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/models.py | 14 | ||||
| -rw-r--r-- | uploader/publications/pubmed.py | 3 | ||||
| -rw-r--r-- | uploader/publications/views.py | 46 |
5 files changed, 50 insertions, 19 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/models.py b/uploader/publications/models.py index dcfa02b..d913144 100644 --- a/uploader/publications/models.py +++ b/uploader/publications/models.py @@ -101,6 +101,20 @@ def fetch_publication_by_id(conn: Connection, publication_id: int) -> dict: return dict(_res) if _res else {} +def fetch_publications_by_ids( + conn: Connection, publications_ids: tuple[int, ...] +) -> tuple[dict, ...]: + """Fetch publications with the given IDs.""" + if len(publications_ids) == 0: + return tuple() + + with conn.cursor(cursorclass=DictCursor) as cursor: + paramstr = ", ".join(["%s"] * len(publications_ids)) + cursor.execute(f"SELECT * FROM Publication WHERE Id IN ({paramstr})", + tuple(publications_ids)) + return tuple(dict(row) for row in cursor.fetchall()) + + def fetch_publication_phenotypes( conn: Connection, publication_id: int) -> Iterable[dict]: """Fetch all phenotypes linked to this publication.""" 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 ee00e67..89e9f5d 100644 --- a/uploader/publications/views.py +++ b/uploader/publications/views.py @@ -1,17 +1,19 @@ """Endpoints for publications""" import json +import datetime from gn_libs.mysqldb import database_connection from flask import ( flash, request, - url_for, 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 ( delete_publications, @@ -81,13 +83,24 @@ 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") + now = datetime.datetime.now() + return render_template( + "publications/create-publication.html", + get_args=_get_args, + current_year=now.year, + current_month=now.strftime("%B")) 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, ({ @@ -105,7 +118,7 @@ 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) @@ -129,14 +142,14 @@ 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: @@ -147,8 +160,10 @@ def edit_publication(publication_id: int): flash("Successfully updated the publication details.", "alert-success") - return redirect(url_for( - "publications.view_publication", publication_id=publication_id)) + return redirect_to_next({ + "uri": "publications.view_publication", + "publication_id": publication_id + }) @pubbp.route("/delete/<int:publication_id>", methods=["GET", "POST"]) @@ -168,7 +183,8 @@ 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)) + "publications.view_publication", + publication_id=publication_id)) if request.method == "GET": return render_template( @@ -179,4 +195,4 @@ def delete_publication(publication_id: int): 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")) |