def upload_archive(config, sdrf_metadata, archive2metadata, exclude_samples, archive_fields, upload_archives, seen_files, nonupload_files, access, log):
'''
uploads the files in the archive that meet the conditions
parameters:
config: the configuration map
sdrf_metadata: metadata map to update
archive2metadata: archive metadata
exclude_samples: list of ffpe preserved samples or samples without a project assigned not to upload
archive_fields: archive name, creation date, and URL
upload_archives: map of level to center to platform of archives to upload
seen_files: files that have been seen in a previously processed archive
nonupload_files: list of file extensions of files not to upload
access: either open or controlled
log: logger to log any messages
'''
archive_path = None
if config['download_archives'] and util.is_upload_archive(archive_fields[0], upload_archives, archive2metadata):
log.info('\tuploading %s-access archive %s.' % (access, archive_fields[0]))
try:
level = archive_fields[0].split('.')[-4].replace('_', ' ')
user_info = config['user_info']
archive_path = util.setup_archive(config, archive_fields, log, user_info['user'], user_info['password'])
file2metadata = process_files(config, archive_path, sdrf_metadata, seen_files, nonupload_files, exclude_samples, level, log)
if 0 < len(file2metadata):
upload_files(config, archive_path, file2metadata, log)
else:
log.warning('did not find files to load for %s' % (archive_fields[0]))
finally:
if archive_path:
shutil.rmtree(archive_path)
log.info('\tfinished uploading %s-access archive %s' % (access, archive_fields[0]))
else:
log.info('\tskipping %s-access archive %s' % (access, archive_fields[0]))
def upload_archive(config, log, archive_fields, archive2metadata,
sdrf_metadata, access):
user_info = config['user_info']
log.info('\tchecking %s-access maf archive %s.' %
(access, archive_fields[0]))
try:
if config['download_archives']:
archive_path = util.setup_archive(archive_fields, log,
user_info['user'],
user_info['password'])
filenames = process_files(archive_path, log)
if 0 < len(filenames):
file2metadata = {}
for file_name in filenames:
if file_name.endswith('maf'):
file2metadata[file_name] = parse_maf_file(
file_name, archive_path, log, archive_fields,
archive2metadata, sdrf_metadata)
upload_archives.upload_files(config, archive_path,
file2metadata, log)
else:
log.warning('\tdid not find files to load for %s' %
(archive_fields[0]))
else:
log.info('\tskipping %s-access archive %s' %
(access, archive_fields[0]))
finally:
shutil.rmtree(archive_path)
def process_sdrf(config, log, magetab_archives, archive2metadata, barcode2annotations):
"""
return types:
barcode2files2term2values: maps aliquot barcode to a map with filenames for that barcode as keys to another map of terms
based on the ['metadata_locations']['sdrf'] section of the config file
"""
log.info('start processing sdrf')
sdrf_pat = re.compile("^.*sdrf.txt$")
anti_pat = re.compile("^.*antibody_annotation.txt$")
barcode2files2term2values = {}
archive2barcodes = {}
for archive_fields in magetab_archives:
try:
log.info('\tprocessing %s' % (archive_fields[0]))
archive_path = util.setup_archive(archive_fields, log)
files = os.listdir(archive_path)
antibody_files = []
cur_barcode2files2term2values = {}
for file_name in files:
if sdrf_pat.match(file_name):
parse_sdrf(config, log, archive_path + file_name, archive2metadata, cur_barcode2files2term2values,
archive2barcodes, archive_fields, file_name, barcode2annotations)
util.merge_metadata(barcode2files2term2values, cur_barcode2files2term2values, archive_fields[0] + ': ' + ','.join([archive_fields[0] for archive_fields in magetab_archives]), log)
upload_sdrf_file(config, archive_path, file_name, barcode2files2term2values.values()[0].values()[0], log)
elif anti_pat.match(file_name):
antibody_files += [file_name]
for file_name in antibody_files:
upload_sdrf_file(config, archive_path, file_name, barcode2files2term2values.values()[0].values()[0], log)
finally:
shutil.rmtree(archive_path)
log.info('finished processing sdrf')
return barcode2files2term2values
def parse_archives(config, log, archives, study, archive2metadata, clinical_metadata, biospecimen_metadata, exclude_samples):
'''
downloads and unpacks the archives. then parses, and if appropriate for the archive, uploads the files to GCS
parameters:
config: the configuration map
log: logger to log any messages
archives: information on the archives to unpack
study: name of the TCGA study the files belongs to
archive2metadata: metadata of the archive
clinical_metadata: the return map for clinical metadata
biospecimen_metadata: the return map for biospecimen metadata
'''
tmp_dir_parent = os.environ.get('ISB_TMP', '/tmp/')
for archive_fields in archives:
if not 'Level_1' in archive_fields[0]:
log.info('skipping bio archive %s' % (archive_fields[0]))
continue
log.info('processing archive %s' % (archive_fields[0]))
archive_path = os.path.join(tmp_dir_parent, archive_fields[0] + '/')
if not os.path.isdir(archive_path):
os.makedirs(archive_path)
archive_path = util.setup_archive(config, archive_fields, log)
files = os.listdir(archive_path)
parse_files(config, log, files, archive_path, archive_fields, study, archive2metadata, exclude_samples, clinical_metadata, biospecimen_metadata)
shutil.rmtree(archive_path)
def parse_archives(config, log, archives, study, archive2metadata, clinical_metadata, biospecimen_metadata):
tmp_dir_parent = os.environ.get('ISB_TMP', '/tmp/')
for archive_fields in archives:
if not 'Level_1' in archive_fields[0]:
log.info('skipping bio archive %s' % (archive_fields[0]))
continue
log.info('processing archive %s' % (archive_fields[0]))
archive_path = os.path.join(tmp_dir_parent, archive_fields[0] + '/')
if not os.path.isdir(archive_path):
os.makedirs(archive_path)
archive_path = util.setup_archive(archive_fields, log)
files = os.listdir(archive_path)
parse_files(config, log, files, archive_path, archive_fields, study, archive2metadata, clinical_metadata, biospecimen_metadata)
shutil.rmtree(archive_path)
def upload_archive(config, sdrf_metadata, archive2metadata, ffpe_samples, archive_fields, upload_archives, seen_files, nonupload_files, access, log):
archive_path = None
if config['download_archives'] and util.is_upload_archive(archive_fields[0], upload_archives, archive2metadata):
log.info('\tuploading %s-access archive %s.' % (access, archive_fields[0]))
try:
level = archive_fields[0].split('.')[-4].replace('_', ' ')
user_info = config['user_info']
archive_path = util.setup_archive(archive_fields, log, user_info['user'], user_info['password'])
file2metadata = process_files(config, archive_path, sdrf_metadata, seen_files, nonupload_files, ffpe_samples, level, log)
if 0 < len(file2metadata):
upload_files(config, archive_path, file2metadata, log)
else:
log.warning('did not find files to load for %s' % (archive_fields[0]))
finally:
if archive_path:
shutil.rmtree(archive_path)
log.info('\tfinished uploading %s-access archive %s' % (access, archive_fields[0]))
else:
log.info('\tskipping %s-access archive %s' % (access, archive_fields[0]))
def upload_archive(config, log, archive_fields, archive2metadata, sdrf_metadata, access):
user_info = config['user_info']
log.info('\tchecking %s-access maf archive %s.' % (access, archive_fields[0]))
try:
if config['download_archives']:
archive_path = util.setup_archive(archive_fields, log, user_info['user'], user_info['password'])
filenames = process_files(archive_path, log)
if 0 < len(filenames):
file2metadata = {}
for file_name in filenames:
if file_name.endswith('maf'):
file2metadata[file_name] = parse_maf_file(file_name, archive_path, log, archive_fields, archive2metadata, sdrf_metadata)
upload_archives.upload_files(config, archive_path, file2metadata, log)
else:
log.warning('\tdid not find files to load for %s' % (archive_fields[0]))
else:
log.info('\tskipping %s-access archive %s' % (access, archive_fields[0]))
finally:
shutil.rmtree(archive_path)
def upload_archive(config, log, archive_fields, archive2metadata, sdrf_metadata, seen_files, access):
'''
uploads and gathers metadata on the maf-related files in the archive
parameters:
config: the configuration map
log: logger to log any messages
archive_fields: archive name, creation date, and URL
archive2metadata: archive metadata
sdrf_metadata: metadata map to update
access: either open or controlled
'''
user_info = config['user_info']
log.info('\tchecking %s-access maf archive %s.' % (access, archive_fields[0]))
archive_path = None
try:
if config['download_archives']:
archive_path = util.setup_archive(config, archive_fields, log, user_info['user'], user_info['password'])
maf_upload_files = config['maf_upload_files']
filenames = process_files(archive_path, maf_upload_files, seen_files, log)
if 0 < len(filenames):
file2metadata = {}
for file_name in filenames:
if file_name.endswith('maf'):
file2metadata[file_name] = parse_maf_file(file_name, archive_path, log, archive_fields, archive2metadata, sdrf_metadata)
elif file_name.endswith('vcf') or file_name.endswith('vcf.gz'):
file2metadata[file_name] = parse_vcf_file(file_name, archive_path, log, archive_fields, archive2metadata, sdrf_metadata)
upload_archives.upload_files(config, archive_path, file2metadata, log)
else:
log.warning('\tdid not find files to load for %s' % (archive_fields[0]))
else:
log.info('\tskipping %s-access archive %s' % (access, archive_fields[0]))
finally:
if archive_path:
shutil.rmtree(archive_path)
