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224 | def main(args):
# HACK: Delete all existing files first
process_functions.rmFiles(database_to_staging.GENIE_RELEASE_DIR)
cbioValidatorPath = os.path.join(
args.cbioportalPath, "core/src/main/scripts/importer/validateData.py"
)
assert os.path.exists(cbioValidatorPath), "Please specify correct cbioportalPath"
assert not (
args.test and args.staging
), "You can only specify --test or --staging, not both"
try:
processingDate = datetime.datetime.strptime(args.processingDate, "%b-%Y")
except ValueError:
raise ValueError(
"Process date must be in the format " "abbreviated_month-YEAR ie. Oct-2017"
)
syn = process_functions.synapse_login(debug=args.debug)
# Get all the possible public releases
# Get configuration
if args.test:
databaseSynIdMappingId = "syn11600968"
args.genieVersion = "TESTpublic"
elif args.staging:
databaseSynIdMappingId = "syn12094210"
else:
databaseSynIdMappingId = "syn10967259"
databaseSynIdMapping = syn.tableQuery("select * from %s" % databaseSynIdMappingId)
databaseSynIdMappingDf = databaseSynIdMapping.asDataFrame()
public_synid = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "public"
].values[0]
# Use release folder fileview
releaseSynId = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "releaseFolder"
].values[0]
processTrackerSynId = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "processTracker"
].values[0]
# TEST run of the infrastructure will always
# Map to a specific folder
if args.test:
officialPublic = {"TESTpublic": "syn12299959"}
else:
officialPublic = extract.get_public_to_consortium_synid_mapping(
syn, releaseSynId
)
if args.genieVersion not in officialPublic.keys():
allowed_public_release_names = ", ".join(officialPublic.keys())
raise ValueError(
f"genieVersion must be one of these: {allowed_public_release_names}."
)
args.releaseId = officialPublic[args.genieVersion]
if not args.test and not args.staging:
load.update_process_trackingdf(
syn=syn,
process_trackerdb_synid=processTrackerSynId,
center="SAGE",
process_type="public",
start=True,
)
caseListEntities, genePanelEntities = consortium_to_public.consortiumToPublic(
syn,
processingDate,
args.genieVersion,
args.releaseId,
databaseSynIdMappingDf,
publicReleaseCutOff=args.publicReleaseCutOff,
)
database_to_staging.revise_metadata_files(syn, public_synid, args.genieVersion)
logger.info("CBIO VALIDATION")
# Must be exit 0 because the validator sometimes fails,
# but we still want to capture the output
command = [
cbioValidatorPath,
"-s",
database_to_staging.GENIE_RELEASE_DIR,
"-n",
"; exit 0",
]
cbio_output = subprocess.check_output(" ".join(command), shell=True)
cbio_decoded_output = cbio_output.decode("utf-8")
logger.info(cbio_decoded_output)
if not args.test and not args.staging:
log_folder_synid = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "logs"
].values[0]
# Use tempfiles
cbio_log_file = "cbioValidatorLogsPublic_{}.txt".format(args.genieVersion)
with open(cbio_log_file, "w") as cbioLog:
cbioLog.write(cbio_decoded_output)
syn.store(synapseclient.File(cbio_log_file, parentId=log_folder_synid))
os.remove(cbio_log_file)
# logger.info("REMOVING OLD FILES")
# process_functions.rmFiles(database_to_staging.CASE_LIST_PATH)
# seg_meta_file = "{}/genie_public_meta_cna_hg19_seg.txt".format(
# database_to_staging.GENIE_RELEASE_DIR
# )
# if os.path.exists(seg_meta_file):
# os.unlink(seg_meta_file)
logger.info("CREATING LINK VERSION")
folders = database_to_staging.create_link_version(
syn,
args.genieVersion,
caseListEntities,
genePanelEntities,
databaseSynIdMappingDf,
release_type="public",
)
# Don't update process tracker is testing or staging
if not args.test and not args.staging:
load.update_process_trackingdf(
syn=syn,
process_trackerdb_synid=processTrackerSynId,
center="SAGE",
process_type="public",
start=False,
)
if not args.test:
logger.info("DASHBOARD UPDATE")
dashboard_table_updater.run_dashboard(
syn, databaseSynIdMappingDf, args.genieVersion, staging=args.staging
)
generate_dashboard_html(args.genieVersion, staging=args.staging)
logger.info("DASHBOARD UPDATE COMPLETE")
logger.info("AUTO GENERATE DATA GUIDE")
# TODO: remove data guide code
# onco_link = databaseSynIdMappingDf["Id"][
# databaseSynIdMappingDf["Database"] == "oncotreeLink"
# ].values[0]
# onco_link_ent = syn.get(onco_link)
# oncotree_link = onco_link_ent.externalURL
# oncotree_version = oncotree_link.split("=")[1]
# data_guide_pdf = generate_data_guide(
# args.genieVersion,
# oncotree_version=oncotree_version,
# database_mapping=databaseSynIdMappingId,
# )
# data_guide_ent = synapseclient.File(
# data_guide_pdf, parent=folders["release_folder"]
# )
# syn.store(data_guide_ent)
logger.info("COMPLETED CONSORTIUM TO PUBLIC")
|