diff options
| -rw-r--r-- | gn3/db/phenotypes.py | 22 |
1 files changed, 21 insertions, 1 deletions
diff --git a/gn3/db/phenotypes.py b/gn3/db/phenotypes.py index 0ed22d4..744df34 100644 --- a/gn3/db/phenotypes.py +++ b/gn3/db/phenotypes.py @@ -1,9 +1,12 @@ # pylint: disable=[R0902, R0903] """This contains all the necessary functions that access the phenotypes from the db""" +from typing import Optional from dataclasses import dataclass -from typing import Optional +from MySQLdb.cursors import DictCursor + +from wqflask.database import Connection as DBConnection @dataclass(frozen=True) @@ -158,3 +161,20 @@ probeset_mapping = { "probe_set_note_by_rw": "Probe_set_Note_by_RW", "flag": "flag" } + +def fetch_trait(conn: DBConnection, dataset_id: int, trait_name: str) -> dict: + """Fetch phenotype 'traits' by `dataset_id` and `trait_name`.""" + query = ( + "SELECT " + "pxr.Id AS _id, pxr.Id as trait_name, pxr.PhenotypeId AS phenotype_id, " + "pxr.PublicationId AS publication_id, pxr.DataId AS data_id, " + "pxr.mean, pxr.locus, pxr.LRS as lrs, pxr.additive, " + "pxr.Sequence as sequence, pxr.comments " + "FROM PublishFreeze AS pf INNER JOIN InbredSet AS iset " + "ON pf.InbredSetId=iset.Id " + "INNER JOIN PublishXRef AS pxr ON iset.Id=pxr.InbredSetId " + "WHERE pf.Id=%(dataset_id)s AND pxr.Id=%(trait_name)s") + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + query, {"dataset_id": dataset_id, "trait_name": trait_name}) + return cursor.fetchone() |