[ARVADOS] created: 1.1.4-369-g10176dd69

Git user git at public.curoverse.com
Fri Aug 24 15:27:01 EDT 2018


        at  10176dd693120301ccc9695310c6ecbd7714cf79 (commit)


commit 10176dd693120301ccc9695310c6ecbd7714cf79
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Aug 24 13:51:56 2018 -0400

    14075: Tweak ruamel.yaml verision range in setup.py
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 8efcb6e7d..bdbe77829 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -33,11 +33,13 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20180524215209',
-          'schema-salad==2.7.20180501211602',
-          'typing >= 3.5.3',
-          'ruamel.yaml >=0.13.11, <0.15',
-          'arvados-python-client>=1.1.4.20180507184611',
+          'cwltool==1.0.20180806194258',
+          'schema-salad==2.7.20180719125426',
+          'typing >= 3.6.4',
+          # Need to limit ruamel.yaml version to 0.15.26 because of bug
+          # https://bitbucket.org/ruamel/yaml/issues/227/regression-parsing-flow-mapping
+          'ruamel.yaml >=0.13.11, <= 0.15.26',
+          'arvados-python-client>=1.1.4.20180607143841',
           'setuptools',
           'ciso8601 >=1.0.6, <2.0.0'
       ],

commit c71619f7d3ec01de2c5a9a517701ecf88381830e
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Aug 24 12:12:47 2018 -0400

    14075: Fix cwl unit tests
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index 2295e934a..0209d2eba 100644
--- 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 30930dd49..1a3f6a9c8 100644
--- 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 f8b557f6c..246d80e50 100644
--- 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 ca51de1fe..5063d75f2 100644
--- 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:

commit c076dcc368300f5e767b6cb946551fd3c9c84a3b
Author: Joshua C. Randall <jcrandall at alum.mit.edu>
Date:   Mon Aug 20 17:31:29 2018 +0100

    fix slow queries in uploadfiles
    
    change uploadfiles to include pdh in name of collection rather then using ensure_unique_names=True
    also don't bother listing existing empty collections
    
    Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall at alum.mit.edu>

diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index 831e496a2..ca51de1fe 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -1,6 +1,19 @@
 # Copyright (C) The Arvados Authors. All rights reserved.
+# Copyright (C) 2018 Genome Research Ltd.
 #
 # SPDX-License-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 from __future__ import print_function
 from __future__ import absolute_import
@@ -22,6 +35,7 @@ import sys
 import errno
 import arvados.commands._util as arv_cmd
 import arvados.collection
+import arvados.config as config
 
 from arvados._version import __version__
 
@@ -206,22 +220,39 @@ def uploadfiles(files, api, dry_run=False, num_retries=0,
                     for src in iterfiles:
                         write_file(collection, pathprefix, os.path.join(root, src))
 
-        filters=[["portable_data_hash", "=", collection.portable_data_hash()]]
-        if name:
-            filters.append(["name", "like", name+"%"])
-        if project:
-            filters.append(["owner_uuid", "=", project])
-
-        exists = api.collections().list(filters=filters, limit=1).execute(num_retries=num_retries)
-
-        if exists["items"]:
-            item = exists["items"][0]
-            pdh = item["portable_data_hash"]
-            logger.info("Using collection %s (%s)", pdh, item["uuid"])
-        elif len(collection) > 0:
-            collection.save_new(name=name, owner_uuid=project, ensure_unique_name=True)
+        pdh = None
+        if len(collection) > 0:
+            # non-empty collection
+            filters = [["portable_data_hash", "=", collection.portable_data_hash()]]
+            name_pdh = "%s (%s)" % (name, collection.portable_data_hash())
+            if name:
+                filters.append(["name", "=", name_pdh])
+            if project:
+                filters.append(["owner_uuid", "=", project])
+
+            # do the list / create in a loop with up to 2 tries as we are using `ensure_unique_name=False`
+            # and there is a potential race with other workflows that may have created the collection
+            # between when we list it and find it does not exist and when we attempt to create it.
+            tries = 2
+            while pdh is None and tries > 0:
+                exists = api.collections().list(filters=filters, limit=1).execute(num_retries=num_retries)
+
+                if exists["items"]:
+                    item = exists["items"][0]
+                    pdh = item["portable_data_hash"]
+                    logger.info("Using collection %s (%s)", pdh, item["uuid"])
+                else:
+                    try:
+                        collection.save_new(name=name_pdh, owner_uuid=project, ensure_unique_name=False)
+                        pdh = collection.portable_data_hash()
+                        logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator())
+                    except arvados.errors.ApiError as ae:
+                        tries -= 1
+        else:
+            # empty collection
             pdh = collection.portable_data_hash()
-            logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator())
+            assert (pdh == config.EMPTY_BLOCK_LOCATOR), "Empty collection portable_data_hash did not have expected locator"
+            logger.info("Using empty collection %s", pdh)
 
     for c in files:
         c.keepref = "%s/%s" % (pdh, c.fn)

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