Add normalization function

src/bio2bel_chebi/manager.py

@@ -5,8 +5,9 @@
 import datetime
 import logging
 import time
-from typing import List, Mapping, Optional
+from typing import Iterable, List, Mapping, Optional, Tuple
 
+from networkx import relabel_nodes
 import pandas as pd
 from tqdm import tqdm
 
@@ -294,28 +295,41 @@ def populate(self,
 
         log.info('populated in %.2f seconds', time.time() - t)
 
+    def normalize_chemicals(self, graph: BELGraph) -> None:
+        mapping = {
+            node: chemical.to_bel()
+            for node, chemical in list(self.iter_chemicals(graph))
+        }
+        relabel_nodes(graph, mapping, copy=False)
+
+    def iter_chemicals(self, graph: BELGraph) -> Iterable[Tuple[BaseEntity, Chemical]]:
+        """Iterate over pairs of BEL nodes and HGNC genes."""
+        for node in graph:
+            chemical = self.get_chemical_from_data(node)
+            if chemical is not None:
+                yield node, chemical
+
     def get_chemical_from_data(self, node: BaseEntity) -> Optional[Chemical]:
         namespace = node.get(NAMESPACE)
 
-        if namespace.lower() not in {'chebi', 'chebiid'}:
+        if not namespace or namespace.lower() not in {'chebi', 'chebiid'}:
             return
 
         identifier = node.get(IDENTIFIER)
         name = node.get(NAME)
 
-        if namespace.lower() == 'chebi':
+        if identifier is None and name is None:
+            raise ValueError
+
+        if namespace.lower() == 'chebiid':
+            return self.get_chemical_by_chebi_id(name)
+
+        elif namespace.lower() == 'chebi':
             if identifier is not None:
                 return self.get_chemical_by_chebi_id(identifier)
-
-            if name is not None:
+            else:  # elif name is not None:
                 return self.get_chemical_by_chebi_name(name)
 
-            else:
-                raise ValueError
-
-        elif namespace.lower() == 'chebiid':
-            return self.get_chemical_by_chebi_id(name)
-
     def enrich_chemical_hierarchy(self, graph: BELGraph) -> None:
         """Enrich the parents for all ChEBI chemicals in the graph."""
         for _, data in graph.nodes(data=True):
@@ -344,8 +358,7 @@ def to_bel(self) -> BELGraph:
             description=_chebi_description,
         )
 
-        namespace = self.upload_bel_namespace()  # Make sure the super id namespace is available
-        graph.namespace_url[namespace.keyword] = namespace.url
+        self.add_namespace_to_graph(graph)
 
         for relation in self._iterate_relations():
             relation.add_to_graph(graph)

src/bio2bel_chebi/models.py

@@ -2,14 +2,14 @@
 
 """SQLAlchemy models for Bio2BEL ChEBI."""
 
-from typing import Mapping
-
 from sqlalchemy import Column, Date, ForeignKey, Index, Integer, String, Text
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import backref, relationship
+from typing import Mapping, Optional
 
-from pybel.constants import NAME, PART_OF
 import pybel.dsl
+from pybel import BELGraph
+from pybel.constants import NAME
 
 __all__ = [
     'Base',
@@ -61,10 +61,10 @@ def safe_name(self) -> str:
         """Either returns this molecule's name, or the parent name."""
         return self.name or self.parent.name
 
-    def to_json(self, include_id: bool = False) -> Mapping:
+    def to_json(self, include_id: bool = False) -> Mapping[str, str]:
         """Export this chemical as dictionary.
 
-        :param bool include_id: Include the database identifier?
+        :param include_id: Include the database identifier?
         """
         rv = {
             'chebi_id': self.chebi_id,
@@ -106,7 +106,7 @@ class Relation(Base):
     target_id = Column(Integer, ForeignKey('{}.id'.format(CHEMICAL_TABLE_NAME)), nullable=False)
     target = relationship('Chemical', foreign_keys=[target_id], backref=backref('in_edges', lazy='dynamic'))
 
-    def add_to_graph(self, graph):
+    def add_to_graph(self, graph: BELGraph) -> Optional[str]:
         """Add this relation to the graph.
 
         :param pybel.BELGraph graph:
@@ -119,7 +119,7 @@ def add_to_graph(self, graph):
             return
 
         if self.type == 'has_part':
-            return graph.add_unqualified_edge(target, source, PART_OF)
+            return graph.add_part_of(target, source)
 
         if self.type == 'is_a':
             return graph.add_is_a(target, source)