From 066f3af7895528dac4a2223183730eae0c02f478 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Mon, 10 Feb 2025 12:59:22 -0800
Subject: [PATCH] Bug fix - "Select hosted genomes" did not download.

---
 src/main/java/org/broad/igv/ucsc/hub/Hub.java             | 3 ---
 src/main/java/org/broad/igv/ui/IGVMenuBar.java            | 5 ++---
 .../java/org/broad/igv/ui/commandbar/GenomeComboBox.java  | 2 +-
 .../igv/ui/commandbar/HostedGenomeSelectionDialog.java    | 8 ++------
 4 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/src/main/java/org/broad/igv/ucsc/hub/Hub.java b/src/main/java/org/broad/igv/ucsc/hub/Hub.java
index 6aaadc188..dcaf9429b 100644
--- a/src/main/java/org/broad/igv/ucsc/hub/Hub.java
+++ b/src/main/java/org/broad/igv/ucsc/hub/Hub.java
@@ -125,9 +125,6 @@ public GenomeConfig getGenomeConfig() {
         if (genomeStanza.hasProperty("chromAliasBb")) {
             config.setChromAliasBbURL(genomeStanza.getProperty("chromAliasBb"));
         }
-        if (genomeStanza.hasProperty("twoBitBptURL")) {
-            config.setTwoBitBptURL(genomeStanza.getProperty("twoBitBptURL"));
-        }
         if (genomeStanza.hasProperty("twoBitBptUrl")) {
             config.setTwoBitBptURL(genomeStanza.getProperty("twoBitBptUrl"));
         }
diff --git a/src/main/java/org/broad/igv/ui/IGVMenuBar.java b/src/main/java/org/broad/igv/ui/IGVMenuBar.java
index c9659150a..2f65cd459 100644
--- a/src/main/java/org/broad/igv/ui/IGVMenuBar.java
+++ b/src/main/java/org/broad/igv/ui/IGVMenuBar.java
@@ -307,7 +307,6 @@ JMenu createFileMenu(Genome genome) {
         // Track hubs
         if (genome.getTrackHubs().size() > 0) {
             menuItems.add(new JSeparator());
-            menuItems.add(new JLabel("Track Hubs"));
             for (Hub trackHub : genome.getTrackHubs()) {
                 menuAction = new SelectHubTracksAction(trackHub.getShortLabel(), igv, trackHub);
                 menuAction.setToolTipText(trackHub.getLongLabel());
@@ -441,8 +440,8 @@ private JMenu createGenomesMenu() {
 
         JMenu menu = new JMenu("Genomes");
 
-        loadGenomeFromServerMenuItem = new JMenuItem("Select Hosted Genome...");
-        loadGenomeFromServerMenuItem.addActionListener(e -> HostedGenomeSelectionDialog.selectHostedGenome());
+        loadGenomeFromServerMenuItem = new JMenuItem("Download Hosted Genome...");
+        loadGenomeFromServerMenuItem.addActionListener(e -> HostedGenomeSelectionDialog.downloadHostedGenome());
         loadGenomeFromServerMenuItem.setToolTipText(LOAD_GENOME_SERVER_TOOLTIP);
         menu.add(loadGenomeFromServerMenuItem);
 
diff --git a/src/main/java/org/broad/igv/ui/commandbar/GenomeComboBox.java b/src/main/java/org/broad/igv/ui/commandbar/GenomeComboBox.java
index 687eee0a1..ea8a2fcda 100644
--- a/src/main/java/org/broad/igv/ui/commandbar/GenomeComboBox.java
+++ b/src/main/java/org/broad/igv/ui/commandbar/GenomeComboBox.java
@@ -96,7 +96,7 @@ public void actionPerformed(ActionEvent actionEvent) {
                 if (genomeListItem != null && genomeListItem.getPath() != null) {
 
                     if (genomeListItem == GenomeListItem.DOWNLOAD_ITEM) {
-                        HostedGenomeSelectionDialog.selectHostedGenome();
+                        HostedGenomeSelectionDialog.downloadHostedGenome();
                     } else {
 
                         try {
diff --git a/src/main/java/org/broad/igv/ui/commandbar/HostedGenomeSelectionDialog.java b/src/main/java/org/broad/igv/ui/commandbar/HostedGenomeSelectionDialog.java
index 4cf472c7d..29eebb844 100644
--- a/src/main/java/org/broad/igv/ui/commandbar/HostedGenomeSelectionDialog.java
+++ b/src/main/java/org/broad/igv/ui/commandbar/HostedGenomeSelectionDialog.java
@@ -88,7 +88,7 @@ public class HostedGenomeSelectionDialog extends org.broad.igv.ui.IGVDialog {
      * Open a selection list to load a genome from the server.   This method is static because its used by multiple
      * UI elements  (menu bar and genome selection pulldown).
      */
-    public static void selectHostedGenome() {
+    public static void downloadHostedGenome() {
 
         Runnable showDialog = () -> {
 
@@ -109,11 +109,7 @@ public static void selectHostedGenome() {
                 boolean downloadSequence = dialog.isDownloadSequence();
                 boolean downloadAnnotations = dialog.isDownloadAnnotations();
 
-                File downloadPath = null;
-                if (downloadSequence || downloadAnnotations || selectedItem.getPath().endsWith(".genome")) {
-                    downloadPath = GenomeManager.getInstance().downloadGenome(selectedItem, downloadSequence, downloadAnnotations);
-                }
-
+                File downloadPath = GenomeManager.getInstance().downloadGenome(selectedItem, downloadSequence, downloadAnnotations);
 
                 try {
                     if (downloadPath != null) {