synGetSubmission encounters error

Description

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 > synGetSubmission("9681792") Traceback (most recent call last): File "<string>", line 1, in <module> File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/synapser/lib/python3.5/site-packages/synapseclient-1.8.2-py3.5.egg/synapseclient/dict_object.py", line 29, in __str__ return json.dumps(self, sort_keys=True, indent=2) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/__init__.py", line 237, in dumps **kw).encode(obj) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 200, in encode chunks = list(chunks) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 429, in _iterencode yield from _iterencode_dict(o, _current_indent_level) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 403, in _iterencode_dict yield from chunks File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 436, in _iterencode o = _default(o) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/synapser/lib/python3.5/site-packages/synapseclient-1.8.2-py3.5.egg/synapseclient/custom_json.py", line 18, in _json_encoder return getattr(obj.__class__, "to_json", _json_encoder.default)(obj) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 179, in default raise TypeError(repr(o) + " is not JSON serializable") TypeError : DockerRepository(isManaged=True, entityType='org.sagebionetworks.repo.model.docker.DockerRepository', id='syn17016672', parentId='syn4990358', createdBy='3324230', modifiedOn='2018-10-26T21:09:08.212Z', annotations='/repo/v1/entity/syn17016672/annotations', repositoryName='docker.synapse.org/syn4990358/challengeworkflowexample', concreteType='org.sagebionetworks.repo.model.docker.DockerRepository', etag='aff734f6-cede-4446-8f12-d95519da0102', accessControlList='/repo/v1/entity/syn17016672/acl', modifiedBy='3324230', name='syn17016672', createdOn='2018-10-26T21:09:08.250Z', uri='/repo/v1/entity/syn17016672') is not JSON serializable Error in pyExec(cmd) : An error has occurred while executing Python code. See traceback above. > synGetSubmission("9681792", downloadFile=False) Error in eval(quote(list(...)), env) : object 'False' not found > synGetSubmission("9681792", downloadFile=FALSE) Traceback (most recent call last): File "<string>", line 1, in <module> File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/synapser/lib/python3.5/site-packages/synapseclient-1.8.2-py3.5.egg/synapseclient/dict_object.py", line 29, in __str__ return json.dumps(self, sort_keys=True, indent=2) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/__init__.py", line 237, in dumps **kw).encode(obj) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 200, in encode chunks = list(chunks) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 429, in _iterencode yield from _iterencode_dict(o, _current_indent_level) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 403, in _iterencode_dict yield from chunks File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 436, in _iterencode o = _default(o) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/synapser/lib/python3.5/site-packages/synapseclient-1.8.2-py3.5.egg/synapseclient/custom_json.py", line 18, in _json_encoder return getattr(obj.__class__, "to_json", _json_encoder.default)(obj) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 179, in default raise TypeError(repr(o) + " is not JSON serializable") TypeError : DockerRepository(isManaged=True, entityType='org.sagebionetworks.repo.model.docker.DockerRepository', id='syn17016672', parentId='syn4990358', createdBy='3324230', modifiedOn='2018-10-26T21:09:08.212Z', annotations='/repo/v1/entity/syn17016672/annotations', repositoryName='docker.synapse.org/syn4990358/challengeworkflowexample', concreteType='org.sagebionetworks.repo.model.docker.DockerRepository', etag='aff734f6-cede-4446-8f12-d95519da0102', accessControlList='/repo/v1/entity/syn17016672/acl', modifiedBy='3324230', name='syn17016672', createdOn='2018-10-26T21:09:08.250Z', uri='/repo/v1/entity/syn17016672') is not JSON serializable Error in pyExec(cmd) : An error has occurred while executing Python code. See traceback above. > synGetSubmission("9681792", download=FALSE) Error in value[[3L]](cond) : Unexpected **kwargs: {'download': False} > ?synGetSubmission > > > > > synGetSubmission("9681792") Traceback (most recent call last): File "<string>", line 1, in <module> File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/synapser/lib/python3.5/site-packages/synapseclient-1.8.2-py3.5.egg/synapseclient/dict_object.py", line 29, in __str__ return json.dumps(self, sort_keys=True, indent=2) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/__init__.py", line 237, in dumps **kw).encode(obj) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 200, in encode chunks = list(chunks) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 429, in _iterencode yield from _iterencode_dict(o, _current_indent_level) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 403, in _iterencode_dict yield from chunks File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 436, in _iterencode o = _default(o) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/synapser/lib/python3.5/site-packages/synapseclient-1.8.2-py3.5.egg/synapseclient/custom_json.py", line 18, in _json_encoder return getattr(obj.__class__, "to_json", _json_encoder.default)(obj) File "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PythonEmbedInR/lib/python3.5/json/encoder.py", line 179, in default raise TypeError(repr(o) + " is not JSON serializable") TypeError : DockerRepository(isManaged=True, entityType='org.sagebionetworks.repo.model.docker.DockerRepository', id='syn17016672', parentId='syn4990358', createdBy='3324230', modifiedOn='2018-10-26T21:09:08.212Z', annotations='/repo/v1/entity/syn17016672/annotations', repositoryName='docker.synapse.org/syn4990358/challengeworkflowexample', concreteType='org.sagebionetworks.repo.model.docker.DockerRepository', etag='aff734f6-cede-4446-8f12-d95519da0102', accessControlList='/repo/v1/entity/syn17016672/acl', modifiedBy='3324230', name='syn17016672', createdOn='2018-10-26T21:09:08.250Z', uri='/repo/v1/entity/syn17016672') is not JSON serializable Error in pyExec(cmd) : An error has occurred while executing Python code. See traceback above.

Environment

None

Status

Assignee

Unassigned

Reporter

Bruce Hoff

Labels

None

Validator

Bruce Hoff

Release Version History

None

Fix versions

Affects versions

synapser-0.6

Priority

Major
Configure