diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 64 |
1 files changed, 37 insertions, 27 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 069f8152..cd5b7893 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -226,8 +226,9 @@ def update_phenotype(dataset_id: str, name: str): ) diff_data = {} with database_connection() as conn: - headers = ["Strain Name", "Value", "SE", "Count"] \ - + list(get_case_attributes(conn).keys()) + headers = ["Strain Name", "Value", "SE", "Count"] + list( + get_case_attributes(conn).keys() + ) diff_data = remove_insignificant_edits( diff_data=csv_diff( base_csv=( @@ -342,9 +343,7 @@ def update_phenotype(dataset_id: str, name: str): conn, "Publication", data=Publication(**publication_), - where=Publication( - id_=data_.get("old_id_") - ), + where=Publication(id_=data_.get("old_id_")), ) if updated_publications: diff_data.update( @@ -543,7 +542,8 @@ def show_history(dataset_id: str, name: str): publish_xref = fetchone( conn=conn, table="PublishXRef", - where=PublishXRef(id_=name, inbred_set_id=dataset_id)) + where=PublishXRef(id_=name, inbred_set_id=dataset_id), + ) json_data = fetchall( conn, @@ -571,7 +571,7 @@ def show_history(dataset_id: str, name: str): "\n".join( difflib.ndiff( [data_.get("old") or ""], - [data_.get("new")] + [data_.get("new")], ) ), ), @@ -583,7 +583,8 @@ def show_history(dataset_id: str, name: str): return render_template( "edit_history.html", diff=diff_data_, - version=os.environ.get("GN_VERSION")) + version=os.environ.get("GN_VERSION"), + ) @metadata_edit.route("<resource_id>/diffs/<file_name>/reject") @@ -719,30 +720,32 @@ def show_case_attribute_columns(): value=author, conn=redis.from_url( current_app.config["REDIS_URL"], decode_responses=True - ) + ), ).get("full_name") - if (m_ := diff.get("Modification")): + if m_ := diff.get("Modification"): m_["author"] = author m_["id"] = id_ if m_.get("description"): m_["description"]["Diff"] = "\n".join( difflib.ndiff( [m_.get("description")["Original"]], - [m_.get("description")["Current"]] - )) + [m_.get("description")["Current"]], + ) + ) if m_.get("name"): m_["name"]["Diff"] = "\n".join( difflib.ndiff( [m_.get("name")["Original"]], - [m_.get("name")["Current"]] - )) + [m_.get("name")["Current"]], + ) + ) if any([m_.get("description"), m_.get("name")]): modifications.append(m_) - if (d_ := diff.get("Deletion")): + if d_ := diff.get("Deletion"): d_["author"] = author d_["id"] = id_ deletions.append(d_) - if (i_ := diff.get("Insert")): + if i_ := diff.get("Insert"): i_["author"] = author i_["id"] = id_ inserts.append(i_) @@ -752,7 +755,7 @@ def show_case_attribute_columns(): case_attributes=get_case_attributes(cursor), modifications=modifications, deletions=deletions, - inserts=inserts + inserts=inserts, ) @@ -768,30 +771,37 @@ def update_case_attributes(): or "" ) with database_connection() as conn: - insert_case_attribute_audit(conn=conn, - status="review", - author=author, - data=data_) + insert_case_attribute_audit( + conn=conn, status="review", author=author, data=data_ + ) return redirect(url_for("metadata_edit.show_case_attribute_columns")) -@metadata_edit.route("/case-attributes/reject", methods=["POST", ]) +@metadata_edit.route( + "/case-attributes/reject", + methods=[ + "POST", + ], +) @case_attributes_edit_access @login_required def reject_case_attribute_data(): case_attr_id = request.form.to_dict().get("id") with database_connection() as conn: - reject_case_attribute(conn=conn, - case_attr_audit_id=int(case_attr_id)) + reject_case_attribute(conn=conn, case_attr_audit_id=int(case_attr_id)) return redirect(url_for("metadata_edit.show_case_attribute_columns")) -@metadata_edit.route("/case-attributes/approve", methods=["POST", ]) +@metadata_edit.route( + "/case-attributes/approve", + methods=[ + "POST", + ], +) @case_attributes_edit_access @login_required def approve_case_attribute_data(): case_attr_id = request.form.to_dict().get("id") with database_connection() as conn: - approve_case_attribute(conn=conn, - case_attr_audit_id=case_attr_id) + approve_case_attribute(conn=conn, case_attr_audit_id=case_attr_id) return redirect(url_for("metadata_edit.show_case_attribute_columns")) |