X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/fbffa8c4d0fa8bd19fe77b82c16395b80f0bb0ce..b5d0e0ad775eb822b9ab4bed5b57c2e9072f4c0b:/sdk/cwl/arvados_cwl/executor.py

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index aa19633d8c..ed57c6dae0 100644
--- 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
@@ -260,46 +261,29 @@ The 'jobs' API is no longer supported.
             if current is None:
                 return
             runtime_status = current.get('runtime_status', {})
-            # In case of status being an error, only report the first one.
-            if kind == 'error':
-                if not runtime_status.get('error'):
-                    runtime_status.update({
-                        'error': message
-                    })
-                    if detail is not None:
-                        runtime_status.update({
-                            'errorDetail': detail
-                        })
-                # Further errors are only mentioned as a count.
-                else:
-                    # Get anything before an optional 'and N more' string.
-                    try:
-                        error_msg = re.match(
-                            r'^(.*?)(?=\s*\(and \d+ more\)|$)', runtime_status.get('error')).groups()[0]
-                        more_failures = re.match(
-                            r'.*\(and (\d+) more\)', runtime_status.get('error'))
-                    except TypeError:
-                        # Ignore tests stubbing errors
-                        return
-                    if more_failures:
-                        failure_qty = int(more_failures.groups()[0])
-                        runtime_status.update({
-                            'error': "%s (and %d more)" % (error_msg, failure_qty+1)
-                        })
-                    else:
-                        runtime_status.update({
-                            'error': "%s (and 1 more)" % error_msg
-                        })
-            elif kind in ['warning', 'activity']:
-                # Record the last warning/activity status without regard of
-                # previous occurences.
+            if kind in ('error', 'warning'):
+                updatemessage = runtime_status.get(kind, "")
+                if not updatemessage:
+                    updatemessage = message
+
+                # Subsequent messages tacked on in detail
+                updatedetail = runtime_status.get(kind+'Detail', "")
+                maxlines = 40
+                if updatedetail.count("\n") < maxlines:
+                    if updatedetail:
+                        updatedetail += "\n"
+                    updatedetail += message + "\n"
+
+                    if detail:
+                        updatedetail += detail + "\n"
+
+                    if updatedetail.count("\n") >= maxlines:
+                        updatedetail += "\nSome messages may have been omitted.  Check the full log."
+
                 runtime_status.update({
-                    kind: message
+                    kind: updatemessage,
+                    kind+'Detail': updatedetail,
                 })
-                if detail is not None:
-                    runtime_status.update({
-                        kind+"Detail": detail
-                    })
             else:
                 # Ignore any other status kind
                 return
@@ -450,7 +434,7 @@ 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)
@@ -560,6 +544,16 @@ The 'jobs' API is no longer supported.
         if not runtimeContext.name:
             runtimeContext.name = self.name = updated_tool.tool.get("label") or updated_tool.metadata.get("label") or os.path.basename(updated_tool.tool["id"])
 
+        if runtimeContext.copy_deps is None and (runtimeContext.create_workflow or runtimeContext.update_workflow):
+            runtimeContext.copy_deps = True
+
+        if runtimeContext.update_workflow and self.project_uuid is None:
+            # If we are updating a workflow, make sure anything that
+            # gets uploaded goes into the same parent project, unless
+            # an alternate --project-uuid was provided.
+            existing_wf = self.api.workflows().get(uuid=runtimeContext.update_workflow).execute()
+            self.project_uuid = existing_wf["owner_uuid"]
+
         # Upload local file references in the job order.
         job_order = upload_job_order(self, "%s input" % runtimeContext.name,
                                      updated_tool, job_order)
@@ -577,8 +571,8 @@ 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
@@ -600,13 +594,12 @@ The 'jobs' API is no longer supported.
         loadingContext.metadata = tool.metadata
         tool = load_tool(tool.tool, loadingContext)
 
-        existing_uuid = runtimeContext.update_workflow
-        if existing_uuid or runtimeContext.create_workflow:
+        if runtimeContext.update_workflow or runtimeContext.create_workflow:
             # Create a pipeline template or workflow record and exit.
             if self.work_api == "containers":
                 uuid = upload_workflow(self, tool, job_order,
                                         self.project_uuid,
-                                        uuid=existing_uuid,
+                                        uuid=runtimeContext.update_workflow,
                                         submit_runner_ram=runtimeContext.submit_runner_ram,
                                         name=runtimeContext.name,
                                         merged_map=merged_map,