def process_zip_archive(file, id):
filename = secure_filename(file.filename)
time_stamp = str(int(round(time.time())))
file_save_directory = os.path.join(current_app.config['CFG_DATADIR'],
str(id), time_stamp)
if not os.path.exists(file_save_directory):
os.makedirs(file_save_directory)
if not filename.endswith('.oldhepdata'):
file_path = os.path.join(file_save_directory, filename)
file.save(file_path)
submission_path = os.path.join(file_save_directory,
remove_file_extension(filename))
if filename.endswith('.yaml'):
# we split the singular yaml file and create a submission directory
error, last_updated = split_files(file_path, submission_path)
if error:
return {
"Single YAML file splitter": [{
"level": "error",
"message": str(error)
}]
}
else:
# we are dealing with a zip, tar, etc. so we extract the contents
extract(filename, file_path, submission_path)
submission_found = find_file_in_directory(
submission_path, lambda x: x == "submission.yaml")
else:
file_path = os.path.join(file_save_directory, 'oldhepdata')
if not os.path.exists(file_path):
os.makedirs(file_path)
print('Saving file to {}'.format(os.path.join(file_path, filename)))
file.save(os.path.join(file_path, filename))
submission_path = os.path.join(file_save_directory, 'oldhepdata')
submission_found = False
if submission_found:
basepath, submission_file_path = submission_found
else:
result = check_and_convert_from_oldhepdata(submission_path, id,
time_stamp)
# Check for errors
if type(result) == dict:
return result
else:
basepath, submission_file_path = result
return process_submission_directory(basepath, submission_file_path, id)
def process_zip_archive(file, id):
filename = secure_filename(file.filename)
time_stamp = str(int(round(time.time())))
file_save_directory = os.path.join(current_app.config['CFG_DATADIR'], str(id), time_stamp)
if not os.path.exists(file_save_directory):
os.makedirs(file_save_directory)
if '.oldhepdata' not in filename:
file_path = os.path.join(file_save_directory, filename)
file.save(file_path)
submission_path = os.path.join(file_save_directory, remove_file_extension(filename))
if 'yaml' in filename:
# we split the singular yaml file and create a submission directory
split_files(file_path, submission_path)
else:
# we are dealing with a zip, tar, etc. so we extract the contents
extract(filename, file_path, submission_path)
submission_found = find_file_in_directory(submission_path,
lambda x: x == "submission.yaml")
else:
file_path = os.path.join(file_save_directory, 'oldhepdata')
if not os.path.exists(file_path):
os.makedirs(file_path)
if filename.endswith('.txt'):
filename = filename.replace(".txt", "")
print('Saving file to {}'.format(os.path.join(file_path, filename)))
file.save(os.path.join(file_path, filename))
submission_path = os.path.join(file_save_directory, 'oldhepdata')
submission_found = False
if submission_found:
basepath, submission_file_path = submission_found
else:
result = check_and_convert_from_oldhepdata(submission_path, id,
time_stamp)
# Check for errors
if type(result) == dict:
return result
else:
basepath, submission_file_path = result
return process_submission_directory(basepath, submission_file_path, id)
def process_zip_archive(file, id):
filename = secure_filename(file.filename)
time_stamp = str(int(round(time.time())))
file_save_directory = os.path.join(current_app.config['CFG_DATADIR'],
str(id), time_stamp)
if not os.path.exists(file_save_directory):
os.makedirs(file_save_directory)
if not filename.endswith('.oldhepdata'):
file_path = os.path.join(file_save_directory, filename)
print('Saving file to {}'.format(file_path))
file.save(file_path)
submission_path = os.path.join(file_save_directory,
remove_file_extension(filename))
submission_temp_path = tempfile.mkdtemp(
dir=current_app.config["CFG_TMPDIR"])
if filename.endswith('.yaml'):
# we split the singular yaml file and create a submission directory
error, last_updated = split_files(file_path, submission_temp_path)
if error:
return {
"Single YAML file splitter": [{
"level": "error",
"message": str(error)
}]
}
else:
# we are dealing with a zip, tar, etc. so we extract the contents
if not extract(file_path, submission_temp_path):
return {
"Archive file extractor": [{
"level":
"error",
"message":
"{} is not a valid zip or tar archive file.".format(
file_path)
}]
}
if not os.path.exists(submission_path):
os.makedirs(submission_path)
# Move files from submission_temp_path to submission_path (try to avoid problems with EOS disk).
if current_app.config.get('PRODUCTION_MODE',
False): # production instance at CERN
copy_command = ['xrdcp', '-N', '-f']
copy_submission_path = submission_path.replace(
current_app.config['CFG_DATADIR'],
current_app.config['EOS_DATADIR'])
else: # local instance
copy_command = ['cp']
copy_submission_path = submission_path
print('Copying with: {} -r {} {}'.format(' '.join(copy_command),
submission_temp_path + '/.',
copy_submission_path))
subprocess.check_output(
copy_command +
['-r', submission_temp_path + '/.', copy_submission_path])
rmtree(submission_temp_path, ignore_errors=True
) # can uncomment when this is definitely working
submission_found = find_file_in_directory(
submission_path, lambda x: x == "submission.yaml")
else:
file_path = os.path.join(file_save_directory, 'oldhepdata')
if not os.path.exists(file_path):
os.makedirs(file_path)
print('Saving file to {}'.format(os.path.join(file_path, filename)))
file.save(os.path.join(file_path, filename))
submission_found = False
if submission_found:
basepath, submission_file_path = submission_found
else:
result = check_and_convert_from_oldhepdata(file_path, id, time_stamp)
# Check for errors
if type(result) == dict:
return result
else:
basepath, submission_file_path = result
return process_submission_directory(basepath, submission_file_path, id)
def process_zip_archive(file_path, id, old_submission_schema=False,
old_data_schema=False):
(file_save_directory, filename) = os.path.split(file_path)
if not filename.endswith('.oldhepdata'):
file_save_directory = os.path.dirname(file_path)
submission_path = os.path.join(file_save_directory, remove_file_extension(filename))
submission_temp_path = tempfile.mkdtemp(dir=current_app.config["CFG_TMPDIR"])
if filename.endswith('.yaml.gz'):
print('Extracting: {} to {}'.format(file_path, file_path[:-3]))
if not extract(file_path, file_path[:-3]):
return {
"Archive file extractor": [{
"level": "error", "message": "{} is not a valid .gz file.".format(file_path)
}]
}
return process_zip_archive(file_path[:-3], id,
old_submission_schema=old_submission_schema,
old_data_schema=False)
elif filename.endswith('.yaml'):
# we split the singular yaml file and create a submission directory
error, last_updated = split_files(file_path, submission_temp_path)
if error:
return {
"Single YAML file splitter": [{
"level": "error",
"message": str(error)
}]
}
else:
# we are dealing with a zip, tar, etc. so we extract the contents
try:
unzipped_path = extract(file_path, submission_temp_path)
except Exception as e:
unzipped_path = None
if not unzipped_path:
return {
"Archive file extractor": [{
"level": "error", "message": "{} is not a valid zip or tar archive file.".format(file_path)
}]
}
copy_errors = move_files(submission_temp_path, submission_path)
if copy_errors:
return copy_errors
submission_found = find_file_in_directory(submission_path, lambda x: x == "submission.yaml")
if not submission_found:
return {
"Archive file extractor": [{
"level": "error", "message": "No submission.yaml file has been found in the archive."
}]
}
basepath, submission_file_path = submission_found
else:
file_dir = os.path.dirname(file_save_directory)
time_stamp = os.path.split(file_dir)[1]
result = check_and_convert_from_oldhepdata(os.path.dirname(file_save_directory), id, time_stamp)
# Check for errors
if type(result) == dict:
return result
else:
basepath, submission_file_path = result
old_data_schema = True
return process_submission_directory(basepath, submission_file_path, id,
old_data_schema=old_data_schema,
old_submission_schema=old_submission_schema)
def _import_record(inspire_id,
update_existing=False,
base_url='https://hepdata.net',
send_email=False):
publication_information, status = get_inspire_record_information(
inspire_id)
if status != "success":
log.error("Failed to retrieve publication information for " +
inspire_id)
return False
current_submission = get_latest_hepsubmission(inspire_id=inspire_id)
if not current_submission:
log.info(
"The record with id {0} does not exist in the database, so we're loading it."
.format(inspire_id))
publication_information["inspire_id"] = inspire_id
record_information = create_record(publication_information)
recid = record_information['recid']
else:
log.info("The record with inspire id {0} already exists.".format(
inspire_id))
if update_existing:
log.info("Updating instead")
recid = current_submission.publication_recid
else:
log.info("Not updating as update_existing is False")
return False
try:
download_path = _download_file(base_url, inspire_id)
filename = os.path.basename(download_path)
time_stamp = str(int(round(time.time())))
file_save_directory = get_data_path_for_record(str(recid), time_stamp)
if not os.path.exists(file_save_directory):
os.makedirs(file_save_directory)
file_path = os.path.join(file_save_directory, filename)
log.info("Moving file to %s" % file_path)
shutil.copy(download_path, file_path)
# Create submission
admin_user_id = 1
hepsubmission = get_or_create_hepsubmission(recid, admin_user_id)
db.session.add(hepsubmission)
db.session.commit()
# Then process the payload as for any other record
errors = process_zip_archive(file_path, recid)
if errors:
log.info("Errors processing archive. Re-trying with old schema.")
# Try again with old schema
# Need to clean up first to avoid errors
# First delete tables
cleanup_submission(recid, 1, [])
# Next remove remaining files
file_save_directory = os.path.dirname(file_path)
submission_path = os.path.join(file_save_directory,
remove_file_extension(filename))
shutil.rmtree(submission_path)
errors = process_zip_archive(file_path,
recid,
old_submission_schema=True,
old_data_schema=True)
if errors:
log.error("Could not process zip archive: ")
for file, file_errors in errors.items():
log.error(" %s:" % file)
for error in file_errors:
log.error(" %s" % error['message'])
raise ValueError("Could not validate record.")
# Delete any previous upload folders
cleanup_old_files(hepsubmission)
log.info("Finalising record %s" % recid)
result_json = do_finalise(recid,
force_finalise=True,
update=(current_submission is not None),
convert=False,
send_email=send_email)
result = json.loads(result_json)
if result and result['success']:
log.info("Imported record %s with %s submissions" %
(recid, result['data_count']))
return True
else:
raise ValueError("Failed to finalise record.")
except Exception as e:
# Unload record
unload_submission(recid)
log.error(e)
return False
