Updated main branch

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 +1,62 @@
+from typing import List
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import relationship
+from api import db
+
+
+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)
+    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)
+
+
+class PublicationFigures(db.Model):
+    __bind_key__ = "gaia"
+    __tablename__ = "publication_figures"
+
+    id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
+    title: db.Mapped[str] = db.mapped_column(db.String(512), nullable=True)
+    abstract: db.Mapped[str] = db.mapped_column(db.Text, nullable=True)
+    children: db.Mapped[List["PubIds"]] = relationship()
+    children: db.Mapped[List["Figures"]] = relationship()
+
+
+class PubIds(db.Model):
+    __bind_key__ = "gaia"
+    __tablename__ = "pub_ids"
+
+    id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
+    publication_figures_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False)
+    publication_figures_id: db.Mapped[int] = db.mapped_column(
+        ForeignKey("publication_figures.id", ondelete="CASCADE"), nullable=False
+    )
+    pubmed: db.Mapped[str] = db.mapped_column(db.String(16), nullable=True)
+    pmc: db.Mapped[str] = db.mapped_column(db.String(16), nullable=True)
+
+
+class Figures(db.Model):
+    __bind_key__ = "gaia"
+    __tablename__ = "figures"
+
+    id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
+    publication_figures_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False)
+    publication_figures_id: db.Mapped[int] = db.mapped_column(
+        ForeignKey("publication_figures.id", ondelete="CASCADE"), nullable=False
+    )
+    img_name: db.Mapped[str] = db.mapped_column(db.String(64), nullable=False)
+    caption: db.Mapped[str] = db.mapped_column(db.Text, nullable=True)
+    img_url: db.Mapped[str] = db.mapped_column(db.String(256), nullable=True)

api/resources/gaia.py

@@ -0,0 +1,176 @@
+from flask import request
+from flask_restx import Namespace, Resource, fields
+from markupsafe import escape
+from api import db
+from api.utils.bar_utils import BARUtils
+from api.models.gaia import Genes, Aliases, PubIds, Figures
+from sqlalchemy import func, or_
+from marshmallow import Schema, ValidationError, fields as marshmallow_fields
+import json
+
+gaia = Namespace("Gaia", description="Gaia", path="/gaia")
+
+parser = gaia.parser()
+parser.add_argument(
+    "terms",
+    type=list,
+    action="append",
+    required=True,
+    help="Publication IDs",
+    default=["32492426", "32550561"],
+)
+
+publication_request_fields = gaia.model(
+    "Publications",
+    {
+        "pubmeds": fields.List(
+            required=True,
+            example=["32492426", "32550561"],
+            cls_or_instance=fields.String,
+        ),
+    },
+)
+
+
+# Validation is done in a different way to keep things simple
+class PublicationSchema(Schema):
+    pubmeds = marshmallow_fields.List(cls_or_instance=marshmallow_fields.String)
+
+
+@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_gaia_alias(identifier):
+            query_ids = []
+            data = []
+
+            # Check if alias exists
+            # Note: This check can be done in on query, but optimizer is not using indexes for some reason
+            query = db.select(Aliases.genes_id, Aliases.alias).filter(Aliases.alias == identifier)
+            rows = db.session.execute(query).fetchall()
+
+            if rows and len(rows) > 0:
+                # Alias exists. Get the genes_ids
+                for row in rows:
+                    query_ids.append(row.genes_id)
+
+            else:
+                # Alias doesn't exist. Get the ids if it's locus or ncbi id
+                query = db.select(Genes.id).filter(or_(Genes.locus == identifier, Genes.geneid == identifier))
+                rows = db.session.execute(query).fetchall()
+
+                if rows and len(rows) > 0:
+                    for row in rows:
+                        query_ids.append(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.in_(query_ids))
+                .group_by(Genes.species, Genes.locus, Genes.geneid)
+            )
+
+            rows = db.session.execute(query).fetchall()
+
+            if rows and len(rows) > 0:
+                for row in rows:
+
+                    # JSONify aliases
+                    if row.aliases:
+                        aliases = json.loads(row.aliases)
+                    else:
+                        aliases = []
+
+                    record = {
+                        "species": row.species,
+                        "locus": row.locus,
+                        "geneid": row.geneid,
+                        "aliases": aliases,
+                    }
+
+                    # Add the record to data
+                    data.append(record)
+
+            # Return final data
+            return BARUtils.success_exit(data)
+
+        else:
+            return BARUtils.error_exit("Invalid identifier"), 400
+
+
+@gaia.route("/publication_figures")
+class GaiaPublicationFigures(Resource):
+    @gaia.expect(publication_request_fields)
+    def post(self):
+        json_data = request.get_json()
+
+        # Validate json
+        try:
+            json_data = PublicationSchema().load(json_data)
+        except ValidationError as err:
+            return BARUtils.error_exit(err.messages), 400
+
+        pubmeds = json_data["pubmeds"]
+
+        # Check if pubmed ids are valid
+        for pubmed in pubmeds:
+            if not BARUtils.is_integer(pubmed):
+                return BARUtils.error_exit("Invalid Pubmed ID"), 400
+
+        # It is valid. Continue
+        data = []
+
+        # Left join is important in case aliases do not exist for the given locus / geneid
+        query = (
+            db.select(Figures.img_name, Figures.caption, Figures.img_url, PubIds.pubmed, PubIds.pmc)
+            .select_from(Figures)
+            .join(PubIds, PubIds.publication_figures_id == Figures.publication_figures_id)
+            .filter(PubIds.pubmed.in_(pubmeds))
+            .order_by(PubIds.pubmed.desc())
+        )
+
+        rows = db.session.execute(query).fetchall()
+
+        record = {}
+
+        if rows and len(rows) > 0:
+            for row in rows:
+
+                # Check if record has an id. If it doesn't, this is first row.
+                if "id" in record:
+                    # Check if this is a new pubmed id
+                    if record["id"]["pubmed"] != row.pubmed:
+                        # new record. Add old now to data and create a new record
+                        data.append(record)
+                        record = {}
+
+                # Check if figures exists, if not add it.
+                if record.get("figures") is None:
+                    # Create a new figures record
+                    record["figures"] = []
+
+                # Now append figure to the record
+                figure = {"img_name": row.img_name, "caption": row.caption, "img_url": row.img_url}
+                record["figures"].append(figure)
+
+                # Now add the id. If it exists don't add
+                if record.get("id") is None:
+                    record["id"] = {}
+                    record["id"]["pubmed"] = row.pubmed
+                    record["id"]["pmc"] = row.pmc
+
+        # The last record
+        data.append(record)
+
+        # Return final data
+        return BARUtils.success_exit(data)

api/utils/bar_utils.py

@@ -252,6 +252,17 @@ def is_integer(data):
         else:
             return False
 
+    @staticmethod
+    def is_gaia_alias(data):
+        """Check if the input is a valid gaia alias.
+        :param data
+        :return: True if valid gaia alias
+        """
+        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

docs/requirements.txt

@@ -1,24 +1,25 @@
 accessible-pygments==0.0.5
 alabaster==1.0.0
 babel==2.17.0
-beautifulsoup4==4.13.4
-certifi==2025.7.14
-charset-normalizer==3.4.2
-docutils==0.21.2
-furo==2025.7.19
-idna==3.10
+beautifulsoup4==4.14.3
+certifi==2026.1.4
+charset-normalizer==3.4.4
+docutils==0.22.4
+furo==2025.12.19
+idna==3.11
 imagesize==1.4.1
 Jinja2==3.1.6
-MarkupSafe==3.0.2
-packaging==25.0
+MarkupSafe==3.0.3
+packaging==26.0
 Pygments==2.19.2
 pytz==2025.2
-requests==2.32.4
+requests==2.32.5
+roman-numerals==4.1.0
 roman-numerals-py==3.1.0
-setuptools==80.9.0
+setuptools==80.10.1
 snowballstemmer==3.0.1
-soupsieve==2.7
-Sphinx==8.2.3
+soupsieve==2.8.3
+Sphinx==9.1.0
 sphinx-basic-ng==1.0.0b2
 sphinx-copybutton==0.5.2
 sphinxcontrib-applehelp==2.0.0
@@ -27,6 +28,6 @@ sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
-typing_extensions==4.14.1
-urllib3==2.5.0
+typing_extensions==4.15.0
+urllib3==2.6.3
 wheel==0.45.1