diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 73 |
1 files changed, 36 insertions, 37 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index cf684bba..b93e9ec4 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -29,6 +29,7 @@ from gn3.authentication import DataRole from gn3.authentication import get_highest_user_access_role from gn3.authentication import get_user_membership from gn3.commands import run_cmd +from gn3.csvcmp import create_dirs_if_not_exists from gn3.db import diff_from_dict from gn3.db import fetchall from gn3.db import fetchone @@ -212,43 +213,41 @@ def display_probeset_metadata(name: str): @edit_access_required @login_required def update_phenotype(dataset_id: str, name: str): - with database_connection() as conn: - data_ = request.form.to_dict() - TMPDIR = current_app.config.get("TMPDIR") - author = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8") - or g.user_session.record.get("user_id") or "") - phenotype_id = str(data_.get('phenotype-id')) - if not (file_ := request.files.get("file")): - flash("No sample-data has been uploaded", "warning") - else: - if not os.path.exists(SAMPLE_DATADIR := os.path.join(TMPDIR, "sample-data")): - os.makedirs(SAMPLE_DATADIR) - if not os.path.exists(os.path.join(SAMPLE_DATADIR, - "diffs")): - os.makedirs(os.path.join(SAMPLE_DATADIR, - "diffs")) - if not os.path.exists(os.path.join(SAMPLE_DATADIR, - "updated")): - os.makedirs(os.path.join(SAMPLE_DATADIR, - "updated")) - current_time = str(datetime.datetime.now().isoformat()) - _file_name = (f"{author}.{request.args.get('resource-id')}." - f"{current_time}") - new_file_name = (os.path.join(TMPDIR, - f"sample-data/updated/{_file_name}.csv")) - uploaded_file_name = (os.path.join( - TMPDIR, "sample-data/updated/", - f"{_file_name}.csv.uploaded")) - file_.save(new_file_name) - with open(uploaded_file_name, "w") as f_: - 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")) - json_data = json.loads(r.get("output")) + 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() + TMPDIR = current_app.config.get("TMPDIR") + author = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8") + or g.user_session.record.get("user_id") or "") + phenotype_id = str(data_.get('phenotype-id')) + if not (file_ := request.files.get("file")): + flash("No sample-data has been uploaded", "warning") + else: + create_dirs_if_not_exists([ + SAMPLE_DATADIR := os.path.join(TMPDIR, "sample-data"), + DIFF_DATADIR := os.path.join(SAMPLE_DATADIR, "diffs"), + UPLOAD_DATADIR := os.path.join(SAMPLE_DATADIR, "updated") + ]) + current_time = str(datetime.datetime.now().isoformat()) + _file_name = (f"{author}.{request.args.get('resource-id')}." + f"{current_time}") + new_file_name = (os.path.join(TMPDIR, + f"sample-data/updated/{_file_name}.csv")) + uploaded_file_name = (os.path.join( + TMPDIR, "sample-data/updated/", + f"{_file_name}.csv.uploaded")) + file_.save(new_file_name) + with open(uploaded_file_name, "w") as f_: + 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")) + json_data = json.loads(r.get("output")) # Only consider values where |ε| < 0.001; otherwise, use the # old value in "Original". |