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 | 14 |
4 files changed, 12 insertions, 11 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 f0ec95a..11732db 100644 --- a/uploader/publications/views.py +++ b/uploader/publications/views.py @@ -140,14 +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: |