From bd84617e054740fbc477f710b4b32a8ffee6b986 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 8 Nov 2024 15:26:00 +0000
Subject: [PATCH 1/4] Add Terra manifest to Download options

---
 .../src/components/FileTable.tsx              | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/packages/data-portal-explore/src/components/FileTable.tsx b/packages/data-portal-explore/src/components/FileTable.tsx
index f3a61726..36aa3d80 100644
--- a/packages/data-portal-explore/src/components/FileTable.tsx
+++ b/packages/data-portal-explore/src/components/FileTable.tsx
@@ -104,6 +104,28 @@ function generateGen3ManifestFile(files: Entity[]): string | undefined {
     return data.length > 0 ? JSON.stringify(data, null, 2) : undefined;
 }
 
+function generateTerraManifestFile(files: Entity[]): string | undefined {
+    const columns = [
+        'entity:drs_id',
+        'drs_uri',
+        'filename',
+    ];
+    const data = _(files)
+        .filter((f) => !!f.viewers?.cds)
+        .map((f) => [
+            f.viewers?.cds?.drs_id, // Assuming drs_id is a property in viewers.cds
+            f.viewers?.cds?.drs_uri,
+            f.name // Use `name` property for the filename
+        ])
+        .value();
+
+    if (data.length > 0) {
+        return [columns, ...data].map((row) => row.join('\t')).join('\n'); // Join with tabs for TSV format
+    } else {
+        return undefined;
+    }
+}
+
 
 const FilenameWithAccessIcon: React.FunctionComponent<{
     file: Entity;
@@ -244,6 +266,28 @@ const gen3ManifestInstructions = (gen3manifestFile: string | undefined) => {
     );
 };
 
+const terra3ManifestInstructions = (terra3manifestFile: string | undefined) => {
+    if (!terra3manifestFile) return null;
+
+    return (
+        <div>
+            <p></p>
+            <p>
+                <strong>Access files in Terra:</strong>{' '}
+                You can add these files to Terra using the following manifest file.
+            </p>
+            <p>
+                <button
+                    className="btn btn-light"
+                    onClick={() => fileDownload(terra3manifestFile, TERRA_MANIFEST_FILENAME)}
+                >
+                    <FontAwesomeIcon icon={faDownload} /> Download <code>terra_manifest.tsv</code>
+                </button>
+            </p>
+        </div>
+    );
+};
+
 const CDSInstructions: React.FunctionComponent<{ files: Entity[] }> = ({ files }) => {
     const dbgapFiles = files.filter(
         (f) => f.downloadSource === DownloadSourceCategory.dbgap
@@ -254,6 +298,7 @@ const CDSInstructions: React.FunctionComponent<{ files: Entity[] }> = ({ files }
 
     const manifestFile = generateCdsManifestFile(files);
     const gen3manifestFile = generateGen3ManifestFile(files);
+    const terra3manifestFile = generateTerraManifestFile(files);
 
     return (
         <div>
@@ -292,6 +337,7 @@ const CDSInstructions: React.FunctionComponent<{ files: Entity[] }> = ({ files }
 
             {/* CDS and Gen3 manifest instructions */}
             {cdsManifestInstructions(manifestFile)}
+            {terra3ManifestInstructions(terra3manifestFile)}
             {gen3ManifestInstructions(gen3manifestFile)}
         </div>
     );

From 1442ae26d6c31b6c8dc2489733f3f952731aca3e Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 8 Nov 2024 15:26:20 +0000
Subject: [PATCH 2/4] Add brief terra instructions

---
 packages/data-portal-explore/src/components/FileTable.tsx | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/packages/data-portal-explore/src/components/FileTable.tsx b/packages/data-portal-explore/src/components/FileTable.tsx
index 36aa3d80..c56cc306 100644
--- a/packages/data-portal-explore/src/components/FileTable.tsx
+++ b/packages/data-portal-explore/src/components/FileTable.tsx
@@ -274,7 +274,11 @@ const terra3ManifestInstructions = (terra3manifestFile: string | undefined) => {
             <p></p>
             <p>
                 <strong>Access files in Terra:</strong>{' '}
-                You can add these files to Terra using the following manifest file.
+                First link your Terra account to NCI CRDC Framework Services from your{' '}
+                <a href="https://app.terra.bio/#profile?tab=externalIdentities" target="_blank" rel="noopener noreferrer">
+                Terra profile External Identities
+                </a> page.{' '}
+                You can then add these files to Terra using the following manifest file.
             </p>
             <p>
                 <button

From f78913d3d719cd45df43f159f1d8390a19516f4c Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Mon, 18 Nov 2024 10:07:18 +0000
Subject: [PATCH 3/4] Define TERRA_MANIFEST_FILENAME

---
 packages/data-portal-explore/src/components/FileTable.tsx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/packages/data-portal-explore/src/components/FileTable.tsx b/packages/data-portal-explore/src/components/FileTable.tsx
index c56cc306..2bcaf99c 100644
--- a/packages/data-portal-explore/src/components/FileTable.tsx
+++ b/packages/data-portal-explore/src/components/FileTable.tsx
@@ -46,6 +46,7 @@ import {
 
 const CDS_MANIFEST_FILENAME = 'cds_manifest.csv';
 const GEN3_MANIFEST_FILENAME = 'gen3_manifest.json';
+const TERRA_MANIFEST_FILENAME = 'terra_manifest.tsv';
 
 interface IFileDownloadModalProps {
     files: Entity[];

From bb9520f7abe88be9c90e952e5b4c2af7536b5d99 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Mon, 18 Nov 2024 10:26:47 +0000
Subject: [PATCH 4/4] Change terra manifest format

---
 .../data-portal-explore/src/components/FileTable.tsx   | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/packages/data-portal-explore/src/components/FileTable.tsx b/packages/data-portal-explore/src/components/FileTable.tsx
index 2bcaf99c..2997884a 100644
--- a/packages/data-portal-explore/src/components/FileTable.tsx
+++ b/packages/data-portal-explore/src/components/FileTable.tsx
@@ -107,16 +107,14 @@ function generateGen3ManifestFile(files: Entity[]): string | undefined {
 
 function generateTerraManifestFile(files: Entity[]): string | undefined {
     const columns = [
-        'entity:drs_id',
-        'drs_uri',
-        'filename',
+        'entity:filename',
+        'drs_uri'
     ];
     const data = _(files)
         .filter((f) => !!f.viewers?.cds)
         .map((f) => [
-            f.viewers?.cds?.drs_id, // Assuming drs_id is a property in viewers.cds
-            f.viewers?.cds?.drs_uri,
-            f.name // Use `name` property for the filename
+            f.name, // Use `name` property for the filename
+            f.viewers?.cds?.drs_uri
         ])
         .value();