def import_cancer_type(jvm_args, data_filename):
args = jvm_args.split(' ')
args.append(IMPORT_CANCER_TYPE_CLASS)
args.append(data_filename)
args.append("false") # don't clobber existing table
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def update_study_status(jvm_args, study_id):
args = jvm_args.split(' ')
args.append(UPDATE_STUDY_STATUS_CLASS)
args.append(study_id)
args.append("AVAILABLE")
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def add_global_case_list(jvm_args, study_id):
args = jvm_args.split(' ')
args.append(ADD_CASE_LIST_CLASS)
args.append(study_id)
args.append("all")
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_cancer_type(jvm_args, data_filename):
args = jvm_args.split(' ')
args.append(IMPORT_CANCER_TYPE_CLASS)
args.append(data_filename)
args.append("false") # don't clobber existing table
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def update_study_status(jvm_args, study_id):
args = jvm_args.split(' ')
args.append(UPDATE_STUDY_STATUS_CLASS)
args.append(study_id)
args.append("AVAILABLE")
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_study_data(jvm_args, meta_filename, data_filename):
args = jvm_args.split(' ')
meta_file_dict, meta_file_type = cbioportal_common.parse_metadata_file(
meta_filename, logger=LOGGER)
if meta_file_type is None:
# invalid file, skip
return
if not data_filename.endswith(meta_file_dict['data_filename']):
print >> ERROR_FILE, ("'data_filename' in meta file contradicts "
"data filename in command, skipping file")
return
importer = IMPORTER_CLASSNAME_BY_META_TYPE[meta_file_type]
args.append(importer)
if IMPORTER_REQUIRES_METADATA[importer]:
args.append("--meta")
args.append(meta_filename)
args.append("--loadMode")
args.append("bulkload")
if importer in ("org.mskcc.cbio.portal.scripts.ImportMutSigData",
"org.mskcc.cbio.portal.scripts.ImportGisticData"):
args.append("--data")
args.append(data_filename)
args.append("--study")
args.append(meta_file_dict['cancer_study_identifier'])
else:
args.append("--data")
args.append(data_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def add_global_case_list(jvm_args, study_id):
args = jvm_args.split(' ')
args.append(ADD_CASE_LIST_CLASS)
args.append(study_id)
args.append("all")
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_study_data(jvm_args, meta_filename, data_filename):
args = jvm_args.split(' ')
meta_file_dict, meta_file_type = cbioportal_common.parse_metadata_file(
meta_filename, logger=LOGGER)
if meta_file_type is None:
# invalid file, skip
return
if not data_filename.endswith(meta_file_dict['data_filename']):
print >> ERROR_FILE, ("'data_filename' in meta file contradicts "
"data filename in command, skipping file")
return
importer = IMPORTER_CLASSNAME_BY_META_TYPE[meta_file_type]
args.append(importer)
if IMPORTER_REQUIRES_METADATA[importer]:
args.append("--meta")
args.append(meta_filename)
args.append("--loadMode")
args.append("bulkload")
if importer in ("org.mskcc.cbio.portal.scripts.ImportMutSigData", "org.mskcc.cbio.portal.scripts.ImportGisticData"):
args.append("--data")
args.append(data_filename)
args.append("--study")
args.append(meta_file_dict['cancer_study_identifier'])
else:
args.append("--data")
args.append(data_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def check_version(jvm_args):
args = jvm_args.split(' ')
args.append(VERSION_UTIL_CLASS)
try:
run_java(*args)
except:
print >> OUTPUT_FILE, 'Error, probably due to this version of the portal being out of sync with the database. Run the database migration script located at PORTAL_HOME/core/src/main/scripts/migrate_db.py before continuing.'
raise
def check_version(jvm_args):
args = jvm_args.split(' ')
args.append(VERSION_UTIL_CLASS)
try:
run_java(*args)
except:
print >> OUTPUT_FILE, 'Error, probably due to this version of the portal being out of sync with the database. Run the database migration script located at PORTAL_HOME/core/src/main/scripts/migrate_db.py before continuing.'
raise
def remove_study(jvm_args, meta_filename):
args = jvm_args.split(" ")
args.append(REMOVE_STUDY_CLASS)
meta_dict, meta_type = cbioportal_common.parse_metadata_file(meta_filename, logger=LOGGER)
if meta_type != MetaFileTypes.STUDY:
# invalid file, skip
print >> ERROR_FILE, "Not a study meta file: " + meta_filename
return
args.append(meta_dict["cancer_study_identifier"])
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def remove_study(jvm_args, meta_filename):
args = jvm_args.split(' ')
args.append(REMOVE_STUDY_CLASS)
meta_dictionary = cbioportal_common.parse_metadata_file(meta_filename,
logger=LOGGER)
if meta_dictionary['meta_file_type'] != MetaFileTypes.STUDY:
# invalid file, skip
print >> ERROR_FILE, 'Not a study meta file: ' + meta_filename
return
args.append(meta_dictionary['cancer_study_identifier'])
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_study_data(jvm_args,
meta_filename,
data_filename,
meta_file_dictionary=None):
args = jvm_args.split(' ')
# In case the meta file is already parsed in a previous function, it is not
# necessary to parse it again
if meta_file_dictionary is None:
meta_file_dictionary = cbioportal_common.parse_metadata_file(
meta_filename, logger=LOGGER)
# Retrieve meta file type
meta_file_type = meta_file_dictionary['meta_file_type']
# invalid file, skip
if meta_file_type is None:
print >> ERROR_FILE, (
"Unrecognized meta file type '%s', skipping file" %
(meta_file_type))
return
if not data_filename.endswith(meta_file_dictionary['data_filename']):
print >> ERROR_FILE, ("'data_filename' in meta file contradicts "
"data filename in command, skipping file")
return
importer = IMPORTER_CLASSNAME_BY_META_TYPE[meta_file_type]
args.append(importer)
if IMPORTER_REQUIRES_METADATA[importer]:
args.append("--meta")
args.append(meta_filename)
args.append("--loadMode")
args.append("bulkload")
if importer in ("org.mskcc.cbio.portal.scripts.ImportMutSigData",
"org.mskcc.cbio.portal.scripts.ImportGisticData"):
args.append("--data")
args.append(data_filename)
args.append("--study")
args.append(meta_file_dictionary['cancer_study_identifier'])
elif importer == "org.mskcc.cbio.portal.scripts.ImportGenePanelProfileMap":
args.append("--meta")
args.append(meta_filename)
args.append("--data")
args.append(data_filename)
else:
args.append("--data")
args.append(data_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_study_data(jvm_args, meta_filename, data_filename, meta_file_dictionary = None):
args = jvm_args.split(' ')
# In case the meta file is already parsed in a previous function, it is not
# necessary to parse it again
if meta_file_dictionary is None:
meta_file_dictionary = cbioportal_common.parse_metadata_file(
meta_filename, logger=LOGGER)
# Retrieve meta file type
meta_file_type = meta_file_dictionary['meta_file_type']
# invalid file, skip
if meta_file_type is None:
print >> ERROR_FILE, ("Unrecognized meta file type '%s', skipping file"
% (meta_file_type))
return
if not data_filename.endswith(meta_file_dictionary['data_filename']):
print >> ERROR_FILE, ("'data_filename' in meta file contradicts "
"data filename in command, skipping file")
return
importer = IMPORTER_CLASSNAME_BY_META_TYPE[meta_file_type]
args.append(importer)
if IMPORTER_REQUIRES_METADATA[importer]:
args.append("--meta")
args.append(meta_filename)
args.append("--loadMode")
args.append("bulkload")
if importer in ("org.mskcc.cbio.portal.scripts.ImportMutSigData", "org.mskcc.cbio.portal.scripts.ImportGisticData"):
args.append("--data")
args.append(data_filename)
args.append("--study")
args.append(meta_file_dictionary['cancer_study_identifier'])
elif importer == "org.mskcc.cbio.portal.scripts.ImportGenePanelProfileMap":
args.append("--meta")
args.append(meta_filename)
args.append("--data")
args.append(data_filename)
else:
args.append("--data")
args.append(data_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_case_list(jvm_args, meta_filename):
args = jvm_args.split(' ')
args.append(IMPORT_CASE_LIST_CLASS)
args.append(meta_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_study(jvm_args, meta_filename):
args = jvm_args.split(' ')
args.append(IMPORT_STUDY_CLASS)
args.append(meta_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_study(jvm_args, meta_filename):
args = jvm_args.split(' ')
args.append(IMPORT_STUDY_CLASS)
args.append(meta_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
def import_case_list(jvm_args, meta_filename):
args = jvm_args.split(' ')
args.append(IMPORT_CASE_LIST_CLASS)
args.append(meta_filename)
args.append("--noprogress") # don't report memory usage and % progress
run_java(*args)
