diff options
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 59 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 58 |
2 files changed, 59 insertions, 58 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 08ff4704..ef9dc127 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -278,3 +278,62 @@ def update_phenotype(dataset_id: str, name: str): flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success") return redirect(f"/datasets/{dataset_id}/traits/{name}" f"?resource-id={request.args.get('resource-id')}") + + +@metadata_edit.route("/traits/<name>", methods=["POST"]) +@edit_access_required +def update_probeset(name: str): + conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), + user=current_app.config.get("DB_USER"), + passwd=current_app.config.get("DB_PASS"), + host=current_app.config.get("DB_HOST")) + data_ = request.form.to_dict() + probeset_ = { + "id_": data_.get("id"), + "symbol": data_.get("symbol"), + "description": data_.get("description"), + "probe_target_description": data_.get("probe_target_description"), + "chr_": data_.get("chr"), + "mb": data_.get("mb"), + "alias": data_.get("alias"), + "geneid": data_.get("geneid"), + "homologeneid": data_.get("homologeneid"), + "unigeneid": data_.get("unigeneid"), + "omim": data_.get("OMIM"), + "refseq_transcriptid": data_.get("refseq_transcriptid"), + "blatseq": data_.get("blatseq"), + "targetseq": data_.get("targetseq"), + "strand_probe": data_.get("Strand_Probe"), + "probe_set_target_region": data_.get("probe_set_target_region"), + "probe_set_specificity": data_.get("probe_set_specificity"), + "probe_set_blat_score": data_.get("probe_set_blat_score"), + "probe_set_blat_mb_start": data_.get("probe_set_blat_mb_start"), + "probe_set_blat_mb_end": data_.get("probe_set_blat_mb_end"), + "probe_set_strand": data_.get("probe_set_strand"), + "probe_set_note_by_rw": data_.get("probe_set_note_by_rw"), + "flag": data_.get("flag") + } + diff_data = {} + author = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8") + or g.user_session.record.get("user_id") or "") + if (updated_probeset := update( + conn, "ProbeSet", + data=Probeset(**probeset_), + where=Probeset(id_=data_.get("id")))): + diff_data.update({"Probeset": diff_from_dict(old={ + k: data_.get(f"old_{k}") for k, v in probeset_.items() + if v is not None}, new=probeset_)}) + if diff_data: + diff_data.update({"probeset_name": data_.get("probeset_name")}) + diff_data.update({"author": author}) + diff_data.update({"resource_id": request.args.get('resource-id')}) + 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("id"), + editor=author.decode("utf-8"), + json_data=json.dumps(diff_data))) + return redirect(f"/datasets/traits/{name}" + f"?resource-id={request.args.get('resource-id')}") + diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 665aabb0..220d9b87 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -416,64 +416,6 @@ def submit_trait_form(): version=GN_VERSION) -@app.route("/probeset/update", methods=["POST"]) -def update_probeset(): - conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), - user=current_app.config.get("DB_USER"), - passwd=current_app.config.get("DB_PASS"), - host=current_app.config.get("DB_HOST")) - data_ = request.form.to_dict() - probeset_ = { - "id_": data_.get("id"), - "symbol": data_.get("symbol"), - "description": data_.get("description"), - "probe_target_description": data_.get("probe_target_description"), - "chr_": data_.get("chr"), - "mb": data_.get("mb"), - "alias": data_.get("alias"), - "geneid": data_.get("geneid"), - "homologeneid": data_.get("homologeneid"), - "unigeneid": data_.get("unigeneid"), - "omim": data_.get("OMIM"), - "refseq_transcriptid": data_.get("refseq_transcriptid"), - "blatseq": data_.get("blatseq"), - "targetseq": data_.get("targetseq"), - "strand_probe": data_.get("Strand_Probe"), - "probe_set_target_region": data_.get("probe_set_target_region"), - "probe_set_specificity": data_.get("probe_set_specificity"), - "probe_set_blat_score": data_.get("probe_set_blat_score"), - "probe_set_blat_mb_start": data_.get("probe_set_blat_mb_start"), - "probe_set_blat_mb_end": data_.get("probe_set_blat_mb_end"), - "probe_set_strand": data_.get("probe_set_strand"), - "probe_set_note_by_rw": data_.get("probe_set_note_by_rw"), - "flag": data_.get("flag") - } - updated_probeset = update( - conn, "ProbeSet", - data=Probeset(**probeset_), - where=Probeset(id_=data_.get("id"))) - - diff_data = {} - author = (g.user_session.record.get(b"user_id", - b"").decode("utf-8") or - g.user_session.record.get("user_id", "")) - if updated_probeset: - diff_data.update({"Probeset": diff_from_dict(old={ - k: data_.get(f"old_{k}") for k, v in probeset_.items() - if v is not None}, new=probeset_)}) - if diff_data: - diff_data.update({"probeset_name": data_.get("probeset_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("id"), - editor=author.decode("utf-8"), - json_data=json.dumps(diff_data))) - return redirect(f"/trait/edit/probeset-name/{data_.get('probeset_name')}") - - @app.route("/create_temp_trait", methods=('POST',)) def create_temp_trait(): logger.info(request.url) |