PLATFORM_MAP = {'133AB': 'AffymetrixU133AB',
'Plus2': 'AffymetrixU133Plus2'}
query = 'select id, name from entity where parentId=="%s"' %OLDPARENTID
df = synapseHelpers.query2df(syn.chunkedQuery(query))
for i in range(1,df.shape[0]):
row = df.ix[i, :]
ent = syn.get(row.id)
fStudy, fTissue, fPlatform, fDatatype, fRest = ent.name.split('_')
name = 'AMP-AD_MSBB_MSSM_%s_%s_%s' % (PLATFORM_MAP[fPlatform],
TISSUEABRMAP[fTissue][0], fRest)
print name
os.rename(ent.path, name)
f = File(name, parentId=NEWPARENTID, name=name[7:])
f.consortium = 'AMP-AD'
f.study = 'MSBB'
f.center = 'MSSM'
f.dataType = 'mRNA'
f.disease = 'Alzheimers Disease'
f.platfrom = PLATFORM_MAP[fPlatform]
f.tissueTypeAbrv = TISSUEABRMAP[fTissue][1]
f.tissueType = TISSUEABRMAP[fTissue][0]
f.dataSubType = 'geneExp'
f.fileType = 'genomicMatrix'
f.organism = 'human'
f = syn.store(f, used = [ent], executed=['https://github.com/Sage-Bionetworks/ampAdScripts/blob/4d7d6b78b1e73058483354a1a18bff7422966a4b/Mount-Sinai/migrateMSBBExpression.py'], activityName='Data migration')
provenance = Activity(name=meta_data['activity'],
desciption=meta_data['description'],
used = meta_data['used']
exectuted = meta_data['used']
)
#prov = syn.store(prov)
name = of.path.basename(input_path)
#Add metadata to files to be uploaded
f = File(input_path, name = name, parentId=DST_FOLDER)
f.dataType = meta_data['dataType']
f.fileType = meta_data['dataType']
f.variant_workflow = meta_data['workflow']
f.variant_workflow_version = meta_data['workflowVersion']
f.call_type = call_type
f.reference_build = meta_data['referenceBuild']
f.center_name = meta_data['center_name']
f.file_md5 = synapseclient.utils.md5_for_file(input_path)
f.study = 'PCAWG 2.0'
f.submitter_donor_id = meta_data['donor_id']
f.alignment_workflow_name='Workflow_Bundle_BWA (UCSC Implementation)'
f.alignment_workflow_source_url='https://github.com/kellrott/tcga_realign'
f.alignment_workflow_version='2.6.0'
#Store metadata and file to Synapse
#f = syn.store(f, activity = provenance)
#Add Description
#wiki = synapseclient.Wiki(TITLE, f, DESCRIPTION)
#wiki = syn.store(wiki)
