def parse_isatab(username, public, path, additional_raw_data_file_extension=None, isa_archive=None, pre_isa_archive=None, file_base_path=None):
"""
Name: parse_isatab
Description:
parses in an ISA-TAB file to create database entries and creates or updates a dataset for the investigation to belong to; returns the dataset UUID or None if something went wrong. Use like this: parse_isatab(username, is_public, folder_name, additional_raw_data_file_extension, isa_archive=<path>, pre_isa_archive=<path>, file_base_path=<path>
Parameters:
username: username of the person the dataset will belong to
public: boolean that determines if the dataset is public or not
path: absolute path of the ISA-Tab file to parse
additional_raw_data_file_extension: an optional argument that will append a suffix to items in Raw Data File as need be
isa_archive: if you're passing a directory, a zipped version of the directory for storage and legacy purposes
pre_isa_archive: optional copy of files that were converted to ISA-Tab
file_base_path: if your file locations are relative paths, this is the base
"""
logger.info("logging from parse_isatab")
p = IsaTabParser()
p.additional_raw_data_file_extension = additional_raw_data_file_extension
p.file_base_path = file_base_path
try:
investigation = p.run(path, isa_archive=isa_archive, preisa_archive=pre_isa_archive)
data_uuid = create_dataset(investigation.uuid, username, public=public)
return data_uuid
except: #prints the error message without breaking things
logger.error("*** print_tb:")
exc_type, exc_value, exc_traceback = sys.exc_info()
logger.error(traceback.print_tb(exc_traceback, file=sys.stdout))
logger.error("*** print_exception:")
logger.error(traceback.print_exception(exc_type, exc_value,
exc_traceback, file=sys.stdout))
return None
def parse_isatab(username,
public,
path,
additional_raw_data_file_extension=None,
isa_archive=None,
pre_isa_archive=None,
file_base_path=None):
"""
Name: parse_isatab
Description:
parses in an ISA-TAB file to create database entries and creates or updates a dataset for the investigation to belong to; returns the dataset UUID or None if something went wrong. Use like this: parse_isatab(username, is_public, folder_name, additional_raw_data_file_extension, isa_archive=<path>, pre_isa_archive=<path>, file_base_path=<path>
Parameters:
username: username of the person the dataset will belong to
public: boolean that determines if the dataset is public or not
path: absolute path of the ISA-Tab file to parse
additional_raw_data_file_extension: an optional argument that will append a suffix to items in Raw Data File as need be
isa_archive: if you're passing a directory, a zipped version of the directory for storage and legacy purposes
pre_isa_archive: optional copy of files that were converted to ISA-Tab
file_base_path: if your file locations are relative paths, this is the base
"""
logger.info("logging from parse_isatab")
p = IsaTabParser()
p.additional_raw_data_file_extension = additional_raw_data_file_extension
p.file_base_path = file_base_path
try:
investigation = p.run(path,
isa_archive=isa_archive,
preisa_archive=pre_isa_archive)
data_uuid = create_dataset(investigation.uuid, username, public=public)
return data_uuid
except: #prints the error message without breaking things
logger.error("*** print_tb:")
exc_type, exc_value, exc_traceback = sys.exc_info()
logger.error(traceback.print_tb(exc_traceback, file=sys.stdout))
logger.error("*** print_exception:")
logger.error(
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=sys.stdout))
return None
def parse_isatab(username, public, path,
additional_raw_data_file_extension=None, isa_archive=None,
pre_isa_archive=None, file_base_path=None):
"""parses in an ISA-TAB file to create database entries and creates or
updates a dataset for the investigation to belong to; returns the dataset
UUID or None if something went wrong. Use like this: parse_isatab(username,
is_public, folder_name, additional_raw_data_file_extension,
isa_archive=<path>, pre_isa_archive=<path>, file_base_path=<path>
Parameters:
username: username of the person the dataset will belong to
public: boolean that determines if the dataset is public or not
path: absolute path of the ISA-Tab file to parse
additional_raw_data_file_extension: an optional argument that will append a
suffix to items in Raw Data File as need be
isa_archive: if you're passing a directory, a zipped version of the
directory for storage and legacy purposes
pre_isa_archive: optional copy of files that were converted to ISA-Tab
file_base_path: if your file locations are relative paths, this is the base
"""
p = IsaTabParser()
p.additional_raw_data_file_extension = additional_raw_data_file_extension
p.file_base_path = file_base_path
"""Get the study title and investigation id and see if anything is in the
database and if so compare the checksum
"""
# 1. First check whether the user exists
try:
user = User.objects.get(username__exact=username)
except:
user = None
# 2. If user exists we need to quickly get the dataset title to see if its
# already in the DB
if user:
checksum = None
(identifier, title) = p.get_dataset_name(path)
if identifier is None or title is None:
datasets = []
else:
dataset_title = "%s: %s" % (identifier, title)
datasets = DataSet.objects.filter(name=dataset_title)
# check if the investigation already exists
if len(datasets): # if not 0, update dataset with new investigation
# go through datasets until you find one with the correct owner
for ds in datasets:
own = ds.get_owner()
if own == user:
# 3. Finally we need to get the checksum so that we can
# compare that to our given file.
investigation = ds.get_investigation()
fileStoreItem = FileStoreItem.objects.get(
uuid=investigation.isarchive_file)
if fileStoreItem:
try:
logger.info("Get file: %s",
fileStoreItem.get_absolute_path())
checksum = calculate_checksum(
fileStoreItem.get_file_object())
except IOError as e:
logger.error(
"Original isatab archive wasn't found. "
"Error: '%s'", e)
# 4. Finally if we got a checksum for an existing file, we calculate
# the checksum for the new file and compare them
if checksum:
new_checksum = None
# TODO: error handling
with open(path, 'rb') as f:
new_checksum = calculate_checksum(f)
if (checksum == new_checksum):
# Checksums are identical so we can skip this file.
logger.info("The checksum of both files is the same: %s",
checksum)
return (
investigation.investigationlink_set.all()[0].data_set.uuid,
os.path.basename(path),
True)
try:
investigation = p.run(path, isa_archive=isa_archive,
preisa_archive=pre_isa_archive)
data_uuid = create_dataset(investigation.uuid, username, public=public)
return (data_uuid, os.path.basename(path), False)
except: # prints the error message without breaking things
logger.error("*** print_tb:")
exc_type, exc_value, exc_traceback = sys.exc_info()
logger.error(traceback.print_tb(exc_traceback, file=sys.stdout))
logger.error("*** print_exception:")
logger.error(
traceback.print_exception(
exc_type,
exc_value,
exc_traceback,
file=sys.stdout
)
)
return None, os.path.basename(path), False
