diff options
| -rw-r--r-- | wqflask/wqflask/views.py | 87 |
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") |