def get_similar_disease(self, disease, **kwargs):
"""
Return targets sharing a similar patter nof association to diseases
Accepts any string as `disease` parameter and fires a search if nothing is retireved on a first attempt
Args:
disease (str): a disease identifier or a string to search for a disease mapping
Keyword Args:
**kwargs: are passed as parameters to the /private/relation/disease method of the REST API
Returns:
IterableResult: Result of the query
"""
if not isinstance(disease, str):
raise AttributeError('disease must be of type str')
result = IterableResult(self.conn)
result(self._relation_disease_endpoint+'/'+disease, **kwargs)
if not result:
search_result = next(self.search(disease, size=1, filter='disease'))
if not search_result:
raise AttributeError('cannot find an disease id for disease {}'.format(disease))
disease_id = search_result['id']
logger.debug('{} resolved to id {}'.format(disease, disease_id))
result = IterableResult(self.conn)
result(self._relation_disease_endpoint + '/' + disease_id, **kwargs)
return result
def get_similar_target(self, target, **kwargs):
"""
Return targets sharing a similar patter nof association to diseases
Accepts any string as `target` parameter and fires a search if it is not an Ensembl Gene identifier
Args:
target (str): an Ensembl Gene identifier or a string to search for a gene mapping
Keyword Args:
**kwargs: are passed as parameters to the /private/relation/target method of the REST API
Returns:
IterableResult: Result of the query
"""
if not isinstance(target, str):
raise AttributeError('target must be of type str')
if not target.startswith('ENSG'):
search_result = next(self.search(target, size=1, filter='target'))
if not search_result:
raise AttributeError('cannot find an ensembl gene id for target {}'.format(target))
target_id = search_result['id']
logger.debug('{} resolved to id {}'.format(target, target_id))
else:
target_id = target
result = IterableResult(self.conn)
result(self._relation_target_endpoint+'/'+target_id, **kwargs)
return result
def get_metrics(self, **kwargs):
"""
Returns metrics about the data served by the REST API
Returns:
IterableResult: Result of the query
"""
result = IterableResult(self.conn)
result(self._metrics_endpoint)
return result
def get_stats(self):
"""
Returns statistics about the data served by the REST API
Returns:
IterableResult: Result of the query
"""
result = IterableResult(self.conn)
result(self._stats_endpoint)
return result
def filter_associations(self,**kwargs):
"""
Retrieve a set of associations by applying a set of filters
Keyword Args:
**kwargs: are passed as parameters to the /public/association/filterby method of the REST API
Returns:
IterableResult: Result of the query
"""
result = IterableResult(self.conn)
result(self._filter_associations_endpoint, **kwargs)
return result
def get_disease(self, disease_id, **kwargs):
"""
Retrieve a specific disease object from the REST API provided its ID
Args:
evidence_id: OT disease ID (EFO, Orphanet, ...)
Keyword Args:
**kwargs: are passed as other parameters to the /private/disease method of the REST API
Returns:
IterableResult: Result of the query
"""
result = IterableResult(self.conn)
result(self._get_disease + '/' + disease_id, **kwargs)
return result
def get_target(self, target_id, **kwargs):
"""
Retrieve a specific target object from the REST API provided its ID
Args:
target_id: Ensembl ID
Keyword Args:
**kwargs: are passed as other parameters to the /private/target method of the REST API
Returns:
IterableResult: Result of the query
"""
result = IterableResult(self.conn)
result(self._get_target + '/' + target_id, **kwargs)
return result
def get_association(self,association_id, **kwargs):
"""
Retrieve a specific Association object from the REST API provided its ID
Args:
association_id (str): Association ID
Keyword Args:
**kwargs: are passed as other parameters to the /public/association method of the REST API
Returns:
IterableResult: Result of the query
"""
kwargs['id']= association_id
result = IterableResult(self.conn)
result(self._get_associations_endpoint, **kwargs)
return result
def get_evidence(self, evidence_id, **kwargs):
"""
Retrieve a specific Evidence object from the REST API provided its ID
Args:
evidence_id:
Keyword Args:
**kwargs: are passed as other parameters to the /public/evidence method of the REST API
Returns:
IterableResult: Result of the query
"""
kwargs['id']= evidence_id
result = IterableResult(self.conn)
result(self._get_evidence_endpoint, **kwargs)
return result
def search(self, query,**kwargs):
"""
Search a string and return a list of objects form the search method of the REST API.
E.g. A returned object could be a target or a disease
Args:
query (str): string to search for
Keyword Args:
**kwargs: are passed as other parameters to the /public/search method of the REST API
Returns:
IterableResult: Result of the query
"""
kwargs['q']=query
result = IterableResult(self.conn)
result(self._search_endpoint,**kwargs)
return result