diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/sample_data.py | 82 |
1 files changed, 29 insertions, 53 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index c620005..49a04d3 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -52,6 +52,23 @@ def get_trait_csv_sample_data(conn: Any, return "No Sample Data Found" +def get_sample_data_ids(conn: Any, publishxref_id: int, + phenotype_id: int, + strain_name: str) -> Tuple: + strain_id, publishdata_id = None, None + with conn.cursor() as cursor: + cursor.execute("SELECT st.id, pd.Id FROM PublishData pd " + "JOIN Strain st ON pd.StrainId = st.Id " + "JOIN PublishXRef px ON px.DataId = pd.Id " + "JOIN PublishFreeze pf ON pf.InbredSetId " + "= px.InbredSetId WHERE px.Id = %s " + "AND px.PhenotypeId = %s AND st.Name = %s", + (publishxref_id, phenotype_id, strain_name)) + if _result := cursor.fetchone(): + strain_id, publishdata_id = _result + return (strain_id, publishdata_id) + + def update_sample_data(conn: Any, # pylint: disable=[R0913] trait_name: str, strain_name: str, @@ -61,28 +78,10 @@ def update_sample_data(conn: Any, # pylint: disable=[R0913] count: Union[int, str]): """Given the right parameters, update sample-data from the relevant table.""" - strain_id, data_id = "", "" + strain_id, data_id = get_sample_data_ids( + conn=conn, publishxref_id=trait_name, + phenotype_id=phenotype_id, strain_name=strain_name) - 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 @@ -167,7 +166,10 @@ def delete_sample_data(conn: Any, phenotype_id: int): """Given the right parameters, delete sample-data from the relevant table.""" - strain_id, data_id = "", "" + strain_id, data_id = get_sample_data_ids( + conn=conn, publishxref_id=trait_name, + phenotype_id=phenotype_id, + strain_name=strain_name) deleted_published_data: int = 0 deleted_se_data: int = 0 @@ -176,29 +178,6 @@ def delete_sample_data(conn: Any, 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 " @@ -240,16 +219,13 @@ def insert_sample_data(conn: Any, # pylint: disable=[R0913] """ inserted_published_data, inserted_se_data, inserted_n_strains = 0, 0, 0 + strain_id, data_id = get_sample_data_ids( + conn=conn, publishxref_id=trait_name, + phenotype_id=phenotype_id, + strain_name=strain_name) + 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", |