From fcbb510713e34b932c216082ebc04d3d4d1e0118 Mon Sep 17 00:00:00 2001
From: Sijie <sijiex@lbl.gov>
Date: Mon, 9 Sep 2024 17:37:22 -0700
Subject: [PATCH] add features_handle_ref && protein_handle_ref before upload

---
 test/data/metagenomes/toy/features_handle_ref |  1 +
 test/data/metagenomes/toy/metagenome.json     |  2 --
 test/data/metagenomes/toy/protein_handle_ref  |  1 +
 test/problematic_tests/save_genome_test.py    | 23 +++++++++++++++++++
 4 files changed, 25 insertions(+), 2 deletions(-)
 create mode 100644 test/data/metagenomes/toy/features_handle_ref
 create mode 100644 test/data/metagenomes/toy/protein_handle_ref

diff --git a/test/data/metagenomes/toy/features_handle_ref b/test/data/metagenomes/toy/features_handle_ref
new file mode 100644
index 00000000..f67a087d
--- /dev/null
+++ b/test/data/metagenomes/toy/features_handle_ref
@@ -0,0 +1 @@
+test features_handle_ref
\ No newline at end of file
diff --git a/test/data/metagenomes/toy/metagenome.json b/test/data/metagenomes/toy/metagenome.json
index 57e42815..95c23ef8 100644
--- a/test/data/metagenomes/toy/metagenome.json
+++ b/test/data/metagenomes/toy/metagenome.json
@@ -15,7 +15,6 @@
         "non_coding_features": 0,
         "protein_encoding_gene": 20
     },
-    "features_handle_ref": "KBH_736245",
     "gc_content": 0.64469,
     "genetic_code": 1,
     "genome_type": "Metagenome",
@@ -36,7 +35,6 @@
         }
     ],
     "original_source_file_name": null,
-    "protein_handle_ref": "KBH_736243",
     "publications": [],
     "scientific_name": "Arabidopsis thaliana",
     "source": "GFF",
diff --git a/test/data/metagenomes/toy/protein_handle_ref b/test/data/metagenomes/toy/protein_handle_ref
new file mode 100644
index 00000000..4e4a8e1f
--- /dev/null
+++ b/test/data/metagenomes/toy/protein_handle_ref
@@ -0,0 +1 @@
+test protein_handle_ref
\ No newline at end of file
diff --git a/test/problematic_tests/save_genome_test.py b/test/problematic_tests/save_genome_test.py
index 5380738c..70eff5c1 100644
--- a/test/problematic_tests/save_genome_test.py
+++ b/test/problematic_tests/save_genome_test.py
@@ -149,6 +149,29 @@ def prepare_data(cls):
         cls.test_metagenome_data = json.load(open('data/metagenomes/toy/metagenome.json'))
         cls.test_metagenome_data['assembly_ref'] = assembly_refs[1]["upa"]
 
+        # Move files to the share folder
+        fhr_path = os.path.join(cls.scratch,'features_handle_ref')
+        phr_path = os.path.join(cls.scratch,'protein_handle_ref')
+
+        shutil.copy('data/metagenomes/toy/features_handle_ref', fhr_path)
+        shutil.copy('data/metagenomes/toy/protein_handle_ref', phr_path)
+
+        # Upload files to the blobstore
+        handle_service_outputs = cls.dfu.file_to_shock_mass(
+            [
+                {'file_path': fhr_path, 'make_handle': 1, 'pack': 'gzip'},
+                {'file_path': phr_path, 'make_handle': 1, 'pack': 'gzip'}
+            ]
+        )
+
+        # Update metagenome
+        cls.test_metagenome_data["features_handle_ref"] = handle_service_outputs[0]["handle"]["hid"]
+        cls.test_metagenome_data["protein_handle_ref"]= handle_service_outputs[1]["handle"]["hid"]
+
+        # Delete shock_ids
+        cls.nodes_to_delete.append(handle_service_outputs[0]["shock_id"])
+        cls.nodes_to_delete.append(handle_service_outputs[1]["shock_id"])
+
     def getWsClient(self):
         return self.__class__.wsClient