Merge pull request #285 from asherpasha/dev

Worked on the new gaia databases

Author: asherpasha

api/models/gaia.py

@@ -1,10 +1,24 @@
+from typing import List
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import relationship
 from api import db
-from sqlalchemy.dialects.mysql import json
+
+
+class Genes(db.Model):
+    __bind_key__ = "gaia"
+    __tablename__ = "genes"
+
+    id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
+    species: db.Mapped[str] = db.mapped_column(db.String(64), nullable=False)
+    locus: db.Mapped[str] = db.mapped_column(db.String(64), nullable=True)
+    geneid: db.Mapped[str] = db.mapped_column(db.String(32), nullable=True)
+    children: db.Mapped[List["Aliases"]] = relationship()
 
 
 class Aliases(db.Model):
     __bind_key__ = "gaia"
     __tablename__ = "aliases"
 
     id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
-    data: db.Mapped[json] = db.mapped_column(db.JSON, nullable=True, primary_key=False)
+    genes_id: db.Mapped[int] = db.mapped_column(ForeignKey("genes.id", ondelete="CASCADE"), nullable=False)
+    alias: db.Mapped[str] = db.mapped_column(db.String(256), nullable=False)

api/resources/gaia.py

@@ -2,8 +2,8 @@
 from markupsafe import escape
 from api import db
 from api.utils.bar_utils import BARUtils
-from api.models.gaia import Aliases
-from sqlalchemy import func
+from api.models.gaia import Genes, Aliases
+from sqlalchemy import func, or_
 import json
 
 gaia = Namespace("Gaia", description="Gaia", path="/gaia")
@@ -18,23 +18,51 @@ def get(self, identifier=""):
         identifier = escape(identifier)
 
         # Is it valid
-        if BARUtils.is_alphanumeric(identifier):
-            # Convert to json
-            identifier_json = json.dumps([identifier])
-
-            # Get data
-            # Note: SQLAlchmemy or_ did not work here. Query had AND for some reason.
-            query = db.select(Aliases).filter(
-                (func.json_contains(func.lower(Aliases.data), func.lower(identifier_json), "$.aliases"))
-                | (func.json_extract(func.lower(Aliases.data), "$.geneid") == func.lower(identifier))
-                | (func.json_extract(func.lower(Aliases.data), "$.locus") == func.lower(identifier)),
-            )
-            row = db.session.execute(query).scalars().first()
+        if BARUtils.is_gaia_alias(identifier):
+
+            # Check if alias exists
+            # Note: This check can be done in on query, but optimizer is not using indexes for some reason
+            # Also, GAIA only uses the first result
+            query = db.select(Aliases.genes_id, Aliases.alias).filter(Aliases.alias == identifier)
+            row = db.session.execute(query).fetchone()
 
             if row:
-                return BARUtils.success_exit(row.data)
+                # Alias exists. Get the genes_id
+                query_id = row.genes_id
+
+            else:
+                # Alias doesn't exist. Get the genes_id if it's locus or ncbi id
+                query = db.select(Genes.id).filter(or_(Genes.locus == identifier, Genes.geneid == identifier))
+                row = db.session.execute(query).fetchone()
+
+                if row:
+                    query_id = row.id
+                else:
+                    return BARUtils.error_exit("Nothing found"), 404
+
+            # Left join is important in case aliases do not exist for the given locus / geneid
+            query = (
+                db.select(Genes.species, Genes.locus, Genes.geneid, func.json_arrayagg(Aliases.alias).label("aliases"))
+                .select_from(Genes)
+                .outerjoin(Aliases, Aliases.genes_id == Genes.id)
+                .filter(Genes.id == query_id)
+            )
+
+            result = db.session.execute(query).fetchone()
+
+            # See if aliases exists
+            if result.aliases:
+                aliases = json.loads(result.aliases)
             else:
-                return BARUtils.error_exit("Nothing found"), 404
+                aliases = []
+
+            data = {
+                "species": result.species,
+                "locus": result.locus,
+                "geneid": result.geneid,
+                "aliases": aliases,
+            }
+            return BARUtils.success_exit(data)
 
         else:
             return BARUtils.error_exit("Invalid identifier"), 400

api/utils/bar_utils.py

@@ -253,12 +253,12 @@ def is_integer(data):
             return False
 
     @staticmethod
-    def is_alphanumeric(data):
-        """Check if the input is alphanumeric.
+    def is_gaia_alias(data):
+        """Check if the input is a valid gaia alias.
         :param data
-        :return: True if alphanumeric
+        :return: True if valid gaia alias
         """
-        if re.search(r"^[a-z0-9]{1,50}$", data, re.I):
+        if re.search(r"^[a-z0-9_]{1,50}$", data, re.I):
             return True
         else:
             return False