Merge tag 'v2.8.5' of https://github.com/genepi/cloudgene into releas…

…e-2.8.5-tis
statgen · Apr 19, 2024 · bbcf49c · bbcf49c
2 parents af3e577 + a8ded7a
commit bbcf49c
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Showing 15 changed files with 84 additions and 21 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.8.2</version>
+	<version>2.8.5</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>

diff --git a/src/main/html/webapp/components/core/job/detail/detail.js b/src/main/html/webapp/components/core/job/detail/detail.js
@@ -76,7 +76,7 @@ export default Control.extend({
   '#delete-btn click': function(el, ev) {
     var that = this;
 
-    bootbox.confirm("Are you sure you want to delete <b>" + that.job.attr('id') + "</b>?", function(result) {
+    bootbox.confirm("Are you sure you want to delete <b>" + that.job.attr('name') + "</b>?", function(result) {
       if (result) {
 
         var okButton = $("button[data-bb-handler='confirm']");
@@ -106,7 +106,7 @@ export default Control.extend({
   '#cancel-btn click': function(el, ev) {
     var that = this;
 
-    bootbox.confirm("Are you sure you want to cancel <b>" + that.job.attr('id') + "</b>?", function(result) {
+    bootbox.confirm("Are you sure you want to cancel <b>" + that.job.attr('name') + "</b>?", function(result) {
       if (result) {
 
         var okButton = $("button[data-bb-handler='confirm']");
@@ -136,7 +136,7 @@ export default Control.extend({
   '#restart-btn click': function(el, ev) {
     var that = this;
 
-    bootbox.confirm("Are you sure you want to restart <b>" + that.job.attr('id') + "</b>?", function(result) {
+    bootbox.confirm("Are you sure you want to restart <b>" + that.job.attr('name') + "</b>?", function(result) {
       if (result) {
 
         var okButton = $("button[data-bb-handler='confirm']");

diff --git a/src/main/html/webapp/components/core/job/list/list.js b/src/main/html/webapp/components/core/job/list/list.js
@@ -48,7 +48,7 @@ export default Control.extend({
     var card = $(el).closest('.card');
     var job = domData.get.call(card[0], 'job');
 
-    bootbox.confirm("Are you sure you want to delete <b>" + job.attr('id') + "</b>?", function(result) {
+    bootbox.confirm("Are you sure you want to delete <b>" + job.attr('name') + "</b>?", function(result) {
       if (result) {
 
         var okButton = $("button[data-bb-handler='confirm']");
@@ -78,7 +78,7 @@ export default Control.extend({
     var card = $(el).closest('.card');
     var job = domData.get.call(card[0], 'job');
 
-    bootbox.confirm("Are you sure you want to cancel <b>" + job.attr('id') + "</b>?", function(result) {
+    bootbox.confirm("Are you sure you want to cancel <b>" + job.attr('name') + "</b>?", function(result) {
       if (result) {
 
         var okButton = $("button[data-bb-handler='confirm']");

diff --git a/src/main/html/webapp/package-lock.json b/src/main/html/webapp/package-lock.json
diff --git a/src/main/html/webapp/package.json b/src/main/html/webapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.8.2",
+  "version": "2.8.5",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <[email protected] (http://www.forer.it)",

diff --git a/src/main/java/cloudgene/mapred/Main.java b/src/main/java/cloudgene/mapred/Main.java
@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.8.2";
+	public static final String VERSION = "2.8.5";
 
 	private Database database;
 

diff --git a/src/main/java/cloudgene/mapred/api/v2/admin/ArchiveJob.java b/src/main/java/cloudgene/mapred/api/v2/admin/ArchiveJob.java
@@ -1,7 +1,9 @@
 package cloudgene.mapred.api.v2.admin;
 
+import cloudgene.mapred.database.ParameterDao;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.restlet.data.Parameter;
 import org.restlet.data.Status;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;

diff --git a/src/main/java/cloudgene/mapred/api/v2/jobs/GetJobDetails.java b/src/main/java/cloudgene/mapred/api/v2/jobs/GetJobDetails.java
@@ -3,6 +3,7 @@
 import java.util.List;
 import java.util.Vector;
 
+import cloudgene.mapred.database.ParameterDao;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.restlet.data.MediaType;

diff --git a/src/main/java/cloudgene/mapred/api/v2/server/GetCounter.java b/src/main/java/cloudgene/mapred/api/v2/server/GetCounter.java
@@ -2,6 +2,7 @@
 
 import java.util.Map;
 
+import cloudgene.mapred.database.JobDao;
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
 import org.restlet.resource.Get;
@@ -17,36 +18,39 @@ public class GetCounter extends BaseResource {
 	public Representation get() {
 
 		JSONObject jsonCounters = new JSONObject();
-		
+
 		// complete
 		Map<String, Long> counters = getWorkflowEngine().getCounters(
-				AbstractJob.STATE_SUCCESS);	
-		JSONObject jsonComplete = new JSONObject();	
+				AbstractJob.STATE_SUCCESS);
+		JSONObject jsonComplete = new JSONObject();
 		for (String key : counters.keySet()) {
 			jsonComplete.put(key, counters.get(key));
 		}
 		jsonCounters.put("complete", jsonComplete);
 
 		// running
 		counters = getWorkflowEngine().getCounters(AbstractJob.STATE_RUNNING);
-		JSONObject jsonRunning = new JSONObject();	
+		JSONObject jsonRunning = new JSONObject();
 		for (String key : counters.keySet()) {
 			jsonRunning.put(key, counters.get(key));
 		}
 		jsonCounters.put("running", jsonRunning);
 
 		// waiting
 		counters = getWorkflowEngine().getCounters(AbstractJob.STATE_WAITING);
-		JSONObject jsonWaiting= new JSONObject();	
+		JSONObject jsonWaiting= new JSONObject();
 		for (String key : counters.keySet()) {
 			jsonWaiting.put(key, counters.get(key));
 		}
 		jsonCounters.put("waiting", jsonWaiting);
 
-		UserDao dao = new UserDao(getDatabase());		
-		jsonCounters.put("users", dao.findAll().size());
-
-
+		UserDao dao = new UserDao(getDatabase());
+		jsonCounters.put("users", dao.countAll());
+
+		JSONObject queue = new JSONObject();
+		queue.put("size", getWorkflowEngine().getSize());
+		jsonCounters.put("queue", queue);
+
 		return new StringRepresentation(jsonCounters.toString());
 
 	}

diff --git a/src/main/java/cloudgene/mapred/cron/CleanUpTasks.java b/src/main/java/cloudgene/mapred/cron/CleanUpTasks.java
@@ -3,6 +3,7 @@
 import java.io.File;
 import java.util.List;
 
+import cloudgene.mapred.database.ParameterDao;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -53,6 +54,7 @@ public static int executeRetire(Database database, Settings settings) {
 				job.setState(AbstractJob.STATE_RETIRED);
 				dao.update(job);
 
+
 				log.info("Job " + job.getId() + " retired.");
 				deleted++;
 

diff --git a/src/main/java/cloudgene/mapred/database/JobDao.java b/src/main/java/cloudgene/mapred/database/JobDao.java
@@ -412,6 +412,31 @@ public List<AbstractJob> findAllByState(int state) {
 		}
 	}
 
+	@SuppressWarnings("unchecked")
+	public int countAllByState(int state) {
+
+		StringBuilder sql = new StringBuilder();
+		sql.append("select count(*) ");
+		sql.append("from job ");
+		sql.append("where state = ? ");
+
+		Object[] params = new Object[1];
+		params[0] = state;
+
+		int result = 0;
+
+		try {
+			result = (Integer) queryForObject(sql.toString(), params, new IntegerMapper());
+			log.debug("count all old jobs successful. results: " + result);
+
+			return result;
+		} catch (SQLException e) {
+			log.error("count all old jobs failed", e);
+			return 0;
+		}
+	}
+
+
 	public AbstractJob findById(String id) {
 
 		return findById(id, true);

diff --git a/src/main/java/cloudgene/mapred/database/ParameterDao.java b/src/main/java/cloudgene/mapred/database/ParameterDao.java
@@ -183,7 +183,7 @@ public CloudgeneParameterOutput findById(int id) {
 		}
 	}
 
-	class ParameterInputMapper implements IRowMapper {
+    class ParameterInputMapper implements IRowMapper {
 
 		@Override
 		public Object mapRow(ResultSet rs, int row) throws SQLException {

diff --git a/src/main/java/cloudgene/mapred/database/UserDao.java b/src/main/java/cloudgene/mapred/database/UserDao.java
@@ -208,7 +208,28 @@ public List<User> findAll() {
 		}
 		return result;
 	}
-
+
+	@SuppressWarnings("unchecked")
+	public int countAll() {
+
+		StringBuilder sql = new StringBuilder();
+		sql.append("select count(*) ");
+		sql.append("from `user` ");
+
+		int result = 0;
+
+		try {
+			result = (Integer) queryForObject(sql.toString(), new IntegerMapper());
+			log.debug("count all users successful. results: " + result);
+
+			return result;
+		} catch (SQLException e) {
+			log.error("count all users failed", e);
+			return 0;
+		}
+	}
+
+
 	@SuppressWarnings("unchecked")
 	public List<User> findByQuery(String query) {
 

diff --git a/src/main/java/cloudgene/mapred/jobs/WorkflowEngine.java b/src/main/java/cloudgene/mapred/jobs/WorkflowEngine.java
@@ -241,6 +241,10 @@ public List<AbstractJob> getAllJobsInLongTimeQueue() {
 		return jobs;
 	}
 
+	public int getSize() {
+		return longTimeQueue.getSize() + shortTimeQueue.getSize();
+	}
+
 	class SetupThread extends PriorityRunnable {
 
 		private AbstractJob job;

diff --git a/src/main/java/cloudgene/mapred/jobs/queue/Queue.java b/src/main/java/cloudgene/mapred/jobs/queue/Queue.java
@@ -305,6 +305,10 @@ public boolean isInQueue(AbstractJob job) {
 		}
 	}
 
+	public int getSize() {
+		return queue.size();
+	}
+
 	protected class PriorityComparator implements Comparator<AbstractJob> {
 
 		@Override