From f4c458f71e94254b05c42c1f1c5caaac2e687e72 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 3 May 2022 18:04:09 +0300
Subject: Replace references of "publish_xref.pubmed_id" with "publication.id"
See: https://issues.genenetwork.org/issues/edit-metadata-bugs.html
* wqflask/wqflask/metadata_edits (edit_phenotype):
When diffing, should there be a null, use a ""
during page display. Also, use the
"publication.id_" instead of
"publication.pubmed_id" when updating a
publication.
* wqflask/wqflask/templates/edit_phenotype.html:
In the HTML form, use values of "publication"
instead of "publish_xref" when referring to a
publication.
---
wqflask/wqflask/metadata_edits.py | 5 +++--
wqflask/wqflask/templates/edit_phenotype.html | 4 ++--
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index 49b03943..10022ae1 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -130,7 +130,7 @@ def edit_phenotype(conn, name, dataset_id):
data_.get("new"),
"\n".join(
difflib.ndiff(
- [data_.get("old")], [data_.get("new")]
+ [data_.get("old") or ""], [data_.get("new")]
)
),
),
@@ -357,6 +357,7 @@ def update_phenotype(dataset_id: str, name: str):
}
)
publication_ = {
+ "pubmed_id": data_.get("pubmed-id"),
"abstract": data_.get("abstract"),
"authors": data_.get("authors"),
"title": data_.get("title"),
@@ -373,7 +374,7 @@ def update_phenotype(dataset_id: str, name: str):
"Publication",
data=Publication(**publication_),
where=Publication(
- id_=data_.get("pubmed-id", data_.get("old_id_"))
+ id_=data_.get("old_id_")
),
)
if updated_publications:
diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index b90c7daf..617848ad 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -81,8 +81,8 @@
Description will be ignored. Do not enter any non-digit
character in this field. -->