diff options
Diffstat (limited to 'uploader/publications')
| -rw-r--r-- | uploader/publications/datatables.py | 2 | ||||
| -rw-r--r-- | uploader/publications/misc.py | 4 | ||||
| -rw-r--r-- | uploader/publications/pubmed.py | 3 | ||||
| -rw-r--r-- | uploader/publications/views.py | 43 |
4 files changed, 32 insertions, 20 deletions
diff --git a/uploader/publications/datatables.py b/uploader/publications/datatables.py index e07fafd..8b3d4a0 100644 --- a/uploader/publications/datatables.py +++ b/uploader/publications/datatables.py @@ -13,7 +13,7 @@ def fetch_publications( search: Optional[str] = None, offset: int = 0, limit: int = -1 -) -> tuple[dict, int, int, int]: +) -> tuple[tuple[dict, ...], int, int, int]: """Fetch publications from the database.""" _query = "SELECT * FROM Publication" _count_query = "SELECT COUNT(*) FROM Publication" diff --git a/uploader/publications/misc.py b/uploader/publications/misc.py index fca6f71..f0ff9c7 100644 --- a/uploader/publications/misc.py +++ b/uploader/publications/misc.py @@ -4,10 +4,10 @@ def publications_differences( filedata: tuple[dict, ...], dbdata: tuple[dict, ...], - pubmedid2pubidmap: tuple[dict, ...] + pubmedid2pubidmap: dict[int, int] ) -> tuple[dict, ...]: """Compute the differences between file data and db data""" - diff = tuple() + diff: tuple[dict, ...] = tuple() for filerow, dbrow in zip( sorted(filedata, key=lambda item: ( item["phenotype_id"], item["xref_id"])), diff --git a/uploader/publications/pubmed.py b/uploader/publications/pubmed.py index 2531c4a..15bf701 100644 --- a/uploader/publications/pubmed.py +++ b/uploader/publications/pubmed.py @@ -1,5 +1,6 @@ """Module to interact with NCBI's PubMed""" import logging +from typing import Optional import requests from lxml import etree @@ -40,7 +41,7 @@ def __pages__(pagination: etree.Element) -> str: )) if start is not None else "" -def __abstract__(article: etree.Element) -> str: +def __abstract__(article: etree.Element) -> Optional[str]: abstract = article.find("Abstract/AbstractText") return abstract.text if abstract is not None else None diff --git a/uploader/publications/views.py b/uploader/publications/views.py index 4ec832f..11732db 100644 --- a/uploader/publications/views.py +++ b/uploader/publications/views.py @@ -10,6 +10,8 @@ from flask import ( render_template, current_app as app) +from uploader.sui import sui_template + from uploader.flask_extensions import url_for from uploader.authorisation import require_login from uploader.route_utils import redirect_to_next @@ -30,7 +32,7 @@ pubbp = Blueprint("publications", __name__) @require_login def index(): """Index page for publications.""" - return render_template("publications/index.html") + return render_template(sui_template("publications/index.html")) @pubbp.route("/list", methods=["GET"]) @@ -72,7 +74,7 @@ def view_publication(publication_id: int): return redirect(url_for('publications.index')) return render_template( - "publications/view-publication.html", + sui_template("publications/view-publication.html"), publication=publication, linked_phenotypes=tuple(fetch_publication_phenotypes( conn, publication_id))) @@ -82,13 +84,21 @@ def view_publication(publication_id: int): @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") + return render_template( + sui_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", **request.args)) + return redirect(url_for("publications.create")) with database_connection(app.config["SQL_URI"]) as conn: publications = create_new_publications(conn, ({ @@ -106,7 +116,7 @@ def create_publication(): return redirect(url_for( request.args.get("return_to") or "publications.view_publication", publication_id=publications[0]["publication_id"], - **request.args)) + **_get_args)) flash("Publication creation failed!", "alert alert-danger") app.logger.debug("Failed to create the new publication.", exc_info=True) @@ -120,7 +130,7 @@ def edit_publication(publication_id: int): with database_connection(app.config["SQL_URI"]) as conn: if request.method == "GET": return render_template( - "publications/edit-publication.html", + sui_template("publications/edit-publication.html"), publication=fetch_publication_by_id(conn, publication_id), linked_phenotypes=tuple(fetch_publication_phenotypes( conn, publication_id)), @@ -130,14 +140,14 @@ def edit_publication(publication_id: int): _pub = update_publications(conn, ({ "publication_id": publication_id, "pubmed_id": form.get("pubmed-id") or None, - "abstract": form.get("publication-abstract").encode("utf8") or None, - "authors": form.get("publication-authors").encode("utf8"), - "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, + "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").encode("utf8") or None + "year": (form.get("publication-year") or "").encode("utf8") or None },)) if not _pub: @@ -171,15 +181,16 @@ def delete_publication(publication_id: int): flash("Cannot delete publication with linked phenotypes!", "alert-warning") return redirect(url_for( - "publications.view_publication", publication_id=publication_id)) + sui_template("publications.view_publication"), + publication_id=publication_id)) if request.method == "GET": return render_template( - "publications/delete-publication.html", + sui_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 render_template("publications/delete-publication-success.html") + return redirect(url_for("publications.index")) |