14075: Fix cwl unit tests

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index 2295e934ac77de76182d04749715a57f730874b4..0209d2eba9f681d5eb8e1ad51d24954b0f2b9f3f 100644 (file)
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -4,6 +4,7 @@
 
 import arvados_cwl
 from arvados_cwl.arvdocker import arv_docker_clear_cache
+import arvados.config
 import logging
 import mock
 import unittest
@@ -21,6 +22,32 @@ if not os.getenv('ARVADOS_DEBUG'):
     logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 
 
+class CollectionMock(object):
+    def __init__(self, vwdmock, *args, **kwargs):
+        self.vwdmock = vwdmock
+        self.count = 0
+
+    def open(self, *args, **kwargs):
+        self.count += 1
+        return self.vwdmock.open(*args, **kwargs)
+
+    def copy(self, *args, **kwargs):
+        self.count += 1
+        self.vwdmock.copy(*args, **kwargs)
+
+    def save_new(self, *args, **kwargs):
+        pass
+
+    def __len__(self):
+        return self.count
+
+    def portable_data_hash(self):
+        if self.count == 0:
+            return arvados.config.EMPTY_BLOCK_LOCATOR
+        else:
+            return "99999999999999999999999999999996+99"
+
+
 class TestContainer(unittest.TestCase):
 
     # The test passes no builder.resources
@@ -215,8 +242,7 @@ class TestContainer(unittest.TestCase):
         runner.fs_access.get_collection.side_effect = get_collection_mock
 
         vwdmock = mock.MagicMock()
-        collection_mock.return_value = vwdmock
-        vwdmock.portable_data_hash.return_value = "99999999999999999999999999999996+99"
+        collection_mock.side_effect = lambda *args, **kwargs: CollectionMock(vwdmock, *args, **kwargs)
 
         tool = cmap({
             "inputs": [],

diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 30930dd49abb1a91fe371cc291cd916feac735df..1a3f6a9c8eb06527856050528ee8de1ea3cb1bee 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -19,6 +19,7 @@ from schema_salad.ref_resolver import Loader
 from schema_salad.sourceline import cmap
 from .mock_discovery import get_rootDesc
 from .matcher import JsonDiffMatcher, StripYAMLComments
+from .test_container import CollectionMock
 
 if not os.getenv('ARVADOS_DEBUG'):
     logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
@@ -342,7 +343,8 @@ class TestWorkflow(unittest.TestCase):
         tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
         metadata["cwlVersion"] = tool["cwlVersion"]
 
-        mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+        mockc = mock.MagicMock()
+        mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mockc, *args, **kwargs)
 
         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
                                               basedir="", make_fs_access=make_fs_access, loader=document_loader,
@@ -366,8 +368,8 @@ class TestWorkflow(unittest.TestCase):
                         'HOME': '$(task.outdir)',
                         'TMPDIR': '$(task.tmpdir)'},
                                'task.vwd': {
-                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
-                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
+                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
                                },
                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
                     'task.stdout': 'cwl.output.json'}]},
@@ -384,8 +386,8 @@ class TestWorkflow(unittest.TestCase):
                      ['docker_image_locator', 'in docker', 'arvados/jobs']],
             find_or_create=True)
 
-        mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
-        mockcollection().open().__enter__().write.assert_has_calls([mock.call(
+        mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
+        mockc.open().__enter__().write.assert_has_calls([mock.call(
 '''{
   "fileblub": {
     "basename": "token.txt",
@@ -428,7 +430,7 @@ class TestWorkflow(unittest.TestCase):
         tool, metadata = document_loader.resolve_ref("tests/wf/echo-wf.cwl")
         metadata["cwlVersion"] = tool["cwlVersion"]
 
-        mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
+        mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mock.MagicMock(), *args, **kwargs)
 
         arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
                                               basedir="", make_fs_access=make_fs_access, loader=document_loader,
@@ -452,8 +454,8 @@ class TestWorkflow(unittest.TestCase):
                         'HOME': '$(task.outdir)',
                         'TMPDIR': '$(task.tmpdir)'},
                                'task.vwd': {
-                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
-                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
+                                   'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
+                                   'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
                                },
                     'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
                     'task.stdout': 'cwl.output.json'}]},

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index f8b557f6cbe86bf4b90bc55a3f4941c88560d948..246d80e506146c3e689ee05bc023c136323294af 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -286,14 +286,14 @@ class TestSubmit(unittest.TestCase):
                 'manifest_text':
                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
                 'replication_desired': None,
-                'name': 'submit_tool.cwl dependencies',
-            }), ensure_unique_name=True),
+                'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+            }), ensure_unique_name=False),
             mock.call(body=JsonDiffMatcher({
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
                 'replication_desired': None,
-                'name': 'submit_wf.cwl input',
-            }), ensure_unique_name=True),
+                'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+            }), ensure_unique_name=False),
             mock.call(body=JsonDiffMatcher({
                 'manifest_text':
                 '. 61df2ed9ee3eb7dd9b799e5ca35305fa+1217 0:1217:workflow.cwl\n',
@@ -473,14 +473,14 @@ class TestSubmit(unittest.TestCase):
                 'manifest_text':
                 '. 5bcc9fe8f8d5992e6cf418dc7ce4dbb3+16 0:16:blub.txt\n',
                 'replication_desired': None,
-                'name': 'submit_tool.cwl dependencies',
-            }), ensure_unique_name=True),
+                'name': 'submit_tool.cwl dependencies (5d373e7629203ce39e7c22af98a0f881+52)',
+            }), ensure_unique_name=False),
             mock.call(body=JsonDiffMatcher({
                 'manifest_text':
                 '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
                 'replication_desired': None,
-                'name': 'submit_wf.cwl input',
-            }), ensure_unique_name=True)])
+                'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+            }), ensure_unique_name=False)])
 
         expect_container = copy.deepcopy(stubs.expect_container_spec)
         stubs.api.container_requests().create.assert_called_with(

diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index ca51de1fe33517c8001fcaef53efabcf7771aeca..5063d75f2a04b22545e7d2589d189139bd6378dc 100644 (file)
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -248,10 +248,19 @@ def uploadfiles(files, api, dry_run=False, num_retries=0,
                         logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator())
                     except arvados.errors.ApiError as ae:
                         tries -= 1
+            if pdh is None:
+                # Something weird going on here, probably a collection
+                # with a conflicting name but wrong PDH.  We won't
+                # able to reuse it but we still need to save our
+                # collection, so so save it with unique name.
+                logger.info("Name conflict on '%s', existing collection has an unexpected portable data hash", name_pdh)
+                collection.save_new(name=name_pdh, owner_uuid=project, ensure_unique_name=True)
+                pdh = collection.portable_data_hash()
+                logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator())
         else:
             # empty collection
             pdh = collection.portable_data_hash()
-            assert (pdh == config.EMPTY_BLOCK_LOCATOR), "Empty collection portable_data_hash did not have expected locator"
+            assert (pdh == config.EMPTY_BLOCK_LOCATOR), "Empty collection portable_data_hash did not have expected locator, was %s" % pdh
             logger.info("Using empty collection %s", pdh)
 
     for c in files: