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authorMuriithi Frederick Muriuki2021-07-28 10:20:18 +0300
committerBonfaceKilz2021-07-29 15:24:51 +0300
commit8d7f8eec5b5d84937e453c9b02de0bd1b1727265 (patch)
tree96ad30948ec15bacfdfd358d88cf054263260853 /gn3/db/traits.py
parent02791f15d6b4940ae8be07fe9d4f8487d8291c78 (diff)
downloadgenenetwork3-8d7f8eec5b5d84937e453c9b02de0bd1b1727265.tar.gz
Make name retrieval more general
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/db/traits.py: make function more general * tests/unit/db/test_traits.py: parametrize the tests Make the name retrieval more general for the different types of traits by changing the column specification and table as appropriate.
Diffstat (limited to 'gn3/db/traits.py')
-rw-r--r--gn3/db/traits.py26
1 files changed, 15 insertions, 11 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 37b111e..fddb8be 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -91,20 +91,24 @@ def insert_publication(pubmed_id: int, publication: Optional[Dict],
with conn.cursor() as cursor:
cursor.execute(insert_query, tuple(publication.values()))
-def retrieve_probeset_trait_name(threshold, name, connection):
+def retrieve_type_trait_name(trait_type, threshold, name, connection):
"""
- Retrieve the name for a Probeset trait
+ Retrieve the name of a trait given the trait's name
- This is extracted from the `webqtlDataset.retrieveName` function,
- specifically the section dealing with 'ProbeSet' type traits
- https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154"""
+ This is extracted from the `webqtlDataset.retrieveName` function as is
+ implemented at
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169
+ """
+ columns = "Id, Name, FullName, ShortName{}".format(
+ ", DataScale" if trait_type == "ProbeSet" else "")
query = (
- 'SELECT Id, Name, FullName, ShortName, DataScale '
- 'FROM ProbeSetFreeze '
- 'WHERE '
- 'public > %(threshold)s '
- 'AND '
- '(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)')
+ "SELECT {columns} "
+ "FROM {trait_type}Freeze "
+ "WHERE "
+ "public > %(threshold)s "
+ "AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format(
+ columns=columns, trait_type=trait_type)
with connection.cursor() as cursor:
cursor.execute(query, {"threshold": threshold, "name": name})
return cursor.fetchone()