diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/csvcmp.py | 2 | ||||
| -rw-r--r-- | gn3/db/sample_data.py | 33 |
2 files changed, 17 insertions, 18 deletions
diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py index 82d74d0..43b795d 100644 --- a/gn3/csvcmp.py +++ b/gn3/csvcmp.py @@ -79,7 +79,7 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp") -> dict: f"{file_name1} {file_name2} " '--format json"')) if _r.get("code") == 0: - _r = json.loads(_r.get("output")) + _r = json.loads(_r.get("output", "")) if any(_r.values()): _r["Columns"] = max(base_csv_header, delta_csv_header) else: diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index e3daa21..2018587 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -14,21 +14,20 @@ _MAP = { def __extract_actions(original_data: str, updated_data: str, - csv_header: str) -> dict: + csv_header: str) -> Dict: """Return a dictionary containing elements that need to be deleted, inserted, or updated. """ - original_data = original_data.strip().split(",") - updated_data = updated_data.strip().split(",") - csv_header = csv_header.strip().split(",") - result = { + result: Dict[str, Any] = { "delete": {"data": [], "csv_header": []}, "insert": {"data": [], "csv_header": []}, "update": {"data": [], "csv_header": []}, } strain_name = "" - for _o, _u, _h in zip(original_data, updated_data, csv_header): + for _o, _u, _h in zip(original_data.strip().split(","), + updated_data.strip().split(","), + csv_header.strip().split(",")): if _h == "Strain Name": strain_name = _o if _o == _u: # No change @@ -74,7 +73,7 @@ def get_trait_csv_sample_data(conn: Any, "LEFT JOIN CaseAttribute ca ON ca.Id = cxref.CaseAttributeId " "WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name") case_attr_columns = set() - csv_data = {} + csv_data: Dict = {} with conn.cursor() as cursor: cursor.execute(__query, (trait_name, phenotype_id)) for data in cursor.fetchall(): @@ -167,11 +166,11 @@ def update_sample_data(conn: Any, return 0 strain_id, data_id, inbredset_id = get_sample_data_ids( - conn=conn, publishxref_id=trait_name, + conn=conn, publishxref_id=int(trait_name), phenotype_id=phenotype_id, strain_name=extract_strain_name(csv_header, original_data)) - none_case_attrs = { + none_case_attrs: Dict[str, Callable] = { "Strain Name": lambda x: 0, "Value": lambda x: __update_data(conn, "PublishData", x), "SE": lambda x: __update_data(conn, "PublishSE", x), @@ -191,11 +190,11 @@ def update_sample_data(conn: Any, header = header.strip() value = value.strip() if header in none_case_attrs: - count += none_case_attrs.get(header)(value) + count += none_case_attrs[header](value) else: count += __update_case_attribute( conn=conn, - value=none_case_attrs.get(header)(value), + value=none_case_attrs[header](value), strain_id=strain_id, case_attr=header, inbredset_id=inbredset_id) @@ -252,11 +251,11 @@ def delete_sample_data(conn: Any, return cursor.rowcount strain_id, data_id, inbredset_id = get_sample_data_ids( - conn=conn, publishxref_id=trait_name, + conn=conn, publishxref_id=int(trait_name), phenotype_id=phenotype_id, strain_name=extract_strain_name(csv_header, data)) - none_case_attrs = { + none_case_attrs: Dict[str, Any] = { "Strain Name": lambda: 0, "Value": lambda: __delete_data(conn, "PublishData"), "SE": lambda: __delete_data(conn, "PublishSE"), @@ -268,7 +267,7 @@ def delete_sample_data(conn: Any, for header in csv_header.split(","): header = header.strip() if header in none_case_attrs: - count += none_case_attrs.get(header)() + count += none_case_attrs[header]() else: count += __delete_case_attribute( conn=conn, @@ -326,11 +325,11 @@ def insert_sample_data(conn: Any, return 0 strain_id, data_id, inbredset_id = get_sample_data_ids( - conn=conn, publishxref_id=trait_name, + conn=conn, publishxref_id=int(trait_name), phenotype_id=phenotype_id, strain_name=extract_strain_name(csv_header, data)) - none_case_attrs = { + none_case_attrs: Dict[str, Any] = { "Strain Name": lambda _: 0, "Value": lambda x: __insert_data(conn, "PublishData", x), "SE": lambda x: __insert_data(conn, "PublishSE", x), @@ -353,7 +352,7 @@ def insert_sample_data(conn: Any, header = header.strip() value = value.strip() if header in none_case_attrs: - count += none_case_attrs.get(header)(value) + count += none_case_attrs[header](value) else: count += __insert_case_attribute( conn=conn, |