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authorFrederick Muriuki Muriithi2023-08-04 10:10:28 +0300
committerFrederick Muriuki Muriithi2023-08-04 10:20:09 +0300
commit8b7c598407a5fea9a3d78473e72df87606998cd4 (patch)
tree8526433a17eca6b511feb082a0574f9b15cb9469 /gn_auth/auth/authorisation/data/mrna.py
parentf7fcbbcc014686ac597b783a8dcb38b43024b9d6 (diff)
downloadgn-auth-8b7c598407a5fea9a3d78473e72df87606998cd4.tar.gz
Copy over files from GN3 repository.
Diffstat (limited to 'gn_auth/auth/authorisation/data/mrna.py')
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diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py
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+"""Handle linking of mRNA Assay data to the Auth(entic|oris)ation system."""
+import uuid
+from typing import Iterable
+from MySQLdb.cursors import DictCursor
+
+import gn3.auth.db as authdb
+import gn3.db_utils as gn3db
+from gn3.auth.dictify import dictify
+from gn3.auth.authorisation.checks import authorised_p
+from gn3.auth.authorisation.groups.models import Group
+
+def linked_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]:
+ """Retrieve mRNA Assay data that is linked to user groups."""
+ with authdb.cursor(conn) as cursor:
+ cursor.execute("SELECT * FROM linked_mrna_data")
+ return (dict(row) for row in cursor.fetchall())
+
+@authorised_p(("system:data:link-to-group",),
+ error_description=(
+ "You do not have sufficient privileges to link data to (a) "
+ "group(s)."),
+ oauth2_scope="profile group resource")
+def ungrouped_mrna_data(# pylint: disable=[too-many-arguments]
+ authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+ search_query: str, selected: tuple[dict, ...] = tuple(),
+ limit: int = 10000, offset: int = 0) -> tuple[
+ dict, ...]:
+ """Retrieve mrna data that is not linked to any user group."""
+ params = tuple(
+ (row["SpeciesId"], row["InbredSetId"], row["ProbeFreezeId"],
+ row["ProbeSetFreezeId"])
+ for row in linked_mrna_data(authconn)) + tuple(
+ (row["SpeciesId"], row["InbredSetId"], row["ProbeFreezeId"],
+ row["ProbeSetFreezeId"])
+ for row in selected)
+ query = (
+ "SELECT s.SpeciesId, iset.InbredSetId, iset.InbredSetName, "
+ "pf.ProbeFreezeId, pf.Name AS StudyName, psf.Id AS ProbeSetFreezeId, "
+ "psf.Name AS dataset_name, psf.FullName AS dataset_fullname, "
+ "psf.ShortName AS dataset_shortname "
+ "FROM Species AS s INNER JOIN InbredSet AS iset "
+ "ON s.SpeciesId=iset.SpeciesId INNER JOIN ProbeFreeze AS pf "
+ "ON iset.InbredSetId=pf.InbredSetId INNER JOIN ProbeSetFreeze AS psf "
+ "ON pf.ProbeFreezeId=psf.ProbeFreezeId ") + (
+ "WHERE " if (len(params) > 0 or bool(search_query)) else "")
+
+ if len(params) > 0:
+ paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(params))
+ query = query + (
+ "(s.SpeciesId, iset.InbredSetId, pf.ProbeFreezeId, psf.Id) "
+ f"NOT IN ({paramstr}) "
+ ) + ("AND " if bool(search_query) else "")
+
+ if bool(search_query):
+ query = query + (
+ "CONCAT(pf.Name, psf.Name, ' ', psf.FullName, ' ', psf.ShortName) "
+ "LIKE %s ")
+ params = params + ((f"%{search_query}%",),)# type: ignore[operator]
+
+ query = query + f"LIMIT {int(limit)} OFFSET {int(offset)}"
+ with gn3conn.cursor(DictCursor) as cursor:
+ cursor.execute(
+ query, tuple(item for sublist in params for item in sublist))
+ return tuple(row for row in cursor.fetchall())
+
+@authorised_p(
+ ("system:data:link-to-group",),
+ error_description=(
+ "You do not have sufficient privileges to link data to (a) "
+ "group(s)."),
+ oauth2_scope="profile group resource")
+def link_mrna_data(
+ conn: authdb.DbConnection, group: Group, datasets: dict) -> dict:
+ """Link genotye `datasets` to `group`."""
+ with authdb.cursor(conn) as cursor:
+ cursor.executemany(
+ "INSERT INTO linked_mrna_data VALUES "
+ "(:data_link_id, :group_id, :SpeciesId, :InbredSetId, "
+ ":ProbeFreezeId, :ProbeSetFreezeId, :dataset_name, "
+ ":dataset_fullname, :dataset_shortname) "
+ "ON CONFLICT "
+ "(SpeciesId, InbredSetId, ProbeFreezeId, ProbeSetFreezeId) "
+ "DO NOTHING",
+ tuple({
+ "data_link_id": str(uuid.uuid4()),
+ "group_id": str(group.group_id),
+ **{
+ key: value for key,value in dataset.items() if key in (
+ "SpeciesId", "InbredSetId", "ProbeFreezeId",
+ "ProbeSetFreezeId", "dataset_fullname", "dataset_name",
+ "dataset_shortname")
+ }
+ } for dataset in datasets))
+ return {
+ "description": (
+ f"Successfully linked {len(datasets)} to group "
+ f"'{group.group_name}'."),
+ "group": dictify(group),
+ "datasets": datasets
+ }