closes #3821

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 13135d0b68499ae5944e3e0f7dd56d30da0412a4..3b14701a9b9480cf6119e6d0e81e478e6da81214 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -11,6 +11,7 @@ import threading
 import hashlib
 import copy
 import json
+import re
 from functools import partial
 import pkg_resources  # part of setuptools
 
@@ -33,7 +34,7 @@ from .arvtool import ArvadosCommandTool
 from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver
 from .perf import Perf
-from .pathmapper import FinalOutputPathMapper
+from .pathmapper import NoFollowPathMapper
 from ._version import __version__
 
 from cwltool.pack import pack
@@ -200,9 +201,6 @@ class ArvCwlRunner(object):
 
     def check_features(self, obj):
         if isinstance(obj, dict):
-            if obj.get("class") == "InitialWorkDirRequirement":
-                if self.work_api == "containers":
-                    raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
             if obj.get("writable"):
                 raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported")
             if obj.get("class") == "CommandLineTool":
@@ -233,7 +231,7 @@ class ArvCwlRunner(object):
         adjustDirObjs(outputObj, capture)
         adjustFileObjs(outputObj, capture)
 
-        generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False)
+        generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False)
 
         final = arvados.collection.Collection(api_client=self.api,
                                               keep_client=self.keep_client,
@@ -317,6 +315,10 @@ class ArvCwlRunner(object):
                                              body={
                                                  'output': self.final_output_collection.portable_data_hash(),
                                              }).execute(num_retries=self.num_retries)
+                self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
+                                              body={
+                                                  'is_trashed': True
+                                              }).execute(num_retries=self.num_retries)
             except Exception as e:
                 logger.info("Setting container output: %s", e)
         elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
@@ -628,6 +630,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
 def add_arv_hints():
     cache = {}
+    cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
     cache["http://arvados.org/cwl"] = res.read()
     res.close()
@@ -680,9 +683,11 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
 
     if arvargs.debug:
         logger.setLevel(logging.DEBUG)
+        logging.getLogger('arvados').setLevel(logging.DEBUG)
 
     if arvargs.quiet:
         logger.setLevel(logging.WARN)
+        logging.getLogger('arvados').setLevel(logging.WARN)
         logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 
     if arvargs.metrics: