def _check_config(self):
if not self.config_path.exists():
logger.info("No config file found so creating empty config file.")
template_path = self.root_path.joinpath(
"datalight/config_template.txt")
with open(template_path) as input_file:
config_text = input_file.read()
with open(self.config_path, 'w') as output_file:
output_file.write(config_text)
def read_schema_from_file() -> dict:
"""Method to read the schema. Reads schema from self.schema_path
Stores schema dictionary in self.schema"""
logger.info(f'Reading schema from: {SCHEMA_FILE}')
try:
with open(SCHEMA_FILE) as input_file:
return json.load(input_file)
except FileNotFoundError:
raise ZenodoMetadataException(f'Schema file: {SCHEMA_FILE} not found.')
def load_yaml(metadata_path: str) -> dict:
"""Method to read metadata from a file.
:param metadata_path: A path to a file which contains zenodo metadata (yaml format).
"""
logger.info(f'Metadata read from file: {metadata_path}')
try:
with open(metadata_path) as input_file:
return yaml.load(input_file, Loader=yaml.FullLoader)
except FileNotFoundError:
raise FileNotFoundError(f'Metadata file {metadata_path} not found.')
def _get_local_open_licenses():
"""Get open license definitions from a local file.
:returns open_licenses: (dict) details of open licenses.
"""
license_path = SCHEMAS_DIR / pathlib.Path(
'zenodo/opendefinition-licenses.json')
try:
with open(license_path) as input_file:
open_licenses = json.load(input_file)
logger.info(f'Using file: {license_path} to validate license')
return open_licenses
except FileNotFoundError:
error = f"Could not get open license definitions from local file {license_path}."
logger.error(error)
raise ZenodoMetadataException(error)
def _get_internet_open_licenses():
"""Download the definition file for open source licenses accepted by Zenodo.
:returns licenses: (dict) Information about the different license types.
if licenses cannot be accessed, returns none.
"""
url = 'https://licenses.opendefinition.org/licenses/groups/all.json'
try:
with urllib.request.urlopen(url) as input_file:
licenses = json.load(input_file)
logger.info(f'open licenses file use for validation: {url}')
return licenses
except urllib.error.URLError:
logger.warning(
f'Not possible to access open license list from: {url}')
return None
def delete_record(deposition_url: str, deposition_id: int,
token: str) -> UploadStatus:
"""Method to delete an unpublished deposition.
If id not provided, use deposition_id, else use provided id
:param deposition_url: URL to make the Zenodo API request.
:param deposition_id: Deposition id of the record to delete. Record can only be deleted
if it was not published.
:param token: API token for connecting to Zenodo.
"""
# Create the request url
request_url = f'{deposition_url}/{deposition_id}'
logger.info('Delete url: {}'.format(request_url))
request = requests.delete(request_url, params={'access_token': token})
return _check_request_response(request)
def _upload_metadata(deposition_url: str, deposition_id: int, token: str,
metadata: dict) -> UploadStatus:
"""Upload metadata to Zenodo repository.
After creating the request and uploading the file(s) we need to update
the metadata needed by Zenodo related to the record.
"""
# Create the url to upload with the deposition_id
url = f'{deposition_url}/{deposition_id}'
logger.info(f'url: {url}')
headers = {"Content-Type": "application/json"}
request = requests.put(url,
params={'access_token': token},
data=json.dumps(metadata),
headers=headers)
return _check_request_response(request)
def _upload_files(upload_url: int, token: str,
filepaths: List[str]) -> UploadStatus:
"""Method to upload a file to Zenodo
:param filepaths: Paths of one or more files to upload.
"""
for filepath in filepaths:
filepath = pathlib.Path(filepath)
logger.info(f'Uploading file "{filepath.name}" from {filepath.parent}')
url = f'{upload_url}/{filepath.name}'
# Open the file to upload in binary mode and upload it.
with open(filepath, 'rb') as input_file:
request = requests.put(url,
data=input_file,
params={'access_token': token})
status = _check_request_response(request)
if status.code not in STATUS_SUCCESS:
return status
return UploadStatus(200, "All files uploaded successfully.")
def validate_metadata(metadata: dict, schema: dict) -> dict:
"""Method which verifies that the metadata have the correct type and that
dependencies are respected."""
# Validate metadata before license to be sure that the "license" and "access_right"
# keys are present.
try:
jsonschema.validate(metadata, schema)
except jsonschema.exceptions.ValidationError as err:
raise ZenodoMetadataException(f'ValidationError: {err.message}')
# Check validity of the license (if open or embargoed)
license_checker = _LicenseStatus(metadata["license"],
metadata["access_right"])
license_checker.validate_license()
if license_checker.license_valid is False:
logger.error(
"Invalid licence type. access_right is 'open' or 'embargoed' and {}"
"is not a valid Open License.".format(license_checker.license))
raise ZenodoMetadataException
logger.info('Metadata have been validated successfully.')
metadata = remove_extra_properties(metadata)
return metadata
def validate_license(self):
"""Method to verify the status of the metadata license."""
if not (self.access_right in ['open', 'embargoed']):
logger.info('No need to check license for Zenodo upload.')
self.license_valid = True
else:
metadata_license = self.license.upper()
logger.info(f'Specified license type is: {self.license}')
logger.info(f'access_right: "{self.access_right}"')
for lic in self.open_licenses.keys():
if lic.startswith(metadata_license):
logger.info(f'license: "{lic}" validated.')
self.license_valid = True
break