[ARVADOS] updated: 1.1.2-51-g75cb314

Git user git at public.curoverse.com
Mon Jan 15 15:51:18 EST 2018


Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py    |  7 ++++++-
 sdk/cwl/arvados_cwl/arvworkflow.py |  3 ++-
 sdk/cwl/arvados_cwl/runner.py      |  2 +-
 sdk/cwl/tests/test_container.py    | 15 ++++++++++-----
 sdk/cwl/tests/test_job.py          |  6 ++++--
 sdk/cwl/tests/test_submit.py       |  4 ++++
 6 files changed, 27 insertions(+), 10 deletions(-)

       via  75cb3149396f6385d6af30deaed74ee87ace696d (commit)
      from  ce7505914ba4c53a7aa1d987aaf92de81af1fb49 (commit)

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commit 75cb3149396f6385d6af30deaed74ee87ace696d
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Jan 15 15:22:49 2018 -0500

    12934: Fix unit tests.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index bb01796..6aa4c8f 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -22,7 +22,6 @@ from cwltool.errors import WorkflowException
 import cwltool.main
 import cwltool.workflow
 import cwltool.process
-import schema_salad
 from schema_salad.sourceline import SourceLine
 
 import arvados
@@ -379,6 +378,12 @@ class ArvCwlRunner(object):
                                   metadata=tool.metadata,
                                   override_tools=override_tools)
 
+        tool.doc_loader.fetcher_constructor = partial(CollectionFetcher,
+                                                api_client=self.api,
+                                                fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
+                                                num_retries=self.num_retries,
+                                                overrides=override_tools)
+
         # Upload local file references in the job order.
         job_order = upload_job_order(self, "%s input" % kwargs["name"],
                                      tool, job_order)
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 79bfacd..4acdc32 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -173,7 +173,8 @@ class ArvadosWorkflow(Workflow):
                         }]
                 }],
                 "hints": self.hints,
-                "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
+                "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
+                "id": "#"
             })
             kwargs["loader"] = self.doc_loader
             kwargs["avsc_names"] = self.doc_schema
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 28de7f3..28c35ad 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -246,7 +246,7 @@ def upload_workflow_deps(arvrunner, tool, override_tools):
                                 False,
                                 include_primary=False)
             document_loader.idx[deptool["id"]] = deptool
-            override_tools[deptool["id"]] = json.dumps(deptool)
+            override_tools[deptool["id"]] = yaml.round_trip_dump(deptool)
 
     tool.visit(upload_tool_deps)
 
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index c516d7b..c206934 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -44,7 +44,8 @@ class TestContainer(unittest.TestCase):
                 "inputs": [],
                 "outputs": [],
                 "baseCommand": "ls",
-                "arguments": [{"valueFrom": "$(runtime.outdir)"}]
+                "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+                "id": "#"
             })
             make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -124,7 +125,8 @@ class TestContainer(unittest.TestCase):
                 "class": "http://arvados.org/cwl#ReuseRequirement",
                 "enableReuse": False
             }],
-            "baseCommand": "ls"
+            "baseCommand": "ls",
+            "id": "#"
         })
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -231,7 +233,8 @@ class TestContainer(unittest.TestCase):
                     "location": "keep:99999999999999999999999999999995+99/subdir"
                 }                        ]
             }],
-            "baseCommand": "ls"
+            "baseCommand": "ls",
+            "id": "#"
         })
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -329,7 +332,8 @@ class TestContainer(unittest.TestCase):
             "stdout": "stdout.txt",
             "stderr": "stderr.txt",
             "stdin": "/keep/99999999999999999999999999999996+99/file.txt",
-            "arguments": [{"valueFrom": "$(runtime.outdir)"}]
+            "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+            "id": "#"
         })
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -449,7 +453,8 @@ class TestContainer(unittest.TestCase):
             ],
             "outputs": [],
             "baseCommand": "ls",
-            "arguments": [{"valueFrom": "$(runtime.outdir)"}]
+            "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+            "id": "#"
         })
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                      collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index faac1f7..309ac09 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -52,7 +52,8 @@ class TestJob(unittest.TestCase):
                 "inputs": [],
                 "outputs": [],
                 "baseCommand": "ls",
-                "arguments": [{"valueFrom": "$(runtime.outdir)"}]
+                "arguments": [{"valueFrom": "$(runtime.outdir)"}],
+                "id": "#"
             })
             make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -142,7 +143,8 @@ class TestJob(unittest.TestCase):
                 "class": "http://arvados.org/cwl#ReuseRequirement",
                 "enableReuse": False
             }],
-            "baseCommand": "ls"
+            "baseCommand": "ls",
+            "id": "#"
         }
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 059b472..9cabea0 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -532,6 +532,10 @@ class TestSubmit(unittest.TestCase):
                 "enableReuse": False,
             },
         ]
+        expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["$namespaces"] = {
+            "arv": "http://arvados.org/cwl#",
+            "cwltool": "http://commonwl.org/cwltool#"
+        }
 
         stubs.api.container_requests().create.assert_called_with(
             body=JsonDiffMatcher(expect_container))

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