Merge pull request #1165 from virtualcell/filter-slurm-user

restrict Slurm job actions to user vcell, not just partition

.github/workflows/codeql-analysis.yml

@@ -49,7 +49,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -60,7 +60,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -74,4 +74,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

vcell-core/src/main/java/cbit/vcell/util/VCellSimStatus.java → vcell-admin/src/main/java/org/vcell/admin/cli/tools/VCellSimStatus_NOT_USED.java

@@ -1,4 +1,4 @@
-package cbit.vcell.util;
+package org.vcell.admin.cli.tools;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -14,6 +14,7 @@
 import java.util.StringTokenizer;
 import java.util.TreeMap;
 
+import cbit.vcell.message.server.htc.HtcProxy;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.util.BeanUtils;
@@ -27,8 +28,8 @@
 import net.schmizz.sshj.userauth.keyprovider.FileKeyProvider;
 import net.schmizz.sshj.userauth.keyprovider.OpenSSHKeyFile;
 
-public class VCellSimStatus {
-    private final static Logger lg = LogManager.getLogger(VCellSimStatus.class);
+public class VCellSimStatus_NOT_USED {
+    private final static Logger lg = LogManager.getLogger(VCellSimStatus_NOT_USED.class);
 
     public static class CommandExecError extends Exception {
         public CommandExecError(String message){
@@ -115,7 +116,7 @@ public VCellSlurmAssoc(VCellSlurmAssoc other){
 
     public static void main(String[] args){
         if(args.length != 6){
-            System.out.println("Usage: " + VCellSimStatus.class.getSimpleName() + " dbHost dbName dbUser dbPassword sshRSAKeyFile slurmHost");
+            System.out.println("Usage: " + VCellSimStatus_NOT_USED.class.getSimpleName() + " dbHost dbName dbUser dbPassword sshRSAKeyFile slurmHost");
             System.exit(1);
         }
         String dbHost = args[0];
@@ -138,7 +139,7 @@ public static void main(String[] args){
             //TO_CHAR(SYSDATE, 'YYYY-MM-DD HH24:MI:SS')
             stmt = con.createStatement();
             String sql =
-                    "select 'V_' || vc_simulationjob.serverid || '_' || simref || '_' || vc_simulationjob.jobindex || '_' || vc_simulationjob.taskid slurnjobname,vc_userinfo.userid," +
+                    "select '"+HtcProxy.JOB_NAME_PREFIX_SIMULATION+"' || vc_simulationjob.serverid || '_' || simref || '_' || vc_simulationjob.jobindex || '_' || vc_simulationjob.taskid slurnjobname,vc_userinfo.userid," +
                             "vc_simulationjob.*" +
                             " from vc_simulationjob,vc_simulation,vc_userinfo" +
                             " where schedulerstatus not in (4,5,6) and vc_simulation.id=vc_simulationjob.simref" +
@@ -230,7 +231,7 @@ public static void main(String[] args){
 //		    			continue;
 //		    		}
 //		    		String s = st.nextToken();
-                    if(nextStr.contains("V_")){
+                    if(nextStr.contains(HtcProxy.JOB_NAME_PREFIX_SIMULATION)){
                         StringTokenizer st = new StringTokenizer(nextStr, " ", false);
                         //GEt slurmjobid (and array job index if present)
                         String slurmJobIDAndArrayIndex = st.nextToken();

vcell-server/src/main/java/cbit/vcell/message/server/dispatcher/SimulationDispatcher.java

@@ -382,6 +382,9 @@ public void run() {
 					for (HtcJobInfo htcJobInfo : runningJobs.keySet()){
 						try {
 							String simJobName = htcJobInfo.getJobName();
+							if (!simJobName.startsWith(HtcProxy.JOB_NAME_PREFIX_SIMULATION)){
+								continue;
+							}
 							HtcProxy.SimTaskInfo simTaskInfo = HtcProxy.getSimTaskInfoFromSimJobName(simJobName);
 							SimulationJobStatus simJobStatus = simulationDatabase.getLatestSimulationJobStatus(simTaskInfo.simId, simTaskInfo.jobIndex);
 							String failureMessage = null;
@@ -404,7 +407,7 @@ public void run() {
 									}
 								}
 							}
-							if (killJob && HtcProxy.isMyJob(htcJobInfo)){
+							if (killJob && HtcProxy.isMySimulationJob(htcJobInfo)){
 								if (lg.isWarnEnabled()) {
 									lg.warn("killing " + htcJobInfo + ", " + failureMessage);
 								}

vcell-server/src/main/java/cbit/vcell/message/server/htc/HtcProxy.java

@@ -32,6 +32,8 @@
 
 public abstract class HtcProxy {
 	public static final Logger LG = LogManager.getLogger(HtcProxy.class);
+	public static final String JOB_NAME_PREFIX_SIMULATION = "V_";
+	public static final String JOB_NAME_PREFIX_COPASI_PAREST = "CopasiParest_";
 
 	public interface HtcProxyFactory {
 		HtcProxy getHtcProxy();
@@ -124,17 +126,28 @@ public boolean equals(Object obj) {
 	 * set {@link HtcProxy#HTC_SIMULATION_JOB_NAME_PREFIX}
 	 * @return V_<i>server<i>
 	 */
-	private static String jobNamePrefix( ){
-		String stub = "V_";
+	private static String simulationJobNamePrefix( ){
+		String stub = JOB_NAME_PREFIX_SIMULATION;
 		String server = PropertyLoader.getRequiredProperty(PropertyLoader.vcellServerIDProperty);
 		return stub + server + "_";
 	}
-
-	public static boolean isMyJob(HtcJobInfo htcJobInfo){
-		return htcJobInfo.getJobName().startsWith(jobNamePrefix());
+
+	/**
+	 * set {@link HtcProxy#HTC_SIMULATION_JOB_NAME_PREFIX}
+	 * @return CopasiParest
+	 */
+	private static String parameterEstimationJobNamePrefix( ){
+		return JOB_NAME_PREFIX_COPASI_PAREST;
 	}
-
-	public final static String HTC_SIMULATION_JOB_NAME_PREFIX = jobNamePrefix();
+
+	public static boolean isMySimulationJob(HtcJobInfo htcJobInfo){
+		return htcJobInfo.getJobName().startsWith(simulationJobNamePrefix());
+	}
+	public static boolean isMyParameterEstimationJob(HtcJobInfo htcJobInfo){
+		return htcJobInfo.getJobName().startsWith(parameterEstimationJobNamePrefix());
+	}
+
+	public final static String HTC_SIMULATION_JOB_NAME_PREFIX = simulationJobNamePrefix();
 	protected final CommandService commandService;
 	protected final String htcUser;
 
@@ -196,7 +209,8 @@ public static SimTaskInfo getSimTaskInfoFromSimJobName(String simJobName) throws
 		if (tokens.hasMoreTokens()){
 			taskIdString = tokens.nextToken();
 		}
-		if (PREFIX.equals("V") && SITE!=null && simIdString!=null && jobIndexString!=null && taskIdString!=null){
+		String expectedSimPrefix = HtcProxy.JOB_NAME_PREFIX_SIMULATION.replace("_","");
+		if (PREFIX.equals(expectedSimPrefix) && SITE!=null && simIdString!=null && jobIndexString!=null && taskIdString!=null){
 			KeyValue simId = new KeyValue(simIdString);
 			int jobIndex = Integer.valueOf(jobIndexString);
 			int taskId = Integer.valueOf(taskIdString);

vcell-server/src/main/java/cbit/vcell/message/server/htc/slurm/SlurmProxy.java

@@ -81,7 +81,7 @@ public static SlurmProxy createLocalProxy(List<String> htcDispatchHostNames, Str
 	@Override
 	public void killJobSafe(HtcJobInfo htcJobInfo) throws ExecutableException, HtcException {
 		final String JOB_CMD_DELETE = PropertyLoader.getProperty(PropertyLoader.slurm_cmd_scancel,"scancel");
-		String[] cmd = new String[]{JOB_CMD_DELETE, "--jobname", htcJobInfo.getJobName(), Long.toString(htcJobInfo.getHtcJobID().getJobNumber())};
+		String[] cmd = new String[]{JOB_CMD_DELETE,"-u",getHtcUser(), "--jobname", htcJobInfo.getJobName(), Long.toString(htcJobInfo.getHtcJobID().getJobNumber())};
 		try {
 			//CommandOutput commandOutput = commandService.command(cmd, new int[] { 0, QDEL_JOB_NOT_FOUND_RETURN_CODE });
 			if (LG.isDebugEnabled()) {
@@ -108,7 +108,7 @@ public void killJobSafe(HtcJobInfo htcJobInfo) throws ExecutableException, HtcEx
 	@Override
 	public void killJobUnsafe(HtcJobID htcJobId) throws ExecutableException, HtcException {
 		final String JOB_CMD_DELETE = PropertyLoader.getProperty(PropertyLoader.slurm_cmd_scancel,"scancel");
-		String[] cmd = new String[]{JOB_CMD_DELETE, Long.toString(htcJobId.getJobNumber())};
+		String[] cmd = new String[]{JOB_CMD_DELETE, "-u", getHtcUser(), Long.toString(htcJobId.getJobNumber())};
 		try {
 			//CommandOutput commandOutput = commandService.command(cmd, new int[] { 0, QDEL_JOB_NOT_FOUND_RETURN_CODE });
 			if (LG.isDebugEnabled()) {
@@ -282,7 +282,7 @@ public Map<HtcJobInfo, HtcJobStatus> getRunningJobs() throws ExecutableException
 		final String JOB_CMD_SQUEUE = PropertyLoader.getProperty(PropertyLoader.slurm_cmd_squeue,"squeue");
 		// squeue -p vcell2 -O jobid:25,name:25,state:13
 		String partition = PropertyLoader.getRequiredProperty(PropertyLoader.slurm_partition);
-		String[] cmds = {JOB_CMD_SQUEUE,"-p",partition,"-O","jobid:25,name:25,state:13,batchhost"};
+		String[] cmds = {JOB_CMD_SQUEUE,"-p",partition,"-u",getHtcUser(),"-O","jobid:25,name:25,state:13,batchhost"};
 		CommandOutput commandOutput = commandService.command(cmds);
 
 		String output = commandOutput.getStandardOutput();
@@ -330,7 +330,7 @@ public Map<HtcJobInfo,HtcJobStatus> getJobStatus(List<HtcJobInfo> requestedHtcJo
 			jobNumbers.add(Long.toString(jobInfo.getHtcJobID().getJobNumber()));
 		}
 		String jobList = String.join(",", jobNumbers);
-		String[] cmds = {JOB_CMD_SACCT,"-P","-j",jobList,"-o","jobid%25,jobname%25,state%13"};
+		String[] cmds = {JOB_CMD_SACCT,"-P","-u",getHtcUser(),"-j",jobList,"-o","jobid%25,jobname%25,state%13"};
 		CommandOutput commandOutput = commandService.command(cmds);
 
 		String output = commandOutput.getStandardOutput();

vcell-server/src/test/java/cbit/vcell/message/server/htc/HtcProxyTest.java

@@ -10,7 +10,7 @@
 import org.vcell.util.document.KeyValue;
 
 import static cbit.vcell.message.server.htc.HtcProxy.getSimTaskInfoFromSimJobName;
-import static cbit.vcell.message.server.htc.HtcProxy.isMyJob;
+import static cbit.vcell.message.server.htc.HtcProxy.isMySimulationJob;
 import static cbit.vcell.server.HtcJobID.BatchSystemType.SLURM;
 import static org.junit.jupiter.api.Assertions.*;
 
@@ -51,11 +51,11 @@ public void test_getSimTaskInfoFromSimJobName() throws NumberFormatException, Ht
 	@Test
 	public void test_isMyJob(){
 		PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, "ALPHA");
-		assertTrue(HtcProxy.isMyJob(new HtcJobInfo(new HtcJobID("1200725", BatchSystemType.SLURM), "V_ALPHA_115785823_0_0")));
-		assertFalse(isMyJob(new HtcJobInfo(new HtcJobID("1200725", SLURM), "V_BETA_115785823_0_0")));
+		assertTrue(HtcProxy.isMySimulationJob(new HtcJobInfo(new HtcJobID("1200725", BatchSystemType.SLURM), "V_ALPHA_115785823_0_0")));
+		assertFalse(isMySimulationJob(new HtcJobInfo(new HtcJobID("1200725", SLURM), "V_BETA_115785823_0_0")));
 
 		PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, "BETA");
-		assertTrue(HtcProxy.isMyJob(new HtcJobInfo(new HtcJobID("1200725", BatchSystemType.SLURM), "V_BETA_115785823_0_0")));
+		assertTrue(HtcProxy.isMySimulationJob(new HtcJobInfo(new HtcJobID("1200725", BatchSystemType.SLURM), "V_BETA_115785823_0_0")));
 	}
 
 }