From 8b7c598407a5fea9a3d78473e72df87606998cd4 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 4 Aug 2023 10:10:28 +0300
Subject: Copy over files from GN3 repository.

---
 gn_auth/auth/authorisation/data/mrna.py | 100 ++++++++++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 gn_auth/auth/authorisation/data/mrna.py

(limited to 'gn_auth/auth/authorisation/data/mrna.py')

diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py
new file mode 100644
index 0000000..bdfc5c1
--- /dev/null
+++ b/gn_auth/auth/authorisation/data/mrna.py
@@ -0,0 +1,100 @@
+"""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
+        }
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