diff options
Diffstat (limited to 'uploader')
| -rw-r--r-- | uploader/phenotypes/models.py | 29 |
1 files changed, 0 insertions, 29 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index 7c051d7..a22497c 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -328,35 +328,6 @@ def save_new_dataset(cursor: Cursor, return {**params, "Id": cursor.lastrowid} -def phenotypes_data_by_ids( - conn: mdb.Connection, - inbred_pheno_xref: dict[str, int] -) -> tuple[dict, ...]: - """Fetch all phenotype data, filtered by the `inbred_pheno_xref` mapping.""" - _paramstr = ",".join(["(%s, %s, %s)"] * len(inbred_pheno_xref)) - _query = ("SELECT " - "pub.PubMed_ID, pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " - "FROM Publication AS pub " - "RIGHT JOIN PublishXRef AS pxr0 ON pub.Id=pxr0.PublicationId " - "INNER JOIN Phenotype AS pheno ON pxr0.PhenotypeId=pheno.id " - "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " - "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " - "INNER JOIN Strain AS str ON pd.StrainId=str.Id " - "INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId " - "INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId " - "INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId " - f"WHERE (pxr.InbredSetId, pheno.Id, pxr.Id) IN ({_paramstr}) " - "ORDER BY pheno.Id") - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute(_query, tuple(item for row in inbred_pheno_xref - for item in (row["population_id"], - row["phenoid"], - row["xref_id"]))) - debug_query(cursor, logger) - return tuple( - reduce(__organise_by_phenotype__, cursor.fetchall(), {}).values()) - - def __pre_process_phenotype_data__(row): _desc = row.get("description", "") _pre_pub_desc = row.get("pre_publication_description", _desc) |