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-rw-r--r--gn3/db/sample_data.py82
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",