def _add_meta(self, *args, **kwargs):
"""Add Ensembl metadata."""
metadata = SourceMeta(
data_license="custom",
data_license_url="https://useast.ensembl.org/info/about"
"/legal/disclaimer.html",
version=self._version,
data_url=self._data_url,
rdp_url=None,
data_license_attributes={
"non_commercial": False,
"share_alike": False,
"attribution": False
},
genome_assemblies=[self._assembly])
self._database.metadata.put_item(
Item={
"src_name": SourceName.ENSEMBL.value,
"data_license": metadata.data_license,
"data_license_url": metadata.data_license_url,
"version": metadata.version,
"data_url": metadata.data_url,
"rdp_url": metadata.rdp_url,
"data_license_attributes": metadata.data_license_attributes,
"genome_assemblies": metadata.genome_assemblies
})
self._load_meta(self._database, metadata, SourceName.ENSEMBL.value)
def _add_meta(self, *args, **kwargs):
"""Add Ensembl metadata."""
metadata = SourceMeta(
data_license='custom',
data_license_url='https://useast.ensembl.org/info/about'
'/legal/disclaimer.html',
version=self._version,
data_url=self._data_url,
rdp_url=None,
data_license_attributes={
'non_commercial': False,
'share_alike': False,
'attribution': False
},
genome_assemblies=[self._assembly])
self._database.metadata.put_item(
Item={
'src_name': SourceName.ENSEMBL.value,
'data_license': metadata.data_license,
'data_license_url': metadata.data_license_url,
'version': metadata.version,
'data_url': metadata.data_url,
'rdp_url': metadata.rdp_url,
'data_license_attributes': metadata.data_license_attributes,
'genome_assemblies': metadata.genome_assemblies
})
self._load_meta(self._database, metadata, SourceName.ENSEMBL.value)
def _add_meta(self, *args, **kwargs):
"""Add HGNC metadata to the gene_metadata table."""
metadata = SourceMeta(
data_license='custom',
data_license_url='https://www.genenames.org/about/',
version=self._version,
data_url=self._data_url,
rdp_url=None,
data_license_attributes={
'non_commercial': False,
'share_alike': False,
'attribution': False
},
genome_assemblies=[])
self._load_meta(self._database, metadata, SourceName.HGNC.value)
def fetch_meta(self, src_name: str) -> SourceMeta:
"""Fetch metadata for src_name.
:param str src_name: name of source to get metadata for
:return: SourceMeta object containing source metadata
"""
if src_name in self.db.cached_sources.keys():
return self.db.cached_sources[src_name]
else:
try:
db_response = self.db.metadata.get_item(
Key={'src_name': src_name})
response = SourceMeta(**db_response['Item'])
self.db.cached_sources[src_name] = response
return response
except ClientError as e:
logger.error(e.response['Error']['Message'])
def _add_meta(self):
"""Load metadata"""
metadata = SourceMeta(
data_license="custom",
data_license_url="https://www.ncbi.nlm.nih.gov/home/"
"about/policies/",
version=self._version,
data_url=self._data_url,
rdp_url="https://reusabledata.org/ncbi-gene.html",
data_license_attributes={
'non_commercial': False,
'share_alike': False,
'attribution': False
},
genome_assemblies=[self._assembly])
self._load_meta(self._database, metadata, SourceName.NCBI.value)