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Errors from cwltool 'make test'
Raw
gistfile1.txt
$ make test
./setup.py test
running pytest
Searching for typing<3.6,>=3.5.2
Best match: typing 3.5.3.0
Processing typing-3.5.3.0-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/typing-3.5.3.0-py2.7.egg
Searching for schema-salad<3,>=2.4.20170308171942
Best match: schema-salad 2.5.20170428142041
Processing schema_salad-2.5.20170428142041-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/schema_salad-2.5.20170428142041-py2.7.egg
Searching for shellescape<3.5,>=3.4.1
Best match: shellescape 3.4.1
Processing shellescape-3.4.1-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/shellescape-3.4.1-py2.7.egg
Searching for rdflib<4.3.0,>=4.2.2
Best match: rdflib 4.2.2
Processing rdflib-4.2.2-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/rdflib-4.2.2-py2.7.egg
Searching for ruamel.yaml>=0.12.4
Best match: ruamel.yaml 0.14.12
Processing ruamel.yaml-0.14.12-py2.7-linux-x86_64.egg
Using /home/takluyver/Code/cwltool/.eggs/ruamel.yaml-0.14.12-py2.7-linux-x86_64.egg
Searching for avro
Best match: avro 1.8.2
Processing avro-1.8.2-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/avro-1.8.2-py2.7.egg
Searching for CacheControl<0.12,>=0.11.7
Best match: CacheControl 0.11.7
Processing CacheControl-0.11.7-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/CacheControl-0.11.7-py2.7.egg
Searching for rdflib-jsonld<0.5.0,>=0.3.0
Best match: rdflib-jsonld 0.4.0
Processing rdflib_jsonld-0.4.0-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/rdflib_jsonld-0.4.0-py2.7.egg
Searching for isodate
Best match: isodate 0.5.4
Processing isodate-0.5.4-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/isodate-0.5.4-py2.7.egg
Searching for ruamel.ordereddict
Best match: ruamel.ordereddict 0.4.9
Processing ruamel.ordereddict-0.4.9-py2.7-linux-x86_64.egg
Using /home/takluyver/Code/cwltool/.eggs/ruamel.ordereddict-0.4.9-py2.7-linux-x86_64.egg
Searching for mock>=2.0.0
Best match: mock 2.0.0
Processing mock-2.0.0-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/mock-2.0.0-py2.7.egg
Searching for pbr>=0.11
Best match: pbr 3.0.1
Processing pbr-3.0.1-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/pbr-3.0.1-py2.7.egg
Searching for funcsigs>=1
Best match: funcsigs 1.0.2
Processing funcsigs-1.0.2-py2.7.egg
Using /home/takluyver/Code/cwltool/.eggs/funcsigs-1.0.2-py2.7.egg
running egg_info
writing requirements to cwltool.egg-info/requires.txt
writing cwltool.egg-info/PKG-INFO
writing top-level names to cwltool.egg-info/top_level.txt
writing dependency_links to cwltool.egg-info/dependency_links.txt
writing entry points to cwltool.egg-info/entry_points.txt
reading manifest file 'cwltool.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
writing manifest file 'cwltool.egg-info/SOURCES.txt'
running build_ext
============================= test session starts ==============================
platform linux2 -- Python 2.7.12, pytest-2.8.7, py-1.4.31, pluggy-0.3.1
rootdir: /home/takluyver/Code/cwltool, inifile:
collected 51 items / 10 errors
test.txt s
build/lib.linux-x86_64-2.7/cwltool/tests/test_check.py .
build/lib.linux-x86_64-2.7/cwltool/tests/test_examples.py .............
build/lib.linux-x86_64-2.7/cwltool/tests/test_ext.py ..........
build/lib.linux-x86_64-2.7/cwltool/tests/test_fetch.py .
build/lib.linux-x86_64-2.7/cwltool/tests/test_js_sandbox.py ..
build/lib.linux-x86_64-2.7/cwltool/tests/test_pack.py F
build/lib.linux-x86_64-2.7/cwltool/tests/test_pathmapper.py ..
build/lib.linux-x86_64-2.7/cwltool/tests/test_relax_path_checks.py .
build/lib.linux-x86_64-2.7/cwltool/tests/test_toolargparse.py ....
cwltool/schemas/draft-3/salad/tests/test_examples.py FFFF
cwltool/schemas/v1.0/salad/tests/test_examples.py FFFFFFFFFF.
==================================== ERRORS ====================================
ERROR collecting cwltool/schemas/v1.1.0-dev1/salad/schema_salad/tests/test_examples.py
/usr/lib/python2.7/dist-packages/py/_path/local.py:664: in pyimport
issame = self.samefile(modfile)
/usr/lib/python2.7/dist-packages/py/_path/local.py:194: in samefile
os.path.samefile, self.strpath, other)
/usr/lib/python2.7/dist-packages/py/_error.py:84: in checked_call
raise cls("%s%r" % (func.__name__, args))
E ENOTDIR: [Not a directory]: samefile('/home/takluyver/Code/cwltool/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/tests/test_examples.py', '/home/takluyver/Code/cwltool/.eggs/schema_salad-2.5.20170428142041-py2.7.egg/schema_salad/tests/test_examples.py')
_____________________ ERROR collecting tests/test_check.py _____________________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_check
___________________ ERROR collecting tests/test_examples.py ____________________
import file mismatch:
imported module 'tests.test_examples' has this __file__ attribute:
/home/takluyver/Code/cwltool/cwltool/schemas/v1.0/salad/tests/test_examples.py
which is not the same as the test file we want to collect:
/home/takluyver/Code/cwltool/tests/test_examples.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
______________________ ERROR collecting tests/test_ext.py ______________________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_ext
_____________________ ERROR collecting tests/test_fetch.py _____________________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_fetch
__________________ ERROR collecting tests/test_js_sandbox.py ___________________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_js_sandbox
_____________________ ERROR collecting tests/test_pack.py ______________________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_pack
__________________ ERROR collecting tests/test_pathmapper.py ___________________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_pathmapper
_______________ ERROR collecting tests/test_relax_path_checks.py _______________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_relax_path_checks
_________________ ERROR collecting tests/test_toolargparse.py __________________
/usr/lib/python2.7/dist-packages/py/_path/local.py:650: in pyimport
__import__(modname)
E ImportError: No module named test_toolargparse
=================================== FAILURES ===================================
______________________________ TestPack.test_pack ______________________________
self = <cwltool.tests.test_pack.TestPack testMethod=test_pack>
def test_pack(self):
self.maxDiff = None
document_loader, workflowobj, uri = fetch_document(
get_data("tests/wf/revsort.cwl"))
document_loader, avsc_names, processobj, metadata, uri = validate_document(
document_loader, workflowobj, uri)
packed = cwltool.pack.pack(document_loader, processobj, uri, metadata)
with open(get_data("tests/wf/expect_packed.cwl")) as f:
expect_packed = json.load(f)
adjustFileObjs(packed, partial(makeRelative,
os.path.abspath(get_data("tests/wf"))))
adjustDirObjs(packed, partial(makeRelative,
os.path.abspath(get_data("tests/wf"))))
self.assertIn("$schemas", packed)
del packed["$schemas"]
del expect_packed["$schemas"]
> self.assertEqual(expect_packed, packed)
E AssertionError: {u'cwlVersion': u'v1.0', u'$graph': [{u'inputs': [{u'default': {u'class': u'File [truncated]... != {'cwlVersion': 'v1.0', '$graph': [CommentedMap([('class', 'Workflow'), ('doc', ' [truncated]...
E + {'$graph': [CommentedMap([('class', 'Workflow'), ('doc', 'Reverse the lines in a document, then sort those lines.'), ('hints', [CommentedMap([('class', 'DockerRequirement'), ('dockerPull', 'debian:8')])]), ('inputs', [CommentedMap([('type', 'File'), ('doc', 'The input file to be processed.'), ('default', CommentedMap([('class', 'File'), ('location', '../../../../../tests/wf/hello.txt')])), ('id', '#main/input')]), CommentedMap([('type', 'boolean'), ('default', True), ('doc', 'If true, reverse (decending) sort'), ('id', '#main/reverse_sort')])]), ('outputs', [CommentedMap([('type', 'File'), ('outputSource', u'#main/sorted/output'), ('doc', 'The output with the lines reversed and sorted.'), ('id', '#main/output')])]), ('steps', [CommentedMap([('in', [CommentedMap([('source', u'#main/input'), ('id', u'#main/rev/input')])]), ('out', [u'#main/rev/output']), ('run', u'#revtool.cwl'), ('id', '#main/rev')]), CommentedMap([('in', [CommentedMap([('source', u'#main/rev/output'), ('id', u'#main/sorted/input')]), CommentedMap([('source', u'#main/reverse_sort'), ('id', u'#main/sorted/reverse')])]), ('out', [u'#main/sorted/output']), ('run', u'#sorttool.cwl'), ('id', '#main/sorted')])]), ('id', '#main')]),
E + CommentedMap([('class', 'CommandLineTool'), ('doc', 'Reverse each line using the `rev` command'), ('inputs', [CommentedMap([('type', 'File'), ('inputBinding', CommentedMap()), ('id', u'#revtool.cwl/input')])]), ('outputs', [CommentedMap([('type', 'File'), ('outputBinding', CommentedMap([('glob', 'output.txt')])), ('id', u'#revtool.cwl/output')])]), ('baseCommand', 'rev'), ('stdout', 'output.txt'), (u'id', u'#revtool.cwl')]),
E + CommentedMap([('class', 'CommandLineTool'), ('doc', 'Sort lines using the `sort` command'), ('inputs', [CommentedMap([('id', u'#sorttool.cwl/reverse'), ('type', 'boolean'), ('inputBinding', CommentedMap([('position', 1), ('prefix', '--reverse')]))]), CommentedMap([('id', u'#sorttool.cwl/input'), ('type', 'File'), ('inputBinding', CommentedMap([('position', 2)]))])]), ('outputs', [CommentedMap([('id', u'#sorttool.cwl/output'), ('type', 'File'), ('outputBinding', CommentedMap([('glob', 'output.txt')]))])]), ('baseCommand', 'sort'), ('stdout', 'output.txt'), (u'id', u'#sorttool.cwl')])],
E - {u'$graph': [{u'class': u'Workflow',
E - u'doc': u'Reverse the lines in a document, then sort those lines.',
E - u'hints': [{u'class': u'DockerRequirement',
E - u'dockerPull': u'debian:8'}],
E - u'id': u'#main',
E - u'inputs': [{u'default': {u'class': u'File',
E - u'location': u'hello.txt'},
E - u'doc': u'The input file to be processed.',
E - u'id': u'#main/input',
E - u'type': u'File'},
E - {u'default': True,
E - u'doc': u'If true, reverse (decending) sort',
E - u'id': u'#main/reverse_sort',
E - u'type': u'boolean'}],
E - u'outputs': [{u'doc': u'The output with the lines reversed and sorted.',
E - u'id': u'#main/output',
E - u'outputSource': u'#main/sorted/output',
E - u'type': u'File'}],
E - u'steps': [{u'id': u'#main/rev',
E - u'in': [{u'id': u'#main/rev/input',
E - u'source': u'#main/input'}],
E - u'out': [u'#main/rev/output'],
E - u'run': u'#revtool.cwl'},
E - {u'id': u'#main/sorted',
E - u'in': [{u'id': u'#main/sorted/input',
E - u'source': u'#main/rev/output'},
E - {u'id': u'#main/sorted/reverse',
E - u'source': u'#main/reverse_sort'}],
E - u'out': [u'#main/sorted/output'],
E - u'run': u'#sorttool.cwl'}]},
E - {u'baseCommand': u'rev',
E - u'class': u'CommandLineTool',
E - u'doc': u'Reverse each line using the `rev` command',
E - u'id': u'#revtool.cwl',
E - u'inputs': [{u'id': u'#revtool.cwl/input',
E - u'inputBinding': {},
E - u'type': u'File'}],
E - u'outputs': [{u'id': u'#revtool.cwl/output',
E - u'outputBinding': {u'glob': u'output.txt'},
E - u'type': u'File'}],
E - u'stdout': u'output.txt'},
E - {u'baseCommand': u'sort',
E - u'class': u'CommandLineTool',
E - u'doc': u'Sort lines using the `sort` command',
E - u'id': u'#sorttool.cwl',
E - u'inputs': [{u'id': u'#sorttool.cwl/reverse',
E - u'inputBinding': {u'position': 1,
E - u'prefix': u'--reverse'},
E - u'type': u'boolean'},
E - {u'id': u'#sorttool.cwl/input',
E - u'inputBinding': {u'position': 2},
E - u'type': u'File'}],
E - u'outputs': [{u'id': u'#sorttool.cwl/output',
E - u'outputBinding': {u'glob': u'output.txt'},
E - u'type': u'File'}],
E - u'stdout': u'output.txt'}],
E - u'cwlVersion': u'v1.0'}
E ? - -
E
E + 'cwlVersion': 'v1.0'}
build/lib.linux-x86_64-2.7/cwltool/tests/test_pack.py:32: AssertionError
----------------------------- Captured stderr call -----------------------------
Resolved '/home/takluyver/Code/cwltool/tests/wf/revsort.cwl' to 'file:///home/takluyver/Code/cwltool/tests/wf/revsort.cwl'
__________________________ TestSchemas.test_examples ___________________________
self = <test_examples.TestSchemas testMethod=test_examples>
def test_examples(self):
self.maxDiff = None
for a in ["field_name", "ident_res", "link_res", "vocab_res"]:
> ldr, _, _ = schema_salad.schema.load_schema("schema_salad/metaschema/%s_schema.yml" % a)
cwltool/schemas/draft-3/salad/tests/test_examples.py:72:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
build/bdist.linux-x86_64/egg/schema_salad/schema.py:200: in load_schema
???
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:493: in resolve_ref
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.sourceline.SourceLine object at 0x7f005daf1a10>
exc_type = <type 'exceptions.RuntimeError'>
exc_value = RuntimeError(u"[Errno 2] No such file or directory: '/home/takluyver/Code/cwltool/schema_salad/metaschema/field_name_schema.yml'",)
traceback = <traceback object at 0x7f005d7c3830>
> ???
E RuntimeError: [Errno 2] No such file or directory: '/home/takluyver/Code/cwltool/schema_salad/metaschema/field_name_schema.yml'
build/bdist.linux-x86_64/egg/schema_salad/sourceline.py:150: RuntimeError
_________________________ TestSchemas.test_jsonld_ctx __________________________
self = <test_examples.TestSchemas testMethod=test_jsonld_ctx>
def test_jsonld_ctx(self):
ldr, _, _ = schema_salad.schema.load_schema({
"$base": "Y",
"name": "X",
"$namespaces": {
"foo": "http://example.com/foo#"
},
"$graph": [{
"name": "ExampleType",
"type": "enum",
> "symbols": ["asym", "bsym"]}]
})
cwltool/schemas/draft-3/salad/tests/test_examples.py:60:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
build/bdist.linux-x86_64/egg/schema_salad/schema.py:200: in load_schema
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005dac8cd0>
ref = {'$base': 'Y', '$graph': [{'name': 'ExampleType', 'symbols': ['asym', 'bsym'], 'type': 'enum'}], '$namespaces': {'foo': 'http://example.com/foo#'}, 'name': 'X'}
base_url = 'file:///home/takluyver/Code/cwltool/', checklinks = True
> ???
E ValueError: Expected CommentedMap or string, got <type 'dict'>: `{'$graph': [{'symbols': ['asym', 'bsym'], 'type': 'enum', 'name': 'ExampleType'}], '$namespaces': {'foo': 'http://example.com/foo#'}, 'name': 'X', '$base': 'Y'}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:465: ValueError
___________________________ TestSchemas.test_schemas ___________________________
self = <test_examples.TestSchemas testMethod=test_schemas>
def test_schemas(self):
l = schema_salad.ref_resolver.Loader({})
ra, _ = l.resolve_all({
"$schemas": ["tests/EDAM.owl"],
"$namespaces": {"edam": "http://edamontology.org/"},
"edam:has_format": "edam:format_1915"
> }, "")
cwltool/schemas/draft-3/salad/tests/test_examples.py:16:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005d827210>
document = {'$namespaces': {'edam': 'http://edamontology.org/'}, '$schemas': ['tests/EDAM.owl'], 'edam:has_format': 'edam:format_1915'}
base_url = '', file_base = '', checklinks = True
> ???
E Exception: Expected CommentedMap or CommentedSeq, got <type 'dict'>: `{'edam:has_format': 'edam:format_1915', '$namespaces': {'edam': 'http://edamontology.org/'}, '$schemas': ['tests/EDAM.owl']}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:727: Exception
________________________ TestSchemas.test_self_validate ________________________
self = <test_examples.TestSchemas testMethod=test_self_validate>
def test_self_validate(self):
> schema_salad.main.main(args=["schema_salad/metaschema/metaschema.yml"])
E TypeError: main() got an unexpected keyword argument 'args'
cwltool/schemas/draft-3/salad/tests/test_examples.py:46: TypeError
_______________________ TestSchemas.test_avro_regression _______________________
self = <tests.test_examples.TestSchemas testMethod=test_avro_regression>
def test_avro_regression(self):
> self.assertEqual(0, schema_salad.main.main(argsl=["tests/Process.yml"]))
cwltool/schemas/v1.0/salad/tests/test_examples.py:58:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
build/bdist.linux-x86_64/egg/schema_salad/main.py:113: in main
???
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:836: in fetch
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.DefaultFetcher object at 0x7f005ce227d0>
url = 'file:///home/takluyver/Code/cwltool/tests/Process.yml'
> ???
E RuntimeError: [Errno 2] No such file or directory: '/home/takluyver/Code/cwltool/tests/Process.yml'
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:146: RuntimeError
----------------------------- Captured stderr call -----------------------------
./setup.py Current version: 2.5.20170428142041
__________________________ TestSchemas.test_examples ___________________________
self = <tests.test_examples.TestSchemas testMethod=test_examples>
def test_examples(self):
self.maxDiff = None
for a in ["field_name", "ident_res", "link_res", "vocab_res"]:
ldr, _, _, _ = schema_salad.schema.load_schema(
> "schema_salad/metaschema/%s_schema.yml" % a)
cwltool/schemas/v1.0/salad/tests/test_examples.py:221:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
build/bdist.linux-x86_64/egg/schema_salad/schema.py:200: in load_schema
???
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:493: in resolve_ref
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.sourceline.SourceLine object at 0x7f005ce22910>
exc_type = <type 'exceptions.RuntimeError'>
exc_value = RuntimeError(u"[Errno 2] No such file or directory: '/home/takluyver/Code/cwltool/schema_salad/metaschema/field_name_schema.yml'",)
traceback = <traceback object at 0x7f005d970878>
> ???
E RuntimeError: [Errno 2] No such file or directory: '/home/takluyver/Code/cwltool/schema_salad/metaschema/field_name_schema.yml'
build/bdist.linux-x86_64/egg/schema_salad/sourceline.py:150: RuntimeError
____________________________ TestSchemas.test_idmap ____________________________
self = <tests.test_examples.TestSchemas testMethod=test_idmap>
def test_idmap(self):
ldr = schema_salad.ref_resolver.Loader({})
ldr.add_context({
"inputs": {
"@id": "http://example.com/inputs",
"mapSubject": "id",
"mapPredicate": "a"
},
"outputs": {
"@type": "@id",
"identity": True,
},
"id": "@id"})
ra, _ = ldr.resolve_all({
"id": "stuff",
"inputs": {
"zip": 1,
"zing": 2
},
"outputs": ["out"],
"other": {
'n': 9
}
> }, "http://example2.com/")
cwltool/schemas/v1.0/salad/tests/test_examples.py:105:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005cdf1e10>
document = {'id': 'stuff', 'inputs': {'zing': 2, 'zip': 1}, 'other': {'n': 9}, 'outputs': ['out']}
base_url = 'http://example2.com/', file_base = 'http://example2.com/'
checklinks = True
> ???
E Exception: Expected CommentedMap or CommentedSeq, got <type 'dict'>: `{'inputs': {'zing': 2, 'zip': 1}, 'other': {'n': 9}, 'id': 'stuff', 'outputs': ['out']}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:727: Exception
_________________________ TestSchemas.test_jsonld_ctx __________________________
self = <tests.test_examples.TestSchemas testMethod=test_jsonld_ctx>
def test_jsonld_ctx(self):
ldr, _, _, _ = schema_salad.schema.load_schema({
"$base": "Y",
"name": "X",
"$namespaces": {
"foo": "http://example.com/foo#"
},
"$graph": [{
"name": "ExampleType",
"type": "enum",
> "symbols": ["asym", "bsym"]}]
})
cwltool/schemas/v1.0/salad/tests/test_examples.py:70:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
build/bdist.linux-x86_64/egg/schema_salad/schema.py:200: in load_schema
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005c74d2d0>
ref = {'$base': 'Y', '$graph': [{'name': 'ExampleType', 'symbols': ['asym', 'bsym'], 'type': 'enum'}], '$namespaces': {'foo': 'http://example.com/foo#'}, 'name': 'X'}
base_url = 'file:///home/takluyver/Code/cwltool/', checklinks = True
> ???
E ValueError: Expected CommentedMap or string, got <type 'dict'>: `{'$graph': [{'symbols': ['asym', 'bsym'], 'type': 'enum', 'name': 'ExampleType'}], '$namespaces': {'foo': 'http://example.com/foo#'}, 'name': 'X', '$base': 'Y'}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:465: ValueError
____________________________ TestSchemas.test_mixin ____________________________
self = <tests.test_examples.TestSchemas testMethod=test_mixin>
def test_mixin(self):
ldr = schema_salad.ref_resolver.Loader({})
ra = ldr.resolve_ref({"$mixin": "mixin.yml", "one": "five"},
> base_url="file://"+os.getcwd()+"/tests/")
cwltool/schemas/v1.0/salad/tests/test_examples.py:329:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005c74b690>
ref = {'$mixin': 'mixin.yml', 'one': 'five'}
base_url = 'file:///home/takluyver/Code/cwltool/tests/', checklinks = True
> ???
E ValueError: Expected CommentedMap or string, got <type 'dict'>: `{'$mixin': 'mixin.yml', 'one': 'five'}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:465: ValueError
___________________________ TestSchemas.test_schemas ___________________________
self = <tests.test_examples.TestSchemas testMethod=test_schemas>
def test_schemas(self):
l = schema_salad.ref_resolver.Loader({})
ra, _ = l.resolve_all({
u"$schemas": [u"tests/EDAM.owl"],
u"$namespaces": {u"edam": u"http://edamontology.org/"},
u"edam:has_format": u"edam:format_1915"
> }, "")
cwltool/schemas/v1.0/salad/tests/test_examples.py:25:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005c08d350>
document = {'$namespaces': {'edam': 'http://edamontology.org/'}, '$schemas': ['tests/EDAM.owl'], 'edam:has_format': 'edam:format_1915'}
base_url = '', file_base = '', checklinks = True
> ???
E Exception: Expected CommentedMap or CommentedSeq, got <type 'dict'>: `{u'edam:has_format': u'edam:format_1915', u'$namespaces': {u'edam': u'http://edamontology.org/'}, u'$schemas': [u'tests/EDAM.owl']}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:727: Exception
__________________________ TestSchemas.test_scoped_id __________________________
self = <tests.test_examples.TestSchemas testMethod=test_scoped_id>
def test_scoped_id(self):
ldr = schema_salad.ref_resolver.Loader({})
ctx = {
"id": "@id",
"location": {
"@id": "@id",
"@type": "@id"
},
"bar": "http://example.com/bar",
"ex": "http://example.com/"
}
ldr.add_context(ctx)
ra, _ = ldr.resolve_all({
"id": "foo",
"bar": {
"id": "baz"
}
> }, "http://example.com")
cwltool/schemas/v1.0/salad/tests/test_examples.py:274:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005c74b4d0>
document = {'bar': {'id': 'baz'}, 'id': 'foo'}, base_url = 'http://example.com'
file_base = 'http://example.com', checklinks = True
> ???
E Exception: Expected CommentedMap or CommentedSeq, got <type 'dict'>: `{'bar': {'id': 'baz'}, 'id': 'foo'}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:727: Exception
_________________________ TestSchemas.test_scoped_ref __________________________
self = <tests.test_examples.TestSchemas testMethod=test_scoped_ref>
def test_scoped_ref(self):
ldr = schema_salad.ref_resolver.Loader({})
ldr.add_context({
"scatter": {
"@type": "@id",
"refScope": 0,
},
"source": {
"@type": "@id",
"refScope": 2,
},
"in": {
"mapSubject": "id",
"mapPredicate": "source"
},
"out": {
"@type": "@id",
"identity": True
},
"inputs": {
"mapSubject": "id",
"mapPredicate": "type"
},
"outputs": {
"mapSubject": "id",
},
"steps": {
"mapSubject": "id"
},
"id": "@id"})
ra, _ = ldr.resolve_all({
"inputs": {
"inp": "string",
"inp2": "string"
},
"outputs": {
"out": {
"type": "string",
"source": "step2/out"
}
},
"steps": {
"step1": {
"in": {
"inp": "inp",
"inp2": "#inp2",
"inp3": ["inp", "inp2"]
},
"out": ["out"],
"scatter": "inp"
},
"step2": {
"in": {
"inp": "step1/out"
},
"scatter": "inp",
"out": ["out"]
}
}
> }, "http://example2.com/")
cwltool/schemas/v1.0/salad/tests/test_examples.py:176:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005c08d290>
document = {'inputs': {'inp': 'string', 'inp2': 'string'}, 'outputs': {'out': {'source': 'step2/out', 'type': 'string'}}, 'steps'... 'inp2']}, 'out': ['out'], 'scatter': 'inp'}, 'step2': {'in': {'inp': 'step1/out'}, 'out': ['out'], 'scatter': 'inp'}}}
base_url = 'http://example2.com/', file_base = 'http://example2.com/'
checklinks = True
> ???
E Exception: Expected CommentedMap or CommentedSeq, got <type 'dict'>: `{'inputs': {'inp2': 'string', 'inp': 'string'}, 'steps': {'step2': {'out': ['out'], 'scatter': 'inp', 'in': {'inp': 'step1/out'}}, 'step1': {'out': ['out'], 'scatter': 'inp', 'in': {'inp3': ['inp', 'inp2'], 'inp2': '#inp2', 'inp': 'inp'}}}, 'outputs': {'out': {'source': 'step2/out', 'type': 'string'}}}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:727: Exception
________________________ TestSchemas.test_self_validate ________________________
self = <tests.test_examples.TestSchemas testMethod=test_self_validate>
def test_self_validate(self):
> self.assertEqual(0, schema_salad.main.main(argsl=["schema_salad/metaschema/metaschema.yml"]))
cwltool/schemas/v1.0/salad/tests/test_examples.py:53:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
build/bdist.linux-x86_64/egg/schema_salad/main.py:113: in main
???
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:836: in fetch
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.DefaultFetcher object at 0x7f005c095dd0>
url = 'file:///home/takluyver/Code/cwltool/schema_salad/metaschema/metaschema.yml'
> ???
E RuntimeError: [Errno 2] No such file or directory: '/home/takluyver/Code/cwltool/schema_salad/metaschema/metaschema.yml'
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:146: RuntimeError
----------------------------- Captured stderr call -----------------------------
./setup.py Current version: 2.5.20170428142041
_________________________ TestSchemas.test_typedsl_ref _________________________
self = <tests.test_examples.TestSchemas testMethod=test_typedsl_ref>
def test_typedsl_ref(self):
ldr = schema_salad.ref_resolver.Loader({})
ldr.add_context({
"File": "http://example.com/File",
"null": "http://example.com/null",
"array": "http://example.com/array",
"type": {
"@type": "@vocab",
"typeDSL": True
}
})
> ra, _ = ldr.resolve_all({"type": "File"}, "")
cwltool/schemas/v1.0/salad/tests/test_examples.py:244:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <schema_salad.ref_resolver.Loader object at 0x7f005c096f90>
document = {'type': 'File'}, base_url = '', file_base = '', checklinks = True
> ???
E Exception: Expected CommentedMap or CommentedSeq, got <type 'dict'>: `{'type': 'File'}`
build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py:727: Exception
========== 15 failed, 35 passed, 1 skipped, 10 error in 23.01 seconds ==========
Makefile:136: recipe for target 'test' failed
make: *** [test] Error 1
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