diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/sample_data.py | 93 |
1 files changed, 49 insertions, 44 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index b2d6aed..e3daa21 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -1,7 +1,8 @@ -from gn3.csvcmp import extract_strain_name -from typing import Any, Tuple +"""Module containing functions that work with sample data""" +from typing import Any, Tuple, Dict, Callable import MySQLdb +from gn3.csvcmp import extract_strain_name _MAP = { @@ -14,6 +15,10 @@ _MAP = { def __extract_actions(original_data: str, updated_data: str, 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(",") @@ -28,7 +33,7 @@ def __extract_actions(original_data: str, strain_name = _o if _o == _u: # No change continue - elif _o and _u == "x": # Deletion + if _o and _u == "x": # Deletion result["delete"]["data"].append(_o) result["delete"]["csv_header"].append(_h) elif _o == "x" and _u: # Insert @@ -84,23 +89,23 @@ def get_trait_csv_sample_data(conn: Any, if not case_attr_columns: return ("Strain Name,Value,SE,Count\n" + "\n".join(csv_data.keys())) - else: - columns = sorted(case_attr_columns) - csv = ("Strain Name,Value,SE,Count," + - ",".join(columns) + "\n") - for key, value in csv_data.items(): - if not value: - csv += (key + (len(case_attr_columns) * ",x") + "\n") - else: - vals = [str(value.get(column, "x")) for column in columns] - csv += (key + "," + ",".join(vals) + "\n") - return csv + columns = sorted(case_attr_columns) + csv = ("Strain Name,Value,SE,Count," + + ",".join(columns) + "\n") + for key, value in csv_data.items(): + if not value: + csv += (key + (len(case_attr_columns) * ",x") + "\n") + else: + vals = [str(value.get(column, "x")) for column in columns] + csv += (key + "," + ",".join(vals) + "\n") + return csv return "No Sample Data Found" def get_sample_data_ids(conn: Any, publishxref_id: int, phenotype_id: int, strain_name: str) -> Tuple: + """Get the strain_id, publishdata_id and inbredset_id for a given strain""" strain_id, publishdata_id, inbredset_id = None, None, None with conn.cursor() as cursor: cursor.execute("SELECT st.id, pd.Id, pf.InbredSetId " @@ -125,7 +130,8 @@ def get_sample_data_ids(conn: Any, publishxref_id: int, return (strain_id, publishdata_id, inbredset_id) -def update_sample_data(conn: Any, # pylint: disable=[R0913] +# pylint: disable=[R0913, R0914] +def update_sample_data(conn: Any, trait_name: str, original_data: str, updated_data: str, @@ -136,12 +142,14 @@ def update_sample_data(conn: Any, # pylint: disable=[R0913] def __update_data(conn, table, value): if value and value != "x": with conn.cursor() as cursor: - sub_query = (" = %s AND ".join(_MAP.get(table)[:2]) + " = %s") + sub_query = (" = %s AND ".join(_MAP.get(table)[:2]) + + " = %s") _val = _MAP.get(table)[-1] cursor.execute((f"UPDATE {table} SET {_val} = %s " f"WHERE {sub_query}"), (value, strain_id, data_id)) return cursor.rowcount + return 0 def __update_case_attribute(conn, value, strain_id, case_attr, inbredset_id): @@ -177,6 +185,7 @@ def update_sample_data(conn: Any, # pylint: disable=[R0913] if __actions.get("update"): _csv_header = __actions["update"]["csv_header"] _data = __actions["update"]["data"] + # pylint: disable=[E1101] for header, value in zip(_csv_header.split(","), _data.split(",")): header = header.strip() @@ -208,9 +217,9 @@ def update_sample_data(conn: Any, # pylint: disable=[R0913] phenotype_id=phenotype_id) if _rowcount: count += 1 - except Exception as e: # pylint: disable=[C0103, W0612] + except Exception as _e: conn.rollback() - raise MySQLdb.Error + raise MySQLdb.Error(_e) from _e conn.commit() return count @@ -223,28 +232,24 @@ def delete_sample_data(conn: Any, """Given the right parameters, delete sample-data from the relevant tables.""" def __delete_data(conn, table): - if value and value != "x": - sub_query = (" = %s AND ".join(_MAP.get(table)[:2]) + " = %s") - with conn.cursor() as cursor: - cursor.execute((f"DELETE FROM {table} " - f"WHERE {sub_query}"), - (strain_id, data_id)) - return cursor.rowcount - return 0 + sub_query = (" = %s AND ".join(_MAP.get(table)[:2]) + " = %s") + with conn.cursor() as cursor: + cursor.execute((f"DELETE FROM {table} " + f"WHERE {sub_query}"), + (strain_id, data_id)) + return cursor.rowcount def __delete_case_attribute(conn, strain_id, case_attr, inbredset_id): - if value != "x": - with conn.cursor() as cursor: - cursor.execute( - "DELETE FROM CaseAttributeXRefNew " - "WHERE StrainId = %s AND CaseAttributeId = " - "(SELECT CaseAttributeId FROM " - "CaseAttribute WHERE Name = %s) " - "AND InbredSetId = %s", - (strain_id, case_attr, inbredset_id)) - return cursor.rowcount - return 0 + with conn.cursor() as cursor: + cursor.execute( + "DELETE FROM CaseAttributeXRefNew " + "WHERE StrainId = %s AND CaseAttributeId = " + "(SELECT CaseAttributeId FROM " + "CaseAttribute WHERE Name = %s) " + "AND InbredSetId = %s", + (strain_id, case_attr, inbredset_id)) + return cursor.rowcount strain_id, data_id, inbredset_id = get_sample_data_ids( conn=conn, publishxref_id=trait_name, @@ -260,9 +265,8 @@ def delete_sample_data(conn: Any, count = 0 try: - for header, value in zip(csv_header.split(","), data.split(",")): + for header in csv_header.split(","): header = header.strip() - value = value.strip() if header in none_case_attrs: count += none_case_attrs.get(header)() else: @@ -271,14 +275,15 @@ def delete_sample_data(conn: Any, strain_id=strain_id, case_attr=header, inbredset_id=inbredset_id) - except Exception as e: # pylint: disable=[C0103, W0612] + except Exception as _e: conn.rollback() - raise MySQLdb.Error + raise MySQLdb.Error(_e) from _e conn.commit() return count -def insert_sample_data(conn: Any, # pylint: disable=[R0913] +# pylint: disable=[R0913, R0914] +def insert_sample_data(conn: Any, trait_name: str, data: str, csv_header: str, @@ -355,6 +360,6 @@ def insert_sample_data(conn: Any, # pylint: disable=[R0913] case_attr=header, value=value) return count - except Exception as e: # pylint: disable=[C0103, W0612] + except Exception as _e: conn.rollback() - raise MySQLdb.Error + raise MySQLdb.Error(_e) from _e |