import uuid
import os
import urllib
-import datetime
+import arvados_cwl.util
import arvados.commands.run
import arvados.collection
pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$')
def __init__(self, arvrunner, referenced_files, input_basedir,
- collection_pattern, file_pattern, name=None, single_collection=False, **kwargs):
+ collection_pattern, file_pattern, name=None, single_collection=False):
self.arvrunner = arvrunner
self.input_basedir = input_basedir
self.collection_pattern = collection_pattern
for l in srcobj.get("listing", []):
self.addentry(l, c, ".", remap)
- info = self._get_intermediate_collection_info()
+ container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
+ info = arvados_cwl.util.get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
c.save_new(name=info["name"],
- owner_uuid=self.arvrunner.project_uuid,
- ensure_unique_name=True,
- trash_at=info["trash_at"],
+ owner_uuid=self.arvrunner.project_uuid,
+ ensure_unique_name=True,
+ trash_at=info["trash_at"],
properties=info["properties"])
ab = self.collection_pattern % c.portable_data_hash()
num_retries=self.arvrunner.num_retries )
self.addentry(srcobj, c, ".", remap)
- info = self._get_intermediate_collection_info()
+ container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
+ info = arvados_cwl.util.get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
c.save_new(name=info["name"],
- owner_uuid=self.arvrunner.project_uuid,
- ensure_unique_name=True,
- trash_at=info["trash_at"],
+ owner_uuid=self.arvrunner.project_uuid,
+ ensure_unique_name=True,
+ trash_at=info["trash_at"],
properties=info["properties"])
ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
else:
return None
- def _get_intermediate_collection_info(self):
- trash_time = None
- if self.arvrunner.intermediate_output_ttl > 0:
- trash_time = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
-
- current_container_uuid = None
- try:
- current_container = self.arvrunner.api.containers().current().execute(num_retries=self.arvrunner.num_retries)
- current_container_uuid = current_container['uuid']
- except ApiError as e:
- # Status code 404 just means we're not running in a container.
- if e.resp.status != 404:
- logger.info("Getting current container: %s", e)
- props = {"type": "Intermediate",
- "container": current_container_uuid}
-
- return {"name" : "Intermediate collection",
- "trash_at" : trash_time,
- "properties" : props}
-
class StagingPathMapper(PathMapper):
_follow_dirs = True