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upload failure from python client (threading)

Description

from collaborator:

">>> syn = synapseclient.Synapse()
>>> syn.login('jishuxu@broadinstitute.org','XXXXXXXX')

UPGRADE AVAILABLE

A more recent version of the Synapse Client (1.5.1) is available. Your version (1.2) can be upgraded by typing:
pip install --upgrade synapseclient

Python Synapse Client version 1.5.1 release notes

Adds Python 3 compatibility and enhanced file upload reliability

Welcome, jishuxu@broadinstitute.org!
>>> results = syn.query('SELECT id, name FROM entity WHERE parentId=="syn5848791"')
>>> results
{u'totalNumberOfResults': 0, u'results': []}
>>> results = syn.query('SELECT id, name FROM entity WHERE parentId=="syn2701448"')
>>> results
{u'totalNumberOfResults': 46, u'results': [{u'entity.id': u'syn5848791', u'entity.name': u'RawData'}, {u'entity.id': u'syn2701453', u'entity.name': u'ill450kAnno_finalQC_chr1.txt'}, {u'entity.id': u'syn2701469', u'entity.name': u'ill450kAnno_finalQC_chr10.txt'}, {u'entity.id': u'syn2701470', u'entity.name': u'ill450kAnno_finalQC_chr11.txt'}, {u'entity.id': u'syn2701471', u'entity.name': u'ill450kAnno_finalQC_chr12.txt'}, {u'entity.id': u'syn2701472', u'entity.name': u'ill450kAnno_finalQC_chr13.txt'}, {u'entity.id': u'syn2701473', u'entity.name': u'ill450kAnno_finalQC_chr14.txt'}, {u'entity.id': u'syn2701474', u'entity.name': u'ill450kAnno_finalQC_chr15.txt'}, {u'entity.id': u'syn2701475', u'entity.name': u'ill450kAnno_finalQC_chr16.txt'}, {u'entity.id': u'syn2701476', u'entity.name': u'ill450kAnno_finalQC_chr17.txt'}, {u'entity.id': u'syn2701477', u'entity.name': u'ill450kAnno_finalQC_chr18.txt'}, {u'entity.id': u'syn2701478', u'entity.name': u'ill450kAnno_finalQC_chr19.txt'}, {u'entity.id': u'syn2701461', u'entity.name': u'ill450kAnno_finalQC_chr2.txt'}, {u'entity.id': u'syn2701479', u'entity.name': u'ill450kAnno_finalQC_chr20.txt'}, {u'entity.id': u'syn2701480', u'entity.name': u'ill450kAnno_finalQC_chr21.txt'}, {u'entity.id': u'syn2701481', u'entity.name': u'ill450kAnno_finalQC_chr22.txt'}, {u'entity.id': u'syn2701462', u'entity.name': u'ill450kAnno_finalQC_chr3.txt'}, {u'entity.id': u'syn2701463', u'entity.name': u'ill450kAnno_finalQC_chr4.txt'}, {u'entity.id': u'syn2701464', u'entity.name': u'ill450kAnno_finalQC_chr5.txt'}, {u'entity.id': u'syn2701465', u'entity.name': u'ill450kAnno_finalQC_chr6.txt'}, {u'entity.id': u'syn2701466', u'entity.name': u'ill450kAnno_finalQC_chr7.txt'}, {u'entity.id': u'syn2701467', u'entity.name': u'ill450kAnno_finalQC_chr8.txt'}, {u'entity.id': u'syn2701468', u'entity.name': u'ill450kAnno_finalQC_chr9.txt'}, {u'entity.id': u'syn2701561', u'entity.name': u'ill450kMeth_chr10_740_imputed.txt'}, {u'entity.id': u'syn2701562', u'entity.name': u'ill450kMeth_chr11_740_imputed.txt'}, {u'entity.id': u'syn2701565', u'entity.name': u'ill450kMeth_chr12_740_imputed.txt'}, {u'entity.id': u'syn2701566', u'entity.name': u'ill450kMeth_chr13_740_imputed.txt'}, {u'entity.id': u'syn2701567', u'entity.name': u'ill450kMeth_chr14_740_imputed.txt'}, {u'entity.id': u'syn2703252', u'entity.name': u'ill450kMeth_chr15_740_imputed.txt'}, {u'entity.id': u'syn2703255', u'entity.name': u'ill450kMeth_chr16_740_imputed.txt'}, {u'entity.id': u'syn2703256', u'entity.name': u'ill450kMeth_chr17_740_imputed.txt'}, {u'entity.id': u'syn2703306', u'entity.name': u'ill450kMeth_chr18_740_imputed.txt'}, {u'entity.id': u'syn2703311', u'entity.name': u'ill450kMeth_chr19_740_imputed.txt'}, {u'entity.id': u'syn2701508', u'entity.name': u'ill450kMeth_chr1_740_imputed.txt'}, {u'entity.id': u'syn2703337', u'entity.name': u'ill450kMeth_chr20_740_imputed.txt'}, {u'entity.id': u'syn2703343', u'entity.name': u'ill450kMeth_chr21_740_imputed.txt'}, {u'entity.id': u'syn2703345', u'entity.name': u'ill450kMeth_chr22_740_imputed.txt'}, {u'entity.id': u'syn2701509', u'entity.name': u'ill450kMeth_chr2_740_imputed.txt'}, {u'entity.id': u'syn2701510', u'entity.name': u'ill450kMeth_chr3_740_imputed.txt'}, {u'entity.id': u'syn2701511', u'entity.name': u'ill450kMeth_chr4_740_imputed.txt'}, {u'entity.id': u'syn2701512', u'entity.name': u'ill450kMeth_chr5_740_imputed.txt'}, {u'entity.id': u'syn2701524', u'entity.name': u'ill450kMeth_chr6_740_imputed.txt'}, {u'entity.id': u'syn2701525', u'entity.name': u'ill450kMeth_chr7_740_imputed.txt'}, {u'entity.id': u'syn2701559', u'entity.name': u'ill450kMeth_chr8_740_imputed.txt'}, {u'entity.id': u'syn2701560', u'entity.name': u'ill450kMeth_chr9_740_imputed.txt'}, {u'entity.id': u'syn5843544', u'entity.name': u'tech_var_748qc_batch.txt'}]}
>>> syn.store(File(path=filetoupload,parent='syn5848791',synapseStore=True))

##################################################
Uploading file to Synapse storage
##################################################
..,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,..,Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/broad/dejagerlab/cogdec/jishu/softwares/Python/lib/python2.7/site-packages/synapseclient-1.2-py2.7.egg/synapseclient/client.py", line 907, in store
mimetype=local_state.get('contentType', None))
File "/broad/dejagerlab/cogdec/jishu/softwares/Python/lib/python2.7/site-packages/synapseclient-1.2-py2.7.egg/synapseclient/client.py", line 1803, in _uploadToFileHandleService
return self._chunkedUploadFile(filename, mimetype=mimetype)
File "/broad/dejagerlab/cogdec/jishu/softwares/Python/lib/python2.7/site-packages/synapseclient-1.2-py2.7.egg/synapseclient/client.py", line 2003, in _chunkedUploadFile
exceptions._raise_for_status(response, verbose=self.debug)
File "/broad/dejagerlab/cogdec/jishu/softwares/Python/lib/python2.7/site-packages/synapseclient-1.2-py2.7.egg/synapseclient/exceptions.py", line 124, in _raise_for_status
raise SynapseHTTPError(message, response=response)
synapseclient.exceptions.SynapseHTTPError: 400 Client Error: Bad Request"

Environment

Status

Assignee

Larsson Omberg

Reporter

Ben Logsdon

Validator

Ben Logsdon

Fix versions

Priority

Critical