[ARVADOS] updated: 1.2.0-428-gd738b8c32

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvcontainer.py |  4 ++--
 sdk/cwl/arvados_cwl/fsaccess.py     |  2 +-
 sdk/cwl/tests/test_container.py     | 13 +++----------
 3 files changed, 6 insertions(+), 13 deletions(-)

       via  d738b8c32940af71462b8aac9bbfdbbc0f2f2642 (commit)
      from  22cad1a48a8bea5a6f46c4241e139b03ee32e877 (commit)

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commit d738b8c32940af71462b8aac9bbfdbbc0f2f2642
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Nov 21 16:39:59 2018 -0500

    Finish fixing setting project_uuid from runtimeContext, fix tests.
    
    refs #14198
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 9a9b8afd3..f1ae65fc0 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -174,7 +174,7 @@ class ArvadosContainer(JobBase):
                     runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
                 info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
                 vwd.save_new(name=info["name"],
-                             owner_uuid=self.arvrunner.project_uuid,
+                             owner_uuid=runtimeContext.project_uuid,
                              ensure_unique_name=True,
                              trash_at=info["trash_at"],
                              properties=info["properties"])
@@ -217,7 +217,7 @@ class ArvadosContainer(JobBase):
         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
                                                                     docker_req,
                                                                     runtimeContext.pull_image,
-                                                                    self.arvrunner.project_uuid)
+                                                                    runtimeContext.project_uuid)
 
         api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement")
         if api_req:
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index b22b2ffd6..598126812 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -265,7 +265,7 @@ class CollectionFetcher(DefaultFetcher):
 
         return super(CollectionFetcher, self).urljoin(base_url, url)
 
-    schemes = [u"file", u"http", u"https", u"mailto", u"keep"]
+    schemes = [u"file", u"http", u"https", u"mailto", u"keep", u"arvwf"]
 
     def supported_schemes(self):  # type: () -> List[Text]
         return self.schemes
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index c875c0785..a34d550f6 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -71,7 +71,9 @@ class TestContainer(unittest.TestCase):
              "make_fs_access": make_fs_access,
              "tmpdir": "/tmp",
              "enable_reuse": enable_reuse,
-             "priority": 500})
+             "priority": 500,
+             "project_uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+            })
 
         return loadingContext, runtimeContext
 
@@ -83,7 +85,6 @@ class TestContainer(unittest.TestCase):
             arv_docker_clear_cache()
 
             runner = mock.MagicMock()
-            runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
             runner.ignore_docker_for_reuse = False
             runner.intermediate_output_ttl = 0
             runner.secret_store = cwltool.secrets.SecretStore()
@@ -147,7 +148,6 @@ class TestContainer(unittest.TestCase):
     def test_resource_requirements(self, keepdocker):
         arv_docker_clear_cache()
         runner = mock.MagicMock()
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 3600
         runner.secret_store = cwltool.secrets.SecretStore()
@@ -243,7 +243,6 @@ class TestContainer(unittest.TestCase):
     def test_initial_work_dir(self, collection_mock, keepdocker):
         arv_docker_clear_cache()
         runner = mock.MagicMock()
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 0
         runner.secret_store = cwltool.secrets.SecretStore()
@@ -373,7 +372,6 @@ class TestContainer(unittest.TestCase):
         arv_docker_clear_cache()
 
         runner = mock.MagicMock()
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 0
         runner.secret_store = cwltool.secrets.SecretStore()
@@ -454,7 +452,6 @@ class TestContainer(unittest.TestCase):
 
         runner = mock.MagicMock()
         runner.api = api
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.num_retries = 0
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 0
@@ -523,7 +520,6 @@ class TestContainer(unittest.TestCase):
         handlerClasses = [h.__class__ for h in root_logger.handlers]
         self.assertTrue(arvados_cwl.RuntimeStatusLoggingHandler in handlerClasses)
 
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.num_retries = 0
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 0
@@ -580,7 +576,6 @@ class TestContainer(unittest.TestCase):
         arv_docker_clear_cache()
 
         runner = mock.MagicMock()
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 0
         runner.secret_store = cwltool.secrets.SecretStore()
@@ -670,7 +665,6 @@ class TestContainer(unittest.TestCase):
         arv_docker_clear_cache()
 
         runner = mock.MagicMock()
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 0
         runner.secret_store = cwltool.secrets.SecretStore()
@@ -768,7 +762,6 @@ class TestContainer(unittest.TestCase):
         arv_docker_clear_cache()
 
         runner = mock.MagicMock()
-        runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
         runner.ignore_docker_for_reuse = False
         runner.intermediate_output_ttl = 0
         runner.secret_store = cwltool.secrets.SecretStore()

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