From 93e9f2a2a26f60e2a09bda1f8f72a6929f66e418 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Sat, 25 Jan 2025 15:09:55 -0800
Subject: [PATCH] Bug fix -- support local path hub.txt files (for testing)

---
 src/main/java/org/broad/igv/ucsc/Hub.java | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/src/main/java/org/broad/igv/ucsc/Hub.java b/src/main/java/org/broad/igv/ucsc/Hub.java
index 2c9e7ff46..86c6db14b 100644
--- a/src/main/java/org/broad/igv/ucsc/Hub.java
+++ b/src/main/java/org/broad/igv/ucsc/Hub.java
@@ -44,12 +44,19 @@ private Hub(String url) throws IOException {
         String baseURL = url.substring(0, idx + 1);
         this.baseURL = baseURL;
 
-        try {
-            this.host = "https://" + (new URL(url)).getHost();
-        } catch (MalformedURLException e) {
-            // This should never happen
-            log.error("Error parsing base URL host", e);
-            throw new RuntimeException(e);
+        if(url.startsWith("https://") || url.startsWith("http://")) {
+            try {
+                URL tmp = new URL(url);
+                this.host = tmp.getProtocol() + "://" + tmp.getHost();
+            } catch (MalformedURLException e) {
+                // This should never happen
+                log.error("Error parsing base URL host", e);
+                throw new RuntimeException(e);
+            }
+        }
+        else {
+            // Local file, no host
+            this.host = "";
         }
 
         List<Stanza> stanzas = loadStanzas(url);
@@ -68,6 +75,8 @@ private Hub(String url) throws IOException {
             throw new RuntimeException("Unexpected hub file -- expected 'genome' stanza but found " + stanzas.get(1).type);
         }
 
+        this.hub = stanzas.get(0);
+
         // Load groups
         this. genomeStanza = stanzas.get(1);
         if (genomeStanza.hasProperty("groups")) {