diff options
| -rw-r--r-- | gn3/db/traits.py | 18 |
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()), |