raise GenestackException(
"The key '%s' must be supplied in the CSV file" %
mandatory_key)
for file_data in reader:
# for each entry, prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# 'link' and 'organism' are treated separately, as they are added to the metainfo using specific methods
if key == "link":
url = file_data[key]
metainfo.add_external_link(key=BioMetainfo.READS_LINK,
text="link",
url=url,
fmt=file_format)
elif key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, file_data[key])
# all the other keys are added as strings
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
metainfo.add_string(metainfo_key, file_data[key])
# create the sequencing assay on Genestack
created_file = importer.create_sequencing_assay(experiment,
metainfo=metainfo)
print "Created file '%s' (%s)" % (file_data['name'], created_file)
print "All done! Bye now..."
reader = csv.DictReader(the_file, delimiter=",")
field_names = reader.fieldnames
# check if mandatory keys are in the CSV file
for mandatory_key in MANDATORY_KEYS:
if mandatory_key not in field_names:
raise GenestackException("The key '%s' must be supplied in the CSV file" % mandatory_key)
for file_data in reader:
# for each entry, prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# 'link' and 'organism' are treated separately, as they are added to the metainfo using specific methods
if key == "link":
url = file_data[key]
metainfo.add_external_link(key=BioMetainfo.READS_LINK, text="link", url=url, fmt=file_format)
elif key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, file_data[key])
# all the other keys are added as strings
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
metainfo.add_string(metainfo_key, file_data[key])
# create the sequencing assay on Genestack
created_file = importer.create_sequencing_assay(experiment, metainfo=metainfo)
print "Created file '%s' (%s)" % (file_data['name'], created_file)
print "All done! Bye now..."
# find the corresponding file
local_identifier = file_data[local_key]
remote_file = identifier_map.get(local_identifier)
if not remote_file:
print "Warning: no match found for file name '%s'" % local_identifier
continue
# prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# key parsing logic
value = file_data[key]
if value == "" or value is None:
continue
if key == args.local_key:
continue
if key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, value)
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
if parse_as_boolean(value) is not None:
metainfo.add_boolean(metainfo_key, parse_as_boolean(value))
else:
metainfo.add_string(metainfo_key, value)
# edit the metadata on Genestack
files_util.add_metainfo_values(remote_file, metainfo)
print "Edited metainfo for '%s' (%s)" % (local_identifier, remote_file)
print "All done!"
remote_file = identifier_map.get(local_identifier)
if not remote_file:
print "Warning: no match found for file name '%s'" % local_identifier
continue
# prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# key parsing logic
value = file_data[key]
if value == "" or value is None:
continue
if key == args.local_key:
continue
if key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, value)
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
if parse_as_boolean(value) is not None:
metainfo.add_boolean(metainfo_key,
parse_as_boolean(value))
else:
metainfo.add_string(metainfo_key, value)
# edit the metadata on Genestack
files_util.add_metainfo_values(remote_file, metainfo)
print "Edited metainfo for '%s' (%s)" % (local_identifier,
remote_file)
print "All done!"
