diff options
Diffstat (limited to 'uploader/publications/views.py')
| -rw-r--r-- | uploader/publications/views.py | 178 |
1 files changed, 169 insertions, 9 deletions
diff --git a/uploader/publications/views.py b/uploader/publications/views.py index 85d3aef..d9eb294 100644 --- a/uploader/publications/views.py +++ b/uploader/publications/views.py @@ -2,13 +2,26 @@ import json from gn_libs.mysqldb import database_connection -from flask import Blueprint, render_template, current_app as app +from flask import ( + flash, + request, + redirect, + Blueprint, + render_template, + current_app as app) +from uploader.flask_extensions import url_for from uploader.authorisation import require_login +from uploader.route_utils import redirect_to_next -from .models import fetch_publications +from .models import ( + delete_publications, + update_publications, + fetch_publication_by_id, + create_new_publications, + fetch_publication_phenotypes) -from gn_libs.debug import __pk__ +from .datatables import fetch_publications pubbp = Blueprint("publications", __name__) @@ -17,18 +30,165 @@ pubbp = Blueprint("publications", __name__) @require_login def index(): """Index page for publications.""" - with database_connection(app.config["SQL_URI"]) as conn: - return render_template("publications/index.html") + return render_template("publications/index.html") @pubbp.route("/list", methods=["GET"]) @require_login def list_publications(): + """Fetch publications that fulfill a specific search, or all of them, if + there is no search term.""" + # 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: + _publications, _current_rows, _totalfiltered, _totalrows = fetch_publications( + conn, + _search, + offset=_start, + limit=_length) + return json.dumps({ - "publications": tuple({ - **row, "index": idx - } for idx,row in enumerate( - fetch_publications(conn), start=1)), + "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: + publication = fetch_publication_by_id(conn, publication_id) + + if not bool(publication): + flash("Requested publication was not found!", "alert-warning") + return redirect(url_for('publications.index')) + + return render_template( + "publications/view-publication.html", + publication=publication, + linked_phenotypes=tuple(fetch_publication_phenotypes( + conn, publication_id))) + + +@pubbp.route("/create", methods=["GET", "POST"]) +@require_login +def create_publication(): + """Create a new publication.""" + _get_args = { + key: request.args[key] + for key in ("species_id", "population_id", "dataset_id", "return_to") + if bool(request.args.get(key)) + } + + if request.method == "GET": + return render_template( + "publications/create-publication.html", + get_args=_get_args) + 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")) + + 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"], + **_get_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")) + + +@pubbp.route("/edit/<int:publication_id>", methods=["GET", "POST"]) +@require_login +def edit_publication(publication_id: int): + """Edit a publication's details.""" + with database_connection(app.config["SQL_URI"]) as conn: + if request.method == "GET": + return render_template( + "publications/edit-publication.html", + publication=fetch_publication_by_id(conn, publication_id), + linked_phenotypes=tuple(fetch_publication_phenotypes( + conn, publication_id)), + publication_id=publication_id) + + form = request.form + _pub = update_publications(conn, ({ + "publication_id": publication_id, + "pubmed_id": form.get("pubmed-id") or None, + "abstract": (form.get("publication-abstract") or "").encode("utf8") or None, + "authors": (form.get("publication-authors") or "").encode("utf8"), + "title": (form.get("publication-title") or "").encode("utf8") or None, + "journal": (form.get("publication-journal") or "").encode("utf8") or None, + "volume": (form.get("publication-volume") or "").encode("utf8") or None, + "pages": (form.get("publication-pages") or "").encode("utf8") or None, + "month": (form.get("publication-month") or "").encode("utf8").capitalize() or None, + "year": (form.get("publication-year") or "").encode("utf8") or None + },)) + + if not _pub: + flash("There was an error updating the publication details.", + "alert-danger") + return redirect(url_for( + "publications.edit_publication", publication_id=publication_id)) + + flash("Successfully updated the publication details.", + "alert-success") + return redirect_to_next({ + "uri": "publications.view_publication", + "publication_id": publication_id + }) + + +@pubbp.route("/delete/<int:publication_id>", methods=["GET", "POST"]) +@require_login +def delete_publication(publication_id: int): + """Delete a particular publication.""" + with database_connection(app.config["SQL_URI"]) as conn: + publication = fetch_publication_by_id(conn, publication_id) + linked_phenotypes=tuple(fetch_publication_phenotypes( + conn, publication_id)) + + if not bool(publication): + flash("Requested publication was not found!", "alert-warning") + return redirect(url_for('publications.index')) + + if len(linked_phenotypes) > 0: + flash("Cannot delete publication with linked phenotypes!", + "alert-warning") + return redirect(url_for( + "publications.view_publication", + publication_id=publication_id)) + + if request.method == "GET": + return render_template( + "publications/delete-publication.html", + publication=publication, + linked_phenotypes=linked_phenotypes, + publication_id=publication_id) + + delete_publications(conn, (publication,)) + flash("Deleted the publication successfully.", "alert-success") + return redirect(url_for("publications.index")) |