[ARVADOS] updated: 7e38c190147681b7d2ce64601b1ac9661812fcd6
Git user
git at public.curoverse.com
Tue Jul 11 18:05:46 EDT 2017
Summary of changes:
sdk/cwl/arvados_cwl/fsaccess.py | 2 +-
sdk/cwl/arvados_cwl/runner.py | 9 ++------
sdk/cwl/tests/test_submit.py | 43 ++++++++++++++++++++++++++++++++------
sdk/cwl/tests/wf/expect_packed.cwl | 5 +++--
4 files changed, 43 insertions(+), 16 deletions(-)
via 7e38c190147681b7d2ce64601b1ac9661812fcd6 (commit)
from d1a7f9691ff2b9d77106f953c714b1455b228c64 (commit)
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commit 7e38c190147681b7d2ce64601b1ac9661812fcd6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Jul 11 18:04:32 2017 -0400
11948: Fix unit tests for additional file checking and nameroot/nameext fields.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curoverse.com>
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 5582d63..93e2819 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -95,7 +95,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
def exists(self, fn):
collection, rest = self.get_collection(fn)
- if collection:
+ if collection is not None:
if rest:
return collection.exists(rest)
else:
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 19ce393..e76d628 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -118,14 +118,9 @@ def upload_dependencies(arvrunner, name, document_loader,
if "location" not in f and "path" in f:
f["location"] = f["path"]
del f["path"]
- if not arvrunner.fs_access.exists(f["location"]):
+ if "location" in f and not arvrunner.fs_access.exists(f["location"]):
# Remove from sc
- i = 0
- while i < len(sc):
- if sc[i]["location"] == f["location"]:
- del sc[i]
- else:
- i += 1
+ sc[:] = [x for x in sc if x["location"] != f["location"]]
# Delete "default" from workflowobj
remove[0] = True
visit_class(obj["default"], ("File", "Directory"), add_default)
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 15cdc1e..3d6b915 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -79,7 +79,12 @@ def stubs(func):
if uuid in (v["uuid"], v["portable_data_hash"]):
return CollectionExecute(v)
- created_collections = {}
+ created_collections = {
+ "99999999999999999999999999999998+99": {
+ "uuid": "",
+ "portable_data_hash": "99999999999999999999999999999998+99",
+ "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
+ }}
stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
@@ -142,10 +147,22 @@ def stubs(func):
'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
'script_parameters': {
'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
- 'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'}},
+ 'x': {"value": {
+ 'basename': 'blorp.txt',
+ 'class': 'File',
+ 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+ "nameext": ".txt",
+ "nameroot": "blorp"
+ }},
'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
'listing': [
- {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ {
+ 'basename': 'renamed.txt',
+ 'class': 'File', 'location':
+ 'keep:99999999999999999999999999999998+99/file1.txt',
+ "nameext": ".txt",
+ "nameroot": "renamed"
+ }
]}},
'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
'arv:enable_reuse': True,
@@ -191,10 +208,24 @@ def stubs(func):
'/var/lib/cwl/cwl.input.json': {
'kind': 'json',
'content': {
- 'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
- 'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'},
+ 'y': {
+ 'basename': '99999999999999999999999999999998+99',
+ 'location': 'keep:99999999999999999999999999999998+99',
+ 'class': 'Directory'},
+ 'x': {
+ 'basename': u'blorp.txt',
+ 'class': 'File',
+ 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+ "nameext": ".txt",
+ "nameroot": "blorp"
+ },
'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
- {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+ {'basename': 'renamed.txt',
+ 'class': 'File',
+ 'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+ "nameext": ".txt",
+ "nameroot": "renamed"
+ }
]}
},
'kind': 'json'
diff --git a/sdk/cwl/tests/wf/expect_packed.cwl b/sdk/cwl/tests/wf/expect_packed.cwl
index 561daf4..32a9255 100644
--- a/sdk/cwl/tests/wf/expect_packed.cwl
+++ b/sdk/cwl/tests/wf/expect_packed.cwl
@@ -24,7 +24,7 @@ $graph:
- id: '#main/x'
type: File
default: {class: File, location: 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- basename: blorp.txt}
+ basename: blorp.txt, nameroot: blorp, nameext: .txt}
- id: '#main/y'
type: Directory
default: {class: Directory, location: 'keep:99999999999999999999999999999998+99',
@@ -32,7 +32,8 @@ $graph:
- id: '#main/z'
type: Directory
default: {class: Directory, basename: anonymous, listing: [{basename: renamed.txt,
- class: File, location: 'keep:99999999999999999999999999999998+99/file1.txt'}]}
+ class: File, location: 'keep:99999999999999999999999999999998+99/file1.txt',
+ nameroot: renamed, nameext: .txt}]}
outputs: []
steps:
- id: '#main/step1'
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