[ARVADOS] updated: 3b68728dd1f6708fa8f2832bb7c8c12fc2fa6820
Git user
git at public.curoverse.com
Thu Aug 11 14:48:31 EDT 2016
Summary of changes:
build/run-build-packages.sh | 2 +-
sdk/cwl/arvados_cwl/__init__.py | 4 ++--
sdk/cwl/arvados_cwl/arvjob.py | 2 +-
sdk/cwl/arvados_cwl/fsaccess.py | 9 +++++++++
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/arvados-tests.yml | 2 +-
sdk/cwl/tests/{dir6.cwl => keep-dir-test-input.cwl} | 0
sdk/cwl/tests/test_job.py | 4 +++-
8 files changed, 18 insertions(+), 7 deletions(-)
rename sdk/cwl/tests/{dir6.cwl => keep-dir-test-input.cwl} (100%)
via 3b68728dd1f6708fa8f2832bb7c8c12fc2fa6820 (commit)
via c48e456e126f8c4a87cb549e4871d6b23dceeb34 (commit)
via bc4f35c648f5414d20ac69501e5955376452ce55 (commit)
from 54f4d656aac507205396969dd16cb01570a9f707 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 3b68728dd1f6708fa8f2832bb7c8c12fc2fa6820
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 14:46:24 2016 -0400
9751: Bump cwltool dependency.
diff --git a/build/run-build-packages.sh b/build/run-build-packages.sh
index fec4950..8cb2330 100755
--- a/build/run-build-packages.sh
+++ b/build/run-build-packages.sh
@@ -467,7 +467,7 @@ fpm_build schema_salad "" "" python 1.14.20160708181155
fpm_build ruamel.yaml "" "" python 0.11.11 --python-setup-py-arguments "--single-version-externally-managed"
# And for cwltool we have the same problem as for schema_salad. Ward, 2016-03-17
-fpm_build cwltool "" "" python 1.0.20160810161358
+fpm_build cwltool "" "" python 1.0.20160811184335
# FPM eats the trailing .0 in the python-rdflib-jsonld package when built with 'rdflib-jsonld>=0.3.0'. Force the version. Ward, 2016-03-25
fpm_build rdflib-jsonld "" "" python 0.3.0
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 35408b7..e22a74f 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160811170313',
+ 'cwltool==1.0.20160811184335',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
commit c48e456e126f8c4a87cb549e4871d6b23dceeb34
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 14:19:37 2016 -0400
9751: Fix unit tests. Rename dir6.cwl to keep-dir-test-input.cwl
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index fd9e74f..f7792cd 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -114,6 +114,8 @@ class ArvCwlRunner(object):
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
self.pipeline = None
+ make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
+ self.fs_access = make_fs_access(kwargs["basedir"])
if kwargs.get("create_template"):
tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse"))
@@ -124,8 +126,6 @@ class ArvCwlRunner(object):
self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
- make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
- self.fs_access = make_fs_access(kwargs["basedir"])
kwargs["make_fs_access"] = make_fs_access
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 99237e1..35408b7 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160811124408',
+ 'cwltool==1.0.20160811170313',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 2526258..1187962 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -6,5 +6,5 @@
"class": "File",
"checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
}
- tool: dir6.cwl
+ tool: keep-dir-test-input.cwl
doc: Test directory in keep
diff --git a/sdk/cwl/tests/dir6.cwl b/sdk/cwl/tests/keep-dir-test-input.cwl
similarity index 100%
rename from sdk/cwl/tests/dir6.cwl
rename to sdk/cwl/tests/keep-dir-test-input.cwl
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 0d3a494..46d2048 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -3,6 +3,7 @@ import logging
import mock
import unittest
import os
+import functools
import cwltool.process
if not os.getenv('ARVADOS_DEBUG'):
@@ -28,7 +29,8 @@ class TestJob(unittest.TestCase):
}
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names, basedir="")
arvtool.formatgraph = None
- for j in arvtool.job({}, mock.MagicMock(), basedir=""):
+ for j in arvtool.job({}, mock.MagicMock(), basedir="",
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)):
j.run()
runner.api.jobs().create.assert_called_with(
body={
commit bc4f35c648f5414d20ac69501e5955376452ce55
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Aug 11 13:01:41 2016 -0400
9751: Override realpath in CollectionFsAccess
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 0035597..9f11058 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -227,7 +227,7 @@ class RunnerJob(Runner):
logger.info("Submitted job %s", response["uuid"])
if kwargs.get("submit"):
- self.pipeline = self.arvrunner.api.pipeline_instances().create(
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
body={
"owner_uuid": self.arvrunner.project_uuid,
"name": shortname(self.tool.tool["id"]),
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 4b129cc..d258937 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -104,3 +104,12 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
return paths[-1]
return os.path.join(path, *paths)
+
+ def realpath(self, path):
+ if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
+ return path
+ collection, rest = self.get_collection(path)
+ if collection:
+ return path
+ else:
+ return os.path.realpath(path)
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 60ea7ab..99237e1 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160810161358',
+ 'cwltool==1.0.20160811124408',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
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