Merge pull request #33 from biolink/27-mart-extensions

[#27] merge routes

biogolr/golr_associations.py

@@ -224,6 +224,7 @@ def translate_docs_compact(ds, field_mapping=None, slim=None, map_identifiers=No
             map_doc(d, field_mapping)
 
         subject = d[M.SUBJECT]
+        subject_label = d[M.SUBJECT_LABEL]
 
         # TODO: use a more robust method; we need equivalence as separate field in solr
         if map_identifiers is not None:
@@ -243,6 +244,7 @@ def translate_docs_compact(ds, field_mapping=None, slim=None, map_identifiers=No
         k = (subject,rel)
         if k not in amap:
             amap[k] = {'subject':subject,
+                       'subject_label':subject_label,
                        'relation':rel,
                        'objects': []}
         if slim is not None and len(slim)>0:
@@ -381,6 +383,7 @@ def search_associations(subject_category=None,
         facet_limit = 0
         select_fields = [
             M.SUBJECT,
+            M.SUBJECT_LABEL,
             M.RELATION,
             M.OBJECT]
 
@@ -501,7 +504,7 @@ def search_associations(subject_category=None,
     logging.info("PARAMS="+str(params))
     results = solr.search(**params)
     n_docs = len(results.docs)
-    logging.info("Num_docs: {}".format(n_docs))
+    logging.info("Docs found: {}".format(results.hits))
 
     if iterate:
         docs = results.docs

biolink/api/mart/endpoints/mart.py

@@ -62,6 +62,11 @@ def get(self, object_category, taxon):
 
         NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.
         """
+
+        # TODO temporary workaround
+        if taxon == "NCBITaxon:9606":
+            taxon = None
+
         assocs = bulk_fetch(subject_category='case',
                             object_category=object_category,
                             taxon=taxon,
@@ -82,30 +87,13 @@ def get(self, object_category, taxon):
 
         NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.
         """
+
+        # TODO temporary workaround
+        if taxon == "NCBITaxon:9606":
+            taxon = None
+
         assocs = bulk_fetch(subject_category='disease',
                             object_category=object_category,
                             taxon=taxon,
                             iterate=True)
         return assocs
-
-@ns.route('/labels/<subject_category>/<objet_category>/<taxon>')
-@api.doc(params={'subject_category': 'CATEGORY of the subject entity, e.g. gene, phenotype, disease'})
-@api.doc(params={'objet_category': 'CATEGORY of the object entity, e.g. phenotype, disease'})
-@api.doc(params={'taxon': 'taxon of gene, must be of form NCBITaxon:9606'})
-class MartLabelsResource(Resource):
-    def get(self, subject_category, objet_category, taxon):
-        """
-        Bulk download of labels.
-
-        Retrieves the labels of the subjects.
-        """
-        myArgs = {
-            "subject_category": subject_category,
-            "object_category": objet_category,
-            "subject_taxon": taxon,
-            "rows": MAX_ROWS,
-            "facet_on": "off",
-            "select_fields": ["subject", "subject_label"],
-            "iterate": True
-        }
-        return search_associations(**myArgs)