From cb6af0224d39e1c96e3813120c71f5ab6bb344d2 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Fri, 11 Oct 2024 10:34:29 -0400
Subject: [PATCH] Fix for Amazon failing.

* Fix the amazon failures due to LogFactory not found by adding a module dependency
* on apache logging.  This is necessary because commons-logging became modularized
* between 1.2.0 and 1.3.0 but amazon is expecting the non-modular 1.2.0 while
* 1.3.0 is being brought in due to changes in htsjdk.
* See https://logging.apache.org/blog/2023/12/02/apache-common-logging-1.3.0.html for
* more info.
* Fix for https://github.com/igvteam/igv/issues/1598
---
 build.gradle                   | 9 ++++++++-
 src/main/java/module-info.java | 4 ++++
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index ab85c1039..16d6f892d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -137,9 +137,16 @@ dependencies {
             [group: 'software.amazon.awssdk', name: 'cognitoidentity', version: amazonVersion],
             [group: 'software.amazon.awssdk', name: 'sts', version: amazonVersion],
             [group: 'software.amazon.awssdk', name: 's3', version: amazonVersion],
-            [group: 'software.amazon.awssdk', name: 'sso', version: amazonVersion]
+            [group: 'software.amazon.awssdk', name: 'sso', version: amazonVersion],
+
+            // This is a transitive dependency from amazon but due to modularization changes between
+            // 1.20 and 1.3.0 we need to specify it here.
+            // This can be removed when amazon moves from 1.2.0 -> 1.3.0 and updates it's module requirements
+            // See https://logging.apache.org/blog/2023/12/02/apache-common-logging-1.3.0.html
+            [group: 'commons-logging', name: 'commons-logging', version: '1.3.0']
     )
 
+
     testImplementation(
             [group: 'junit', name: 'junit', version: '4.13.2'],
             [group: 'com.sparkjava', name: 'spark-core', version: '2.9.4'],
diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
index fb0b4a1f3..20ea2ca08 100644
--- a/src/main/java/module-info.java
+++ b/src/main/java/module-info.java
@@ -43,5 +43,9 @@
     requires software.amazon.awssdk.http;
     requires software.amazon.awssdk.utils;
 
+    // Transitive dependency of amazon modules that is required to be specified
+    // because amazon resolves the unmodularized 1.2.0 version while htjsdk brings in the modular 1.3.0
+    requires org.apache.commons.logging;
+
     requires jide.oss;
 }