From acde4fc57250cf2ecc0bb12b34d523d8cf306c3e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 10 Apr 2023 10:08:54 +0300
Subject: Enable search, filtering out selected, but not linked data

When a user selects some datasets and does a new search, we filter out the
selected datasets too, even though they are yet to be linked.
---
 gn3/auth/authorisation/data/genotypes.py | 16 +++++++++-------
 gn3/auth/authorisation/data/views.py     | 23 +++++++++++++++++++----
 2 files changed, 28 insertions(+), 11 deletions(-)

(limited to 'gn3/auth/authorisation/data')

diff --git a/gn3/auth/authorisation/data/genotypes.py b/gn3/auth/authorisation/data/genotypes.py
index fe06726..8f901a5 100644
--- a/gn3/auth/authorisation/data/genotypes.py
+++ b/gn3/auth/authorisation/data/genotypes.py
@@ -21,14 +21,17 @@ def linked_genotype_data(conn: authdb.DbConnection) -> Iterable[dict]:
                   "You do not have sufficient privileges to link data to (a) "
                   "group(s)."),
               oauth2_scope="profile group resource")
-def ungrouped_genotype_data(
+def ungrouped_genotype_data(# pylint: disable=[too-many-arguments]
         authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
-        search_query: str, limit: int = 10000, offset: int = 0) -> tuple[
+        search_query: str, selected: tuple[dict, ...] = tuple(),
+        limit: int = 10000, offset: int = 0) -> tuple[
             dict, ...]:
     """Retrieve genotype data that is not linked to any user group."""
     params = tuple(
         (row["SpeciesId"], row["InbredSetId"], row["GenoFreezeId"])
-            for row in linked_genotype_data(authconn))
+            for row in linked_genotype_data(authconn)) + tuple(
+                    (row["SpeciesId"], row["InbredSetId"], row["GenoFreezeId"])
+                    for row in selected)
     query = (
         "SELECT s.SpeciesId, iset.InbredSetId, iset.InbredSetName, "
         "gf.Id AS GenoFreezeId, gf.Name AS dataset_name, "
@@ -50,14 +53,13 @@ def ungrouped_genotype_data(
 
     if bool(search_query):
         query = query + (
-            "CONCAT(gf.Name, ' ', gf.FullName, ' ', gf.ShortName) LIKE '%%?%%' ")
-        params = params + ((search_query,),)# type: ignore[operator]
+            "CONCAT(gf.Name, ' ', gf.FullName, ' ', gf.ShortName) LIKE %s ")
+        params = params + ((f"%{search_query}%",),)# type: ignore[operator]
 
     query = query + f"LIMIT {int(limit)} OFFSET {int(offset)}"
-    final_params = tuple(item for sublist in params for item in sublist)
     with gn3conn.cursor(DictCursor) as cursor:
         cursor.execute(
-            query, final_params)
+            query, tuple(item for sublist in params for item in sublist))
         return tuple(row for row in cursor.fetchall())
 
 @authorised_p(
diff --git a/gn3/auth/authorisation/data/views.py b/gn3/auth/authorisation/data/views.py
index 55a7373..9a924b4 100644
--- a/gn3/auth/authorisation/data/views.py
+++ b/gn3/auth/authorisation/data/views.py
@@ -313,13 +313,28 @@ def migrate_users_data() -> Response:
 def __search_mrna__():
     pass
 
+def __request_key__(key: str, default: Any = ""):
+    if bool(request.json):
+        return request.json.get(#type: ignore[union-attr]
+            key, request.args.get(key, request.form.get(key, default)))
+    return request.args.get(key, request.form.get(key, default))
+
+def __request_key_list__(key: str, default: tuple[Any, ...] = tuple()):
+    if bool(request.json):
+        return (request.json.get(key,[])#type: ignore[union-attr]
+                or request.args.getlist(key) or request.form.getlist(key)
+                or list(default))
+    return (request.args.getlist(key)
+            or request.form.getlist(key) or list(default))
+
 def __search_genotypes__():
-    query = request.form.get("query", request.args.get("query", ""))
-    limit = int(request.form.get("limit", request.args.get("limit", 10000)))
-    offset = int(request.form.get("offset", request.args.get("offset", 0)))
+    query = __request_key__("query", "")
+    limit = int(__request_key__("limit", 10000))
+    offset = int(__request_key__("offset", 0))
     with gn3db.database_connection() as gn3conn:
         __ungrouped__ = partial(
             ungrouped_genotype_data, gn3conn=gn3conn, search_query=query,
+            selected=__request_key_list__("selected"),
             limit=limit, offset=offset)
         return jsonify(with_db_connection(__ungrouped__))
 
@@ -330,7 +345,7 @@ def __search_phenotypes__():
 @require_oauth("profile group resource")
 def search_unlinked_data():
     """Search for various unlinked data."""
-    dataset_type = request.form["dataset_type"]
+    dataset_type = request.json["dataset_type"]
     search_fns = {
         "mrna": __search_mrna__,
         "genotype": __search_genotypes__,
-- 
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