Merge pull request #284 from asherpasha/dev

GAIA: initial commit

Author: asherpasha

api/__init__.py

@@ -52,6 +52,7 @@ def create_app():
 
     # Now add routes
     from api.resources.gene_information import gene_information
+    from api.resources.gaia import gaia
     from api.resources.rnaseq_gene_expression import rnaseq_gene_expression
     from api.resources.microarray_gene_expression import microarray_gene_expression
     from api.resources.proxy import bar_proxy
@@ -66,6 +67,7 @@ def create_app():
     from api.resources.llama3 import llama3
 
     bar_api.add_namespace(gene_information)
+    bar_api.add_namespace(gaia)
     bar_api.add_namespace(rnaseq_gene_expression)
     bar_api.add_namespace(microarray_gene_expression)
     bar_api.add_namespace(bar_proxy)

api/models/gaia.py

@@ -0,0 +1,10 @@
+from api import db
+from sqlalchemy.dialects.mysql import json
+
+
+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)

api/resources/gaia.py

@@ -0,0 +1,40 @@
+from flask_restx import Namespace, Resource
+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
+import json
+
+gaia = Namespace("Gaia", description="Gaia", path="/gaia")
+
+
+@gaia.route("/aliases/<string:identifier>")
+class GaiaAliases(Resource):
+    @gaia.param("identifier", _in="path", default="ABI3")
+    def get(self, identifier=""):
+
+        # Escape input
+        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 row:
+                return BARUtils.success_exit(row.data)
+            else:
+                return BARUtils.error_exit("Nothing found"), 404
+
+        else:
+            return BARUtils.error_exit("Invalid identifier"), 400

api/utils/bar_utils.py

@@ -252,6 +252,17 @@ def is_integer(data):
         else:
             return False
 
+    @staticmethod
+    def is_alphanumeric(data):
+        """Check if the input is alphanumeric.
+        :param data
+        :return: True if alphanumeric
+        """
+        if re.search(r"^[a-z0-9]{1,50}$", data, re.I):
+            return True
+        else:
+            return False
+
     @staticmethod
     def format_poplar(poplar_gene):
         """Format Poplar gene ID to be Potri.016G107900, i.e. capitalized P and G