Merge branch 'master' into fixes/job-names

genepi · Mar 21, 2024 · 9975ed9 · 9975ed9
2 parents 640ff6f + 2872374
commit 9975ed9
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Showing 8 changed files with 44 additions and 6 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>2.8.3</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>

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": "2.8.3",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <lukas.forer@i-med.ac.at (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 = "2.8.3";
 
 	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;
@@ -81,6 +83,9 @@ public Representation get() {
 				job.setState(AbstractJob.STATE_RETIRED);
 				dao.update(job);
 
+				ParameterDao parameterDao = new ParameterDao(getDatabase());
+				parameterDao.deleteAllByJob(job);
+
 				if (externalWorkspace != null) {
 					try {
 						externalWorkspace.delete(job.getId());

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;
@@ -148,6 +149,9 @@ public Representation deleteJob(Representation entity) {
 		job.setState(AbstractJob.STATE_DELETED);
 		dao.update(job);
 
+		ParameterDao parameterDao = new ParameterDao(getDatabase());
+		parameterDao.deleteAllByJob(job);
+
 		Settings settings = getSettings();
 
 		IExternalWorkspace externalWorkspace = null;

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;
 
@@ -25,6 +26,8 @@ public class CleanUpTasks {
 	public static int executeRetire(Database database, Settings settings) {
 		JobDao dao = new JobDao(database);
 
+		ParameterDao parameterDao = new ParameterDao(database);
+
 		List<AbstractJob> oldJobs = dao.findAllNotifiedJobs();
 
 		int deleted = 0;
@@ -53,6 +56,9 @@ public static int executeRetire(Database database, Settings settings) {
 				job.setState(AbstractJob.STATE_RETIRED);
 				dao.update(job);
 
+
+				parameterDao.deleteAllByJob(job);
+
 				log.info("Job " + job.getId() + " retired.");
 				deleted++;
 

diff --git a/src/main/java/cloudgene/mapred/database/ParameterDao.java b/src/main/java/cloudgene/mapred/database/ParameterDao.java
@@ -183,7 +183,30 @@ public CloudgeneParameterOutput findById(int id) {
 		}
 	}
 
-	class ParameterInputMapper implements IRowMapper {
+    public boolean deleteAllByJob(AbstractJob job) {
+		try {
+
+			StringBuilder sql = new StringBuilder();
+			sql.append("delete ");
+			sql.append("from parameter ");
+			sql.append("where job_id = ?");
+
+			Object[] params = new Object[1];
+			params[0] = job.getId();
+
+			update(sql.toString(), params);
+
+			log.debug("delete all parameters by job_id '" + job.getId() + "' successful.");
+
+			return true;
+
+		} catch (SQLException e) {
+			log.error("delete all parameters by job_id '" + job.getId() + "' failed.", e);
+			return false;
+		}
+    }
+
+    class ParameterInputMapper implements IRowMapper {
 
 		@Override
 		public Object mapRow(ResultSet rs, int row) throws SQLException {