Merge branch 'master' into search_page

Author: haohangyan

indra/ontology/bio/__init__.py

@@ -4,8 +4,14 @@
 
 from indra.config import get_config
 from .ontology import BioOntology
+from .sqlite_ontology import SqliteOntology, DEFAULT_SQLITE_ONTOLOGY
 from ..virtual import VirtualOntology
 
 indra_ontology_url = get_config('INDRA_ONTOLOGY_URL')
-bio_ontology = BioOntology() if not indra_ontology_url else \
-    VirtualOntology(url=indra_ontology_url)
+if indra_ontology_url is None:
+    bio_ontology = BioOntology()
+elif indra_ontology_url == "sqlite":
+    sqlite_ontology_path = get_config("SQLITE_ONTOLOGY_PATH") or DEFAULT_SQLITE_ONTOLOGY
+    bio_ontology = SqliteOntology(db_path=sqlite_ontology_path)
+else:
+    bio_ontology = VirtualOntology(url=indra_ontology_url)

indra/ontology/bio/sqlite_ontology.py

@@ -7,8 +7,7 @@
 import logging
 from collections import defaultdict
 from indra.ontology.ontology_graph import IndraOntology
-from indra.ontology.bio.ontology import CACHE_DIR
-from indra.ontology.bio import bio_ontology
+from indra.ontology.bio.ontology import CACHE_DIR, BioOntology
 
 
 logger = logging.getLogger(__name__)
@@ -24,6 +23,10 @@ def __init__(self, db_path=DEFAULT_SQLITE_ONTOLOGY):
         build_sqlite_ontology(db_path)
         conn = sqlite3.connect(db_path)
         self.cur = conn.cursor()
+        self._initialized = True
+
+    def initialize(self):
+        pass
 
     def isa_or_partof(self, ns1, id1, ns2, id2):
         q = """SELECT 1 FROM relationships
@@ -36,18 +39,28 @@ def child_rel(self, ns, id, rel_types):
         q = """SELECT children FROM child_lookup
                WHERE parent_id=? AND parent_ns=?
                LIMIT 1;"""
+        if rel_types and 'isa' in rel_types or 'partof' in rel_types:
+            rel_types |= {'isa_or_partof'}
         self.cur.execute(q, (id, ns))
         res = self.cur.fetchone()
         if res is None:
             yield from []
         else:
-            yield from [tuple(x.split(':', 1)) for x in res[0].split(',')]
+            children = res[0].split(',')
+            for child in children:
+                curie, rel_type = child.split('|', 1)
+                if rel_type in rel_types:
+                    yield tuple(curie.split(':', 1))
 
     def get_parents(self, ns, id):
-        return list(self.parent_rel(ns, id, {'isa', 'partof'}))
+        # Note that for isa/partof ontological child/parent is the
+        # opposite of the graph-based child/parent
+        return list(self.child_rel(ns, id, {'isa_or_partof'}))
 
     def get_children(self, ns, id, ns_filter=None):
-        children = list(self.child_rel(ns, id, {'isa', 'partof'}))
+        # Note that for isa/partof ontological child/parent is the
+        # opposite of the graph-based child/parent
+        children = list(self.parent_rel(ns, id, {'isa_or_partof'}))
         if ns_filter:
             children = [(cns, cid) for cns, cid in children
                         if cns in ns_filter]
@@ -57,12 +70,18 @@ def parent_rel(self, ns, id, rel_types):
         q = """SELECT parents FROM parent_lookup
                WHERE child_id=? AND child_ns=?
                LIMIT 1;"""
+        if rel_types and 'isa' in rel_types or 'partof' in rel_types:
+            rel_types |= {'isa_or_partof'}
         self.cur.execute(q, (id, ns))
         res = self.cur.fetchone()
         if res is None:
             yield from []
         else:
-            yield from [tuple(x.split(':', 1)) for x in res[0].split(',')]
+            parents = res[0].split(',')
+            for parent in parents:
+                curie, rel_type = parent.split('|', 1)
+                if rel_type in rel_types:
+                    yield tuple(curie.split(':', 1))
 
     def get_node_property(self, ns, id, property):
         q = """SELECT properties FROM node_properties
@@ -92,6 +111,7 @@ def build_sqlite_ontology(db_path=DEFAULT_SQLITE_ONTOLOGY, force=False):
             pass
 
     # Initialize the bio ontology and build the transitive closure
+    bio_ontology = BioOntology()
     bio_ontology.initialize()
     bio_ontology._build_transitive_closure()
 
@@ -107,26 +127,51 @@ def build_sqlite_ontology(db_path=DEFAULT_SQLITE_ONTOLOGY, force=False):
         child_ns TEXT NOT NULL,
         parent_id TEXT NOT NULL,
         parent_ns TEXT NOT NULL,
+        rel_type TEXT NOT NULL,
         UNIQUE (child_id, child_ns, parent_id, parent_ns)
     );"""
     cur.execute(q)
 
     # Insert into the database in chunks
     chunk_size = 10000
+    # Note: the transitive closure consists of pairs with the first element
+    # being the ontological child and the second the parent. However,
+    # in a graph representation isa/partof edges point from the ontological
+    # child to the ontological parent. Here, we need to follow the graph-based
+    # parent->child relationships, not the ontological ones.
     tc = sorted(bio_ontology.transitive_closure)
     all_children = defaultdict(set)
     all_parents = defaultdict(set)
     for i in range(0, len(tc), chunk_size):
         chunk = tc[i:i+chunk_size]
-        chunk_values = [(child.split(':', 1)[1], child.split(':')[0],
-                         parent.split(':', 1)[1], parent.split(':')[0])
+        chunk_values = [(parent.split(':', 1)[1], parent.split(':')[0],
+                         child.split(':', 1)[1], child.split(':')[0])
                         for child, parent in chunk]
         for cid, cns, pid, pns in chunk_values:
-            all_children[(pid, pns)].add('%s:%s' % (cns, cid))
-            all_parents[(cid, cns)].add('%s:%s' % (pns, pid))
-        cur.executemany("""INSERT INTO relationships (child_id, 
-                        child_ns, parent_id, parent_ns) 
-                        VALUES (?, ?, ?, ?);""", chunk_values)
+            all_children[(pid, pns)].add(
+                '%s:%s|%s' % (cns, cid, 'isa_or_partof'))
+            all_parents[(cid, cns)].add(
+                '%s:%s|%s' % (pns, pid, 'isa_or_partof'))
+        cur.executemany("""INSERT INTO relationships (parent_id, 
+                            parent_ns, child_id, child_ns, rel_type)
+                            VALUES (?, ?, ?, ?, 'isa_or_partof');""",
+                        chunk_values)
+
+    for parent, child, data in bio_ontology.edges(data=True):
+        parent_ns, parent_id = bio_ontology.get_ns_id(parent)
+        child_ns, child_id = bio_ontology.get_ns_id(child)
+        rel_type = data.get('type')
+        if rel_type in {'isa', 'partof'}:
+            continue
+        all_children[(parent_id, parent_ns)].add(
+            '%s:%s|%s' % (child_ns, child_id, rel_type))
+        all_parents[(child_id, child_ns)].add(
+            '%s:%s|%s' % (parent_ns, parent_id, rel_type))
+        cur.execute("""INSERT INTO relationships (parent_id,
+                        parent_ns, child_id, child_ns, rel_type)
+                        VALUES (?, ?, ?, ?, ?);""",
+                    (parent_id, parent_ns, child_id, child_ns, rel_type))
+
     q = """CREATE INDEX idx_child_parent ON relationships 
         (child_id, child_ns, parent_id, parent_ns);"""
     cur.execute(q)

indra/tests/test_pmc_client.py

@@ -95,7 +95,7 @@ def test_get_xml_PMC():
 
 @pytest.mark.webservice
 def test_get_xml_invalid():
-    pmc_id = '9999999'
+    pmc_id = '123456789000'
     xml_str = pmc_client.get_xml(pmc_id)
     assert xml_str is None