enhancement to filter by the produced_by information issue #545

ontobio/golr/golr_associations.py

@@ -118,7 +118,7 @@ def top_species(**kwargs):
     else:
         d = fcs['subject_taxon']
     return sorted(d.items(), key=lambda t: -t[1])
-    
+
 
 
 def bulk_fetch(subject_category, object_category, taxon, rows=MAX_ROWS, **kwargs):
@@ -178,7 +178,7 @@ def pivot_query_as_matrix(facet=None, facet_pivot_fields=[], **kwargs):
     xlabels=set()
     ylabels=set()
 
-    
+
     for r in results:
         logging.info("R={}".format(r))
         xtype=r['field']
@@ -204,7 +204,7 @@ def pivot_query_as_matrix(facet=None, facet_pivot_fields=[], **kwargs):
          'yaxis':ylabels,
          'z':z}
     return m
-         
+
 
 
 # TODO: unify this with the monarch-specific instance
@@ -294,5 +294,3 @@ def get_homologs(gene, relation=HomologyTypes.Ortholog.value):
                         object_category='gene',
                         relation=relation,
                         subject=gene)
-
-

ontobio/golr/golr_query.py

@@ -45,7 +45,7 @@
 
 class GolrFields:
     """
-    Enumeration of fields in Golr.
+    Enumeration of fields in Monarch Golr.
     Note the Monarch golr schema is taken as canonical here
     """
 
@@ -427,6 +427,11 @@ class GolrAssociationQuery(GolrAbstractQuery):
         compact_associations contains a more compact representation
         consisting of objects with (subject, relation and objects)
 
+    provided_by: String
+
+        indicates the original source that provided the assertions
+        will only return assertions from this source
+
     config : Config
 
         See :ref:`Config` for details. The config object can be used
@@ -471,6 +476,7 @@ def __init__(self,
                  facet_mincount=1,
                  facet_pivot_fields=[],
                  facet_on = 'on',
+                 provided_by=None,
                  pivot_subject_object=False,
                  unselect_evidence=False,
                  rows=10,
@@ -519,6 +525,7 @@ def __init__(self,
         self.facet_mincount=facet_mincount
         self.facet_pivot_fields=facet_pivot_fields
         self.facet_on=facet_on
+        self.provided_by=provided_by
         self.pivot_subject_object=pivot_subject_object
         self.unselect_evidence=unselect_evidence
         self.max_rows=100000
@@ -708,6 +715,12 @@ def solr_params(self):
             else:
                 fq['evidence_object_closure'] = e
 
+        provided_by=self.provided_by
+        if provided_by is not None:
+            # want to be able to select by whoever provided this assertion see:
+            # Dataset URIs in metadata and in main tll dumps are not connected #545
+            fq[M.IS_DEFINED_BY] = 'https://data.monarchinitiative.org/ttl/'+provided_by+'.ttl'
+
         if self.exclude_automatic_assertions:
             fq['-evidence_object_closure'] = 'ECO:0000501'
 

tests/test_golr_associations.py

@@ -3,7 +3,6 @@
 """
 from ontobio.golr.golr_associations import search_associations, search_associations_compact, select_distinct_subjects, get_objects_for_subject, get_subjects_for_object
 
-
 HUMAN_SHH = 'NCBIGene:6469'
 HOLOPROSENCEPHALY = 'HP:0001360'
 TWIST_ZFIN = 'ZFIN:ZDB-GENE-050417-357'
@@ -47,7 +46,7 @@ def test_go_assocs_negated():
     # we also place NOT as a qualifier
     neg_assocs2 = [a for a in assocs if 'not' in a['qualifiers']]
     assert len(neg_assocs2) > 0
-    
+
 def test_go_assocs_compact():
     assocs = search_associations_compact(subject=TWIST_ZFIN,
                                           object_category='function'
@@ -70,8 +69,8 @@ def test_go_assocs_compact():
             print("  QUERY FOR {} -> {}".format(obj,a))
         m = [a for a in rassocs if a['subject'] == TWIST_ZFIN]
         assert len(m) == 1
-    
-    
+
+
 def test_pheno_assocs():
     payload = search_associations(subject=TWIST_ZFIN,
                                   object_category='phenotype'
@@ -92,7 +91,7 @@ def test_pheno_assocs_compact():
     a = assocs[0]
     assert a['subject'] == TWIST_ZFIN
     assert 'ZP:0007631' in a['objects']
-    
+
 def test_pheno_objects():
     results = search_associations(subject=TWIST_ZFIN,
                                   fetch_objects=True,
@@ -103,7 +102,7 @@ def test_pheno_objects():
     print(str(objs))
     assert len(objs) > 1
     assert 'ZP:0007631' in objs
-    
+
 def test_func_objects():
     results = search_associations(subject=TWIST_ZFIN,
                                   fetch_objects=True,
@@ -114,7 +113,7 @@ def test_func_objects():
     print(objs)
     assert DVPF in objs
     assert len(objs) > 1
-    
+
 def test_pheno_objects_shh_2():
     """
     Equivalent to above, using convenience method
@@ -136,7 +135,7 @@ def test_pheno2gene():
     print(len(subjs))
     assert HUMAN_SHH in subjs
     assert len(subjs) > 50
-    
+
 def test_disease_assocs():
     payload = search_associations(subject=HUMAN_SHH,
                                   object_category='disease'
@@ -153,7 +152,7 @@ def test_disease2gene():
     for a in assocs:
         print(str(a))
     assert len(assocs) > 0
- 
+
 def test_species_facet():
     payload = search_associations(subject_category='gene',
                                   object_category='phenotype',
@@ -162,5 +161,17 @@ def test_species_facet():
     fcs = payload['facet_counts']
     print(str(fcs))
     assert 'Homo sapiens' in fcs['subject_taxon_label'].keys()
-
-
+
+def test_provided_by(capsys):
+    with capsys.disabled():
+        payload = search_associations(subject_category='gene',
+                                      object_category='gene',
+                                      subject='HGNC:10848',
+                                      relation_closure='RO:HOM0000017',
+                                      homology_type='O',
+                                      provided_by='zfin',
+                                      facet_fields=['is_defined_by'],
+                                      rows=100)
+        fcs = payload['facet_counts']
+        print('FCS: {}'.format(fcs))
+        assert 'https://data.monarchinitiative.org/ttl/zfin.ttl' in fcs['is_defined_by'].keys()