Release 2024-01-26-1200

MD-Anderson-Bioinformatics · Jan 26, 2024 · 59c9404 · 59c9404
1 parent 917197f
commit 59c9404
Show file tree

Hide file tree

Showing 65 changed files with 70 additions and 58 deletions.
diff --git a/README.md b/README.md
@@ -17,10 +17,10 @@ Make the following directories.
  - /MBA/PROPS
  - /MBA/UTIL
  - /MBA/WEBSITE
- - /MBA/MW_CONFIG
+ - /MBA/MW_CACHE
  - /MBA/MW_ZIP
 
- 1. Copy the contents of inst/ext/MW_CONFIG into /MBA/MW_CONFIG.
+ 1. Copy the contents of inst/ext/MW_CACHE into /MBA/MW_CACHE.
  2. Copy the contents of inst/ext/OUTPUT into /MBA/OUTPUT.
  3. Copy the contents of inst/ext/PROPS into /MBA/PROPS.
  4. Copy the contents of inst/ext/UTIL into /MBA/UTIL.

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/authorization/Authorization.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/authorization/Authorization.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/authorization/UserAndRoleData.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/authorization/UserAndRoleData.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/processes/BatchdataObj.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/processes/BatchdataObj.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/AuthOut.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/AuthOut.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/AuthUpdate.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/AuthUpdate.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/AuthUser.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/AuthUser.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/Batchdata.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/Batchdata.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/MBAServletMixin.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/MBAServletMixin.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/MBAproperties.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/MBAproperties.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/MBatchConfig.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/MBatchConfig.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/RBNConfig.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/RBNConfig.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadBatch.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadBatch.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadLinkMap.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadLinkMap.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadManifest.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadManifest.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadMatrix.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/UploadMatrix.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBGDCDownload.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBGDCDownload.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBMWDownload.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBMWDownload.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBRunMBatch.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBRunMBatch.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBdelete.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBdelete.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //
@@ -46,28 +46,38 @@ protected void internalProcess(HttpServletRequest request, StringBuffer theBuffe
 		if ((jobId!=null)&&!("".equals(jobId)))
 		{
 			File jobDir = new File(MBAUtils.M_OUTPUT, jobId);
+			log("JOBdelete jobDir = " + jobDir);
 			boolean success = deleteWebsiteFiles(jobId, this);
+			log("JOBdelete deleteWebsiteFiles = " + success);
 			if(true==success)
 			{
+				log("JOBdelete deleteQuietly before");
 				success = FileUtils.deleteQuietly(jobDir);
+				log("JOBdelete deleteQuietly = " + success);
 				if(true==success)
 				{
+					log("JOBdelete deleteJob before");
 					JobStatus.deleteJob(jobId, this);
+					log("JOBdelete deleteJob after");
 					theBuffer.append("Successfully deleted " + jobId);
+					log("Successfully deleted " + jobId);
 				}
 				else
 				{
 					theBuffer.append("Unable to delete " + jobId);
+					log("Unable to delete " + jobId);
 				}
 			}
 			else
 			{
 				theBuffer.append("Unable to delete website directory " + jobId);
+				log("Unable to delete website directory " + jobId);
 			}
 		}
 		else
 		{
 			theBuffer.append("No job specified");
+			log("No job specified");
 		}
 	}
 

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBdownload.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBdownload.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBinfo.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBinfo.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBlist.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBlist.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBnew.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBnew.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBnext.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBnext.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBstatus.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBstatus.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBupdate.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBupdate.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBwsurl.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/servlets/job/JOBwsurl.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/FileTail.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/FileTail.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/JOB_STATUS.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/JOB_STATUS.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/JobStatus.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/JobStatus.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/SendEmail.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/status/SendEmail.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/utils/MBAUtils.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/utils/MBAUtils.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/utils/PropertiesEsc.java b/apps/MetaBatchAnalyzer/src/main/java/edu/mda/bcb/mba/utils/PropertiesEsc.java
@@ -1,5 +1,5 @@
 /*
- *  Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+ *  Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
  *  
  *  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
  *  

diff --git a/apps/MetaBatchAnalyzer/src/test/java/edu/mda/bcb/mba/MBASuite.java b/apps/MetaBatchAnalyzer/src/test/java/edu/mda/bcb/mba/MBASuite.java
@@ -1,4 +1,4 @@
-// Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+// Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 //
 // This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 //

diff --git a/docker-build/mba-stack/02_dockerSed.bash b/docker-build/mba-stack/02_dockerSed.bash
@@ -49,7 +49,7 @@ JOB_OUTPUT_DIR=${LOCAL_PATH_ENV}/MBA/OUTPUT
 ### directory for the Batch Effects Website
 WEBSITE_DIR=${LOCAL_PATH_ENV}/MBA/WEBSITE
 ### read-only directory for util files
-UTIL_DIR=${LOCAL_PATH_ENV}/MBA/UTIL
+UTIL_DIR=${LOCAL_PATH_ENV}/MBA/UTILS
 
 # URL and tag to use as image name for MBA image, such as mdabcb/mba_image:DAP_BEA_VERSION_TIMESTAMP
 MBA_IMAGEURL=${9}

diff --git a/docker-build/mba-stack/bev-image/Dockerfile_template b/docker-build/mba-stack/bev-image/Dockerfile_template
@@ -64,7 +64,7 @@ ENV LD_LIBRARY_PATH=/usr/lib/jvm/java-17-openjdk/lib/server
 
 # install Tomcat 10, set to run as bcbuser
 ENV TOMCAT_MAJOR=10 \
-    TOMCAT_VERSION=10.1.13 \
+    TOMCAT_VERSION=10.1.18 \
     TOMCAT_HOME=/opt/tomcat \
     CATALINA_HOME=/opt/tomcat \
     CATALINA_OUT=/dev/null

diff --git a/docker-build/mba-stack/docker-compose.yml b/docker-build/mba-stack/docker-compose.yml
@@ -1,7 +1,7 @@
 # this is the docker compose version
 version: '3.0'
 
-# file version 2023-09-22-1600
+# file version 2024-01-26-1200
 
 
 networks:
@@ -23,7 +23,7 @@ services:
             context: ./mba-image
             dockerfile: Dockerfile
         container_name: mbaMBA_cont_hub
-        image: mdabcb/mba_image:2023-09-22-1600
+        image: mdabcb/mba_image:2024-01-26-1200
         volumes:
             # external:internal
             # external log path
@@ -35,9 +35,9 @@ services:
             # directory for the Batch Effects Website (must be on Linux file system since links to /MBA/OUTOUT are created here)
             - /MBA/MBA/WEBSITE:/BEA/MBA/WEBSITE
             # read-only directory for HG38 map
-            - /MBA/MBA/UTIL:/BEA/MBA/UTILS:ro
+            - /MBA/MBA/UTILS:/BEA/MBA/UTILS:ro
             # SMW paths for Metabolomics Workbench DAta
-            - /MBA/MW_CONFIG:/BEA/SMW/MW_CACHE:ro
+            - /MBA/MW_CACHE:/BEA/SMW/MW_CACHE:ro
             - /MBA/MW_ZIP:/BEA/SMW/MW_ZIP
             # read-only file to set time to same in image as on server
             - /etc/localtime:/etc/localtime:ro
@@ -55,14 +55,14 @@ services:
             context: ./mbatch-image
             dockerfile: Dockerfile
         container_name: mbatchMBA_cont_hub
-        image: mdabcb/mbatch_image:2023-09-22-1600
+        image: mdabcb/mbatch_image:2024-01-26-1200
         volumes:
             # directory for output from MBA, GDCDownload, and MBatch Results external:internal
             - /MBA/MBA/OUTPUT:/BEA/MBA/OUTPUT
             # directory for the Batch Effects Website (must be on Linux file system since links to /MBA/OUTOUT are created here)
             - /MBA/MBA/WEBSITE:/BEA/MBA/WEBSITE
             # SMW paths for Metabolomics Workbench DAta
-            - /MBA/MW_CONFIG:/BEA/SMW/MW_CACHE:ro
+            - /MBA/MW_CACHE:/BEA/SMW/MW_CACHE:ro
             - /MBA/MW_ZIP:/BEA/SMW/MW_ZIP
             # read-only file to set time to same in image as on server
             - /etc/localtime:/etc/localtime:ro
@@ -80,7 +80,7 @@ services:
             dockerfile: Dockerfile
         container_name: bevMBA_cont_hub
         # update :latest to desired version
-        image: mdabcb/bev_image:2023-09-22-1600
+        image: mdabcb/bev_image:2024-01-26-1200
         volumes:
             # external:internal
             # external log path

diff --git a/docker-build/mba-stack/mba-image/Dockerfile_template b/docker-build/mba-stack/mba-image/Dockerfile_template
@@ -64,7 +64,7 @@ ENV LD_LIBRARY_PATH=/usr/lib/jvm/java-17-openjdk/lib/server
 
 # install Tomcat 10, set to run as bcbuser
 ENV TOMCAT_MAJOR=10 \
-    TOMCAT_VERSION=10.1.13 \
+    TOMCAT_VERSION=10.1.18 \
     TOMCAT_HOME=/opt/tomcat \
     CATALINA_HOME=/opt/tomcat \
     CATALINA_OUT=/dev/null

diff --git a/docker-build/mba-stack/mbatch-image/installations/runMBatch1.R b/docker-build/mba-stack/mbatch-image/installations/runMBatch1.R
@@ -1,4 +1,4 @@
-# MBatch Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+# MBatch Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 #
 # This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 #

diff --git a/docker-build/mba-stack/mbatch-image/installations/runMBatch2.R b/docker-build/mba-stack/mbatch-image/installations/runMBatch2.R
@@ -1,4 +1,4 @@
-# MBatch Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+# MBatch Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 #
 # This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 #

diff --git a/docker-build/mba-stack/mbatch-image/installations/runMBatch3.R b/docker-build/mba-stack/mbatch-image/installations/runMBatch3.R
@@ -1,4 +1,4 @@
-# MBatch Copyright (c) 2011-2022 University of Texas MD Anderson Cancer Center
+# MBatch Copyright (c) 2011-2024 University of Texas MD Anderson Cancer Center
 #
 # This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
 #