From ac17bffa647b2da4c2e0e6ce6e31f5975e3f143a Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Wed, 21 Aug 2024 16:44:52 -0700
Subject: [PATCH] Remove manifest entries for links.json (#4565)

---
 .../plugins/repository/tdr_hca/__init__.py    | 20 +++----------------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...318dbb86000.2019-01-03T163633.780215Z.json | 12 -----------
 ...61d6da02d44.2019-09-20T103932.395795Z.json | 12 -----------
 ...a3fb4204953.2018-03-29T142048.835519Z.json | 12 -----------
 ...d019d1c9439.2019-05-15T222432.561000Z.json | 12 -----------
 ...08092b2dabe.2019-04-17T175706.867000Z.json | 12 -----------
 ...68e20ec4a2e.2019-02-02T065454.662896Z.json | 12 -----------
 ...19c1c2d9018.2018-10-07T130111.835234Z.json | 12 -----------
 ...406a478d5ab.2018-09-05T182535.846470Z.json | 12 -----------
 ...95a3f8deb9c.2019-04-03T103426.471000Z.json | 12 -----------
 ...720f33a5dde.2019-03-17T220646.332108Z.json | 12 -----------
 ...3-5e9d-52cd-b32d-af88edccabfa.dss.hca.json | 11 ----------
 ...5-71e2-48ca-a87b-e256938c6a98.dss.hca.json | 11 ----------
 ...3-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json | 11 ----------
 ...c-6778-423d-8fe9-869e2a515d35.dss.hca.json | 11 ----------
 ...8-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json | 12 -----------
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json | 11 ----------
 ...5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json | 11 ----------
 ...8-658e-4c51-9de4-a768322f84c5.dss.hca.json | 11 ----------
 ...a-940e-49b1-9bcc-25699a55b295.dss.hca.json | 12 -----------
 ...f-61a7-4504-a57c-fc70f38d5b13.dss.hca.json | 12 -----------
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json | 12 -----------
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json | 12 -----------
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json | 11 ----------
 ...e-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json | 11 ----------
 ...4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json | 12 -----------
 ...0.2020-12-10T10:30:00.000000Z.dss.hca.json | 11 ----------
 ...f-8346-5420-b7e4-b486f99451a8.dss.hca.json | 11 ----------
 ...e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json | 11 ----------
 ...1-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json | 11 ----------
 ...e-9a5d-4e3d-ada2-0414b666b880.dss.hca.json | 12 -----------
 ...2-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json | 12 -----------
 ...3-f0ac-417a-8a29-221c77debde8.dss.hca.json | 12 -----------
 ...d.2018-11-02T11:33:44.698028Z.dss.hca.json | 12 -----------
 ...d.2018-11-04T11:33:44.698028Z.dss.hca.json | 12 -----------
 ...e-9b7b-4800-8977-fe7c94e131df.dss.hca.json | 12 -----------
 ...4-dc9f-439e-af29-f8eb75b0729d.dss.hca.json | 12 -----------
 ...4-9a58-4763-9e66-59894efbdaa8.dss.hca.json | 12 -----------
 ...d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json | 12 -----------
 ...1-4766-4210-966c-f9ee25d19190.dss.hca.json | 12 -----------
 ...a-2b51-4419-9cde-34df44c6458a.dss.hca.json | 12 -----------
 ...e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json | 12 -----------
 ...4-6b80-4eed-97c9-4984de81a47c.dss.hca.json | 12 -----------
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json | 12 -----------
 ...b-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json | 12 -----------
 ...7-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json | 11 ----------
 ...f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json | 12 -----------
 test/integration_test.py                      |  9 +--------
 55 files changed, 4 insertions(+), 647 deletions(-)

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index df9b25986..c1043a682 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -343,10 +343,7 @@ def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
                               manifest=[],
                               metadata_files={})
         entities, root_entities, links_jsons = self._stitch_bundles(bundle)
-        bundle.add_entity(entity_key='links.json',
-                          entity_type='links',
-                          entity_row=self._merge_links(links_jsons),
-                          is_stitched=False)
+        bundle.metadata_files['links.json'] = self._merge_links(links_jsons)
 
         with ThreadPoolExecutor(max_workers=config.num_tdr_workers) as executor:
             futures = {
@@ -555,12 +552,6 @@ def _merge_links(self, links_jsons: JSONs) -> JSON:
         """
         root, *stitched = links_jsons
         if stitched:
-            merged = {
-                'links_id': root['links_id'],
-                'version': root['version']
-            }
-            for common_key in ('project_id', 'schema_type'):
-                merged[common_key] = one({row[common_key] for row in links_jsons})
             source_contents = [row['content'] for row in links_jsons]
             # FIXME: Explicitly verify compatible schema versions for stitched subgraphs
             #        https://github.com/DataBiosphere/azul/issues/3215
@@ -574,14 +565,9 @@ def _merge_links(self, links_jsons: JSONs) -> JSON:
                 'describedBy': str(schema_url),
                 'links': sum((sc['links'] for sc in source_contents), start=[])
             }
-            merged['content'] = merged_content  # Keep result of parsed JSON for reuse
-            merged['content_size'] = len(json.dumps(merged_content))
-            assert merged.keys() == one({
-                frozenset(row.keys()) for row in links_jsons
-            }), merged
             assert merged_content.keys() == one({
                 frozenset(sc.keys()) for sc in source_contents
             }), merged_content
-            return merged
+            return merged_content
         else:
-            return root
+            return root['content']
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 01627b98e..1f5712e7e 100644
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -48,18 +48,6 @@
             "uuid": "821601f1-64e8-4427-8680-34a743b35b69",
             "version": "1"
         },
-        {
-            "crc32c": "DDAABBB6",
-            "sha1": "82c4c5273e31923bf6e12139804c3a4cf10b338d",
-            "sha256": "3de258c171a757d80e53a617ce1834e14710c87db0289c9b2012d0a14a3ea705",
-            "s3_etag": "4dc6069c891063f28a0ee155c6cd7b65",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1856,
-            "uuid": "04e79979-489e-4cd8-93c3-1d8e99d09ec8",
-            "version": "1"
-        },
         {
             "crc32c": "522D96A7",
             "sha1": "9876adb67827ea0328566811a1304bcf49a31b02",
diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 1a798a5a8..ce91f3795 100644
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -84,18 +84,6 @@
             "uuid": "5910c207-1093-4ef1-9537-dc614d128d14",
             "version": "1"
         },
-        {
-            "crc32c": "1CAA5E57",
-            "sha1": "e3d6064f20fa85351d9446be179ebb15458324e6",
-            "sha256": "e4529c8501160b286824388a51f50b6e94110d3f9a55998a3b088f918e92ae53",
-            "s3_etag": "1e11ded031de78c2c7cec5e5fb3b48a7",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 2381,
-            "uuid": "2aea848d-fbe7-472a-953d-2cd77716b939",
-            "version": "1"
-        },
         {
             "crc32c": "17049723",
             "sha1": "df812b18c751efd55e21318be9411200f3066513",
diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index eb9525ed0..959b66bbf 100644
--- a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
+++ b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
@@ -156,18 +156,6 @@
             "uuid": "597f5fae-db6a-4ebc-b2f0-b9c527f5b3ed",
             "version": "1"
         },
-        {
-            "crc32c": "E8D34C5D",
-            "sha1": "e3336e075787d319a239533d8620a4a60a793bac",
-            "sha256": "062e56b2f314b8fd81b916985767abaedc4e22923e80607b023a3bf68554d4e0",
-            "s3_etag": "3ae64d0365c9c2d857c4194f41b471a6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 7860,
-            "uuid": "19f9d2c2-2d30-4262-8d19-a5de9ca13dd7",
-            "version": "1"
-        },
         {
             "crc32c": "27917E6E",
             "sha1": "6be5be8c979bf95b9be25df1f16c9856bb55bff3",
diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 3f9f9b81a..c7b3b4a1f 100644
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -48,18 +48,6 @@
             "uuid": "3b8ffd02-7a9e-44ff-bec5-1387b87b0e34",
             "version": "1"
         },
-        {
-            "crc32c": "5AE674D4",
-            "sha1": "a2c43b27d4cdcd769ea9aa5fb6dc38d144a19448",
-            "sha256": "5444d86b7f7dde2c7521dde5821b12d04cd544ecae07464b45ee75ad98c9becc",
-            "s3_etag": "f2fb4a3a21e54e7b6455fcd9fac1e1b1",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1856,
-            "uuid": "d6284ed3-ff4c-4153-90b5-a3f5fb10c799",
-            "version": "1"
-        },
         {
             "crc32c": "22B1F2B5",
             "sha1": "24335fec0fbe49e182b9a25d9953a7ef34f797fa",
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 5c0f7246f..57480d942 100644
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -60,18 +60,6 @@
             "uuid": "6aa1f675-a3be-4def-8da9-259ae0fcad68",
             "version": "1"
         },
-        {
-            "crc32c": "837B6FBF",
-            "sha1": "4534daa77cd865f34273f6c8a8d0fd3a96361bfe",
-            "sha256": "26c92efa3719bda131663c452d7b385925d927eb5a49f6b2e5ebb1497e871c64",
-            "s3_etag": "dc518a7c1b8faea79320eb70e7c239e6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 2027,
-            "uuid": "447bd719-baa7-4f32-b4d6-7f64fabfe0f1",
-            "version": "1"
-        },
         {
             "crc32c": "93A97712",
             "sha1": "4365e3dbeeff6b4c23c9057e5b30aab65807a405",
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 2acf73c7f..95a14aad9 100644
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -36,18 +36,6 @@
             "uuid": "6ce66ac8-1e0f-49b4-a278-468f7b677ffe",
             "version": "1"
         },
-        {
-            "crc32c": "C0EF71FC",
-            "sha1": "79e8137293c18fc1ef1a4b2a532e59f6223fbec3",
-            "sha256": "d333cfe228457aaa476b4ccf39bdd4c620bfcf0f2c11ccfff83c9aacb7a17c13",
-            "s3_etag": "cbacd6ba075487820bcd49e2667581b6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1727,
-            "uuid": "169acedb-1e56-4b6d-a3d7-0d3e56d74098",
-            "version": "1"
-        },
         {
             "crc32c": "8D88697D",
             "sha1": "cfbab7537d593e0b1765b65b755e88244bd88ebc",
diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 6eea5c58b..31d2472cb 100644
--- a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -60,18 +60,6 @@
             "uuid": "1d64e884-84c1-438e-8f1b-7d42698942ad",
             "version": "1"
         },
-        {
-            "crc32c": "C1574314",
-            "sha1": "086e0e40e88c2ed0b4a1c68a3f2fd88e66454e6e",
-            "sha256": "88fa107073946ff3a01455ebeca62cb7a8c8253a10f90c68f8c37078f00be627",
-            "s3_etag": "151fe404519e0934fa5e24772d8002d6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1643,
-            "uuid": "62f4b747-7bf2-4af5-b710-723a060f0d35",
-            "version": "1"
-        },
         {
             "crc32c": "D044B620",
             "sha1": "15c4e8085308b8f297b9b682c8aa892514e476de",
diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
index bb2a50bf8..0ca2b6573 100644
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
+++ b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
@@ -512,18 +512,6 @@
             "uuid": "baa3a061-534c-4b6e-8c51-a11a8307f537",
             "version": "2019-01-03T120758.911000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "8296c70e",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "dcda06d2eb79d368ac84a47a06689773",
-            "sha1": "3d4d918d7deae23cade8abb3269ca957c315ad0d",
-            "sha256": "a0c53628a804b864567b1c6a87879a040dba1d24b539418710dc3979599301e1",
-            "size": 7860,
-            "uuid": "5b71a545-1f04-477b-98b5-f15664311970",
-            "version": "2019-01-03T163557.511721Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "dec968a1",
diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
index 8b58a1e79..816ed60ed 100644
--- a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
+++ b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
@@ -228,18 +228,6 @@
             "uuid": "b3cddf6f-65ee-4aa8-8682-60f00c55be73",
             "version": "2019-09-20T082959.366000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "afe1de7d",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "e00d35caa8374da25b82de4a4358611d",
-            "sha1": "769e482e1902871370aa269dc264379a7bdb64b9",
-            "sha256": "e237b747a7f00824d9e7fca8285500dcf26c335c31a7169b2b5a655f1145776b",
-            "size": 2322,
-            "uuid": "774029ec-ba28-49e6-ae47-6403f5a9555e",
-            "version": "2019-09-20T104007.387625Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "759039c3",
diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
index 9f0938781..678119b86 100644
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
@@ -84,18 +84,6 @@
             "uuid": "7db5a820-e612-402c-aaf3-d2676e19d862",
             "version": "2018-03-29T142047.303889Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "4e6ce5dd",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "14c01392fd55df2b2cdbd08994009e24",
-            "sha1": "6ab7fdb229d9f0971a05e781ef52cbcfbf680e00",
-            "sha256": "be6a5c420109f6208e2a663c7d9fdc66de6dac9b08180c4aa0993ada30754645",
-            "size": 5963,
-            "uuid": "8c45f35c-c070-4bf4-999a-1de1676ad598",
-            "version": "2018-03-29T142047.912393Z"
-        }
     ],
     "metadata": {
         "project_0.json": {
diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
index c50b63a0f..3de125e26 100644
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
@@ -120,18 +120,6 @@
             "uuid": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
             "version": "2019-05-14T122652.545000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "2c25a3c2",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "1f7c2cbccc797da2d885bb52de52232d",
-            "sha1": "39ba144902ba5d1095af5b8d5dace8dd19a4b08d",
-            "sha256": "33052247612f39f6ea48568a12c761842af30030e1242943bb2c5eb238722488",
-            "size": 2083,
-            "uuid": "51168054-6dad-45aa-916a-ef71135651b2",
-            "version": "2019-05-16T015324.197421Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "86192092",
diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
index dfb5dc797..fa59f5ed9 100644
--- a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
@@ -192,18 +192,6 @@
             "uuid": "4276c1dd-50aa-4ffa-a618-dee757bff479",
             "version": "2019-04-17T165959.680000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "4392f0e2",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "ddce74cad640a9a30b2b3b6ac6c4f0c8",
-            "sha1": "8e596d873bf15ebc9f1ff405e17ec633248ebe0a",
-            "sha256": "024b37f1635851b6100974e5318170fbbca1875a02a43c25ce65cb4ac0e5e1e9",
-            "size": 2643,
-            "uuid": "468bd567-e319-4dcc-a636-daf90a534f6d",
-            "version": "2019-04-17T185612.241223Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "9e612174",
diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
index b1eeeff62..fbb9c6a02 100644
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
@@ -612,18 +612,6 @@
             "uuid": "832b39e3-ebba-4686-a724-52babb96056f",
             "version": "2019-01-23T110544.002000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "290d41eb",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "0d6d83e234cf9a884a96403bbfc56d67",
-            "sha1": "3fee9537a1391d0ba0060e53d42e0a2186f6344d",
-            "sha256": "792cc5459ebf45cef1ef1fb5f62f44fbd79e6f73281d1f4622bb2b1b35abcca3",
-            "size": 7448,
-            "uuid": "700f28bc-8f57-4276-9fce-6b7774bf5210",
-            "version": "2019-02-02T065434.323908Z"
-        },
         {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "82ad16f4",
diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
index c301e8a49..00eb2a89c 100644
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
+++ b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
@@ -168,18 +168,6 @@
             "uuid": "5a15ed38-5e37-44ff-ba35-0d17bb8564bd",
             "version": "2018-10-07T120517.018000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "56d56718",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "70623328382d0927e3242efc726fe29d",
-            "sha1": "a947b0283b948cf08e1197064506bfa2491d8b3a",
-            "sha256": "0bc6c6fa6a9093caddd8a4921826cd47c6a0773312cc62f51abcd55f93e52ecb",
-            "size": 2393,
-            "uuid": "a1681a39-e8d2-43f7-8781-ac4edab527fe",
-            "version": "2018-10-07T130110.624725Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "a3f89844",
diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
index 15a52e8e6..67fe8541e 100644
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
+++ b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
@@ -156,18 +156,6 @@
             "uuid": "6284381f-de72-4015-ae51-fa17e13677f8",
             "version": "2018-09-05T182534.886667Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "ac18a06b",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "46cce577c8cfc281c8e33233f0366f99",
-            "sha1": "da4381b79641d4de4fe15ff2e7385aa75b79d79f",
-            "sha256": "0d881b169fbc809219d9eaf6b1c77349b9bbd298ac5c7ce9714517f01ca47a0b",
-            "size": 2095,
-            "uuid": "d33848ba-a9f8-4aa9-a72c-26755f0273d1",
-            "version": "2018-09-05T182535.148513Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "4ef74578",
diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
index 6072f329f..f0ef040f7 100644
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
+++ b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
@@ -2844,18 +2844,6 @@
             "uuid": "fee8a188-5783-44cd-a1c1-ed9d5d7c32a9",
             "version": "2019-04-03T101353.834000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "70bbc6b8",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "7385add25e1c482b4d9b4881fb3e196f",
-            "sha1": "df323c0304644ec6c9cc94694198f568fa43ca86",
-            "sha256": "3cec4e10f26331a01ccea9741267a9d5a59a00a39b5a67059cd3f18eb3030663",
-            "size": 14532,
-            "uuid": "48f0d8a4-fd04-4fee-8301-7441b6efcf48",
-            "version": "2019-04-03T105534.952135Z"
-        },
         {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "d1fbf93a",
diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
index 6b5bd4ff6..f1be1bff2 100644
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
+++ b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
@@ -180,18 +180,6 @@
             "uuid": "b147df84-443b-4dd2-8327-7ea42adcd151",
             "version": "2019-03-17T220103.254000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "5356a6ba",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "9b3b812e32f35e5406449b2b4221da39",
-            "sha1": "0881415da33135bb54802129c3fec9b462035ab4",
-            "sha256": "82606b3dc782eeacdcc0d5a670d4e6bf5fc453998c63fc40a2f0318ac5dfc1ef",
-            "size": 2335,
-            "uuid": "feb61912-5a3c-4e12-a4ba-28a0207835fd",
-            "version": "2019-03-17T220643.786686Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "da1a6040",
diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
index 8c4d7a98e..6a577e48d 100644
--- a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
@@ -1,16 +1,5 @@
 {
     "manifest": [
-        {
-            "name": "links.json",
-            "uuid": "00f48893-5e9d-52cd-b32d-af88edccabfa",
-            "version": "2020-02-03T10:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 12651,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "Retina_Wong_scRNA_Sample5_I1.fastq.gz",
             "uuid": "07b45ad4-7797-4c16-bfae-493fb41d6600",
diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
index 3aa26458d..52244e823 100644
--- a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
+++ b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
@@ -33,17 +33,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "02e69c25-71e2-48ca-a87b-e256938c6a98",
-            "version": "2021-06-28T14:21:18.700000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 23068,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "process_0.json",
             "uuid": "02e69c25-71e2-48ca-a87b-e256938c6a98",
diff --git a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
index 8ce7cebd5..d4bed59fe 100644
--- a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
+++ b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
@@ -178,17 +178,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "04836733-0449-4e57-be2e-6f3b8fbdfb12",
-            "version": "2021-05-10T23:25:12.412000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 358661,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "process_0.json",
             "uuid": "04836733-0449-4e57-be2e-6f3b8fbdfb12",
diff --git a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
index d2d1e73cc..21d4beb7f 100644
--- a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
+++ b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
@@ -11,17 +11,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "0722b70c-6778-423d-8fe9-869e2a515d35",
-            "version": "2021-03-18T11:38:49.863000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 1697,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "process_0.json",
             "uuid": "0722b70c-6778-423d-8fe9-869e2a515d35",
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
index c3e399acd..769139153 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
@@ -312,18 +312,6 @@
             "sha256": "55b54e2b1001ad02aa4d319138aee07492653efb25df7c029d2ec915147bb0a7",
             "s3_etag": "b275f550a67f0f13bd9d72b4c7ab2965"
         },
-        {
-            "name": "links.json",
-            "uuid": "3bdcee29-2225-4033-95e1-8330208629e9",
-            "version": "2019-09-24T09:35:06.958773Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 3451,
-            "indexed": true,
-            "crc32c": "28463345",
-            "sha1": "65c1b41dc541d3c0b70c6303c9776cd0b886fce4",
-            "sha256": "8df416fbfb97a4ec0941575294eff77124e635fe4cc4e5cf6a17e78bd2fd3884",
-            "s3_etag": "dda677a4c7cba00d4708e9246e3bc12a"
-        },
         {
             "name": "IDC9_L001_I1.fastq.gz",
             "uuid": "08bc2234-5157-4f5c-b348-5d63cc9f14e1",
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index 5f92b228c..2e377a6ca 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -96,17 +96,6 @@
             "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_385feda5-d1e3-5a51-8e55-f4f491a4e7bf"
         },
-        {
-            "name": "links.json",
-            "uuid": "1b6d8348-d6e9-406a-aa6a-7ee886e52bf9",
-            "version": "2019-09-24T09:35:06.958773Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 3786,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
-        },
         {
             "name": "IDC9_L001_R2.fastq.gz",
             "uuid": "1b9d4386-97ac-402d-a93d-40740b2c3c28",
diff --git a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
index a09cbdaf4..5db6250e6 100644
--- a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
+++ b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
@@ -33,17 +33,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "1fd499c5-f397-4bff-9af0-eb42c37d5fbe",
-            "version": "2021-03-18T11:38:49.884000Z",
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-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "process_1.json",
             "uuid": "1fd499c5-f397-4bff-9af0-eb42c37d5fbe",
diff --git a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
index 3eb746590..4f7fc5d64 100644
--- a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
+++ b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
@@ -1,16 +1,5 @@
 {
     "manifest": [
-        {
-            "name": "links.json",
-            "uuid": "2c7d06b8-658e-4c51-9de4-a768322f84c5",
-            "version": "2021-09-21T17:27:23.898000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 1638,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
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             "name": "process_0.json",
             "uuid": "2c7d06b8-658e-4c51-9de4-a768322f84c5",
diff --git a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
index 0140db290..c2694b954 100644
--- a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
+++ b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
@@ -360,18 +360,6 @@
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             "version": "2018-11-02T17:38:45.850000Z"
         },
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-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "567cca4c",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "4a7aeb9e5b2d42d416248c035df24104",
-            "sha1": "2f9e6ece95cd5a7484f9b1913c00a0e0e168712c",
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-            "uuid": "a45e08a3-a4c0-4710-8be0-0fc3ab52ceb8",
-            "version": "2018-11-02T18:40:10.540316Z"
-        },
         {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "ce4f092f",
diff --git a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
index 3a1276a7d..a232a860d 100644
--- a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
+++ b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
@@ -576,18 +576,6 @@
             "uuid": "4a1432a1-ae18-45f2-b574-9869b7242289",
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-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "2bc3ad5f",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "d96e6fda9532e606b44d0ff2fcb0cc6d",
-            "sha1": "f3c05d096a45d3a3dc494268b358816e35b77c61",
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-            "uuid": "302206c2-e1d8-49d9-a4b9-7ffe15a77581",
-            "version": "2018-10-24T23:43:45.969008Z"
-        },
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             "content-type": "text/plain; dcp-type=data",
             "crc32c": "7fea1984",
diff --git a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index c32bc21ec..6d7cb2625 100644
--- a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -684,18 +684,6 @@
             "uuid": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
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-            "crc32c": "e90e51d2",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "850967c36ce39ca1c39cb50fbbce2e3a",
-            "sha1": "f8819c84b8a3243f8383e044824ed418c4b9c123",
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-            "uuid": "4e4a6937-c54a-4933-913a-0ab2cddaaa6f",
-            "version": "2018-10-18T20:46:11.972661Z"
-        },
         {
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             "crc32c": "e511d1cf",
diff --git a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 678ee4be7..185506e10 100644
--- a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -684,18 +684,6 @@
             "uuid": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
             "version": "2018-10-11T21:18:10.586000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "e90e51d2",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "850967c36ce39ca1c39cb50fbbce2e3a",
-            "sha1": "f8819c84b8a3243f8383e044824ed418c4b9c123",
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-            "uuid": "4e4a6937-c54a-4933-913a-0ab2cddaaa6f",
-            "version": "2018-10-18T20:46:11.972661Z"
-        },
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             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "e511d1cf",
diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index 8ff3547e7..93c70d14a 100644
--- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
+++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
@@ -78,17 +78,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "4426adc5-b3c5-5aab-ab86-51d8ce44dfbe",
-            "version": "2020-08-10T21:24:26.174274Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 3322,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "library_preparation_protocol_0.json",
             "uuid": "5b503dcb-dca6-4e4f-988b-f7100c030dc5",
diff --git a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
index c0f2574fe..1363f86b3 100644
--- a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
+++ b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
@@ -23,17 +23,6 @@
             "crc32c": "5bf9776f",
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         },
-        {
-            "name": "links.json",
-            "uuid": "4b03c1ce-9df1-5cd5-a8e4-48a2fe095081",
-            "version": "2021-02-10T16:56:40.419579Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 935,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "supplementary_file_1.json",
             "uuid": "5b465aad-0981-5152-b468-e615e20f5884",
diff --git a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
index e8f318774..920040235 100644
--- a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
+++ b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
@@ -528,18 +528,6 @@
             "uuid": "908d468a-eb62-4d19-8706-c5f708a14940",
             "version": "2018-10-10T02:23:43.104000Z"
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-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "7b8cabc3",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "56f651d69c90f007ae6457f2bc7b1480",
-            "sha1": "b98a0163f28458ed17a4f30c7592e58d93870eb8",
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-            "uuid": "07086553-f0ef-446a-af5c-cd96295214b7",
-            "version": "2018-10-10T03:10:31.063705Z"
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         {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "074766b5",
diff --git a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
index 7254cc7cf..850a472aa 100644
--- a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
+++ b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
@@ -2222,17 +2222,6 @@
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-            "uuid": "79fa91b4-f1fc-534b-a935-b57342804a70",
-            "version": "2020-12-10T10:30:00.000000Z",
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-            "size": 76574,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "sequence_file_29.json",
             "uuid": "7a058660-f594-4eb5-b02f-bace314f6d76",
diff --git a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
index bd480066d..14032393d 100644
--- a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
+++ b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
@@ -143,17 +143,6 @@
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-            "uuid": "7eb74d9f-8346-5420-b7e4-b486f99451a8",
-            "version": "2020-02-03T10:30:00.000000Z",
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-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
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         {
             "name": "project_0.json",
             "uuid": "8185730f-4113-40d3-9cc3-929271784c2b",
diff --git a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
index 89ff6add9..4f8d05032 100644
--- a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
+++ b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
@@ -138,17 +138,6 @@
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-            "uuid": "80baee6e-00a5-4fdc-bfe3-d339ff8a7178",
-            "version": "2021-03-12T22:43:32.330000Z",
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-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
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         {
             "name": "process_1.json",
             "uuid": "80baee6e-00a5-4fdc-bfe3-d339ff8a7178",
diff --git a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
index 146a0f535..658d4936f 100644
--- a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
@@ -57,17 +57,6 @@
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-        {
-            "name": "links.json",
-            "uuid": "8338b891-f3fa-5e7b-885f-e4ee5689ee15",
-            "version": "2020-12-03T10:39:17.144517Z",
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-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
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         {
             "name": "supplementary_file_2.json",
             "uuid": "8d2ba1c1-bc9f-5c2a-a74d-fe5e09bdfb18",
diff --git a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
index 6df1142ce..b8c0e4669 100644
--- a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
+++ b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
@@ -348,18 +348,6 @@
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-            "uuid": "50f1b06c-511b-4145-b9d2-67b5a75dd573",
-            "version": "2019-10-14T19:54:58.503698Z",
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             "uuid": "f4146a80-2737-4299-8d9a-0ec685dbac8b",
diff --git a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
index 88cb2f9df..78a1a3649 100644
--- a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
+++ b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
@@ -2844,18 +2844,6 @@
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diff --git a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
index 8403358ef..28629f6db 100644
--- a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
+++ b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
@@ -168,18 +168,6 @@
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             "name": "E8.75_anterior_Rep1_barcodes.fastq.gz",
             "uuid": "1fdcd06c-ea5b-4e5a-b382-ae42dcfc8aca",
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
index 35179cfc3..bbd43843e 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
@@ -156,18 +156,6 @@
             "uuid": "4674255d-5ecd-4860-9b8d-beae98772cd9",
             "version": "2018-11-02T10:12:03.520000Z"
         },
-        {
-            "content-type": "application/json; dcp-type='metadata/links'",
-            "crc32c": "aace07f3",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "77a21047cf9b7c706e72663090e67d4d",
-            "sha1": "766cefe20615e3f8aa5e0fc2042e4192d0494041",
-            "sha256": "e4163bdffb83d5cdf9f00b51febd05962fbc728189fc7c836ab0d4a667680c6c",
-            "size": 2083,
-            "uuid": "b09d8a5a-550c-425f-baaa-1c963a8a3312",
-            "version": "2018-11-02T11:33:44.257057Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "54bb9c82",
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
index 4eb03b66e..b624f9147 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
@@ -156,18 +156,6 @@
             "uuid": "4674255d-5ecd-4860-9b8d-beae98772cd9",
             "version": "2018-11-04T10:12:03.520000Z"
         },
-        {
-            "content-type": "application/json; dcp-type='metadata/links'",
-            "crc32c": "aace07f3",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "77a21047cf9b7c706e72663090e67d4d",
-            "sha1": "766cefe20615e3f8aa5e0fc2042e4192d0494041",
-            "sha256": "e4163bdffb83d5cdf9f00b51febd05962fbc728189fc7c836ab0d4a667680c6c",
-            "size": 2083,
-            "uuid": "b09d8a5a-550c-425f-baaa-1c963a8a3312",
-            "version": "2018-11-04T11:33:44.257057Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "54bb9c82",
diff --git a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
index 842fb2e3c..ae2cf7e90 100644
--- a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
+++ b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
@@ -180,18 +180,6 @@
             "uuid": "34aa8a89-27d0-4a03-8196-72da4d701efb",
             "version": "2018-09-12T12:11:53.497592Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "8dabafdc",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "9187a3a62eac5c71798be5606a5db5b0",
-            "sha1": "590f7e494654860bfe36d95d180b604ae7291f0f",
-            "sha256": "18d00a235d016427f344e22e9b27f757c620dead17b1e9f14d887128efa666e3",
-            "size": 2748,
-            "uuid": "372dfa6d-fc17-4a6b-be36-9ddeebb8544b",
-            "version": "2018-09-12T12:11:53.763631Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "13312585",
diff --git a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
index bb295fec4..d3d010a16 100644
--- a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
+++ b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
@@ -180,18 +180,6 @@
             "uuid": "8b1f44be-7eaa-4030-b6c5-697c5fc388eb",
             "version": "2019-07-18T21:12:44.455000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "6fa63916",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "3d2c1f5323d5645a4946394ae97156f3",
-            "sha1": "801cfabd504abfd3d72c23367c0e7f6686f8db65",
-            "sha256": "12f0d3f084cb9f87ba0f72b8923ea8fc4548808915a4d8ebf889d887f31065e5",
-            "size": 2465,
-            "uuid": "67d2808f-f774-4f00-96a9-9ef6d1ebb817",
-            "version": "2019-07-18T21:29:49.279115Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "64e45095",
diff --git a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
index edfb64ef2..cfdb0d0b0 100644
--- a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
+++ b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
@@ -9372,18 +9372,6 @@
             "uuid": "3197c12d-693c-49c9-992b-9051a4794814",
             "version": "2018-10-03T14:41:35.677792Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "00c67c50",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "284c852451692ae94a19fcabddfd74eb",
-            "sha1": "33b37aea194d1903fefb76e2b08d291c0e7d35eb",
-            "sha256": "25b4bbc69b4eb48f3758d75dcf3af7a8ce8579e9a5a0fd48004fa053d0d6398e",
-            "size": 523539,
-            "uuid": "df99abec-3681-4216-98e0-dcef817edc4d",
-            "version": "2018-10-03T14:41:35.975980Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "db304acb",
diff --git a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
index e7ea43adb..833ab0476 100644
--- a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
+++ b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
@@ -528,18 +528,6 @@
             "uuid": "44edcce5-152d-401c-ba29-ed73cd9ec57f",
             "version": "2018-09-06T18:57:40.546407Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "9f74bbaf",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "f686b75d62d09a84479046f497db0831",
-            "sha1": "bc9ee2d73c5228a3b56a4f40442b86e09ac8696a",
-            "sha256": "0900e839b6924ad0ba3a4f1f0266761989d0901358f7d6f7819d809ead8980c2",
-            "size": 5783,
-            "uuid": "77a7b5fd-01e1-40a9-a87a-d7c146c35c75",
-            "version": "2018-09-06T18:57:41.197346Z"
-        },
         {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "7171048d",
diff --git a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
index bc0849cc5..8d7d20190 100644
--- a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
@@ -684,18 +684,6 @@
             "uuid": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
             "version": "2018-10-11T21:18:10.586000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "e90e51d2",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "850967c36ce39ca1c39cb50fbbce2e3a",
-            "sha1": "f8819c84b8a3243f8383e044824ed418c4b9c123",
-            "sha256": "ef3b8c62921e5b016ec1609d93f348c7e48ec5452a7c9e0a9968b649c69c84f4",
-            "size": 24588,
-            "uuid": "4e4a6937-c54a-4933-913a-0ab2cddaaa6f",
-            "version": "2018-10-18T20:46:11.972661Z"
-        },
         {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "e511d1cf",
diff --git a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
index 277d529c1..2e9d79780 100644
--- a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
+++ b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
@@ -216,18 +216,6 @@
             "uuid": "84d06811-a6b5-4a37-809c-842b0ca9e093",
             "version": "2018-12-04T16:22:57.045000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "2b78e964",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "f0743e4e7e807d6bc26f51264eb0358d",
-            "sha1": "35255cc50616f8367ae7b238457e1f609b5c6897",
-            "sha256": "b496c0bb5fbcedb42e505afbe402b9c12fb6969e6aff506742b59521562d65b8",
-            "size": 3043,
-            "uuid": "c159c5f6-200e-4451-b387-9368d70a8442",
-            "version": "2018-12-05T23:08:45.226963Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "43d9f66a",
diff --git a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
index 3cea1a695..aaeaf6953 100644
--- a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
@@ -576,18 +576,6 @@
             "uuid": "4a1432a1-ae18-45f2-b574-9869b7242289",
             "version": "2018-10-16T08:06:34.625000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "bb93ecdd",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "bf6bd20beb3c637e3a2349449f16fa39",
-            "sha1": "82dc9911a05a3f1e705dee87ecee09dc5f12adb8",
-            "sha256": "d670b1c7ec77b4928ccd7c6de6c1552c473e2727d76a90a4ba523dfd2d58855f",
-            "size": 6414,
-            "uuid": "3c293e25-0410-4d51-b52e-ec7e74b3fb4f",
-            "version": "2018-10-24T23:42:14.241258Z"
-        },
         {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "6bb92520",
diff --git a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
index 828c98423..2990aa646 100644
--- a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
+++ b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
@@ -3600,18 +3600,6 @@
             "uuid": "8b1f44be-7eaa-4030-b6c5-697c5fc388eb",
             "version": "2019-07-18T21:12:44.455000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "927d1da3",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "0617fdd7789db13775d2ffafd4dcefc9",
-            "sha1": "477428b0566112cf9a50d4b7fdf6716ad0b7d630",
-            "sha256": "5cc8bd0f57369d910fe69c742c42d6ead90397a01ecdece4ceb0a83963800384",
-            "size": 18864,
-            "uuid": "a3c7cdcb-131d-467e-852d-b556d307c40e",
-            "version": "2019-07-23T06:45:53.877413Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "28590550",
diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index 9c6007653..f34a77fe3 100644
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -204,18 +204,6 @@
             "uuid": "c0f05fdb-8375-4c39-adba-24a63c004b9d",
             "version": "2018-09-14T12:33:43.318246Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "9ce4b69a",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "4ecdc10304fec328a6a2bb79b73a848c",
-            "sha1": "7b4ad28babc0027e0cce3e6151f9de3dc3d0d2cf",
-            "sha256": "e228e25a5404cfb724b4804de5cecff96695a652dafd1c6abdaa32fa0207598a",
-            "size": 2095,
-            "uuid": "6db034c3-0060-4cb7-a86b-15545b7fef61",
-            "version": "2018-09-14T12:33:43.485382Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "980453cc",
diff --git a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
index 3498a6ab3..b7df8b085 100644
--- a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
+++ b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
@@ -360,18 +360,6 @@
             "uuid": "85b60548-5e15-4efa-8baa-966f0de7d11c",
             "version": "2019-02-14T18:29:48.758000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "1c529673",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "ff78ad1cfe4bb03be728b85903c5853b",
-            "sha1": "2c8afbe3fa187b24364dec2153885b9f1240204e",
-            "sha256": "3c118283ff5de04792e598df38a523920ddb5068e211c591f6efbcc881e184f0",
-            "size": 7988,
-            "uuid": "81b98ed4-e366-4c18-ba60-398abb4359fa",
-            "version": "2019-02-14T19:24:27.259003Z"
-        },
         {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "1e03bc76",
diff --git a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
index 45262fb29..acabe1388 100644
--- a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
+++ b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
@@ -7104,17 +7104,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "fce68057-b0f0-5d11-b9a7-30e8fa3259a8",
-            "version": "2021-02-09T01:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 101562,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "sequence_file_118.json",
             "uuid": "fd0752c7-210b-4acd-a7ef-df7ffcdfbd3d",
diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
index cc54819b5..2cd51a806 100644
--- a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
+++ b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
@@ -168,18 +168,6 @@
             "uuid": "c7070951-ec8a-492f-a7be-354b5670c056",
             "version": "2019-10-09T15:36:21.507000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "78d21cea",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "ea8c58448e80259d02399dd65103f32f",
-            "sha1": "f1fca16d8ecabb2833b896b1994dcbe11a92db03",
-            "sha256": "e1046b17e04ae20586dccb8b771248f05085bbdc8f719d068554e1368968927f",
-            "size": 2266,
-            "uuid": "29b2a53c-299e-4062-a87a-c2aa393fc347",
-            "version": "2019-10-09T17:22:51.165978Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "49a9085f",
diff --git a/test/integration_test.py b/test/integration_test.py
index 537690956..6f421705b 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -1937,14 +1937,7 @@ def _test_catalog(self, catalog: config.Catalog):
                 self.assertIsInstance(metadata, dict)
                 manifest_files = sorted(e['name'] for e in manifest if e['indexed'])
                 metadata_files = sorted(metadata.keys())
-
-                if catalog.plugins['repository'].name == 'canned':
-                    # FIXME: Manifest entry not generated for links.json by
-                    #        StagingArea.get_bundle
-                    #        https://github.com/DataBiosphere/hca-metadata-api/issues/52
-                    assert 'links.json' not in manifest_files
-                    metadata_files.remove('links.json')
-
+                metadata_files.remove('links.json')
                 self.assertListEqual(manifest_files, metadata_files)
             elif metadata_plugin_name == 'anvil':
                 self.assertEqual({'entities', 'links'}, bundle_json.keys())