Merge pull request #291 from asherpasha/dev

GAIA publications collection initial commit.

Author: asherpasha

api/models/gaia.py

@@ -22,3 +22,41 @@ class Aliases(db.Model):
     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

@@ -1,13 +1,41 @@
-from flask_restx import Namespace, Resource
+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
+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):
@@ -78,3 +106,71 @@ def get(self, identifier=""):
 
         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)

requirements.txt

@@ -1,23 +1,23 @@
 aniso8601==10.0.1
 async-timeout==5.0.1
 attrs==25.4.0
-black==25.9.0
+black==25.12.0
 blinker==1.9.0
 cachelib==0.13.0
-certifi==2025.10.5
+certifi==2025.11.12
 charset-normalizer==3.4.4
-click==8.3.0
-coverage==7.11.0
-Deprecated==1.2.18
+click==8.3.1
+coverage==7.13.0
+Deprecated==1.3.1
 flake8==7.3.0
 Flask==3.1.2
 Flask-Caching==2.3.1
 flask-cors==6.0.1
-Flask-Limiter==4.0.0
+Flask-Limiter==4.1.1
 flask-marshmallow==1.3.0
 flask-restx==1.3.2
 Flask-SQLAlchemy==3.1.1
-greenlet==3.2.4
+greenlet==3.3.0
 idna==3.11
 importlib_resources==6.5.2
 iniconfig==2.3.0
@@ -28,34 +28,34 @@ jsonschema-specifications==2025.9.1
 limits==5.6.0
 markdown-it-py==4.0.0
 MarkupSafe==3.0.3
-marshmallow==4.0.1
+marshmallow==4.1.1
 mccabe==0.7.0
 mdurl==0.1.2
 mypy_extensions==1.1.0
 mysqlclient==2.2.7
 ordered-set==4.1.0
 packaging==25.0
 pathspec==0.12.1
-platformdirs==4.5.0
+platformdirs==4.5.1
 pluggy==1.6.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
 Pygments==2.19.2
 pyrsistent==0.20.0
-pytest==8.4.2
+pytest==9.0.2
 python-dateutil==2.9.0.post0
-pytokens==0.2.0
+pytokens==0.3.0
 pytz==2025.2
-redis==7.0.1
+redis==7.1.0
 referencing==0.37.0
 requests==2.32.5
 rich==14.2.0
-rpds-py==0.28.0
+rpds-py==0.30.0
 setuptools==80.9.0
 six==1.17.0
 SQLAlchemy==2.0.44
 typing_extensions==4.15.0
-urllib3==2.5.0
-Werkzeug==3.1.3
+urllib3==2.6.1
+Werkzeug==3.1.4
 wheel==0.45.1
-wrapt==1.17.3
+wrapt==2.0.1