From 620ff2d3020142da5208879d43e56931f74c40e9 Mon Sep 17 00:00:00 2001
From: Son Chau <soncqb@gmail.com>
Date: Fri, 9 Aug 2024 12:38:05 -0700
Subject: [PATCH 1/2] change katsu path to v3

---
 defaults/paths.json | 44 ++++++++++++++++++--------------------------
 1 file changed, 18 insertions(+), 26 deletions(-)

diff --git a/defaults/paths.json b/defaults/paths.json
index 63c60ca..171ac47 100644
--- a/defaults/paths.json
+++ b/defaults/paths.json
@@ -2,16 +2,16 @@
     "paths": {
         "read": {
             "get": [
-                "/v2/discovery/?.*",
-                "/v2/authorized/?.*",
-                "/htsget/v1/variants/?.*",
-                "/htsget/v1/variants/search",
-                "/htsget/v1/reads/?.*",
-                "/htsget/v1/samples/?.*",
-                "/ga4gh/drs/v1/objects/?.*",
-                "/ga4gh/drs/v1/cohorts/?.*",
-                "/ga4gh/drs/v1/cohorts/?.*/status",
-                "/beacon/v2/g_variants/?.*"
+              "/v3/discovery/?.*",
+              "/v3/authorized/?.*",
+              "/htsget/v1/variants/?.*",
+              "/htsget/v1/variants/search",
+              "/htsget/v1/reads/?.*",
+              "/htsget/v1/samples/?.*",
+              "/ga4gh/drs/v1/objects/?.*",
+              "/ga4gh/drs/v1/cohorts/?.*",
+              "/ga4gh/drs/v1/cohorts/?.*/status",
+              "/beacon/v2/g_variants/?.*"
             ],
             "post": [
                 "/htsget/v1/variants/search",
@@ -20,22 +20,14 @@
             ]
         },
         "curate": {
-            "get": [
-                "/htsget/v1/variants/?.*/index",
-                "/htsget/v1/variants/?.*/verify",
-                "/htsget/v1/reads/?.*/index",
-                "/htsget/v1/reads/?.*/verify"
-            ],
-            "post": [
-                "/ingest/?.*",
-                "/ga4gh/drs/v1/?.*",
-                "/v2/ingest/?.*"
-            ],
-            "delete": [
-                "/ingest/?.*",
-                "/ga4gh/drs/v1/?.*",
-                "/v2/ingest/?.*"
-            ]
+          "get": [
+            "/htsget/v1/variants/?.*/index",
+            "/htsget/v1/variants/?.*/verify",
+            "/htsget/v1/reads/?.*/index",
+            "/htsget/v1/reads/?.*/verify"
+          ],
+          "post": ["/ingest/?.*", "/ga4gh/drs/v1/?.*", "/v3/ingest/?.*"],
+          "delete": ["/ingest/?.*", "/ga4gh/drs/v1/?.*", "/v3/ingest/?.*"]
         }
     }
 }
\ No newline at end of file

From 3e52283230986a75ae90de3b7344358af4c05eac Mon Sep 17 00:00:00 2001
From: Son Chau <soncqb@gmail.com>
Date: Fri, 9 Aug 2024 12:38:19 -0700
Subject: [PATCH 2/2] change katsu test path to v3

---
 tests/test_opa_permissions.py | 46 ++++++++++-------------------------
 1 file changed, 13 insertions(+), 33 deletions(-)

diff --git a/tests/test_opa_permissions.py b/tests/test_opa_permissions.py
index fb83b8b..6b5f2fc 100644
--- a/tests/test_opa_permissions.py
+++ b/tests/test_opa_permissions.py
@@ -243,47 +243,27 @@ def test_site_admin(user, expected_result, site_roles, users, programs):
 
 def get_user_datasets():
     return [
-        ( # site admin should be able to read all datasets
+        (  # site admin should be able to read all datasets
             "site_admin",
-            {
-                "body": {
-                  "path": "/ga4gh/drs/v1/cohorts/",
-                  "method": "GET"
-                }
-            },
-            ["SYNTHETIC-1", "SYNTHETIC-2", "SYNTHETIC-3", "SYNTHETIC-4"]
+            {"body": {"path": "/ga4gh/drs/v1/cohorts/", "method": "GET"}},
+            ["SYNTHETIC-1", "SYNTHETIC-2", "SYNTHETIC-3", "SYNTHETIC-4"],
         ),
-        ( # user1 can view the datasets it's a member of
+        (  # user1 can view the datasets it's a member of
             "user1",
-            {
-                "body": {
-                  "path": "/v2/discovery/programs/",
-                  "method": "GET"
-                }
-            },
-            ["SYNTHETIC-1", "SYNTHETIC-3", "SYNTHETIC-4"]
+            {"body": {"path": "/v3/discovery/programs/", "method": "GET"}},
+            ["SYNTHETIC-1", "SYNTHETIC-3", "SYNTHETIC-4"],
         ),
-        ( # user3 can view the datasets it's a member of + DAC programs,
-          # but SYNTHETIC-1's authorized dates are in the past
+        (  # user3 can view the datasets it's a member of + DAC programs,
+            # but SYNTHETIC-1's authorized dates are in the past
             "user3",
-            {
-                "body": {
-                  "path": "/v2/discovery/programs/",
-                  "method": "GET"
-                }
-            },
-            ["SYNTHETIC-3", "SYNTHETIC-4"]
+            {"body": {"path": "/v3/discovery/programs/", "method": "GET"}},
+            ["SYNTHETIC-3", "SYNTHETIC-4"],
         ),
         (
             "dac_user",
-            {
-                "body": {
-                  "path": "/ga4gh/drs/v1/cohorts",
-                  "method": "GET"
-                }
-            },
-            ["SYNTHETIC-3"]
-        )
+            {"body": {"path": "/ga4gh/drs/v1/cohorts", "method": "GET"}},
+            ["SYNTHETIC-3"],
+        ),
     ]