diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 95 |
1 files changed, 55 insertions, 40 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 76dd50d9..fa6cfea3 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -45,6 +45,8 @@ from gn3.db.phenotypes import PublishXRef from gn3.db.phenotypes import probeset_mapping from gn3.db.traits import get_trait_csv_sample_data from gn3.db.traits import update_sample_data +from gn3.db.traits import delete_sample_data +from gn3.db.traits import insert_sample_data metadata_edit = Blueprint('metadata_edit', __name__) @@ -249,23 +251,11 @@ def update_phenotype(dataset_id: str, name: str): TMPDIR, "sample-data/updated/", f"{_file_name}.csv.uploaded")) file_.save(new_file_name) - publishdata_id = "" - lines = [] - split_point = "" - with open(new_file_name, "r") as f: - lines = f.read() - for line in lines.split("\n"): - if "# Publish Data Id:" in line: - split_point = line - publishdata_id = re.findall(r'\b\d+\b', line)[0] - break - with open(new_file_name, "w") as f: - f.write(lines.split(f"{split_point}\n")[-1].strip()) - csv_ = get_trait_csv_sample_data(conn=conn, - trait_name=str(name), - phenotype_id=str(phenotype_id)) with open(uploaded_file_name, "w") as f_: - f_.write(csv_.split(str(publishdata_id))[-1].strip()) + f_.write(get_trait_csv_sample_data( + conn=conn, + trait_name=str(name), + phenotype_id=str(phenotype_id))) r = run_cmd(cmd=("csvdiff " f"'{uploaded_file_name}' '{new_file_name}' " "--format json")) @@ -274,9 +264,9 @@ def update_phenotype(dataset_id: str, name: str): with open(diff_output, "w") as f: dict_ = json.loads(r.get("output")) dict_.update({ + "trait_name": str(name), + "phenotype_id": str(phenotype_id), "author": author, - "publishdata_id": publishdata_id, - "dataset_id": name, "timestamp": datetime.datetime.now().strftime( "%Y-%m-%d %H:%M:%S") }) @@ -324,11 +314,16 @@ def update_phenotype(dataset_id: str, name: str): k: data_.get(f"old_{k}") for k, v in publication_.items() if v is not None}, new=publication_)}) if diff_data: - diff_data.update({"dataset_id": name}) - diff_data.update({"resource_id": request.args.get('resource-id')}) - diff_data.update({"author": author}) - diff_data.update({"timestamp": datetime.datetime.now().strftime( - "%Y-%m-%d %H:%M:%S")}) + diff_data.update({ + "phenotype_id": str(phenotype_id), + "dataset_id": name, + "resource_id": request.args.get('resource-id'), + "author": author, + "timestamp": (datetime + .datetime + .now() + .strftime("%Y-%m-%d %H:%M:%S")), + }) insert(conn, table="metadata_audit", data=MetadataAudit(dataset_id=name, @@ -473,34 +468,54 @@ def approve_data(resource_id:str, file_name: str): with open(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), 'r') as myfile: sample_data = json.load(myfile) - modifications = [d for d in sample_data.get("Modifications")] - for modification in modifications: + for modification in ( + modifications := [d for d in sample_data.get("Modifications")]): if modification.get("Current"): - (strain_id, - strain_name, + (strain_name, value, se, count) = modification.get("Current").split(",") update_sample_data( conn=conn, + trait_name=sample_data.get("trait_name"), strain_name=strain_name, - strain_id=int(strain_id), - publish_data_id=int(sample_data.get("publishdata_id")), + phenotype_id=int(sample_data.get("phenotype_id")), value=value, error=se, - count=count - ) - insert(conn, - table="metadata_audit", - data=MetadataAudit( - dataset_id=sample_data.get("dataset_id"), - editor=sample_data.get("author"), - json_data=json.dumps(sample_data))) - if modifications: + count=count) + for deletion in (deletions := [d for d in sample_data.get("Deletions")]): + strain_name, _, _, _ = deletion.split(",") + delete_sample_data( + conn=conn, + trait_name=sample_data.get("trait_name"), + strain_name=strain_name, + phenotype_id=int(sample_data.get("phenotype_id"))) + for insertion in ( + insertions := [d for d in sample_data.get("Additions")]): + (strain_name, + value, se, count) = insertion.split(",") + insert_sample_data( + conn=conn, + trait_name=sample_data.get("trait_name"), + strain_name=strain_name, + phenotype_id=int(sample_data.get("phenotype_id")), + value=value, + error=se, + count=count) + + if any([any(modifications), any(deletions), any(insertions)]): + insert(conn, + table="metadata_audit", + data=MetadataAudit( + dataset_id=sample_data.get("trait_name"), + editor=sample_data.get("author"), + json_data=json.dumps(sample_data))) # Once data is approved, rename it! os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), os.path.join(f"{TMPDIR}/sample-data/diffs", f"{file_name}.approved")) - flash((f"Just updated data from: {file_name}; {len(modifications)} " - "row(s) modified!"), + flash((f"Just updated data from: {file_name};\n" + f"# Modifications: {len(modifications)}; " + f"# Additions: {len(insertions)}; " + f"# Deletions: {len(deletions)}"), "success") return redirect(url_for('metadata_edit.list_diffs')) |