def validate_archive(self, filename):
reader = CombineArchiveReader()
name = os.path.relpath(filename, EXAMPLES_DIR)
temp_dirname = os.path.join(self.temp_dirname, name)
if not os.path.isdir(temp_dirname):
os.makedirs(temp_dirname)
archive = reader.run(filename, temp_dirname)
config = Config(
OMEX_METADATA_SCHEMA=OmexMetadataSchema.biosimulations, )
error_msgs, warning_msgs = validate(
archive,
temp_dirname,
formats_to_validate=list(
CombineArchiveContentFormat.__members__.values()),
config=config,
)
if warning_msgs:
msg = 'The COMBINE/OMEX archive may be invalid.\n {}'.format(
flatten_nested_list_of_strings(warning_msgs).replace(
'\n', '\n '))
warnings.warn(msg, BioSimulatorsWarning)
if error_msgs:
msg = 'The COMBINE/OMEX archive is not valid.\n {}'.format(
flatten_nested_list_of_strings(error_msgs).replace(
'\n', '\n '))
raise ValueError(msg)
def handler(body, file=None):
''' Validate a COMBINE/OMEX archive
Args:
body (:obj:`dict`): dictionary in schema ``ValidateCombineArchiveFileOrUrl`` with keys
* ``url`` whose value has schema ``Url`` with the URL for a COMBINE/OMEX archive
* ``omexMetadataFormat`` (:obj:`str`): format of the OMEX Metadata files
* ``omexMetadataSchema`` (:obj:`str`): schema for validating the OMEX Metadata files
* ``validateOmexManifest`` (:obj:`bool`, optional): Whether to validate the OMEX manifest file in the archive
* ``validateSedml`` (:obj:`bool`, optional): Whether to validate the SED-ML files in the archive
* ``validateSedmlModels`` (:obj:`bool`, optional): Whether to validate the sources of the models in the SED-ML files in the archive
* ``validateOmexMetadata`` (:obj:`bool`, optional): Whether to validate the OMEX metdata files in the archive according to
`BioSimulators' conventions <https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/>`_
* ``validateImages`` (:obj:`bool`, optional): Whether to validate the images (BMP, GIF, JPEG, PNG, TIFF WEBP) files in the archive
file (:obj:`werkzeug.datastructures.FileStorage`): COMBINE/OMEX archive file
Returns:
``ValidationReport``: information about the validity or
lack thereof of a COMBINE/OMEX archive
'''
try:
omexMetadataInputFormat = OmexMetadataInputFormat(
body['omexMetadataFormat'])
except ValueError as exception:
raise BadRequestException(
title='`omexMetadataFormat` must be a recognized format.',
exception=exception)
try:
omexMetadataSchema = OmexMetadataSchema(body['omexMetadataSchema'])
except ValueError as exception:
raise BadRequestException(
title='`omexMetadataSchema` must be a recognized schema.',
exception=exception)
config = Config(
OMEX_METADATA_INPUT_FORMAT=omexMetadataInputFormat,
OMEX_METADATA_SCHEMA=omexMetadataSchema,
VALIDATE_OMEX_MANIFESTS=body.get('validateOmexManifest', True),
VALIDATE_SEDML=body.get('validateSedml', True),
VALIDATE_SEDML_MODELS=body.get('validateSedmlModels', True),
VALIDATE_OMEX_METADATA=body.get('validateOmexMetadata', True),
VALIDATE_IMAGES=body.get('validateImages', True),
)
archive_file = file
archive_url = body.get('url', None)
if archive_url and archive_file:
raise BadRequestException(
title='Only one of `file` or `url` can be used at a time.',
instance=ValueError(),
)
if not archive_url and not archive_file:
raise BadRequestException(
title='One of `file` or `url` must be used.',
instance=ValueError(),
)
# create temporary working directory
temp_dirname = get_temp_dir()
archive_filename = os.path.join(temp_dirname, 'archive.omex')
# get COMBINE/OMEX archive
if archive_file:
archive_file.save(archive_filename)
else:
try:
response = requests.get(archive_url)
response.raise_for_status()
except requests.exceptions.RequestException as exception:
title = 'COMBINE/OMEX archive could not be loaded from `{}`'.format(
archive_url)
raise BadRequestException(
title=title,
instance=exception,
)
# save archive to local temporary file
with open(archive_filename, 'wb') as file:
file.write(response.content)
# read archive
archive_dirname = os.path.join(temp_dirname, 'archive')
reader = CombineArchiveReader()
errors = []
warnings = []
try:
archive = reader.run(archive_filename, archive_dirname, config=config)
except Exception as exception:
errors = [[
'The file could not be parsed as a COMBINE/OMEX archive.',
[[str(exception)]]
]]
if not errors:
errors, warnings = validate(
archive,
archive_dirname,
formats_to_validate=list(
CombineArchiveContentFormat.__members__.values()),
config=config,
)
return make_validation_report(errors,
warnings,
filenames=[archive_filename])
