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Diffstat (limited to 'uploader/publications/views.py')
-rw-r--r-- | uploader/publications/views.py | 107 |
1 files changed, 107 insertions, 0 deletions
diff --git a/uploader/publications/views.py b/uploader/publications/views.py new file mode 100644 index 0000000..0608a35 --- /dev/null +++ b/uploader/publications/views.py @@ -0,0 +1,107 @@ +"""Endpoints for publications""" +import json + +from MySQLdb.cursors import DictCursor +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_publication_by_id, + create_new_publications, + fetch_publication_phenotypes) + +from .datatables import fetch_publications + +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(): + # request breakdown: + # https://datatables.net/manual/server-side + _page = int(request.args.get("draw")) + _length = int(request.args.get("length") or '-1') + _start = int(request.args.get("start") or '0') + _search = request.args["search[value]"] + with (database_connection(app.config["SQL_URI"]) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): + _publications, _current_rows, _totalfiltered, _totalrows = fetch_publications( + conn, + _search, + offset=_start, + limit=_length) + + return json.dumps({ + "draw": _page, + "recordsTotal": _totalrows, + "recordsFiltered": _totalfiltered, + "publications": _publications, + "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") or None, + "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")) |