arvrunner.num_retries)
- if not collections["items"]:
- raise WorkflowException(
- "[job %s] output '%s' cannot be found on API server" % (
- self.name, record["output"]))
+ if not collection_exists["items"]:
+ # Create a collection located in the same project as the
+ # pipeline with the contents of the output/log.
+ # First, get output/log record.
+ collections = self.arvrunner.api.collections().list(
+ limit=1,
+ filters=[['portable_data_hash', '=', colpdh]],
+ select=["manifest_text"]
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ if not collections["items"]:
+ raise WorkflowException(
+ "[job %s] %s '%s' cannot be found on API server" % (
+ self.name, coltype, colpdh))
- # Create new collection in the parent project
- # with the output contents.
- self.arvrunner.api.collections().create(body={
- "owner_uuid": self.arvrunner.project_uuid,
- "name": colname,
- "portable_data_hash": record["output"],
- "manifest_text": collections["items"][0]["manifest_text"]
- }, ensure_unique_name=True).execute(
- num_retries=self.arvrunner.num_retries)
+ # Create new collection in the parent project
+ # with the output/log contents.
+ self.arvrunner.api.collections().create(body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": colname,
+ "portable_data_hash": colpdh,
+ "manifest_text": collections["items"][0]["manifest_text"]
+ }, ensure_unique_name=True).execute(
+ num_retries=self.arvrunner.num_retries)
return done_outputs(self, record, tmpdir, outdir, keepdir)
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
- runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
+ runner.api.collections().get().execute.return_value = {"portable_data_hash": "99999999999999999999999999999993+99"}
+ # Simulate reused job from another project so that we can check is a can_read
+ # link is added.
+ runner.api.jobs().create().execute.return_value = {
+ 'state': 'Complete' if enable_reuse else 'Queued',
+ 'owner_uuid': 'zzzzz-tpzed-yyyyyyyyyyyyyyy' if enable_reuse else 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'uuid': 'zzzzz-819sb-yyyyyyyyyyyyyyy',
+ 'output': None,
+ }
tool = cmap({
"inputs": [],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
['docker_image_locator', 'in docker', 'arvados/jobs']]
)
+ if enable_reuse:
+ runner.api.links().create.assert_called_with(
+ body=JsonDiffMatcher({
+ 'link_class': 'can_read',
+ "tail_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
+ "head_uuid": "zzzzz-819sb-yyyyyyyyyyyyyyy",
+ })
+ )
+ else:
+ assert not runner.api.links().create.called
# The test passes some fields in builder.resources
# For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
""")
api.collections().list().execute.side_effect = ({"items": []},
- {"items": [{"manifest_text": "XYZ"}]})
+ {"items": [{"manifest_text": "XYZ"}]},
+ {"items": []},
+ {"items": [{"manifest_text": "ABC"}]})
arvjob = arvados_cwl.ArvadosJob(runner)
arvjob.name = "testjob"
api.collections().list.assert_has_calls([
mock.call(),
+ # Output collection check
mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
['portable_data_hash', '=', '99999999999999999999999999999993+99'],
['name', '=', 'Output 9999999 of testjob']]),
mock.call().execute(num_retries=0),
mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999993+99']],
select=['manifest_text']),
+ mock.call().execute(num_retries=0),
+ # Log collection's turn
+ mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
+ ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
+ ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
+ mock.call().execute(num_retries=0),
+ mock.call(limit=1, filters=[['portable_data_hash', '=', '99999999999999999999999999999994+99']],
+ select=['manifest_text']),
mock.call().execute(num_retries=0)])
- api.collections().create.assert_called_with(
- ensure_unique_name=True,
- body={'portable_data_hash': '99999999999999999999999999999993+99',
- 'manifest_text': 'XYZ',
- 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
- 'name': 'Output 9999999 of testjob'})
+ api.collections().create.assert_has_calls([
+ mock.call(ensure_unique_name=True,
+ body={'portable_data_hash': '99999999999999999999999999999993+99',
+ 'manifest_text': 'XYZ',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'name': 'Output 9999999 of testjob'}),
+ mock.call().execute(num_retries=0),
+ mock.call(ensure_unique_name=True,
+ body={'portable_data_hash': '99999999999999999999999999999994+99',
+ 'manifest_text': 'ABC',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'name': 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
+ mock.call().execute(num_retries=0),
+ ])
arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
2016-11-02_23:12:18 c97qk-8i9sb-cryqw2blvzy4yaj 13358 0 stderr 2016/11/02 23:12:18 crunchrunner: $(task.keep)=/keep
""")
- api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},)
+ api.collections().list().execute.side_effect = (
+ {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
+ {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzz2"}]},
+ )
arvjob = arvados_cwl.ArvadosJob(runner)
arvjob.name = "testjob"
api.collections().list.assert_has_calls([
mock.call(),
+ # Output collection
mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
['portable_data_hash', '=', '99999999999999999999999999999993+99'],
['name', '=', 'Output 9999999 of testjob']]),
- mock.call().execute(num_retries=0)])
+ mock.call().execute(num_retries=0),
+ # Log collection
+ mock.call(filters=[['owner_uuid', '=', 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'],
+ ['portable_data_hash', '=', '99999999999999999999999999999994+99'],
+ ['name', '=', 'Log of zzzzz-8i9sb-zzzzzzzzzzzzzzz']]),
+ mock.call().execute(num_retries=0)
+ ])
self.assertFalse(api.collections().create.called)
projects / arvados.git / commitdiff