Merge pull request #51 from biolink/obo-obsolete

handing of obsoletion

ontobio/io/assocwriter.py

@@ -98,4 +98,59 @@ class GafWriter(AssocWriter):
     """
     Writes Associations in GAF format. Not yet implemented
     """
-    pass
+    def __init__(self, file=None):
+        self.file = file
+
+    def write_assoc(self, assoc):
+        """
+        Write a single association to a line in the output file
+        """
+        subj = assoc['subject']
+
+        db, db_object_id = self._split_prefix(subj)
+
+        rel = assoc['relation']
+        qualifier = rel['id']
+        if assoc['negated']:
+            qualifier = 'NOT|' + qualifier
+
+        goid = assoc['object']['id']
+
+        ev = assoc['evidence']
+        evidence = ev['type']
+        withfrom = "|".join(ev['with_support_from'])
+        reference = "|".join(ev['has_supporting_reference'])
+
+        date = assoc['date']
+        assigned_by = assoc['provided_by']
+
+        annotation_xp = '' # TODO
+        annotation_properties = '' # TODO
+        interacting_taxon_id = '' ## TODO
+        gene_product_isoform = '' ## TODO
+
+        aspect = None
+        taxon = None
+        if 'taxon' in subj:
+            taxon = subj['taxon']['id']
+
+        vals = [db,
+                db_object_id,
+                subj.get('label'),
+                qualifier,
+                goid,
+                reference,
+                evidence,
+                withfrom,
+                aspect,
+                subj.get('full_name'),
+                subj.get('synonyms'),
+                subj.get('type'),
+                taxon,
+                date,
+                assigned_by,
+                annotation_xp,
+                gene_product_isoform]
+
+        self._write_row(vals)
+

ontobio/obograph_util.py

@@ -39,7 +39,7 @@ def add_obograph_digraph(og, digraph, node_type=None, predicates=None, xref_grap
         if 'lbl' in n:
             digraph.node[id]['label'] = n['lbl']
         if parse_meta and 'meta' in n:
-            meta = n['meta']
+            meta = transform_meta(n['meta'])
             if xref_graph is not None and 'xrefs' in meta:
                 for x in meta['xrefs']:
                     xref_graph.add_edge(contract_uri_wrap(x['val']), id, source=id)
@@ -71,7 +71,12 @@ def add_obograph_digraph(og, digraph, node_type=None, predicates=None, xref_grap
                                      contract_uri_wrap(x['fillerId'])) for x in a['restrictions'] if x is not None])
             logical_definitions.append(ld)
 
-
+def transform_meta(m):
+    if 'basicPropertyValues' in m:
+        for x in m['basicPropertyValues']:
+            x['pred'] = contract_uri_wrap(x['pred'])
+            x['val'] = contract_uri_wrap(x['val'])
+    return m
 
 def convert_json_file(obographfile, **args):
     """

ontobio/ontol.py

@@ -619,11 +619,15 @@ def _get_meta(self, nid):
         return None
 
     def _get_basic_property_values(self, nid):
-        return self._get_meta_prop(nid, 'basicPropertyValues')
+        r =  self._get_meta_prop(nid, 'basicPropertyValues')
+        if r is None:
+            return []
+        else:
+            return r
 
     def _get_basic_property_value(self, nid, prop):
-        bpvs = self._get_basic_property_values()
-        return [x['val'] for x in bpvs in x['pred'] == prop]
+        bpvs = self._get_basic_property_values(nid)
+        return [x['val'] for x in bpvs if x['pred'] == prop]
 
     def is_obsolete(self, nid):
         """

tests/resources/obsolete.json

@@ -0,0 +1,73 @@
+{
+  "graphs" : [ {
+    "nodes" : [ {
+      "id" : "http://purl.obolibrary.org/obo/IAO_0100001",
+      "type" : "PROPERTY",
+      "lbl" : "term replaced by"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_2",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/GO_1"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_1",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:2"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "x1"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_4",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "GO:1"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "x4"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#consider",
+      "type" : "PROPERTY",
+      "lbl" : "consider"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+      "type" : "PROPERTY",
+      "lbl" : "has_alternative_id"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_3",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "GO:1"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "x3"
+    } ],
+    "edges" : [ ],
+    "id" : "http://purl.obolibrary.org/obo/test-obsolete.owl",
+    "meta" : {
+      "subsets" : [ ],
+      "xrefs" : [ ],
+      "basicPropertyValues" : [ ]
+    },
+    "equivalentNodesSets" : [ ],
+    "logicalDefinitionAxioms" : [ ],
+    "domainRangeAxioms" : [ ],
+    "propertyChainAxioms" : [ ]
+  } ]
+}

tests/test_local_json.py

@@ -219,3 +219,24 @@ def test_subontology():
     ancs = subont.ancestors(PERM)
     print(str(ancs))
     assert len(ancs) > 0
+
+def test_obsolete():
+    """
+    Test obsoletion metadata
+    """
+    factory = OntologyFactory()
+    print("Creating ont")
+    ont = factory.create('tests/resources/obsolete.json')
+    print("ONT NODES: {}".format(ont.nodes()))
+    n_obs = 0
+    for nid in ont.nodes():
+        is_obs = ont.is_obsolete(nid)
+        if is_obs:
+            print("OBS: {} {}".format(nid, ont.label(nid)))
+            n_obs += 1
+        rb = ont.replaced_by(nid)
+        if rb is not None:
+            print("REPLACED BY: {} {}".format(rb, ont.label(rb)))
+    assert ont.replaced_by('GO:2') == 'GO:1'
+    assert ont.replaced_by('GO:3') == 'GO:1'
+    assert n_obs == 3