18994: Fix for colon characters in filenames

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

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index edb9d5b523c09bee4aa43f16705e27f2f15194d9..5f24d2407d1ad727a9aa534382973399f89b0090 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -18,6 +18,7 @@ import json
 import re
 from functools import partial
 import time
+import urllib
 
 from cwltool.errors import WorkflowException
 import cwltool.workflow
@@ -99,7 +100,8 @@ class ArvCwlExecutor(object):
                  arvargs=None,
                  keep_client=None,
                  num_retries=4,
-                 thread_count=4):
+                 thread_count=4,
+                 stdout=sys.stdout):
 
         if arvargs is None:
             arvargs = argparse.Namespace()
@@ -132,6 +134,7 @@ class ArvCwlExecutor(object):
         self.should_estimate_cache_size = True
         self.fs_access = None
         self.secret_store = None
+        self.stdout = stdout
 
         if keep_client is not None:
             self.keep_client = keep_client
@@ -448,7 +451,7 @@ The 'jobs' API is no longer supported.
             srccollection = sp[0][5:]
             try:
                 reader = self.collection_cache.get(srccollection)
-                srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
+                srcpath = urllib.parse.unquote("/".join(sp[1:]) if len(sp) > 1 else ".")
                 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
             except arvados.errors.ArgumentError as e:
                 logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
@@ -549,7 +552,7 @@ The 'jobs' API is no longer supported.
         if runtimeContext.submit_request_uuid and self.work_api != "containers":
             raise Exception("--submit-request-uuid requires containers API, but using '{}' api".format(self.work_api))
 
-        default_storage_classes = ",".join([k for k,v in self.api.config()["StorageClasses"].items() if v.get("Default") is True])
+        default_storage_classes = ",".join([k for k,v in self.api.config().get("StorageClasses", {"default": {"Default": True}}).items() if v.get("Default") is True])
         if runtimeContext.storage_classes == "default":
             runtimeContext.storage_classes = default_storage_classes
         if runtimeContext.intermediate_storage_classes == "default":
@@ -575,8 +578,8 @@ The 'jobs' API is no longer supported.
 
         loadingContext = self.loadingContext.copy()
         loadingContext.do_validate = False
-        loadingContext.do_update = False
         if submitting:
+            loadingContext.do_update = False
             # Document may have been auto-updated. Reload the original
             # document with updating disabled because we want to
             # submit the document with its original CWL version, not
@@ -602,14 +605,15 @@ The 'jobs' API is no longer supported.
         if existing_uuid or runtimeContext.create_workflow:
             # Create a pipeline template or workflow record and exit.
             if self.work_api == "containers":
-                return (upload_workflow(self, tool, job_order,
+                uuid = upload_workflow(self, tool, job_order,
                                         self.project_uuid,
                                         uuid=existing_uuid,
                                         submit_runner_ram=runtimeContext.submit_runner_ram,
                                         name=runtimeContext.name,
                                         merged_map=merged_map,
-                                        submit_runner_image=runtimeContext.submit_runner_image),
-                        "success")
+                                        submit_runner_image=runtimeContext.submit_runner_image)
+                self.stdout.write(uuid + "\n")
+                return (None, "success")
 
         self.apply_reqs(job_order, tool)
 
@@ -679,7 +683,8 @@ The 'jobs' API is no longer supported.
         if runtimeContext.submit and not runtimeContext.wait:
             runnerjob = next(jobiter)
             runnerjob.run(runtimeContext)
-            return (runnerjob.uuid, "success")
+            self.stdout.write(runnerjob.uuid+"\n")
+            return (None, "success")
 
         current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
         if current_container: