diff options
Diffstat (limited to 'uploader/phenotypes/models.py')
| -rw-r--r-- | uploader/phenotypes/models.py | 112 |
1 files changed, 82 insertions, 30 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index 73b1cce..4a229e6 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -54,6 +54,20 @@ def phenotypes_count(conn: mdb.Connection, return int(cursor.fetchone()["total_phenos"]) +def phenotype_publication_data(conn, phenotype_id) -> Optional[dict]: + """Retrieve the publication data for a phenotype if it exists.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT DISTINCT pxr.PhenotypeId, pub.* FROM PublishXRef AS pxr " + "INNER JOIN Publication as pub ON pxr.PublicationId=pub.Id " + "WHERE pxr.PhenotypeId=%s", + (phenotype_id,)) + res = cursor.fetchone() + if res is None: + return res + return dict(res) + + def dataset_phenotypes(conn: mdb.Connection, population_id: int, dataset_id: int, @@ -61,7 +75,7 @@ def dataset_phenotypes(conn: mdb.Connection, limit: Optional[int] = None) -> tuple[dict, ...]: """Fetch the actual phenotypes.""" _query = ( - "SELECT pheno.*, pxr.Id, ist.InbredSetCode FROM Phenotype AS pheno " + "SELECT pheno.*, pxr.Id AS xref_id, pxr.InbredSetId, ist.InbredSetCode FROM Phenotype AS pheno " "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " "INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId " "INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id " @@ -73,31 +87,41 @@ def dataset_phenotypes(conn: mdb.Connection, return tuple(dict(row) for row in cursor.fetchall()) -def __phenotype_se__(cursor: Cursor, - species_id: int, - population_id: int, - dataset_id: int, - xref_id: str) -> dict: +def __phenotype_se__(cursor: Cursor, xref_id, dataids_and_strainids): """Fetch standard-error values (if they exist) for a phenotype.""" - _sequery = ( - "SELECT pxr.Id AS xref_id, pxr.DataId, str.Id AS StrainId, pse.error, nst.count " - "FROM Phenotype AS pheno " - "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " - "INNER JOIN PublishSE AS pse ON pxr.DataId=pse.DataId " - "INNER JOIN NStrain AS nst ON pse.DataId=nst.DataId " - "INNER JOIN Strain AS str ON nst.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 " - "WHERE (str.SpeciesId, pxr.InbredSetId, pf.Id, pxr.Id)=(%s, %s, %s, %s)") - cursor.execute(_sequery, - (species_id, population_id, dataset_id, xref_id)) - return {(row["DataId"], row["StrainId"]): { - "xref_id": row["xref_id"], - "DataId": row["DataId"], - "error": row["error"], - "count": row["count"] - } for row in cursor.fetchall()} + paramstr = ", ".join(["(%s, %s)"] * len(dataids_and_strainids)) + flat = tuple(item for sublist in dataids_and_strainids for item in sublist) + cursor.execute("SELECT * FROM PublishSE WHERE (DataId, StrainId) IN " + f"({paramstr})", + flat) + debug_query(cursor, app.logger) + _se = { + (row["DataId"], row["StrainId"]): { + "DataId": row["DataId"], + "StrainId": row["StrainId"], + "error": row["error"] + } + for row in cursor.fetchall() + } + + cursor.execute("SELECT * FROM NStrain WHERE (DataId, StrainId) IN " + f"({paramstr})", + flat) + debug_query(cursor, app.logger) + _n = { + (row["DataId"], row["StrainId"]): { + "DataId": row["DataId"], + "StrainId": row["StrainId"], + "count": row["count"] + } + for row in cursor.fetchall() + } + + keys = set(tuple(_se.keys()) + tuple(_n.keys())) + return { + key: {"xref_id": xref_id, **_se.get(key,{}), **_n.get(key,{})} + for key in keys + } def __organise_by_phenotype__(pheno, row): """Organise disparate data rows into phenotype 'objects'.""" @@ -117,6 +141,7 @@ def __organise_by_phenotype__(pheno, row): **(_pheno["data"] if bool(_pheno) else {}), (row["DataId"], row["StrainId"]): { "DataId": row["DataId"], + "StrainId": row["StrainId"], "mean": row["mean"], "Locus": row["Locus"], "LRS": row["LRS"], @@ -170,11 +195,9 @@ def phenotype_by_id( **_pheno, "data": tuple(__merge_pheno_data_and_se__( _pheno["data"], - __phenotype_se__(cursor, - species_id, - population_id, - dataset_id, - xref_id)).values()) + __phenotype_se__( + cursor, xref_id, tuple(_pheno["data"].keys())) + ).values()) } if bool(_pheno) and len(_pheno.keys()) > 1: raise Exception( @@ -231,3 +254,32 @@ def save_new_dataset(cursor: Cursor, params) debug_query(cursor, app.logger) 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, app.logger) + return tuple( + reduce(__organise_by_phenotype__, cursor.fetchall(), {}).values()) |