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/groups/data.py | 106 ++++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 gn_auth/auth/authorisation/groups/data.py

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

diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/groups/data.py
new file mode 100644
index 0000000..ee6f70e
--- /dev/null
+++ b/gn_auth/auth/authorisation/groups/data.py
@@ -0,0 +1,106 @@
+"""Handles the resource objects' data."""
+from MySQLdb.cursors import DictCursor
+
+from gn3 import db_utils as gn3db
+from gn3.auth import db as authdb
+from gn3.auth.authorisation.groups import Group
+from gn3.auth.authorisation.checks import authorised_p
+from gn3.auth.authorisation.errors import NotFoundError
+
+def __fetch_mrna_data_by_ids__(
+        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+            dict, ...]:
+    """Fetch mRNA Assay data by ID."""
+    with conn.cursor(DictCursor) as cursor:
+        paramstr = ", ".join(["%s"] * len(dataset_ids))
+        cursor.execute(
+            "SELECT psf.Id, psf.Name AS dataset_name, "
+            "psf.FullName AS dataset_fullname, "
+            "ifiles.GN_AccesionId AS accession_id FROM ProbeSetFreeze AS psf "
+            "INNER JOIN InfoFiles AS ifiles ON psf.Name=ifiles.InfoPageName "
+            f"WHERE psf.Id IN ({paramstr})",
+            dataset_ids)
+        res = cursor.fetchall()
+        if res:
+            return tuple(dict(row) for row in res)
+        raise NotFoundError("Could not find mRNA Assay data with the given ID.")
+
+def __fetch_geno_data_by_ids__(
+        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+            dict, ...]:
+    """Fetch genotype data by ID."""
+    with conn.cursor(DictCursor) as cursor:
+        paramstr = ", ".join(["%s"] * len(dataset_ids))
+        cursor.execute(
+            "SELECT gf.Id, gf.Name AS dataset_name, "
+            "gf.FullName AS dataset_fullname, "
+            "ifiles.GN_AccesionId AS accession_id FROM GenoFreeze AS gf "
+            "INNER JOIN InfoFiles AS ifiles ON gf.Name=ifiles.InfoPageName "
+            f"WHERE gf.Id IN ({paramstr})",
+            dataset_ids)
+        res = cursor.fetchall()
+        if res:
+            return tuple(dict(row) for row in res)
+        raise NotFoundError("Could not find Genotype data with the given ID.")
+
+def __fetch_pheno_data_by_ids__(
+        conn: gn3db.Connection, dataset_ids: tuple[str, ...]) -> tuple[
+            dict, ...]:
+    """Fetch phenotype data by ID."""
+    with conn.cursor(DictCursor) as cursor:
+        paramstr = ", ".join(["%s"] * len(dataset_ids))
+        cursor.execute(
+            "SELECT pxf.Id, iset.InbredSetName, pf.Id AS dataset_id, "
+            "pf.Name AS dataset_name, pf.FullName AS dataset_fullname, "
+            "ifiles.GN_AccesionId AS accession_id "
+            "FROM PublishXRef AS pxf "
+            "INNER JOIN InbredSet AS iset ON pxf.InbredSetId=iset.InbredSetId "
+            "INNER JOIN PublishFreeze AS pf ON iset.InbredSetId=pf.InbredSetId "
+            "INNER JOIN InfoFiles AS ifiles ON pf.Name=ifiles.InfoPageName "
+            f"WHERE pxf.Id IN ({paramstr})",
+            dataset_ids)
+        res = cursor.fetchall()
+        if res:
+            return tuple(dict(row) for row in res)
+        raise NotFoundError(
+            "Could not find Phenotype/Publish data with the given IDs.")
+
+def __fetch_data_by_id(
+        conn: gn3db.Connection, dataset_type: str,
+        dataset_ids: tuple[str, ...]) -> tuple[dict, ...]:
+    """Fetch data from MySQL by IDs."""
+    fetch_fns = {
+        "mrna": __fetch_mrna_data_by_ids__,
+        "genotype": __fetch_geno_data_by_ids__,
+        "phenotype": __fetch_pheno_data_by_ids__
+    }
+    return fetch_fns[dataset_type](conn, dataset_ids)
+
+@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_data_to_group(
+        authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
+        dataset_type: str, dataset_ids: tuple[str, ...], group: Group) -> tuple[
+            dict, ...]:
+    """Link the given data to the specified group."""
+    the_data = __fetch_data_by_id(gn3conn, dataset_type, dataset_ids)
+    with authdb.cursor(authconn) as cursor:
+        params = tuple({
+            "group_id": str(group.group_id), "dataset_type": {
+                "mrna": "mRNA", "genotype": "Genotype",
+                "phenotype": "Phenotype"
+            }[dataset_type],
+            "dataset_or_trait_id": item["Id"],
+            "dataset_name": item["dataset_name"],
+            "dataset_fullname": item["dataset_fullname"],
+            "accession_id": item["accession_id"]
+        } for item in the_data)
+        cursor.executemany(
+            "INSERT INTO linked_group_data VALUES"
+            "(:group_id, :dataset_type, :dataset_or_trait_id, :dataset_name, "
+            ":dataset_fullname, :accession_id)",
+            params)
+        return params
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