1 files changed, 92 insertions, 0 deletions
diff --git a/uploader/publications/views.py b/uploader/publications/views.py
new file mode 100644
index 0000000..ebb8740
--- /dev/null
+++ b/uploader/publications/views.py
@@ -0,0 +1,92 @@
+"""Endpoints for publications"""
+import json
+
+from gn_libs.mysqldb import database_connection
+from flask import (
+    flash,
+    request,
+    url_for,
+    redirect,
+    Blueprint,
+    render_template,
+    current_app as app)
+
+from uploader.authorisation import require_login
+
+from .models import (
+    fetch_publications,
+    fetch_publication_by_id,
+    create_new_publications,
+    fetch_publication_phenotypes)
+
+from gn_libs.debug import __pk__
+
+pubbp = Blueprint("publications", __name__)
+
+
+@pubbp.route("/", methods=["GET"])
+@require_login
+def index():
+    """Index page for publications."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        return render_template("publications/index.html")
+
+
+@pubbp.route("/list", methods=["GET"])
+@require_login
+def list_publications():
+    with database_connection(app.config["SQL_URI"]) as conn:
+        return json.dumps({
+            "publications": tuple({
+                **row, "index": idx
+            } for idx,row in enumerate(
+                fetch_publications(conn), start=1)),
+            "status": "success"
+        })
+
+
+@pubbp.route("/view/<int:publication_id>", methods=["GET"])
+@require_login
+def view_publication(publication_id: int):
+    """View more details on a particular publication."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        return render_template(
+            "publications/view-publication.html",
+            publication=fetch_publication_by_id(conn, publication_id),
+            linked_phenotypes=tuple(fetch_publication_phenotypes(
+                conn, publication_id)))
+
+
+@pubbp.route("/create", methods=["GET", "POST"])
+@require_login
+def create_publication():
+    """Create a new publication."""
+    if(request.method == "GET"):
+        return render_template("publications/create-publication.html")
+    form = request.form
+    authors = form.get("publication-authors").encode("utf8")
+    if authors is None or authors == "":
+        flash("The publication's author(s) MUST be provided!", "alert alert-danger")
+        return redirect(url_for("publications.create", **request.args))
+
+    with database_connection(app.config["SQL_URI"]) as conn:
+        publications = create_new_publications(conn, ({
+            "pubmed_id": form.get("pubmed-id"),
+            "abstract": form.get("publication-abstract").encode("utf8") or None,
+            "authors": authors,
+            "title":  form.get("publication-title").encode("utf8") or None,
+            "journal": form.get("publication-journal").encode("utf8") or None,
+            "volume": form.get("publication-volume").encode("utf8") or None,
+            "pages": form.get("publication-pages").encode("utf8") or None,
+            "month": (form.get("publication-month") or "").encode("utf8").capitalize() or None,
+            "year": form.get("publication-year").encode("utf8") or None
+        },))
+        flash("New publication created!", "alert alert-success")
+        return redirect(url_for(
+            request.args.get("return_to") or "publications.view_publication",
+            publication_id=publications[0]["publication_id"],
+            **request.args))
+
+    flash("Publication creation failed!", "alert alert-danger")
+    app.logger.debug("Failed to create the new publication.", exc_info=True)
+    return redirect(url_for("publications.create_publication"))