Release 2021-08-13-1100

BEA#143 PIPELINE: data in archive BEA#147 SDB/BEV/BEI: JS file anti-cache timestamps BEA#366 NGCHM: html/ngchm? BEA#390 Data: some legacy data lack titles BEA#404 Docker: tomcat startup BEA#405 MBA: duplicate features BEA#407 MQA: next at last dataset BEA#408 MBatch: Add UMAP BEA#409 MQA: Add UMAP BEA#410 MQA: GUI Buttons BEA#411 MOB: More MW Data BEA#412 NGCHM: widget loading BEA#413 NGCHM/SuperClust: one only? BEA#414 MQA: Small Space Support BEA#415 NGCHM: annotation bar height BEA#417 ALL: WebInspect Remediation BEA#418 MtOB: allfactors support BEA#419 MQA: missing somatic mutation data BEA#420 Docker: PanDoc and TexLive revisit BEA#428 ALL: CentOS to AlmaLinux BEA#430 MQA: make query scroll BEA#433 BEV: resize results better BEA#434 BEV: no results message locks GUI BEA#435 MBatch: static PNG legend title BEA#436 LR: log report CI/CD BEA#437 MBatch: UTF-8 features and batch names BEA#439 BEV: fix histogram plots BEA#440 BEV: handle no results indexes
MD-Anderson-Bioinformatics · Aug 20, 2021 · 0045d76 · 0045d76
1 parent 9e31911
commit 0045d76
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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
@@ -42,24 +42,33 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
 	{
 		try
 		{
+			try
+			{
+				// *******************************************************************
+				// logout user
+				request.logout();
+			}
+			catch (Exception exp)
+			{
+				log("AuthOut::processRequest logout", exp);
+			}
 			// *******************************************************************
-			// logout user
-			request.logout();
+			// redirect user to main index
+			String url = request.getHeader("referer");
+			log("AuthOut referer=" + url);
+			if ((null==url)||("".equals(url)))
+			{
+				url = "/BEI/BEI/index.html";
+			}
+			String urlWithSessionID = response.encodeRedirectURL(url);
+			response.sendRedirect( urlWithSessionID );
 		}
-		catch (Exception exp)
+		catch(Exception exp)
 		{
 			log("AuthOut::processRequest failed", exp);
+			response.setStatus(400);
+			response.sendError(400);
 		}
-		// *******************************************************************
-		// redirect user to main index
-		String url = request.getHeader("referer");
-		log("AuthOut referer=" + url);
-		if ((null==url)||("".equals(url)))
-		{
-			url = "/BEI/BEI/index.html";
-		}
-		String urlWithSessionID = response.encodeRedirectURL(url);
-		response.sendRedirect( urlWithSessionID );
 	}
 
 	// <editor-fold defaultstate="collapsed" desc="HttpServlet methods. Click on the + sign on the left to edit the code.">

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
@@ -52,47 +52,56 @@ synchronized protected void processRequest(HttpServletRequest request, HttpServl
 		// TODO: replace synchronized if needed to speed up login process
 		try
 		{
-			// *******************************************************************
-			// Update User List and Role Information
-			log("request.getRemoteUser() = " + request.getRemoteUser());
-			String userName = getUserName(request);
-			if (null==userName)
-			{
-				log("nobody logged in");
-			}
-			else
+			try
 			{
-				Properties props = new Properties();
-				if (new File(BEIUtils.M_PROPS, "user.properties").exists())
+				// *******************************************************************
+				// Update User List and Role Information
+				log("request.getRemoteUser() = " + request.getRemoteUser());
+				String userName = getUserName(request);
+				if (null==userName)
 				{
-					try (FileInputStream is = new FileInputStream(new File(BEIUtils.M_PROPS, "user.properties")))
-					{
-						props.loadFromXML(is);
-					}
+					log("nobody logged in");
 				}
-				props.setProperty(userName, getUserRoleString(request));
-				try (FileOutputStream os = new FileOutputStream(new File(BEIUtils.M_PROPS, "user.properties")))
+				else
 				{
-					props.storeToXML(os, "user properties");
+					Properties props = new Properties();
+					if (new File(BEIUtils.M_PROPS, "user.properties").exists())
+					{
+						try (FileInputStream is = new FileInputStream(new File(BEIUtils.M_PROPS, "user.properties")))
+						{
+							props.loadFromXML(is);
+						}
+					}
+					props.setProperty(userName, getUserRoleString(request));
+					try (FileOutputStream os = new FileOutputStream(new File(BEIUtils.M_PROPS, "user.properties")))
+					{
+						props.storeToXML(os, "user properties");
+					}
+					log("AuthUpdate::processRequest updateUserAndRoleData");
+					UserAndRoleData.updateUserAndRoleData(props);
 				}
-				log("AuthUpdate::processRequest updateUserAndRoleData");
-				UserAndRoleData.updateUserAndRoleData(props);
 			}
+			catch (Exception exp)
+			{
+				log("AuthUpdate::processRequest failed", exp);
+			}
+			// *******************************************************************
+			// redirect user to main index
+			String url = request.getHeader("referer");
+			log("AuthOut referer=" + url);
+			if ((null==url)||("".equals(url)))
+			{
+				url = "/BEI/BEI/index.html";
+			}
+			String urlWithSessionID = response.encodeRedirectURL(url);
+			response.sendRedirect( urlWithSessionID );
 		}
-		catch (Exception exp)
+		catch(Exception exp)
 		{
 			log("AuthUpdate::processRequest failed", exp);
+			response.setStatus(400);
+			response.sendError(400);
 		}
-		// *******************************************************************
-		// redirect user to main index
-		String url = request.getHeader("referer");
-		log("AuthOut referer=" + url);
-		if ((null==url)||("".equals(url)))
-		{
-			url = "/BEI/BEI/index.html";
-		}
-		String urlWithSessionID = response.encodeRedirectURL(url);
-		response.sendRedirect( urlWithSessionID );
 	}
 
 	static public String getUserName(HttpServletRequest request)

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
@@ -35,6 +35,7 @@ public AuthUser()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent class
 		theBuffer.append("{");
 		String userName = "";
 		if (null!=request.getRemoteUser())

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
@@ -13,6 +13,7 @@
 
 import edu.mda.bcb.bei.utils.BEIUtils;
 import edu.mda.bcb.bei.authorization.Authorization;
+import edu.mda.bcb.bei.status.JobStatus;
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
@@ -69,6 +70,10 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
 			log("version = " + edu.mda.bcb.bei.utils.BEIUtils.M_VERSION);
 			String jobId = request.getParameter("jobId");
 			log("passed in jobId is " + jobId);
+			if (null!=jobId)
+			{
+				JobStatus.checkJobId(jobId);
+			}
 			if ((null!=jobId)&&(false!=mCheckUserAuthorization))
 			{
 				log("auth jobId is " + jobId);
@@ -97,8 +102,8 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
 		{
 			log("BEIServletMixin::processRequest failed", exp);
 			response.setContentType("text;charset=UTF-8");
-			response.setStatus(500);
-			response.sendError(500, exp.getMessage());
+			response.setStatus(400);
+			response.sendError(400);
 			if (null!=mErrorFile)
 			{
 				Files.write(mErrorFile.toPath(), exp.getMessage().getBytes(), StandardOpenOption.CREATE, StandardOpenOption.APPEND);

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
@@ -61,6 +61,7 @@ public BEIproperties()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		long start = System.currentTimeMillis();
 		theBuffer.append(getResponseString(this));
 		long finish = System.currentTimeMillis();

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
@@ -15,6 +15,7 @@
 import edu.mda.bcb.bei.processes.BatchdataObj;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
+import edu.mda.bcb.bei.status.JobStatus;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
@@ -43,8 +44,10 @@ public Batchdata()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		String jobId = request.getParameter("jobId");
 		log("passed in jobId is " + jobId);
+		JobStatus.checkJobId(jobId);
 		String isAlternate = request.getParameter("isAlternate");
 		// NO, YES, YES-IGNORE
 		log("passed in isAlternate is " + isAlternate);

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/GDCdatasets.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/GDCdatasets.java
@@ -41,6 +41,7 @@ public GDCdatasets()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		long start = System.currentTimeMillis();
 		theBuffer.append(getResponseString(this));
 		long finish = System.currentTimeMillis();

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
@@ -11,6 +11,7 @@
 
 package edu.mda.bcb.bei.servlets;
 
+import edu.mda.bcb.bei.status.JobStatus;
 import edu.mda.bcb.bei.utils.BEIUtils;
 import java.io.BufferedWriter;
 import java.io.File;
@@ -44,8 +45,10 @@ public MBatchConfig()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		String jobId = request.getParameter("jobId");
 		log("passed in jobId is " + jobId);
+		JobStatus.checkJobId(jobId);
 		String action = request.getParameter("action");
 		log("passed in action is " + action);
 		// action options

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/MWdatasets.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/MWdatasets.java
@@ -45,6 +45,7 @@ public MWdatasets()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		long start = System.currentTimeMillis();
 		theBuffer.append(getResponseString(this));
 		long finish = System.currentTimeMillis();

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
@@ -42,19 +42,28 @@ public class RBNConfig extends HttpServlet
 	protected void processRequest(HttpServletRequest request, HttpServletResponse response)
 			throws ServletException, IOException
 	{
-		response.setContentType("text/html;charset=UTF-8");
-		try (PrintWriter out = response.getWriter())
+		try
 		{
-			/* TODO output your page here. You may use following sample code. */
-			out.println("<!DOCTYPE html>");
-			out.println("<html>");
-			out.println("<head>");
-			out.println("<title>Servlet RBNConfig</title>");			
-			out.println("</head>");
-			out.println("<body>");
-			out.println("<h1>Servlet RBNConfig at " + request.getContextPath() + "</h1>");
-			out.println("</body>");
-			out.println("</html>");
+			response.setContentType("text/html;charset=UTF-8");
+			try (PrintWriter out = response.getWriter())
+			{
+				/* TODO output your page here. You may use following sample code. */
+				out.println("<!DOCTYPE html>");
+				out.println("<html>");
+				out.println("<head>");
+				out.println("<title>Servlet RBNConfig</title>");			
+				out.println("</head>");
+				out.println("<body>");
+				out.println("<h1>Servlet RBNConfig at " + request.getContextPath() + "</h1>");
+				out.println("</body>");
+				out.println("</html>");
+			}
+		}
+		catch(Exception exp)
+		{
+			log("RBNConfig::processRequest failed", exp);
+			response.setStatus(400);
+			response.sendError(400);
 		}
 	}
 

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
@@ -67,7 +67,9 @@ public UploadBatch()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		String jobId = request.getParameter("jobId");
+		JobStatus.checkJobId(jobId);
 		boolean keepOriginal = paramStringToBool(request.getParameter("keepOriginal"));
 		// No rectangle flag should be logically inverted
 		boolean noRectangle = !paramStringToBool(request.getParameter("noRectangle"));
@@ -168,15 +170,15 @@ public static String saveFileUpload(Part thePart, String theSavePath, HttpServle
 			message = "You either did not specify a file to upload or are trying to upload a file to a protected or nonexistent location. "
 					+ fne.getMessage();
 			theServlet.log("Problems during file upload. Error: " + fne.getMessage(), fne);
-			//response.setStatus(500);
-			//response.sendError(500, exp.getMessage());
+			//response.setStatus(400);
+			//response.sendError(400, exp.getMessage());
 		}
 		catch (Exception exp)
 		{
 			message = exp.getMessage();
 			theServlet.log("Problems during file upload. Error: " + exp.getMessage(), exp);
-			//response.setStatus(500);
-			//response.sendError(500, exp.getMessage());
+			//response.setStatus(400);
+			//response.sendError(400, exp.getMessage());
 		}
 		finally
 		{

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
@@ -10,6 +10,7 @@
 // MD Anderson Cancer Center Bioinformatics at MDA <https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/bioinformatics-and-computational-biology.html>
 package edu.mda.bcb.bei.servlets;
 
+import edu.mda.bcb.bei.status.JobStatus;
 import edu.mda.bcb.bei.utils.BEIUtils;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -58,7 +59,9 @@ public UploadLinkMap()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// reutnr to user handled in parent
 		String jobId = request.getParameter("jobId");
+		JobStatus.checkJobId(jobId);
 		String isAlternate = request.getParameter("isAlternate");
 		boolean isAlternateP = isAlternate.equals("YES");
 		File jobDir = new File(BEIUtils.M_OUTPUT, jobId);
@@ -118,15 +121,15 @@ public static String saveFileUpload(Part thePart, String theSavePath, HttpServle
 			message = "You either did not specify a file to upload or are trying to upload a file to a protected or nonexistent location. "
 					+ fne.getMessage();
 			theServlet.log("Problems during file upload. Error: " + fne.getMessage(), fne);
-			//response.setStatus(500);
-			//response.sendError(500, exp.getMessage());
+			//response.setStatus(400);
+			//response.sendError(400, exp.getMessage());
 		}
 		catch (Exception exp)
 		{
 			message = exp.getMessage();
 			theServlet.log("Problems during file upload. Error: " + exp.getMessage(), exp);
-			//response.setStatus(500);
-			//response.sendError(500, exp.getMessage());
+			//response.setStatus(400);
+			//response.sendError(400, exp.getMessage());
 		}
 		finally
 		{

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
@@ -58,7 +58,9 @@ public UploadManifest()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		String jobId = request.getParameter("jobId");
+		JobStatus.checkJobId(jobId);
 		String isAlternate = request.getParameter("isAlternate");
 		String dataset = request.getParameter("dataset");
 		String dstype = request.getParameter("dstype");

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadMatrix.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/UploadMatrix.java
@@ -66,7 +66,9 @@ public UploadMatrix()
 	@Override
 	protected void internalProcess(HttpServletRequest request, StringBuffer theBuffer) throws Exception
 	{
+		// return to user handled in parent
 		String jobId = request.getParameter("jobId");
+		JobStatus.checkJobId(jobId);
 		boolean keepOriginalFlag = paramStringToBool(request.getParameter("keepOriginal"));
 		// No rectangle flag should be logically inverted
 		boolean noRectangleFlag = !paramStringToBool(request.getParameter("noRectangle"));

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBGDCDownload.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBGDCDownload.java
@@ -42,6 +42,7 @@ protected void internalProcess(HttpServletRequest request, StringBuffer theBuffe
 	{
 		////////////////////////////////////////////////////////////////////
 		String jobId = request.getParameter("jobId");
+		JobStatus.checkJobId(jobId);
 		log("passed in jobId is " + jobId);
 		String isAlternate = request.getParameter("isAlternate");
 		log("passed in isAlternate is " + isAlternate);

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBMWDownload.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBMWDownload.java
@@ -43,6 +43,7 @@ protected void internalProcess(HttpServletRequest request, StringBuffer theBuffe
 		////////////////////////////////////////////////////////////////////
 		String jobId = request.getParameter("jobId");
 		log("passed in jobId is " + jobId);
+		JobStatus.checkJobId(jobId);
 		String isAlternate = request.getParameter("isAlternate");
 		log("passed in isAlternate is " + isAlternate);
 		File jobDir = new File(BEIUtils.M_OUTPUT, jobId);

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBRunMBatch.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBRunMBatch.java
@@ -37,6 +37,7 @@ protected void internalProcess(HttpServletRequest request, StringBuffer theBuffe
 	{
 		String jobId = request.getParameter("jobId");
 		log("passed in jobId is " + jobId);
+		JobStatus.checkJobId(jobId);
 		JobStatus.setJobStatus(jobId, JOB_STATUS.MBATCHCONFIG_END, request, this);
 		JobStatus.setJobStatus(jobId, JOB_STATUS.MBATCHRUN_START_WAIT, request, this);
 		theBuffer.append(jobId);

diff --git a/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBdelete.java b/apps/BatchEffectsInterface/src/main/java/edu/mda/bcb/bei/servlets/job/JOBdelete.java
@@ -40,6 +40,7 @@ protected void internalProcess(HttpServletRequest request, StringBuffer theBuffe
 	{
 		String jobId = request.getParameter("jobId");
 		log("passed in jobId is " + jobId);
+		JobStatus.checkJobId(jobId);
 		if ((jobId!=null)&&!("".equals(jobId)))
 		{
 			File jobDir = new File(BEIUtils.M_OUTPUT, jobId);