From 769e91e49529834da57ca8277a05cf4c4250b49b Mon Sep 17 00:00:00 2001
From: ZihengSun <szhwhu@gmail.com>
Date: Sat, 7 Dec 2019 04:33:56 -0500
Subject: [PATCH 1/4] update

---
 src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java | 2 +-
 .../gmu/csiss/earthcube/cyberconnector/ssh/WorkflowTool.java    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
index 6a2b6fa5a..9d16332ed 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
@@ -530,7 +530,7 @@ public static String executeShell(String id, String hid, String pswd, String tok
 			
 			if(token == null) {
 				
-				token = new RandomString(12).nextString();
+				token = hid; //new RandomString(12).nextString();
 				
 			}
 			
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/WorkflowTool.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/WorkflowTool.java
index 637a30f91..f6016031d 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/WorkflowTool.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/WorkflowTool.java
@@ -349,7 +349,7 @@ public static String execute(String id, String mode, String[] hosts, String[] ps
 			
 			if(BaseTool.isNull(token)) {
 				
-				token = new RandomString(12).nextString(); //this token will be used to establish websocket session
+				token = task.getHistory_id(); //new RandomString(12).nextString(); //this token will be used to establish websocket session
 				
 			}
 			

From 9aff7ad8f861666a1b66fab037586c4b1638d594 Mon Sep 17 00:00:00 2001
From: Ziheng Sun <zsun@gmu.edu>
Date: Wed, 18 Dec 2019 16:17:29 -0500
Subject: [PATCH 2/4] update

---
 WebContent/WEB-INF/lib/jtar-2.3.jar           | Bin 0 -> 17178 bytes
 .../geoweaver/js/edu.gmu.csiss.geoweaver.js   |   2 +-
 pom.xml                                       |   7 +-
 .../cyberconnector/ssh/FileTool.java          |  78 +++++++++-
 .../cyberconnector/ssh/ProcessTool.java       | 137 ++++++++++++++++--
 .../cyberconnector/ssh/SSHSession.java        |   2 +-
 .../cyberconnector/ssh/SSHSessionImpl.java    |  25 +++-
 .../cyberconnector/utils/BaseTool.java        |  47 ++++++
 8 files changed, 279 insertions(+), 19 deletions(-)
 create mode 100644 WebContent/WEB-INF/lib/jtar-2.3.jar

diff --git a/WebContent/WEB-INF/lib/jtar-2.3.jar b/WebContent/WEB-INF/lib/jtar-2.3.jar
new file mode 100644
index 0000000000000000000000000000000000000000..454957124c15562296ce1e252a93c074729b354d
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zEU-q6oGs~k;|W<b@O57$HE#oy^}=Gec$gn3Pp$<@P}^-L!eKK>HXUdg+6Jg;zU+bL
zehtc}&ZN#=korONDHN+x^5G%^J(akc?IK`z&mx>{-3C0aB{wRX%`=4E4O(?pEobrz
zsx&-V?ux!(Y5)MgU=OxD<5PYz)2C%&sM@p!eEsuS-qUTNZ8lIxVX6(kId!lvN(qVR
z%hB~rrHs-@v^2B*zcvc(p2rU+i$DSu3^l<EX1^pzPMm(VxJw}_H>Clq3T;`-s`Dch
z4QA7%_;!5fOh7EP5=xbhLY7rYOte)cgD*?}Q_6-AVHQx1G&B`X<#}TiMoRguS@_Vb
zYSX9PE#q4jwn!dYl&D}4veR;UIP{FYA6gyk8N4(H_ppN1*byy!D?;H?E+7HvzWOsP
z0);4ONO!!u&3C{ArcC<*sFmWEBHxm$Hrtd|g@|Fw8I)K*8qqkNDtX=a;x0xAzE*M0
ztGt!&t$J$<lU3at)xAA9w5^ngjOOGod)0gt!d95WUn}E<QO?DXO6fkk6sZJP4vy8g
z6<bO#g*F<{Y`5~IYqqTroCK?ijD26Rue8BZtG5<4Pm>Jg=9bES@oNXGRYf)-y|Dh3
z`x33s@3i$Su)DtZP@^+J*SHal4KtR%f{(r&w<Z&LHw-$&I40LC)w4g50h=)*u-AMu
z7(KRNI&hk>C{%-OUGPSVB>Z-pcyvMO_SWRMv-Zp3%b=DFgaWEEz#e=Ova)WOR9j84
z7(J3%y+GLgif^U%o%OyJ%@~}ymH%;l*2gI`v%l)-jqp`2gT5Ms<Sg92^Q%AXtGH}7
zzjWQ+t1UBvi?F(&x?GrVE#B@R*R^1kR`H{8=GTp(C^Q5ic%&Q>`uGB$?yKPL-ibS(
zSu3@ibpS4Ks065j?;2!h{@b;S$j|oJ`ba+7UU>YoAA-le9Y2ls=`$Sd_J<B^t#4Wh
zOgBXB?pUs@+!&c8NOaZ(RN&?%UkZ*xW=%=6Cp>T6eO<(g%^3JQD$_;0i@@_3w$D1{
z`~qAxpL|ZS-NEf8y6U2Arq~kSAc$X}{#pe7m^$(#<DHE@2E6IV#q|GU;M+Ue*_${z
zS(pIeMrz;%7!ZM`I`kaEbn0jFkRwE4i=X}bkor~RB!7AgrlidElVDl|zWJlu87BRV
z=$QrPf;flXg|^AN!Aq6Va!$yU-kK?FNhj47XHFJ8aO%^E)yq^smC`1|-O;mp{q;e9
zfk99~|FdrTquw6{5$ODn1K_`AzrWo6JSzTONBxKKAEnU$kLB-wC(VCQRsV(XuR`Vz
z`u(?p2=q&E@Z<hZ;qzZr{X@I`cbh*x|BycaS^n@i`ndhW<DaMX|LpyT6#CEdhd27i
zqW!z~-{$qdL;Tt3-=)!i2dVd${7(@7PAL6XPy7k{yUgk@Smh5T`@gN(2kbwHu6_sn
zJ@xf3K%@`N`@aSJheX)l(SFaY`wI;S^FN^d6$ki-UDNNlzsJx2!gVD054is}n*KZP
z?@^4ua78}8oBy`;zt#7@#x#C^-0vsCe?89ZBM<T4KJK^k;olK|-;w@>$oVm?{3pc!
z($l}Q)4u?H*#0x%Z(Q}STK;=V_9rMJ(EIxa`#;P8e<x^vA4&h}{0Bw*%Nd5_Uz|T$
z{2O8W&tQL0w!gq6{@-B#GSL4Wh5I|^FaPlWBjVo(-Cvys`9J@q;`b%u@4)r`UwQtY
h?f##t{sH{gf}tP{{&8#p1cdVO`XkYujrWhA{y)Zq;JN?+

literal 0
HcmV?d00001

diff --git a/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.js b/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.js
index 58024ed69..8ba3a8461 100644
--- a/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.js
+++ b/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.js
@@ -18,7 +18,7 @@ edu = {
 							
 					sponsor: "ESIPLab incubator project",
 					
-					version: "0.7.7",
+					version: "0.7.8",
 					
 					author: "Ziheng Sun",
 					
diff --git a/pom.xml b/pom.xml
index 48df8115a..083fe266e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,7 +1,7 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <artifactId>Geoweaver</artifactId>
-    <version>0.7.7</version>
+    <version>0.7.8</version>
     <packaging>war</packaging>
     <name>Geoweaver</name>
     <description>ESIPLab incubator project</description>
@@ -54,6 +54,11 @@
 	        <version>4.12</version>
 	        <scope>test</scope>
 	    </dependency>
+	    <dependency>
+		    <groupId>org.kamranzafar</groupId>
+		    <artifactId>jtar</artifactId>
+		    <version>2.3</version>
+		</dependency>
         <dependency>
             <groupId>aopalliance</groupId>
             <artifactId>aopalliance</artifactId>
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/FileTool.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/FileTool.java
index f8f134ee4..27a78938e 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/FileTool.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/FileTool.java
@@ -15,6 +15,7 @@
 import net.schmizz.sshj.sftp.RemoteResourceInfo;
 import net.schmizz.sshj.sftp.SFTPClient;
 import net.schmizz.sshj.xfer.FilePermission;
+import net.schmizz.sshj.xfer.scp.SCPFileTransfer;
 
 public class FileTool {
 	
@@ -24,6 +25,79 @@ public class FileTool {
 
 	static Map<String, SFTPClient> token2ftpclient = new HashMap();
 	
+	/**
+	 * Upload a file from local to a specific location on a remote host
+	 * @param hid
+	 * @param passwd
+	 * @param localPath
+	 * @param remoteLoc
+	 * @return
+	 */
+	public static String scp_upload(String hid, String passwd, String localPath, String remoteLoc, boolean removelocal) {
+		
+		String resp = null;
+		
+		SSHSession session = new SSHSessionImpl();
+		
+		try {
+			
+			//get host ip, port, user name and password
+			
+//			String[] hostdetails = HostTool.getHostDetailsById(hid);
+			
+			//establish SSH session and generate a token for it
+			
+			session.login(hid, passwd, null, false);
+			
+			File localfile = new File(localPath);
+			
+			String filename = localfile.getName();
+			
+			String fileloc = remoteLoc + "/" + filename; //upload file to temporary folder
+			
+			log.info("upload " + localPath + " to " + remoteLoc);
+			
+//			session.getSsh().newSCPFileTransfer().download(file_path, fileloc);
+			
+			session.getSsh().newSCPFileTransfer().upload(localPath, remoteLoc);
+			
+			//remove the local temporal files
+			
+			if(removelocal) localfile.delete();
+			
+			session.getSsh().close();
+			
+//			session.getSSHJSession().newSCPFileTransfer().download("test_file", new FileSystemFile("/tmp/"));
+			
+//			session.runBash(code, id, false); 
+			
+			String file_url = null;
+			
+			resp = "{\"filename\": \"" + fileloc + "\", \"ret\": \"success\"}";
+			
+		} catch (Exception e) {
+			
+			e.printStackTrace();
+			
+			throw new RuntimeException(e.getLocalizedMessage());
+			
+		}  finally {
+			
+			
+			
+		}
+        		
+		return resp;
+		
+	}
+	
+	/**
+	 * Upload a file from local to the home directory of remote host
+	 * @param hid
+	 * @param passwd
+	 * @param localPath
+	 * @return
+	 */
 	public static String scp_upload(String hid, String passwd, String localPath) {
 		
 		String resp = null;
@@ -50,7 +124,9 @@ public static String scp_upload(String hid, String passwd, String localPath) {
 			
 //			session.getSsh().newSCPFileTransfer().download(file_path, fileloc);
 			
-			session.getSsh().newSCPFileTransfer().upload(localPath, fileloc);
+			SCPFileTransfer transfer = session.getSsh().newSCPFileTransfer();
+			
+			transfer.upload(localPath, fileloc);
 			
 			//remove the local temporal files
 			
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
index 01dc4239a..e260b5bce 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
@@ -1,7 +1,10 @@
 package edu.gmu.csiss.earthcube.cyberconnector.ssh;
 
+import java.io.File;
 import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.lang3.StringUtils;
@@ -367,6 +370,39 @@ public static String del(String id) {
 		
 	}
 	
+	/**
+	 * Get process name by id
+	 * @param pid
+	 * @return
+	 */
+	public static String getNameById(String pid) {
+
+		StringBuffer sql = new StringBuffer("select name from process_type where id = '").append(pid).append("';");
+		
+		ResultSet rs = DataBaseOperation.query(sql.toString());
+		
+		String name = null;
+		
+		try {
+			
+			if(rs.next()) {
+				
+				name = rs.getString("name");
+				
+			}
+			
+			DataBaseOperation.closeConnection();
+			
+		} catch (SQLException e) {
+			
+			e.printStackTrace();
+			
+		}
+		
+		return name;
+		
+	}
+	
 	/**
 	 * Get code by Id
 	 * @param pid
@@ -374,7 +410,7 @@ public static String del(String id) {
 	 */
 	public static String getCodeById(String pid) {
 		
-		StringBuffer sql = new StringBuffer("select code from process_type where id = '").append(pid).append("';");
+		StringBuffer sql = new StringBuffer("select name,code from process_type where id = '").append(pid).append("';");
 		
 		ResultSet rs = DataBaseOperation.query(sql.toString());
 		
@@ -732,12 +768,82 @@ public static String executeBuiltInProcess(String id, String hid, String pswd, S
 		
 	}
 	
+	/**
+	 * Package all python files into one zip file
+	 */
+	public static String packageAllPython(String hid) {
+		
+		StringBuffer sql = new StringBuffer("select name,code from process_type where description = 'python';");
+		
+		logger.info(sql.toString());
+		
+		ResultSet rs = DataBaseOperation.query(sql.toString());
+		
+		String resp = null, code = null, name = null;
+		
+		try {
+			
+			String folderpath = BaseTool.getCyberConnectorRootPath() + SysDir.temp_file_path + "/" + hid + "/";
+			
+			resp = BaseTool.getCyberConnectorRootPath() + SysDir.temp_file_path + "/" + hid + ".tar";
+			
+			new File(folderpath).mkdirs(); //make a temporary folder
+			
+			List<String> files = new ArrayList();
+			
+			while(rs.next()) {
+				
+				code = rs.getString("code");
+				
+				name = rs.getString("name");
+				
+				String filepath = folderpath;
+				
+				if(name.endsWith(".py")) {
+					
+					filepath += name;
+					
+				}else{
+				
+					filepath += name + ".py";
+					
+				}
+				
+				logger.info(filepath);
+				
+				BaseTool.writeString2File(code, filepath);
+				
+				files.add(filepath);
+				
+			}
+			
+			if(files.size()==0) {
+				
+				throw new RuntimeException("No python is found in the database");
+				
+			}
+			//zip the files into a tar file
+			BaseTool.tar(files, resp);
+			
+			DataBaseOperation.closeConnection();
+			
+		} catch (SQLException e) {
+			
+			e.printStackTrace();
+			
+		}
+		
+		return resp;
+		
+	}
+	
 	/**
 	 * Execute Python process
 	 * @param id
 	 * @param hid
 	 * @param pswd
 	 * @param token
+	 * for security reasons
 	 * @param isjoin
 	 * @return
 	 */
@@ -748,11 +854,30 @@ public static String executePythonProcess(String id, String hid, String pswd,
 		
 		try {
 			
+			if(token == null) {
+				
+				token = new RandomString(12).nextString();
+				
+			}
+			
+			//package all the python files into a tar
+			String packagefile = ProcessTool.packageAllPython(token);
+			
+			if(basedir!=null) {
+				
+				FileTool.scp_upload(hid, pswd, packagefile, basedir, true);
+				
+			}else {
+				
+				FileTool.scp_upload(hid, pswd, packagefile);
+				
+			}
+			
 			//get code of the process
 			
 			String code = getCodeById(id);
 			
-			logger.info(code);
+//			logger.info(code);
 			
 			//get host ip, port, user name and password
 			
@@ -760,19 +885,13 @@ public static String executePythonProcess(String id, String hid, String pswd,
 			
 			//establish SSH session and generate a token for it
 			
-			if(token == null) {
-				
-				token = new RandomString(12).nextString();
-				
-			}
-			
 			SSHSession session = new SSHSessionImpl();
 			
 			session.login(hid, pswd, token, false);
 			
 			GeoweaverController.sshSessionManager.sessionsByToken.put(token, session);
 			
-			session.runPython(code, id, isjoin, bin, pyenv, basedir); 
+			session.runPython(code, id, isjoin, bin, pyenv, basedir, token); 
 			
 			String historyid = session.getHistory_id();
 			
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java
index 937ffbc3e..dafa9e745 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java
@@ -77,7 +77,7 @@ public interface SSHSession {
 	
 	public void runJupyter(String script, String processid, boolean isjoin, String bin, String env, String basedir);
 	
-	public void runPython(String script, String processid, boolean isjoin, String bin, String pyenv, String basedir);
+	public void runPython(String script, String processid, boolean isjoin, String bin, String pyenv, String basedir, String token);
 	
 	public void runMultipleBashes(String[] script, String processid);
 	
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java
index 9a25fc0a5..de882bd28 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java
@@ -344,7 +344,7 @@ public static String escapeJupter(String json) {
     }
     
     @Override
-	public void runPython(String python, String processid, boolean isjoin, String bin, String pyenv, String basedir) {
+	public void runPython(String python, String processid, boolean isjoin, String bin, String pyenv, String basedir, String token) {
     	
 		this.history_id = new RandomString(12).nextString();
 		
@@ -375,13 +375,26 @@ public void runPython(String python, String processid, boolean isjoin, String bi
     			
     		}
     		
-    		cmdline += "printf \"" + python + "\" > python-" + history_id + ".py; ";
+    		//new version of execution in which all the python files are copied in the host
     		
-    		cmdline += "chmod +x python-" + history_id + ".py;";
+    		cmdline += "mkdir " + basedir + "/" + token + ";";
+    		
+    		cmdline += "tar -xvf " + token + ".tar -C " + basedir + "/" + token + "/; ";
+    		
+    		cmdline += "cd "+ basedir + "/" + token + "/; ";
+    		
+//    		cmdline += "printf \"" + python + "\" > python-" + history_id + ".py; ";
+    		
+    		cmdline += "chmod +x *.py;";
+    		
+    		String filename = ProcessTool.getNameById(processid);
+    		
+    		filename = filename.trim().endsWith(".py")? filename: filename+".py";
     		
     		if(BaseTool.isNull(bin)||"default".equals(bin)) {
 
-    			cmdline += "python python-" + history_id + ".py;";
+//    			cmdline += "python python-" + history_id + ".py;";
+    			cmdline += "python " + filename + "; ";
     			
     		}else {
     			
@@ -389,13 +402,13 @@ public void runPython(String python, String processid, boolean isjoin, String bi
     			
     			cmdline += "source activate " + pyenv + "; "; //for demo only
     			
-    			cmdline += bin + " python-" + history_id + ".py;";
+    			cmdline += bin + " " + filename + "; ";
     			
     		}
     		
     		cmdline += "echo \"==== Geoweaver Bash Output Finished ====\"";
     		
-    		cmdline += "rm python-" + history_id + ".py;";
+    		cmdline += "cd ..; rm -R " + token + "*;";
     		
     		log.info(cmdline);
     		
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/utils/BaseTool.java b/src/edu/gmu/csiss/earthcube/cyberconnector/utils/BaseTool.java
index 54d32ea20..845dbbf81 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/utils/BaseTool.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/utils/BaseTool.java
@@ -1,5 +1,7 @@
 package edu.gmu.csiss.earthcube.cyberconnector.utils;
 
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.DataInputStream;
@@ -24,6 +26,7 @@
 import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 import javax.xml.soap.SOAPException;
@@ -40,6 +43,8 @@
 import org.dom4j.Node;
 import org.dom4j.XPath;
 import org.dom4j.io.SAXReader;
+import org.kamranzafar.jtar.TarEntry;
+import org.kamranzafar.jtar.TarOutputStream;
 
 
 /**
@@ -221,6 +226,48 @@ public static String getCyberConnectorRootPath(){
 		return rootpath;
 	}
 	
+	/**
+	 * Zip the files into a tar file
+	 * @param files
+	 * @param targetfile
+	 */
+	public static void tar(List<String> files, String targetfile) {
+		
+		try {
+			
+			// Output file stream
+			FileOutputStream dest = new FileOutputStream( targetfile );
+			
+			// Create a TarOutputStream
+			TarOutputStream out = new TarOutputStream( new BufferedOutputStream( dest ) );
+			  
+			// Files to tar
+			for(String fp:files){
+				 File f = new File(fp);
+			     out.putNextEntry(new TarEntry(f, f.getName()));
+			     BufferedInputStream origin = new BufferedInputStream(new FileInputStream( f ));
+			     int count;
+			     byte data[] = new byte[2048];
+			  
+			     while((count = origin.read(data)) != -1) {
+			        out.write(data, 0, count);
+			     }
+			  
+			     out.flush();
+			     origin.close();
+			}
+			  
+			out.close();
+			
+		}catch(Exception e) {
+			
+			e.printStackTrace();
+			throw new RuntimeException("Fail to tar the files" + e.getLocalizedMessage());
+			
+		}
+		
+	}
+	
 	/**
 	 * Get classpath
 	 * @return

From 649da3c6368730d7a8ef1e3bc901238a9e008e7f Mon Sep 17 00:00:00 2001
From: ZihengSun <szhwhu@gmail.com>
Date: Wed, 18 Dec 2019 21:08:20 -0500
Subject: [PATCH 3/4] update

---
 sync.ffs_db | Bin 5825 -> 6266 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sync.ffs_db b/sync.ffs_db
index 46c37050531d996677701d64d20ff8830a2af84e..bb9bda1f2f25c617f5452f3f7f5b1295739b8e39 100644
GIT binary patch
delta 6033
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z1)yB!RRtT;)lXqcMP^hI=G@t*%oB6|hk?~XOE71ZMU~#CRwvQ^a#1Gh-xZ>|(zeM&
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From 4ee188fe3bb16f6079b3caeb1d6bd64b1b4f8b4a Mon Sep 17 00:00:00 2001
From: ZihengSun <szhwhu@gmail.com>
Date: Wed, 18 Dec 2019 23:55:33 -0500
Subject: [PATCH 4/4] fix the python run and stop process function

---
 .../js/edu.gmu.csiss.geoweaver.process.js     |  6 ++++-
 .../cyberconnector/ssh/ProcessTool.java       | 10 ++++-----
 .../cyberconnector/ssh/SSHSession.java        |  4 ++--
 .../cyberconnector/ssh/SSHSessionImpl.java    | 22 +++++++++----------
 .../cyberconnector/tools/HistoryTool.java     |  6 +++++
 5 files changed, 29 insertions(+), 19 deletions(-)

diff --git a/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.process.js b/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.process.js
index 8bed00c0d..572c21ea6 100644
--- a/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.process.js
+++ b/WebContent/geoweaver/js/edu.gmu.csiss.geoweaver.process.js
@@ -564,6 +564,10 @@ edu.gmu.csiss.geoweaver.process = {
 				
 				status_col = "      <td id=\"status_"+hid+"\"><span class=\"label label-warning\">Running</span></td> ";
 				
+			}else if(status == "Stopped"){
+				
+				status_col = "      <td id=\"status_"+hid+"\"><span class=\"label label-default\">Stopped</span></td> ";
+				
 			}else{
 				
 				status_col = "      <td id=\"status_"+hid+"\"><span class=\"label label-primary\">Unknown</span></td> ";
@@ -737,7 +741,7 @@ edu.gmu.csiss.geoweaver.process = {
 					
 //					<span id=\"status_"+msg[i].id+"\" class=\"label label-warning\">Pending</span>
 					
-					$("#status_" + history_id).html("<span class=\"label label-success\">Stopped</span>");
+					$("#status_" + history_id).html("<span class=\"label label-default\">Stopped</span>");
 					
 				}else{
 
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
index 3a5b8b80d..b9778147e 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/ProcessTool.java
@@ -566,7 +566,7 @@ public static String executeShell(String id, String hid, String pswd, String tok
 			
 			if(token == null) {
 				
-				token = hid; //new RandomString(12).nextString();
+				token = new RandomString(12).nextString();
 				
 			}
 			
@@ -574,12 +574,12 @@ public static String executeShell(String id, String hid, String pswd, String tok
 			
 			session.login(hid, pswd, token, false);
 			
-			GeoweaverController.sshSessionManager.sessionsByToken.put(token, session);
-			
-			session.runBash(code, id, isjoin); 
+			session.runBash(code, id, isjoin, token); 
 			
 			String historyid = session.getHistory_id();
 			
+			GeoweaverController.sshSessionManager.sessionsByToken.put(token, session);
+			
 			resp = "{\"history_id\": \""+historyid+
 					
 					"\", \"token\": \""+token+
@@ -646,7 +646,7 @@ public static String executeJupyterProcess(String id, String hid, String pswd, S
 			
 			GeoweaverController.sshSessionManager.sessionsByToken.put(token, session);
 			
-			session.runJupyter(code, id, isjoin, bin, pyenv, basedir); 
+			session.runJupyter(code, id, isjoin, bin, pyenv, basedir, token); 
 			
 			String historyid = session.getHistory_id();
 			
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java
index dafa9e745..496d9c6a6 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSession.java
@@ -73,9 +73,9 @@ public interface SSHSession {
     
 	public void setWebSocketSession(WebSocketSession session);
 	
-	public void runBash(String script, String processid, boolean isjoin);
+	public void runBash(String script, String processid, boolean isjoin, String token);
 	
-	public void runJupyter(String script, String processid, boolean isjoin, String bin, String env, String basedir);
+	public void runJupyter(String script, String processid, boolean isjoin, String bin, String env, String basedir, String token);
 	
 	public void runPython(String script, String processid, boolean isjoin, String bin, String pyenv, String basedir, String token);
 	
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java
index de882bd28..821802218 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/ssh/SSHSessionImpl.java
@@ -56,13 +56,13 @@ public class SSHSessionImpl implements SSHSession {
 	
     protected final Logger   log = LoggerFactory.getLogger(getClass());
     
-    private SSHClient        ssh;
+    private SSHClient        ssh; //SSHJ creates a new client
     
     private String 			 hostid;
     
-    private Session          session; //sshj session
+    private Session          session; //SSHJ client creates SSHJ session
     
-    private Shell            shell;
+    private Shell            shell; //SSHJ session creates SSHJ shell
     
     private String           username;
     
@@ -166,7 +166,7 @@ public boolean login(String host, String port, String username, String password,
             logout();
             // ssh.authPublickey(System.getProperty("user.name"));
             log.info("new SSHClient");
-            ssh = new SSHClient();
+            ssh = new SSHClient(); //create a new SSH client
             log.info("verify all hosts");
             ssh.addHostKeyVerifier(new HostKeyVerifier() {
                 public boolean verify(String arg0, int arg1, PublicKey arg2) {
@@ -178,7 +178,7 @@ public boolean verify(String arg0, int arg1, PublicKey arg2) {
             log.info("authenticating: {}", username);
             ssh.authPassword(username, password);
             log.info("starting session");
-            session = ssh.startSession();
+            session = ssh.startSession(); //SSH client creates new SSH session
             log.info("allocating PTY");
             session.allocateDefaultPTY(); 
             this.username = username;
@@ -188,7 +188,7 @@ public boolean verify(String arg0, int arg1, PublicKey arg2) {
             if(isShell) {
             	//shell
             	log.info("starting shell");
-                shell = session.startShell(); //if shell is null, it is in command mode.
+                shell = session.startShell(); //SSH session creates SSH Shell. if shell is null, it is in command mode.
                 log.info("SSH session established");
                 input = new BufferedReader(new InputStreamReader(shell.getInputStream()));
                 output = shell.getOutputStream();
@@ -346,7 +346,7 @@ public static String escapeJupter(String json) {
     @Override
 	public void runPython(String python, String processid, boolean isjoin, String bin, String pyenv, String basedir, String token) {
     	
-		this.history_id = new RandomString(12).nextString();
+		this.history_id = token; //new RandomString(12).nextString();
 		
 		this.history_process = processid.split("-")[0]; //only retain process id, remove object id
 		
@@ -459,9 +459,9 @@ public void runPython(String python, String processid, boolean isjoin, String bi
 	}
     
     @Override
-	public void runJupyter(String notebookjson, String processid, boolean isjoin, String bin, String pyenv, String basedir) {
+	public void runJupyter(String notebookjson, String processid, boolean isjoin, String bin, String pyenv, String basedir, String token) {
     	
-		this.history_id = new RandomString(12).nextString();
+		this.history_id = token; //new RandomString(12).nextString();
 		
 		this.history_process = processid.split("-")[0]; //only retain process id, remove object id
 		
@@ -558,9 +558,9 @@ public void runJupyter(String notebookjson, String processid, boolean isjoin, St
 	}
 
 	@Override
-	public void runBash(String script, String processid, boolean isjoin) {
+	public void runBash(String script, String processid, boolean isjoin, String token) {
     	
-		this.history_id = new RandomString(12).nextString();
+		this.history_id = token; //new RandomString(12).nextString();
 		
 		this.history_process = processid.split("-")[0]; //only retain process id, remove object id
 		
diff --git a/src/edu/gmu/csiss/earthcube/cyberconnector/tools/HistoryTool.java b/src/edu/gmu/csiss/earthcube/cyberconnector/tools/HistoryTool.java
index 5a721b3ac..ef70bda62 100644
--- a/src/edu/gmu/csiss/earthcube/cyberconnector/tools/HistoryTool.java
+++ b/src/edu/gmu/csiss/earthcube/cyberconnector/tools/HistoryTool.java
@@ -1,7 +1,9 @@
 package edu.gmu.csiss.earthcube.cyberconnector.tools;
 
 import edu.gmu.csiss.earthcube.cyberconnector.database.DataBaseOperation;
+import edu.gmu.csiss.earthcube.cyberconnector.ssh.SSHSession;
 import edu.gmu.csiss.earthcube.cyberconnector.utils.BaseTool;
+import edu.gmu.csiss.earthcube.cyberconnector.web.GeoweaverController;
 
 public class HistoryTool {
 	
@@ -13,6 +15,10 @@ public static void stop(String history_id) {
 		
 		try {
 			
+			SSHSession session = GeoweaverController.sshSessionManager.sessionsByToken.get(history_id);
+			
+			session.getSsh().close(); //this line close the shell session and the associated command is stopped
+			
 			String history_end_time = BaseTool.getCurrentMySQLDatetime();
 
 			StringBuffer sql = new StringBuffer("update history set end_time = '");