diff options
| -rw-r--r-- | gn3/db/sample_data.py | 284 | ||||
| -rw-r--r-- | gn3/db/traits.py | 283 |
2 files changed, 284 insertions, 283 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py new file mode 100644 index 0000000..c620005 --- /dev/null +++ b/gn3/db/sample_data.py @@ -0,0 +1,284 @@ +from typing import Any, Tuple, Union + +import MySQLdb + +def get_trait_csv_sample_data(conn: Any, + trait_name: int, phenotype_id: int) -> str: + """Fetch a trait and return it as a csv string""" + __query = ("SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',', " + "ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) as 'Data' " + ",ifnull(ca.Name, 'x') as 'CaseAttr', " + "ifnull(cxref.value, 'x') as 'Value' " + "FROM PublishFreeze pf " + "JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId " + "JOIN PublishData pd ON pd.Id = px.DataId " + "JOIN Strain st ON pd.StrainId = st.Id " + "LEFT JOIN PublishSE ps ON ps.DataId = pd.Id " + "AND ps.StrainId = pd.StrainId " + "LEFT JOIN NStrain ns ON ns.DataId = pd.Id " + "AND ns.StrainId = pd.StrainId " + "LEFT JOIN CaseAttributeXRefNew cxref ON " + "(cxref.InbredSetId = px.InbredSetId AND " + "cxref.StrainId = st.Id) " + "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 = {} + with conn.cursor() as cursor: + cursor.execute(__query, (trait_name, phenotype_id)) + for data in cursor.fetchall(): + if data[1] == "x": + csv_data[data[0]] = None + else: + sample, case_attr, value = data[0], data[1], data[2] + if not csv_data.get(sample): + csv_data[sample] = {} + csv_data[sample][case_attr] = None if value == "x" else value + case_attr_columns.add(case_attr) + 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 + return "No Sample Data Found" + + +def update_sample_data(conn: Any, # pylint: disable=[R0913] + trait_name: str, + strain_name: str, + phenotype_id: int, + value: Union[int, float, str], + error: Union[int, float, str], + count: Union[int, str]): + """Given the right parameters, update sample-data from the relevant + table.""" + strain_id, data_id = "", "" + + with conn.cursor() as cursor: + cursor.execute( + ("SELECT Strain.Id, PublishData.Id FROM " + "(PublishData, Strain, PublishXRef, PublishFreeze) " + "LEFT JOIN PublishSE ON " + "(PublishSE.DataId = PublishData.Id AND " + "PublishSE.StrainId = PublishData.StrainId) " + "LEFT JOIN NStrain ON " + "(NStrain.DataId = PublishData.Id AND " + "NStrain.StrainId = PublishData.StrainId) " + "WHERE PublishXRef.InbredSetId = " + "PublishFreeze.InbredSetId AND " + "PublishData.Id = PublishXRef.DataId AND " + "PublishXRef.Id = %s AND " + "PublishXRef.PhenotypeId = %s " + "AND PublishData.StrainId = Strain.Id " + "AND Strain.Name = \"%s\"") % (trait_name, + phenotype_id, + str(strain_name))) + strain_id, data_id = cursor.fetchone() + updated_published_data: int = 0 + updated_se_data: int = 0 + updated_n_strains: int = 0 + + with conn.cursor() as cursor: + # Update the PublishData table + if value == "x": + cursor.execute(("DELETE FROM PublishData " + "WHERE StrainId = %s AND Id = %s") + % (strain_id, data_id)) + updated_published_data = cursor.rowcount + else: + cursor.execute(("UPDATE PublishData SET value = %s " + "WHERE StrainId = %s AND Id = %s"), + (value, strain_id, data_id)) + updated_published_data = cursor.rowcount + + if not updated_published_data: + cursor.execute( + "SELECT * FROM " + "PublishData WHERE StrainId = " + "%s AND Id = %s" % (strain_id, data_id)) + if not cursor.fetchone(): + cursor.execute(("INSERT INTO PublishData (Id, StrainId, " + " value) VALUES (%s, %s, %s)") % + (data_id, strain_id, value)) + updated_published_data = cursor.rowcount + + # Update the PublishSE table + if error == "x": + cursor.execute(("DELETE FROM PublishSE " + "WHERE StrainId = %s AND DataId = %s") % + (strain_id, data_id)) + updated_se_data = cursor.rowcount + else: + cursor.execute(("UPDATE PublishSE SET error = %s " + "WHERE StrainId = %s AND DataId = %s"), + (None if error == "x" else error, + strain_id, data_id)) + updated_se_data = cursor.rowcount + if not updated_se_data: + cursor.execute( + "SELECT * FROM " + "PublishSE WHERE StrainId = " + "%s AND DataId = %s" % (strain_id, data_id)) + if not cursor.fetchone(): + cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, " + " error) VALUES (%s, %s, %s)") % + (strain_id, data_id, + None if error == "x" else error)) + updated_se_data = cursor.rowcount + + # Update the NStrain table + if count == "x": + cursor.execute(("DELETE FROM NStrain " + "WHERE StrainId = %s AND DataId = %s" % + (strain_id, data_id))) + updated_n_strains = cursor.rowcount + else: + cursor.execute(("UPDATE NStrain SET count = %s " + "WHERE StrainId = %s AND DataId = %s"), + (count, strain_id, data_id)) + updated_n_strains = cursor.rowcount + if not updated_n_strains: + cursor.execute( + "SELECT * FROM " + "NStrain WHERE StrainId = " + "%s AND DataId = %s" % (strain_id, data_id)) + if not cursor.fetchone(): + cursor.execute(("INSERT INTO NStrain " + "(StrainId, DataId, count) " + "VALUES (%s, %s, %s)") % + (strain_id, data_id, count)) + updated_n_strains = cursor.rowcount + return (updated_published_data, + updated_se_data, updated_n_strains) + + +def delete_sample_data(conn: Any, + trait_name: str, + strain_name: str, + phenotype_id: int): + """Given the right parameters, delete sample-data from the relevant + table.""" + strain_id, data_id = "", "" + + deleted_published_data: int = 0 + deleted_se_data: int = 0 + deleted_n_strains: int = 0 + + with conn.cursor() as cursor: + # Delete the PublishData table + try: + cursor.execute( + ("SELECT Strain.Id, PublishData.Id FROM " + "(PublishData, Strain, PublishXRef, PublishFreeze) " + "LEFT JOIN PublishSE ON " + "(PublishSE.DataId = PublishData.Id AND " + "PublishSE.StrainId = PublishData.StrainId) " + "LEFT JOIN NStrain ON " + "(NStrain.DataId = PublishData.Id AND " + "NStrain.StrainId = PublishData.StrainId) " + "WHERE PublishXRef.InbredSetId = " + "PublishFreeze.InbredSetId AND " + "PublishData.Id = PublishXRef.DataId AND " + "PublishXRef.Id = %s AND " + "PublishXRef.PhenotypeId = %s " + "AND PublishData.StrainId = Strain.Id " + "AND Strain.Name = \"%s\"") % (trait_name, + phenotype_id, + str(strain_name))) + + # Check if it exists if the data was already deleted: + if _result := cursor.fetchone(): + strain_id, data_id = _result + + # Only run if the strain_id and data_id exist + if strain_id and data_id: + cursor.execute(("DELETE FROM PublishData " + "WHERE StrainId = %s AND Id = %s") + % (strain_id, data_id)) + deleted_published_data = cursor.rowcount + + # Delete the PublishSE table + cursor.execute(("DELETE FROM PublishSE " + "WHERE StrainId = %s AND DataId = %s") % + (strain_id, data_id)) + deleted_se_data = cursor.rowcount + + # Delete the NStrain table + cursor.execute(("DELETE FROM NStrain " + "WHERE StrainId = %s AND DataId = %s" % + (strain_id, data_id))) + deleted_n_strains = cursor.rowcount + except Exception as e: #pylint: disable=[C0103, W0612] + conn.rollback() + raise MySQLdb.Error + conn.commit() + cursor.close() + cursor.close() + + return (deleted_published_data, + deleted_se_data, deleted_n_strains) + + +def insert_sample_data(conn: Any, # pylint: disable=[R0913] + trait_name: str, + strain_name: str, + phenotype_id: int, + value: Union[int, float, str], + error: Union[int, float, str], + count: Union[int, str]): + """Given the right parameters, insert sample-data to the relevant table. + + """ + + inserted_published_data, inserted_se_data, inserted_n_strains = 0, 0, 0 + with conn.cursor() as cursor: + try: + cursor.execute("SELECT DataId FROM PublishXRef WHERE Id = %s AND " + "PhenotypeId = %s", (trait_name, phenotype_id)) + data_id = cursor.fetchone() + + cursor.execute("SELECT Id FROM Strain WHERE Name = %s", + (strain_name,)) + strain_id = cursor.fetchone() + + # Return early if an insert already exists! + cursor.execute("SELECT Id FROM PublishData where Id = %s " + "AND StrainId = %s", + (data_id, strain_id)) + if cursor.fetchone(): # This strain already exists + return (0, 0, 0) + + # Insert the PublishData table + cursor.execute(("INSERT INTO PublishData (Id, StrainId, value)" + "VALUES (%s, %s, %s)"), + (data_id, strain_id, value)) + inserted_published_data = cursor.rowcount + + # Insert into the PublishSE table if error is specified + if error and error != "x": + cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, " + " error) VALUES (%s, %s, %s)") % + (strain_id, data_id, error)) + inserted_se_data = cursor.rowcount + + # Insert into the NStrain table + if count and count != "x": + cursor.execute(("INSERT INTO NStrain " + "(StrainId, DataId, count) " + "VALUES (%s, %s, %s)") % + (strain_id, data_id, count)) + inserted_n_strains = cursor.rowcount + except Exception: # pylint: disable=[C0103, W0612] + conn.rollback() + raise MySQLdb.Error + return (inserted_published_data, + inserted_se_data, inserted_n_strains) diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 04b2a70..2e634fe 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -79,289 +79,6 @@ def export_trait_data( return reduce(__exporter, samplelist, tuple()) -def get_trait_csv_sample_data(conn: Any, - trait_name: int, phenotype_id: int) -> str: - """Fetch a trait and return it as a csv string""" - __query = ("SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',', " - "ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) as 'Data' " - ",ifnull(ca.Name, 'x') as 'CaseAttr', " - "ifnull(cxref.value, 'x') as 'Value' " - "FROM PublishFreeze pf " - "JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId " - "JOIN PublishData pd ON pd.Id = px.DataId " - "JOIN Strain st ON pd.StrainId = st.Id " - "LEFT JOIN PublishSE ps ON ps.DataId = pd.Id " - "AND ps.StrainId = pd.StrainId " - "LEFT JOIN NStrain ns ON ns.DataId = pd.Id " - "AND ns.StrainId = pd.StrainId " - "LEFT JOIN CaseAttributeXRefNew cxref ON " - "(cxref.InbredSetId = px.InbredSetId AND " - "cxref.StrainId = st.Id) " - "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 = {} - with conn.cursor() as cursor: - cursor.execute(__query, (trait_name, phenotype_id)) - for data in cursor.fetchall(): - if data[1] == "x": - csv_data[data[0]] = None - else: - sample, case_attr, value = data[0], data[1], data[2] - if not csv_data.get(sample): - csv_data[sample] = {} - csv_data[sample][case_attr] = None if value == "x" else value - case_attr_columns.add(case_attr) - 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 - return "No Sample Data Found" - - -def update_sample_data(conn: Any, # pylint: disable=[R0913] - trait_name: str, - strain_name: str, - phenotype_id: int, - value: Union[int, float, str], - error: Union[int, float, str], - count: Union[int, str]): - """Given the right parameters, update sample-data from the relevant - table.""" - strain_id, data_id = "", "" - - with conn.cursor() as cursor: - cursor.execute( - ("SELECT Strain.Id, PublishData.Id FROM " - "(PublishData, Strain, PublishXRef, PublishFreeze) " - "LEFT JOIN PublishSE ON " - "(PublishSE.DataId = PublishData.Id AND " - "PublishSE.StrainId = PublishData.StrainId) " - "LEFT JOIN NStrain ON " - "(NStrain.DataId = PublishData.Id AND " - "NStrain.StrainId = PublishData.StrainId) " - "WHERE PublishXRef.InbredSetId = " - "PublishFreeze.InbredSetId AND " - "PublishData.Id = PublishXRef.DataId AND " - "PublishXRef.Id = %s AND " - "PublishXRef.PhenotypeId = %s " - "AND PublishData.StrainId = Strain.Id " - "AND Strain.Name = %s"), - (trait_name, phenotype_id, str(strain_name))) - strain_id, data_id = cursor.fetchone() - updated_published_data: int = 0 - updated_se_data: int = 0 - updated_n_strains: int = 0 - - with conn.cursor() as cursor: - # Update the PublishData table - if value == "x": - cursor.execute(("DELETE FROM PublishData " - "WHERE StrainId = %s AND Id = %s"), - (strain_id, data_id)) - updated_published_data = cursor.rowcount - else: - cursor.execute(("UPDATE PublishData SET value = %s " - "WHERE StrainId = %s AND Id = %s"), - (value, strain_id, data_id)) - updated_published_data = cursor.rowcount - - if not updated_published_data: - cursor.execute( - ("SELECT * FROM " - "PublishData WHERE StrainId = " - "%s AND Id = %s"), - (strain_id, data_id)) - if not cursor.fetchone(): - cursor.execute(("INSERT INTO PublishData (Id, StrainId, " - " value) VALUES (%s, %s, %s)"), - (data_id, strain_id, value)) - updated_published_data = cursor.rowcount - - # Update the PublishSE table - if error == "x": - cursor.execute(("DELETE FROM PublishSE " - "WHERE StrainId = %s AND DataId = %s"), - (strain_id, data_id)) - updated_se_data = cursor.rowcount - else: - cursor.execute(("UPDATE PublishSE SET error = %s " - "WHERE StrainId = %s AND DataId = %s"), - (None if error == "x" else error, - strain_id, data_id)) - updated_se_data = cursor.rowcount - if not updated_se_data: - cursor.execute( - ("SELECT * FROM " - "PublishSE WHERE StrainId = " - "%s AND DataId = %s"), - (strain_id, data_id)) - if not cursor.fetchone(): - cursor.execute( - ("INSERT INTO PublishSE (StrainId, DataId, " - " error) VALUES (%s, %s, %s)"), - (strain_id, data_id, None if error == "x" else error)) - updated_se_data = cursor.rowcount - - # Update the NStrain table - if count == "x": - cursor.execute(("DELETE FROM NStrain " - "WHERE StrainId = %s AND DataId = %s"), - (strain_id, data_id)) - updated_n_strains = cursor.rowcount - else: - cursor.execute(("UPDATE NStrain SET count = %s " - "WHERE StrainId = %s AND DataId = %s"), - (count, strain_id, data_id)) - updated_n_strains = cursor.rowcount - if not updated_n_strains: - cursor.execute( - ("SELECT * FROM " - "NStrain WHERE StrainId = " - "%s AND DataId = %s"), - (strain_id, data_id)) - if not cursor.fetchone(): - cursor.execute(("INSERT INTO NStrain " - "(StrainId, DataId, count) " - "VALUES (%s, %s, %s)"), - (strain_id, data_id, count)) - updated_n_strains = cursor.rowcount - return (updated_published_data, - updated_se_data, updated_n_strains) - - -def delete_sample_data(conn: Any, - trait_name: str, - strain_name: str, - phenotype_id: int): - """Given the right parameters, delete sample-data from the relevant - table.""" - strain_id, data_id = "", "" - - deleted_published_data: int = 0 - deleted_se_data: int = 0 - deleted_n_strains: int = 0 - - with conn.cursor() as cursor: - # Delete the PublishData table - try: - cursor.execute( - ("SELECT Strain.Id, PublishData.Id FROM " - "(PublishData, Strain, PublishXRef, PublishFreeze) " - "LEFT JOIN PublishSE ON " - "(PublishSE.DataId = PublishData.Id AND " - "PublishSE.StrainId = PublishData.StrainId) " - "LEFT JOIN NStrain ON " - "(NStrain.DataId = PublishData.Id AND " - "NStrain.StrainId = PublishData.StrainId) " - "WHERE PublishXRef.InbredSetId = " - "PublishFreeze.InbredSetId AND " - "PublishData.Id = PublishXRef.DataId AND " - "PublishXRef.Id = %s AND " - "PublishXRef.PhenotypeId = %s " - "AND PublishData.StrainId = Strain.Id " - "AND Strain.Name = %s"), - (trait_name, phenotype_id, str(strain_name))) - - # Check if it exists if the data was already deleted: - if _result := cursor.fetchone(): - strain_id, data_id = _result - - # Only run if the strain_id and data_id exist - if strain_id and data_id: - cursor.execute(("DELETE FROM PublishData " - "WHERE StrainId = %s AND Id = %s"), - (strain_id, data_id)) - deleted_published_data = cursor.rowcount - - # Delete the PublishSE table - cursor.execute(("DELETE FROM PublishSE " - "WHERE StrainId = %s AND DataId = %s"), - (strain_id, data_id)) - deleted_se_data = cursor.rowcount - - # Delete the NStrain table - cursor.execute(("DELETE FROM NStrain " - "WHERE StrainId = %s AND DataId = %s"), - (strain_id, data_id)) - deleted_n_strains = cursor.rowcount - except Exception as e: #pylint: disable=[C0103, W0612] - conn.rollback() - raise MySQLdb.Error - conn.commit() - cursor.close() - cursor.close() - - return (deleted_published_data, - deleted_se_data, deleted_n_strains) - - -def insert_sample_data(conn: Any, # pylint: disable=[R0913] - trait_name: str, - strain_name: str, - phenotype_id: int, - value: Union[int, float, str], - error: Union[int, float, str], - count: Union[int, str]): - """Given the right parameters, insert sample-data to the relevant table. - - """ - - inserted_published_data, inserted_se_data, inserted_n_strains = 0, 0, 0 - with conn.cursor() as cursor: - try: - cursor.execute("SELECT DataId FROM PublishXRef WHERE Id = %s AND " - "PhenotypeId = %s", (trait_name, phenotype_id)) - data_id = cursor.fetchone() - - cursor.execute("SELECT Id FROM Strain WHERE Name = %s", - (strain_name,)) - strain_id = cursor.fetchone() - - # Return early if an insert already exists! - cursor.execute("SELECT Id FROM PublishData where Id = %s " - "AND StrainId = %s", - (data_id, strain_id)) - if cursor.fetchone(): # This strain already exists - return (0, 0, 0) - - # Insert the PublishData table - cursor.execute(("INSERT INTO PublishData (Id, StrainId, value)" - "VALUES (%s, %s, %s)"), - (data_id, strain_id, value)) - inserted_published_data = cursor.rowcount - - # Insert into the PublishSE table if error is specified - if error and error != "x": - cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, " - " error) VALUES (%s, %s, %s)"), - (strain_id, data_id, error)) - inserted_se_data = cursor.rowcount - - # Insert into the NStrain table - if count and count != "x": - cursor.execute(("INSERT INTO NStrain " - "(StrainId, DataId, count) " - "VALUES (%s, %s, %s)"), - (strain_id, data_id, count)) - inserted_n_strains = cursor.rowcount - except Exception: # pylint: disable=[C0103, W0612] - conn.rollback() - raise MySQLdb.Error - return (inserted_published_data, - inserted_se_data, inserted_n_strains) - - def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any): """Retrieve trait information for type `Publish` traits. |