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)