Release 2023-09-22-1600

MD-Anderson-Bioinformatics · Oct 2, 2023 · 19e10db · 19e10db
1 parent 80f7e1b
commit 19e10db
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Showing 58 changed files with 14,968 additions and 12,920 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,9 +1,12 @@
 apps/*/build
 apps/*/dist
+apps/*/target
 apps/*/nbproject/private
 apps/*/.Rproj.user
 apps/*/.Rbuildignore
 apps/*/.Rhistory
 data/apps_out/*
 data/testing_dynamic/*
 .Rproj.user
+/apps/SamplesValidation/target/
+/apps/BatchEffectsInterface/target/
diff --git a/apps/BatchEffectsInterface/nb-configuration.xml b/apps/BatchEffectsInterface/nb-configuration.xml
@@ -13,7 +13,7 @@ You can copy and paste the single properties, into the pom.xml file and the IDE
 That way multiple projects can share the same settings (useful for formatting rules for example).
 Any value defined here will override the pom.xml file value but is only applicable to the current project.
 -->
-        <org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_j2eeVersion>1.7-web</org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_j2eeVersion>
+        <org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_j2eeVersion>10-web</org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_j2eeVersion>
         <org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_deploy_2e_server>Tomcat</org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_deploy_2e_server>
     </properties>
 </project-shared-configuration>
diff --git a/apps/BatchEffectsInterface/pom.xml b/apps/BatchEffectsInterface/pom.xml
@@ -15,22 +15,11 @@
 	</properties>
 
 	<dependencies>
-		<dependency>
-			<groupId>org.apache.tomcat</groupId>
-			<artifactId>tomcat-catalina</artifactId>
-			<version>9.0.74</version>
-			<scope>provided</scope>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-text</artifactId>
 			<version>1.10.0</version>
 		</dependency>
-		<dependency>
-			<groupId>javax.mail</groupId>
-			<artifactId>javax.mail-api</artifactId>
-			<version>1.6.2</version>
-		</dependency>
 		<dependency>
 			<groupId>${project.groupId}</groupId>
 			<artifactId>SamplesValidation</artifactId>
@@ -41,12 +30,6 @@
 			<artifactId>StdMWUtils</artifactId>
 			<version>${project.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>javax</groupId>
-			<artifactId>javaee-web-api</artifactId>
-			<version>8.0.1</version>
-			<scope>provided</scope>
-		</dependency>
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
@@ -56,18 +39,28 @@
 		<dependency>
 			<groupId>org.apache.tika</groupId>
 			<artifactId>tika-core</artifactId>
-			<version>2.7.0</version>
+			<version>2.8.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.tika</groupId>
 			<artifactId>tika-parsers</artifactId>
-			<version>2.7.0</version>
+			<version>2.8.0</version>
 			<type>pom</type>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.tika</groupId>
 			<artifactId>tika-parser-text-module</artifactId>
-			<version>2.7.0</version>
+			<version>2.8.0</version>
+		</dependency>
+		<dependency>
+			<groupId>jakarta.servlet</groupId>
+			<artifactId>jakarta.servlet-api</artifactId>
+			<version>6.0.0</version>
+		</dependency>
+		<dependency>
+			<groupId>jakarta.mail</groupId>
+			<artifactId>jakarta.mail-api</artifactId>
+			<version>2.1.2</version>
 		</dependency>
 	</dependencies>
 
@@ -97,7 +90,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-dependency-plugin</artifactId>
-				<version>2.6</version>
+				<version>3.6.0</version>
 				<executions>
 					<execution>
 						<phase>validate</phase>
@@ -109,9 +102,9 @@
 							<silent>true</silent>
 							<artifactItems>
 								<artifactItem>
-									<groupId>javax</groupId>
-									<artifactId>javaee-endorsed-api</artifactId>
-									<version>7.0</version>
+									<groupId>jakarta.servlet</groupId>
+									<artifactId>jakarta.servlet-api</artifactId>
+									<version>6.0.0</version>
 									<type>jar</type>
 								</artifactItem>
 							</artifactItems>

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/authorization/Authorization.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/authorization/Authorization.java
@@ -24,8 +24,8 @@
 import java.util.HashMap;
 import java.util.Map.Entry;
 import java.util.TreeSet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/AuthOut.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/AuthOut.java
@@ -13,11 +13,11 @@
 
 import edu.mda.bcb.bei.utils.ScanCheck;
 import java.io.IOException;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/AuthUpdate.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/AuthUpdate.java
@@ -21,12 +21,11 @@
 import java.io.IOException;
 import java.security.Principal;
 import java.util.TreeSet;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import org.apache.catalina.realm.GenericPrincipal;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 /**
  *
@@ -119,40 +118,40 @@ static public String getUserName(HttpServletRequest request)
 
 	static public TreeSet<String> getUserRoles(HttpServletRequest request)
 	{
-		Principal p = request.getUserPrincipal();
+		// Principal p = request.getUserPrincipal();
 		TreeSet<String> roles = new TreeSet<>();
-		if (null!=p)
-		{
-			System.out.println("request.getUserPrincipal().getClass() = " + request.getUserPrincipal().getClass());
-			GenericPrincipal gp = (GenericPrincipal)p;
-			for (String role : gp.getRoles())
-			{
-				roles.add(role);
-			}
-		}
+//		if (null!=p)
+//		{
+//			System.out.println("request.getUserPrincipal().getClass() = " + request.getUserPrincipal().getClass());
+//			GenericPrincipal gp = (GenericPrincipal)p;
+//			for (String role : gp.getRoles())
+//			{
+//				roles.add(role);
+//			}
+//		}
 		return roles;
 	}
 
 	static public String getUserRoleString(HttpServletRequest request)
 	{
-		Principal p = request.getUserPrincipal();
+		//Principal p = request.getUserPrincipal();
 		String roleString = null;
-		if (null!=p)
-		{
-			System.out.println("request.getUserPrincipal().getClass() = " + request.getUserPrincipal().getClass());
-			GenericPrincipal gp = (GenericPrincipal)p;
-			for (String role : gp.getRoles())
-			{
-				if (null==roleString)
-				{
-					roleString = role;
-				}
-				else
-				{
-					roleString = roleString + "|" + role;
-				}
-			}
-		}
+//		if (null!=p)
+//		{
+//			System.out.println("request.getUserPrincipal().getClass() = " + request.getUserPrincipal().getClass());
+//			GenericPrincipal gp = (GenericPrincipal)p;
+//			for (String role : gp.getRoles())
+//			{
+//				if (null==roleString)
+//				{
+//					roleString = role;
+//				}
+//				else
+//				{
+//					roleString = roleString + "|" + role;
+//				}
+//			}
+//		}
 		return roleString;
 	}
 

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/AuthUser.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/AuthUser.java
@@ -14,8 +14,8 @@
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import edu.mda.bcb.bei.authorization.UserAndRoleData;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServletRequest;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/BEIServletMixin.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/BEIServletMixin.java
@@ -20,10 +20,10 @@
 import java.io.PrintWriter;
 import java.nio.file.Files;
 import java.nio.file.StandardOpenOption;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/BEIproperties.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/BEIproperties.java
@@ -17,9 +17,9 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.StringWriter;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/Batchdata.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/Batchdata.java
@@ -24,8 +24,8 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.TreeMap;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServletRequest;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/MBatchConfig.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/MBatchConfig.java
@@ -22,8 +22,8 @@
 import java.nio.file.StandardOpenOption;
 import java.util.Enumeration;
 import java.util.List;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.text.StringEscapeUtils;
 
@@ -64,6 +64,7 @@ protected void checkMbatchConfigData(HttpServletRequest theRequest) throws Excep
 			String paraName = sEnum.nextElement();
 			String paraValue = theRequest.getParameter(paraName);
 			if (("jobId".equals(paraName)) || ("configDesc".equals(paraName))
+					|| ("Title".equals(paraName))
 					|| ("DataVersion".equals(paraName)) || ("TestVersion".equals(paraName))
 					|| ("mutBatchMem".equals(paraName)) || ("RBN_InvariantId".equals(paraName))
 					|| ("RBN_VariantId".equals(paraName)) || ("EBNPlus_GroupId1".equals(paraName))
@@ -216,7 +217,7 @@ public void writeConfigFile(HttpServletRequest theRequest, File theConfigFile,
 				String value = null;
 				if ((!"_".equals(paraName)) && (!"action".equals(paraName)))
 				{
-					if ("title".equals(paraName))
+					if ("Title".equals(paraName))
 					{
 						foundTitle = true;
 					}
@@ -265,7 +266,7 @@ public void writeConfigFile(HttpServletRequest theRequest, File theConfigFile,
 			}
 			if (false == foundTitle)
 			{
-				bw.write("title\tBatch Effects Run from BEI");
+				bw.write("Title\tBatch Effects Run from BEI");
 				bw.newLine();
 			}
 			File mafFiles = new File(new File(new File(theJobDir, "ZIP-DATA"), "original"), "MUT_MAFS");

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/RBNConfig.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/RBNConfig.java
@@ -14,11 +14,11 @@
 import edu.mda.bcb.bei.utils.ScanCheck;
 import java.io.IOException;
 import java.io.PrintWriter;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadBatch.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadBatch.java
@@ -24,12 +24,12 @@
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.nio.file.StandardCopyOption;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.MultipartConfig;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.Part;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.MultipartConfig;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.Part;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadLinkMap.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadLinkMap.java
@@ -16,12 +16,12 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.MultipartConfig;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.Part;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.MultipartConfig;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.Part;
 
 /**
  *

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadManifest.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadManifest.java
@@ -19,11 +19,11 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.MultipartConfig;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.MultipartConfig;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 /**
  *