10129: Ensure that directory literals get preserved when trimming keep directory...

[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 20bbc41bd32627d020f156c4b4e86ac31663971b..cd38003daef65d1c64007818c193ce2bd3398513 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -23,9 +23,8 @@ import arvados.config
 from .arvcontainer import ArvadosContainer, RunnerContainer
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
 from .arvtool import ArvadosCommandTool
-from .arvworkflow import ArvadosWorkflow
+from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .fsaccess import CollectionFsAccess
-from .arvworkflow import upload_workflow
 from .perf import Perf
 from cwltool.pack import pack
 
@@ -56,6 +55,7 @@ class ArvCwlRunner(object):
         self.work_api = work_api
         self.stop_polling = threading.Event()
         self.poll_api = None
+        self.pipeline = None
 
         if self.work_api is None:
             # todo: autodetect API to use.
@@ -368,12 +368,13 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 def add_arv_hints():
     cache = {}
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
-    cache["https://w3id.org/cwl/arv-cwl-schema.yml"] = res.read()
+    cache["http://arvados.org/cwl"] = res.read()
     res.close()
     _, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
-    _, extnames, _, _ = schema_salad.schema.load_schema("https://w3id.org/cwl/arv-cwl-schema.yml", cache=cache)
+    _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", cache=cache)
     for n in extnames.names:
-        cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
+        if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""):
+            cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
 
 def main(args, stdout, stderr, api_client=None):
     parser = arg_parser()