sdk/cwl/arvados_cwl/util.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 import datetime
   6 from arvados.errors import ApiError
   7
   8 collectionUUID =  "http://arvados.org/cwl#collectionUUID"
   9
  10 def get_intermediate_collection_info(workflow_step_name, current_container, intermediate_output_ttl):
  11         if workflow_step_name:
  12             name = "Intermediate collection for step %s" % (workflow_step_name)
  13         else:
  14             name = "Intermediate collection"
  15         trash_time = None
  16         if intermediate_output_ttl > 0:
  17             trash_time = datetime.datetime.utcnow() + datetime.timedelta(seconds=intermediate_output_ttl)
  18         container_uuid = None
  19         props = {"type": "intermediate"}
  20         if current_container:
  21             props["container_uuid"] = current_container['uuid']
  22
  23         return {"name" : name, "trash_at" : trash_time, "properties" : props}
  24
  25 def get_current_container(api, num_retries=0, logger=None):
  26     current_container = None
  27     try:
  28         current_container = api.containers().current().execute(num_retries=num_retries)
  29     except ApiError as e:
  30         # Status code 404 just means we're not running in a container.
  31         if e.resp.status != 404:
  32             if logger:
  33                 logger.info("Getting current container: %s", e)
  34             raise e
  35
  36     return current_container
  37
  38
  39 def common_prefix(firstfile, all_files):
  40     common_parts = firstfile.split('/')
  41     common_parts[-1] = ''
  42     for f in all_files:
  43         f_parts = f.split('/')
  44         for index, (a, b) in enumerate(zip(common_parts, f_parts)):
  45             if a != b:
  46                 common_parts = common_parts[:index + 1]
  47                 common_parts[-1] = ''
  48                 break
  49         if not any(common_parts):
  50             break
  51     return '/'.join(common_parts)