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 .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 .fsaccess import CollectionFsAccess

-from .arvworkflow import upload_workflow

 from .perf import Perf
 from cwltool.pack import pack
 
 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.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.
 
         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')
 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")
     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:
     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()
 
 def main(args, stdout, stderr, api_client=None):
     parser = arg_parser()