first draft of the biokb wrapper

biokb/biokb.py

+from typing import List
+from interface.TextMiningService import TextMiningService
+from models.publication import Publication
+from models.coocurrence import CoOccurrence
+from biokb.utils import uri_to_code
+
+from SPARQLWrapper import SPARQLWrapper, JSON
+from SPARQLWrapper.SPARQLExceptions import EndPointNotFound, EndPointInternalError, QueryBadFormed
+
+import logging
+logger = logging.getLogger(__name__)
+
+class BioKBClientException(Exception):
+    pass
+
+
+class MalformedQueryException(BioKBClientException):
+    pass
+
+
+class BioKBservice(TextMiningService):
+    def __init__(self, sparql_url="https://biokb.lcsb.uni.lu/sparql"):
+        self.sparql = SPARQLWrapper(sparql_url)
+        super().__init__('BioKB',
+                         'This client communicates with BioKB triple store and Publication Solr index.')
+
+    def _run_sparql_query(self, sparql_query):
+        try:
+            self.sparql.setQuery(sparql_query)
+            self.sparql.setReturnFormat(JSON)
+            results = self.sparql.query().convert()
+            return results
+        except QueryBadFormed as e:
+            logger.error(e)
+            raise MalformedQueryException(e)
+
+    def get_mentions(self, entities: List[str], limit: int = 20) -> List[Publication]:
+
+        entity_subquery = ""
+        for entity in entities:
+            entity_subquery += f"?publication <http://lcsb.uni.lu/biokb#containsEntity> <http://lcsb.uni.lu/biokb/entities/{entity}> .\n"
+
+        query = """
+            select ?publication str(?solrId) as ?solrId where {{
+                {} 
+                ?publication <http://lcsb.uni.lu/biokb#solrId> ?solrId	.
+            }} LIMIT {}
+            """.format(entity_subquery, limit)
+
+        results = self._run_sparql_query(query)
+        values = []
+        for result in results['results']['bindings']:
+            solr_id = result['solrId']['value']
+            publication_uri = result['publication']['value']
+            values.append(
+                {"solr_id": solr_id, "publication_uri": publication_uri})
+
+        return values
+
+    def get_co_occurrences(self, entity: str) -> List[CoOccurrence]:
+        query = """
+            select * where {
+    
+                select ?other_entity, (COUNT(*) AS ?count) where {
+                    
+                    ?s <http://lcsb.uni.lu/biokb#containsEntity> <http://lcsb.uni.lu/biokb/entities/%ENTITY%> .
+                    ?s a  <http://lcsb.uni.lu/biokb#Publication> .
+                    ?s <http://lcsb.uni.lu/biokb#containsEntity> ?other_entity .
+                
+                    OPTIONAL {?ss rdfs:subClassOf ?other_entity} .
+                
+                    FILTER (!bound(?ss)) .
+                    FILTER(?other_entity != <http://lcsb.uni.lu/biokb/entities/%ENTITY%>) .
+                    
+                    OPTIONAL {
+                        ?other_entity owl:sameAs ?o_original .
+                    } .
+                    
+                    OPTIONAL {
+                        ?other_entity a <http://lcsb.uni.lu/biokb#Protein> .
+                        ?other_entity owl:sameAs ?ensembl_protein .
+                    }
+
+                }
+                
+                GROUP BY ?other_entity 
+
+            } ORDER BY DESC(?count)
+        """.replace('%ENTITY', entity)
+
+        results = self._run_sparql_query(query)
+        values = []
+        values = []
+        for result in results['results']['bindings']:
+            entity_code = uri_to_code(result['other_entity']['value'])
+            count       = int(result['count']['value'])
+            co_occur    = CoOccurrence(entity_code, count)
+            values.append(co_occur)
+        return values