diff options
Diffstat (limited to 'gn3/csvcmp.py')
| -rw-r--r-- | gn3/csvcmp.py | 17 |
1 files changed, 8 insertions, 9 deletions
diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py index 8db89ca..4e8cc0f 100644 --- a/gn3/csvcmp.py +++ b/gn3/csvcmp.py @@ -52,8 +52,7 @@ def clean_csv_text(csv_text: str) -> str: """Remove extra white space elements in all elements of the CSV file""" _csv_text = [] for line in csv_text.strip().split("\n"): - _csv_text.append( - ",".join([el.strip() for el in line.split(",")])) + _csv_text.append(",".join([el.strip() for el in line.split(",")])) return "\n".join(_csv_text) @@ -73,8 +72,9 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp") -> dict: if base_csv_header != delta_csv_header: if longest_header != base_csv_header: - base_csv = base_csv.replace("Strain Name,Value,SE,Count", - longest_header, 1) + base_csv = base_csv.replace( + "Strain Name,Value,SE,Count", longest_header, 1 + ) else: delta_csv = delta_csv.replace( "Strain Name,Value,SE,Count", longest_header, 1 @@ -89,9 +89,9 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp") -> dict: _f.write(fill_csv(delta_csv, width=_l)) # Now we can run the diff! - _r = run_cmd(cmd=('"csvdiff ' - f"{file_name1} {file_name2} " - '--format json"')) + _r = run_cmd( + cmd=('"csvdiff ' f"{file_name1} {file_name2} " '--format json"') + ) if _r.get("code") == 0: _r = json.loads(_r.get("output", "")) if any(_r.values()): @@ -127,8 +127,7 @@ def get_allowable_sampledata_headers(conn: Any) -> List: attributes = ["Strain Name", "Value", "SE", "Count"] with conn.cursor() as cursor: cursor.execute("SELECT Name from CaseAttribute") - attributes += [attributes[0] for attributes in - cursor.fetchall()] + attributes += [attributes[0] for attributes in cursor.fetchall()] return attributes |