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authorBonfaceKilz2021-04-13 16:54:55 +0300
committerBonfaceKilz2021-05-08 19:19:47 +0300
commite4487b7dbbb8e2c93417019b33b7f4fbd5de655e (patch)
tree19d0c62c35428fbc3415badc5155254e132c7f7f /gn3/db/traits.py
parentd87f0e63159ffc6e56e0c596eccca4a158522c4d (diff)
downloadgenenetwork3-e4487b7dbbb8e2c93417019b33b7f4fbd5de655e.tar.gz
Add method for inserting publication_data
Diffstat (limited to 'gn3/db/traits.py')
-rw-r--r--gn3/db/traits.py18
1 files changed, 17 insertions, 1 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 8ba8a53..fc1463c 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,8 +1,9 @@
"""This contains all the necessary functions that are required to add traits
to the published database"""
-from typing import Any, Dict, Optional
from dataclasses import dataclass
+from itertools import chain
from typing import Optional
+from typing import Any, Dict, List, Optional
@dataclass(frozen=True)
@@ -76,6 +77,21 @@ def insert_publication(pubmed_id: int, publication: Optional[Dict],
cursor.execute(insert_query, tuple(publication.values()))
+def insert_publication_data(riset_id: int, strains: List, conn: Any):
+ species_id = None
+ with conn.cursor() as cursor:
+ cursor.execute("SELECT SpeciesId from InbredSet where "
+ "Id=%s" % riset_id)
+ species_id, *_ = cursor.fetchone()
+ cursor.execute(
+ "SELECT Id FROM Strain WHERE SpeciesId="
+ "%s AND Name in (%s)"
+ % (riset_id, ", ".join(f"'{strain}'" for strain in strains)))
+ strain_ids = cursor.fetchall()
+ if strain_ids:
+ strain_ids = list(chain(*strain_ids))
+
+
def insert_phenotype(phenotype: Optional[Dict], conn: Any):
insert_query = ("INSERT into Phenotype (%s) Values (%s)" %
(", ".join(phenotype.keys()),