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authorBonfaceKilz2021-06-07 09:53:38 +0300
committerBonfaceKilz2021-06-07 18:43:44 +0300
commit134c683877195fe7b18778f75da8c3f88588728b (patch)
treee49002370d08aab9d69e9b0cfe0af93b574177a5 /wqflask
parentd8ca52eaca18aa5a638e8b9aa01f66f67f44d021 (diff)
downloadgenenetwork2-134c683877195fe7b18778f75da8c3f88588728b.tar.gz
wqflask: views: Insert data into metadata_audit table
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/views.py87
1 files changed, 50 insertions, 37 deletions
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1ca0a71a..a853048e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -23,11 +23,14 @@ import array
import sqlalchemy
from wqflask import app
+from gn3.db import diff_from_dict
from gn3.db import fetchone
+from gn3.db import insert
from gn3.db import update
+from gn3.db.metadata_audit import MetadataAudit
from gn3.db.phenotypes import Phenotype
-from gn3.db.phenotypes import PublishXRef
from gn3.db.phenotypes import Publication
+from gn3.db.phenotypes import PublishXRef
from flask import current_app
@@ -462,47 +465,57 @@ def update_trait():
host=current_app.config.get("DB_HOST"))
data_ = request.form.to_dict()
# Run updates:
+ phenotype_ = {
+ "pre_pub_description": data_.get("pre-pub-desc"),
+ "post_pub_description": data_.get("post-pub-desc"),
+ "original_description": data_.get("orig-desc"),
+ "units": data_.get("units"),
+ "pre_pub_abbreviation": data_.get("pre-pub-abbrev"),
+ "post_pub_abbreviation": data_.get("post-pub-abbrev"),
+ "lab_code": data_.get("labcode"),
+ "submitter": data_.get("submitter"),
+ "owner": data_.get("owner"),
+ "authorized_users": data_.get("authorized-users"),
+ }
updated_phenotypes = update(
conn, "Phenotype",
- data=Phenotype(
- pre_pub_description=data_.get("pre-pub-desc"),
- post_pub_description=data_.get("post-pub-desc"),
- original_description=data_.get("orig-desc"),
- units=data_.get("units"),
- pre_pub_abbreviation=data_.get("pre-pub-abbrev"),
- post_pub_abbreviation=data_.get("post-pub-abbrev"),
- lab_code=data_.get("labcode"),
- submitter=data_.get("submitter"),
- owner=data_.get("owner"),
- ),
+ data=Phenotype(**phenotype_),
where=Phenotype(id_=data_.get("phenotype-id")))
+ diff_data = {}
+ if updated_phenotypes:
+ diff_data.update({"Phenotype": diff_from_dict(old={
+ k: data_.get(f"old_{k}") for k, v in phenotype_.items()
+ if v is not None}, new=phenotype_)})
+ publication_ = {
+ "abstract": data_.get("abstract"),
+ "authors": data_.get("authors"),
+ "title": data_.get("title"),
+ "journal": data_.get("journal"),
+ "volume": data_.get("volume"),
+ "pages": data_.get("pages"),
+ "month": data_.get("month"),
+ "year": data_.get("year")
+ }
updated_publications = update(
conn, "Publication",
- data=Publication(
- abstract=data_.get("abstract"),
- authors=data_.get("authors"),
- title=data_.get("title"),
- journal=data_.get("journal"),
- volume=data_.get("volume"),
- pages=data_.get("pages"),
- month=data_.get("month"),
- year=data_.get("year")),
- where=Publication(id_=data_.get("pubmed-id")))
- if updated_phenotypes or updated_publications:
- comments = data_.get("comments")
- if comments:
- comments = (f"{comments}\r\n"
- f"{g.user_session.record.get(b'user_name')}")
- update(conn, "PublishXRef",
- data=PublishXRef(
- comments=(f"{data_.get('comments')}\r\n"
- "Modified by: "
- f"{g.user_session.record.get(b'user_name').decode('utf-8')} "
- f"on {str(datetime.datetime.now())}"),
- publication_id=data_.get("pubmed-id")),
- where=PublishXRef(
- id_=data_.get("dataset-name"),
- inbred_set_id=data_.get("inbred-set-id")))
+ data=Publication(**publication_),
+ where=Publication(id_=data_.get("pubmed-id",
+ data_.get("old_id_"))))
+ if updated_publications:
+ diff_data.update({"Publication": diff_from_dict(old={
+ k: data_.get(f"old_{k}") for k, v in publication_.items()
+ if v is not None}, new=publication_)})
+ author = g.user_session.record.get(b'user_name')
+ if diff_data:
+ diff_data.update({"dataset_id": data_.get("dataset-name")})
+ diff_data.update({"author": author.decode('utf-8')})
+ diff_data.update({"timestamp": datetime.datetime.now().strftime(
+ "%Y-%m-%d %H:%M:%S")})
+ insert(conn,
+ table="metadata_audit",
+ data=MetadataAudit(dataset_id=data_.get("dataset-name"),
+ editor=author.decode("utf-8"),
+ json_data=json.dumps(diff_data)))
return redirect("/trait/10007/edit/1")