From 72f9ef8934292b3ae8e5622288002b0ed27dd692 Mon Sep 17 00:00:00 2001
From: OganM <ogan.mancarci@gmail.com>
Date: Fri, 5 Jun 2026 18:24:57 -0700
Subject: [PATCH 1/5] default to currently installed hdf5

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 6f984f2170..ddb47ef604 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1668,7 +1668,7 @@
 		<!-- You may override these in ~/.m2/settings.xml. On macOS install with the HDF Group
 		     binary tarball (which ships libhdf5_java.dylib and jarhdf5-X.Y.Z.jar) and set
 		     hdf5.libDir to the bundled lib/ directory. -->
-		<hdf5.version>1.12.3</hdf5.version>
+		<hdf5.version>1.12.1</hdf5.version>
 		<!-- directory containing the HDF5 JNI shared library -->
 		<hdf5.libDir>/usr/lib64/hdf5</hdf5.libDir>
 		<mysql.version>8.4.0</mysql.version>

From c6ae4487edb382a42ec7f686588298e161a77972 Mon Sep 17 00:00:00 2001
From: OganM <ogan.mancarci@gmail.com>
Date: Fri, 5 Jun 2026 20:54:04 -0700
Subject: [PATCH 2/5] configuration for gemma-rest set to 8181

---
 .idea/runConfigurations/Gemma_Rest.xml | 91 ++++++++++++++++++++++++++
 1 file changed, 91 insertions(+)
 create mode 100644 .idea/runConfigurations/Gemma_Rest.xml

diff --git a/.idea/runConfigurations/Gemma_Rest.xml b/.idea/runConfigurations/Gemma_Rest.xml
new file mode 100644
index 0000000000..dfda70c9a4
--- /dev/null
+++ b/.idea/runConfigurations/Gemma_Rest.xml
@@ -0,0 +1,91 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Gemma Rest" type="#com.intellij.j2ee.web.tomcat.TomcatRunConfigurationFactory" factoryName="Local" APPLICATION_SERVER_NAME="Tomcat" ALTERNATIVE_JRE_ENABLED="false">
+    <option name="COMMON_VM_ARGUMENTS" value="-Dspring.profiles.active=dev -Dgemma.mail.username=dev -Dgemma.runas.password=dev-runas-pw -Dgemma.anonymousAuth.key=dev-anon-key -Dgemma.agent.password=dev-agent-pw" />
+    <option name="UPDATING_POLICY" value="restart-server" />
+    <deployment>
+      <artifact name="gemma-rest:war exploded">
+        <settings>
+          <option name="CONTEXT_PATH" value="/" />
+        </settings>
+      </artifact>
+    </deployment>
+    <server-settings>
+      <option name="BASE_DIRECTORY_NAME" value="d57f1d5c-7d9c-4543-98a4-d3fc72e5ae01" />
+      <option name="HTTP_PORT" value="8181" />
+    </server-settings>
+    <predefined_log_file enabled="true" id="Tomcat" />
+    <predefined_log_file enabled="true" id="Tomcat Catalina" />
+    <predefined_log_file id="Tomcat Manager" />
+    <predefined_log_file id="Tomcat Host Manager" />
+    <predefined_log_file id="Tomcat Localhost Access" />
+    <RunnerSettings RunnerId="Debug">
+      <option name="DEBUG_PORT" value="36821" />
+    </RunnerSettings>
+    <ConfigurationWrapper VM_VAR="JAVA_OPTS" RunnerId="Cover">
+      <option name="USE_ENV_VARIABLES" value="true" />
+      <STARTUP>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </STARTUP>
+      <SHUTDOWN>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </SHUTDOWN>
+    </ConfigurationWrapper>
+    <ConfigurationWrapper VM_VAR="JAVA_OPTS" RunnerId="Debug">
+      <option name="USE_ENV_VARIABLES" value="true" />
+      <STARTUP>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </STARTUP>
+      <SHUTDOWN>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </SHUTDOWN>
+    </ConfigurationWrapper>
+    <ConfigurationWrapper VM_VAR="JAVA_OPTS" RunnerId="Profile">
+      <option name="USE_ENV_VARIABLES" value="true" />
+      <STARTUP>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </STARTUP>
+      <SHUTDOWN>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </SHUTDOWN>
+    </ConfigurationWrapper>
+    <ConfigurationWrapper VM_VAR="JAVA_OPTS" RunnerId="Run">
+      <option name="USE_ENV_VARIABLES" value="true" />
+      <STARTUP>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </STARTUP>
+      <SHUTDOWN>
+        <option name="USE_DEFAULT" value="true" />
+        <option name="SCRIPT" value="" />
+        <option name="VM_PARAMETERS" value="" />
+        <option name="PROGRAM_PARAMETERS" value="" />
+      </SHUTDOWN>
+    </ConfigurationWrapper>
+    <method v="2">
+      <option name="Make" enabled="true" />
+      <option name="BuildArtifacts" enabled="true">
+        <artifact name="gemma-rest:war exploded" />
+      </option>
+    </method>
+  </configuration>
+</component>
\ No newline at end of file

From 5c30e4bd79f7f0868f7ffca035cabb3d4bf4d0e4 Mon Sep 17 00:00:00 2001
From: OganM <ogan.mancarci@gmail.com>
Date: Tue, 9 Jun 2026 19:00:21 -0700
Subject: [PATCH 3/5] specific tomcat for configuration

---
 .idea/runConfigurations/Gemma_Rest.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.idea/runConfigurations/Gemma_Rest.xml b/.idea/runConfigurations/Gemma_Rest.xml
index dfda70c9a4..e04a1ab8fa 100644
--- a/.idea/runConfigurations/Gemma_Rest.xml
+++ b/.idea/runConfigurations/Gemma_Rest.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Gemma Rest" type="#com.intellij.j2ee.web.tomcat.TomcatRunConfigurationFactory" factoryName="Local" APPLICATION_SERVER_NAME="Tomcat" ALTERNATIVE_JRE_ENABLED="false">
+  <configuration default="false" name="Gemma Rest" type="#com.intellij.j2ee.web.tomcat.TomcatRunConfigurationFactory" factoryName="Local" APPLICATION_SERVER_NAME="Tomcat 10.1.34" ALTERNATIVE_JRE_ENABLED="false">
     <option name="COMMON_VM_ARGUMENTS" value="-Dspring.profiles.active=dev -Dgemma.mail.username=dev -Dgemma.runas.password=dev-runas-pw -Dgemma.anonymousAuth.key=dev-anon-key -Dgemma.agent.password=dev-agent-pw" />
     <option name="UPDATING_POLICY" value="restart-server" />
     <deployment>

From 50f538378be9e356497361e916e35e1cbc285237 Mon Sep 17 00:00:00 2001
From: OganM <ogan.mancarci@gmail.com>
Date: Tue, 9 Jun 2026 19:00:37 -0700
Subject: [PATCH 4/5] shift java versions on jenkins

---
 .jenkins/Jenkinsfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.jenkins/Jenkinsfile b/.jenkins/Jenkinsfile
index fa9f7613a2..5a5df54732 100644
--- a/.jenkins/Jenkinsfile
+++ b/.jenkins/Jenkinsfile
@@ -23,6 +23,7 @@ pipeline {
     agent any
     tools {
         maven 'Maven 3.6.3'
+        jdk 'Java 25'
     }
     environment {
         GEMMA_CLI_WIKI_DEPLOY_TOKEN = credentials('confluence-wiki-token')
@@ -210,7 +211,7 @@ pipeline {
                 }
                 stage('SonarQube Analysis') {
                     tools {
-                        jdk 'Java 17'
+                        jdk 'Java 25'
                     }
                     when {
                         anyOf {

From aa71c9ba7620d42810a1e44fd47fbb406260a700 Mon Sep 17 00:00:00 2001
From: OganM <ogan.mancarci@gmail.com>
Date: Thu, 18 Jun 2026 12:52:46 -0700
Subject: [PATCH 5/5] differential expression with subsets fix

---
 .../diff/DifferentialExpressionAnalysisReadServiceImpl.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisReadServiceImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisReadServiceImpl.java
index 0e92f47228..86b5478e12 100644
--- a/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisReadServiceImpl.java
+++ b/gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/DifferentialExpressionAnalysisReadServiceImpl.java
@@ -267,8 +267,8 @@ public Map<ExpressionExperimentDetailsValueObject, Collection<DifferentialExpres
                 Collection<ExpressionAnalysisResultSet> results = analysis.getResultSets();
 
                 DifferentialExpressionAnalysisValueObject avo = new DifferentialExpressionAnalysisValueObject( analysis );
-
-                BioAssaySet experimentAnalyzed = analysis.getExperimentAnalyzed();
+                
+                BioAssaySet experimentAnalyzed = ( BioAssaySet ) Hibernate.unproxy( analysis.getExperimentAnalyzed() );
 
                 avo.setExperimentAnalyzedId( experimentAnalyzed.getId() ); // might be a subset.