[ARVADOS] updated: 540adbf18728558df8797bf176ec666061cea934

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvworkflow.py |  2 +-
 sdk/cwl/tests/test_submit.py       | 44 +++++++++++++++++++++++++++-
 sdk/cwl/tests/wf/expect_packed.cwl | 60 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 104 insertions(+), 2 deletions(-)
 create mode 100644 sdk/cwl/tests/wf/expect_packed.cwl

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      from  0f53d219c91812baeac4cff3387196c6501ec0c0 (commit)

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commit 540adbf18728558df8797bf176ec666061cea934
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Aug 30 10:46:47 2016 -0400

    9766: Add test for workflow create.

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 0e1ad9f..dcef67f 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -27,7 +27,7 @@ def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
             "owner_uuid": project_uuid,
             "name": tool.tool.get("label", name),
             "description": tool.tool.get("doc", ""),
-            "workflow":json.dumps(packed, sort_keys=True, indent=4)
+            "workflow":json.dumps(packed, sort_keys=True, indent=4, separators=(',',': '))
         }}
 
     if update_uuid:
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 21be5c7..6ea9314 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -9,6 +9,7 @@ import hashlib
 import mock
 import sys
 import unittest
+import json
 
 from .matcher import JsonDiffMatcher
 
@@ -128,6 +129,12 @@ def stubs(func):
                 'ram': 268435456
             }
         }
+
+        stubs.expect_workflow_uuid = "zzzzz-7fd4e-zzzzzzzzzzzzzzz"
+        stubs.api.workflows().create().execute.return_value = {
+            "uuid": stubs.expect_workflow_uuid,
+        }
+
         return func(self, stubs, *args, **kwargs)
     return wrapped
 
@@ -244,7 +251,7 @@ class TestCreateTemplate(unittest.TestCase):
         capture_stdout = cStringIO.StringIO()
 
         exited = arvados_cwl.main(
-            ["--create-template", "--no-wait", "--debug",
+            ["--create-template", "--debug",
              "--project-uuid", project_uuid,
              "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
             capture_stdout, sys.stderr, api_client=stubs.api)
@@ -274,6 +281,41 @@ class TestCreateTemplate(unittest.TestCase):
                          stubs.expect_pipeline_template_uuid + '\n')
 
 
+class TestCreateWorkflow(unittest.TestCase):
+    @stubs
+    def test_create(self, stubs):
+        project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+
+        capture_stdout = cStringIO.StringIO()
+
+        exited = arvados_cwl.main(
+            ["--create-workflow", "--debug",
+             "--project-uuid", project_uuid,
+             "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+            capture_stdout, sys.stderr, api_client=stubs.api)
+        self.assertEqual(exited, 0)
+
+        stubs.api.pipeline_templates().create.refute_called()
+        stubs.api.container_requests().create.refute_called()
+
+        with open("tests/wf/expect_packed.cwl") as f:
+            expect_workflow = f.read()
+
+        body = {
+            "workflow": {
+                "owner_uuid": project_uuid,
+                "name": "submit_wf.cwl",
+                "description": "",
+                "workflow": expect_workflow
+            }
+        }
+        stubs.api.workflows().create.assert_called_with(
+            body=JsonDiffMatcher(body))
+
+        self.assertEqual(capture_stdout.getvalue(),
+                         stubs.expect_workflow_uuid + '\n')
+
+
 class TestTemplateInputs(unittest.TestCase):
     expect_template = {
         "components": {
diff --git a/sdk/cwl/tests/wf/expect_packed.cwl b/sdk/cwl/tests/wf/expect_packed.cwl
new file mode 100644
index 0000000..84b89af
--- /dev/null
+++ b/sdk/cwl/tests/wf/expect_packed.cwl
@@ -0,0 +1,60 @@
+{
+    "$graph": [
+        {
+            "baseCommand": "cat",
+            "class": "CommandLineTool",
+            "id": "#submit_tool.cwl",
+            "inputs": [
+                {
+                    "default": {
+                        "class": "File",
+                        "location": "keep:99999999999999999999999999999991+99/tool/blub.txt"
+                    },
+                    "id": "#submit_tool.cwl/x",
+                    "inputBinding": {
+                        "position": 1
+                    },
+                    "type": "File"
+                }
+            ],
+            "outputs": [],
+            "requirements": [
+                {
+                    "class": "DockerRequirement",
+                    "dockerImageId": "debian:8",
+                    "dockerPull": "debian:8"
+                }
+            ]
+        },
+        {
+            "class": "Workflow",
+            "id": "#main",
+            "inputs": [
+                {
+                    "default": {
+                        "basename": "blorp.txt",
+                        "class": "File",
+                        "location": "keep:99999999999999999999999999999991+99/input/blorp.txt"
+                    },
+                    "id": "#main/x",
+                    "type": "File"
+                }
+            ],
+            "outputs": [],
+            "steps": [
+                {
+                    "id": "#main/step1",
+                    "in": [
+                        {
+                            "id": "#main/step1/x",
+                            "source": "#main/x"
+                        }
+                    ],
+                    "out": [],
+                    "run": "#submit_tool.cwl"
+                }
+            ]
+        }
+    ],
+    "cwlVersion": "v1.0"
+}
\ No newline at end of file

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