Update documentation

src/bio2bel_wikipathways/manager.py

@@ -3,7 +3,7 @@
 """This module populates the tables of bio2bel_wikipathways."""
 
 import logging
-from typing import Optional
+from typing import List, Mapping, Optional
 
 from tqdm import tqdm
 
@@ -13,7 +13,7 @@
 from bio2bel.manager.namespace_manager import BELNamespaceManagerMixin
 from compath_utils import CompathManager
 from pybel.constants import BIOPROCESS, NAME, PROTEIN
-from pybel.manager.models import NamespaceEntry
+from pybel.manager.models import Namespace, NamespaceEntry
 from pybel.struct.graph import BELGraph
 from .constants import MODULE_NAME, WIKIPATHWAYS
 from .models import Base, Pathway, Protein, protein_pathway
@@ -72,22 +72,18 @@ class ProteinView(ModelView):
         admin.add_view(ProteinView(Protein, self.session))
         return admin
 
-    def summarize(self):
-        """Summarize the database.
-
-        :rtype: dict[str,int]
-        """
+    def summarize(self) -> Mapping[str, int]:
+        """Summarize the database."""
         return dict(
             pathways=self._count_model(Pathway),
             proteins=self._count_model(Protein),
         )
 
-    def query_pathway_by_name(self, query, limit=None):
+    def query_pathway_by_name(self, query: str, limit: Optional[int] = None) -> List[Pathway]:
         """Return all pathways having the query in their names.
 
         :param query: query string
-        :param Optional[int] limit: limit result query
-        :rtype: list[Pathway]
+        :param limit: limit result query
         """
         q = self.session.query(Pathway).filter(Pathway.name.contains(query))
 
@@ -96,12 +92,11 @@ def query_pathway_by_name(self, query, limit=None):
 
         return q.all()
 
-    def get_or_create_pathway(self, wikipathways_id, name=None):
+    def get_or_create_pathway(self, wikipathways_id: str, name: Optional[str] = None) -> Pathway:
         """Get an pathway from the database or creates it.
 
-        :param str wikipathways_id: wikipathways identifier
-        :param Optional[str] name: name of the pathway
-        :rtype: Pathway
+        :param wikipathways_id: WikiPathways identifier
+        :param name: name of the pathway
         """
         pathway = self.get_pathway_by_id(wikipathways_id)
 
@@ -114,13 +109,12 @@ def get_or_create_pathway(self, wikipathways_id, name=None):
 
         return pathway
 
-    def get_or_create_protein(self, entrez_id, hgnc_symbol, hgnc_id):
+    def get_or_create_protein(self, entrez_id: str, hgnc_symbol: str, hgnc_id: str) -> Protein:
         """Get an pathway from the database or creates it.
 
-        :param str entrez_id: entrez identifier
-        :param str hgnc_symbol: hgnc symbol
-        :param str hgnc_id: hgnc identifier
-        :rtype: Protein
+        :param entrez_id: entrez identifier
+        :param hgnc_symbol: hgnc symbol
+        :param hgnc_id: hgnc identifier
         """
         protein = self.get_protein_by_entrez_id(entrez_id)
 
@@ -135,36 +129,24 @@ def get_or_create_protein(self, entrez_id, hgnc_symbol, hgnc_id):
 
         return protein
 
-    def get_protein_by_entrez_id(self, entrez_id):
-        """Get a protein by its wikipathways id.
-
-        :param entrez_id: entrez identifier
-        :rtype: Optional[Protein]
-        """
+    def get_protein_by_entrez_id(self, entrez_id: str) -> Optional[Protein]:
+        """Get a protein by its Entrez gene identifier."""
         return self.session.query(Protein).filter(Protein.entrez_id == entrez_id).one_or_none()
 
-    def get_protein_by_hgnc_id(self, hgnc_id):
-        """Get a protein by its hgnc_id.
-
-        :param hgnc_id: hgnc_id
-        :rtype: Optional[Protein]
-        """
+    def get_protein_by_hgnc_id(self, hgnc_id: str) -> Optional[Protein]:
+        """Get a protein by its HGNC identifier."""
         return self.session.query(Protein).filter(Protein.hgnc_id == hgnc_id).one_or_none()
 
-    def get_protein_by_hgnc_symbol(self, hgnc_symbol):
-        """Get a protein by its hgnc symbol.
-
-        :param hgnc_symbol: hgnc identifier
-        :rtype: Optional[Protein]
-        """
+    def get_protein_by_hgnc_symbol(self, hgnc_symbol: str) -> Optional[Protein]:
+        """Get a protein by its HGNC gene symbol."""
         return self.session.query(Protein).filter(Protein.hgnc_symbol == hgnc_symbol).one_or_none()
 
     """Methods to populate the DB"""
 
-    def populate(self, url=None):
+    def populate(self, url: Optional[str] = None):
         """Populate the database.
 
-        :param Optional[str] url: url from a GMT file
+        :param url: url from a GMT file
         """
         hgnc_manager = bio2bel_hgnc.Manager(engine=self.engine, session=self.session)
         if not hgnc_manager.is_populated():
@@ -239,9 +221,8 @@ def to_bel(self) -> BELGraph:
     def get_pathway_graph_by_id(self, wikipathways_id: str) -> Optional[BELGraph]:
         """Return a new graph corresponding to the pathway.
 
-        :param wikipathways_id: wikipathways identifier
-        :rtype: Optional[pybel.BELGraph]
-        :return: A BEL Graph corresponding to the wikipathway id
+        :param wikipathways_id: WikiPathways identifier
+        :return: A BEL Graph corresponding to the WikiPathways identifier
 
         Example Usage:
 
@@ -288,13 +269,8 @@ def enrich_wikipathways_protein(self, graph: BELGraph) -> None:
                 for pathway in protein.pathways:
                     graph.add_part_of(node, pathway.serialize_to_pathway_node())
 
-    def _create_namespace_entry_from_model(self, model, namespace):
-        """Create a namespace entry from the model.
-
-        :param Pathway model: The model to convert
-        :type namespace: pybel.manager.models.Namespace
-        :rtype: Optional[pybel.manager.models.NamespaceEntry]
-        """
+    def _create_namespace_entry_from_model(self, model: Pathway, namespace: Namespace) -> NamespaceEntry:
+        """Create a namespace entry from the model."""
         return NamespaceEntry(encoding='B', name=model.name, identifier=model.wikipathways_id, namespace=namespace)
 
     @staticmethod

src/bio2bel_wikipathways/models.py

@@ -34,6 +34,8 @@ class Protein(Base):
     entrez_id = Column(String(255), doc='entrez id of the protein')
     hgnc_id = Column(String(255), doc='hgnc id of the protein')
     hgnc_symbol = Column(String(255), doc='hgnc symbol of the protein')
+    uniprot_id = Column()
+    uniprot_accession = Column()
 
     def __repr__(self):  # noqa: D105
         return self.hgnc_id