Merge branch '2069-createproject-should-not-be-transactional' into 'master'

Resolve "CreateProject should not be transactional"

Closes #2069

See merge request !1756

CHANGELOG

+minerva (17.1.1) unstable; urgency=medium
+  * Bug fix: sometimes there was a deadlock when uploading a project due (#2069)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Aug 2024 13:00:00 +0200
+
 minerva (17.1.0) unstable; urgency=medium
   * Improvement: downloadModel API call contains strictCutoff parameter
     (default=true) to allow selecting reaction that cross polygon (#1769)

CellDesigner-plugin/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>CellDesigner-plugin</artifactId>
 	<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>commons</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>

annotation/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>annotation</artifactId>
 	<name>Annotation module</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer dao -->
@@ -27,7 +27,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer cell designer parser (we need access 
@@ -35,13 +35,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorImpl.java

@@ -50,7 +50,7 @@ public class TairAnnotatorImpl extends ElementAnnotator implements TairAnnotator
 
   private static final Logger logger = LogManager.getLogger();
 
-  private static final String URL_SOURCE_DATABASE = "https://www.arabidopsis.org/api/download-files/download?filePath=Proteins%2FId_conversions%2FArchived%2FTAIR2UniprotMapping-Jul2023.txt";
+  private static final String URL_SOURCE_DATABASE = "https://minerva-dev.lcsb.uni.lu/TAIR2UniprotMapping-Jul2023.txt";
 
   private static final int BUFFER_SIZE = 1024;
 

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java

 package lcsb.mapviewer.annotation.services.annotators;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.Collection;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.util.ReflectionTestUtils;
-
 import lcsb.mapviewer.annotation.AnnotationTestFunctions;
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -21,6 +9,17 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.util.ReflectionTestUtils;
+
+import java.util.Collection;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
 
 public class TairAnnotatorTest extends AnnotationTestFunctions {
 
@@ -30,7 +29,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
   @Autowired
   private GeneralCacheInterface cache;
 
-  private WebPageDownloader webPageDownloader = new WebPageDownloader();
+  private final WebPageDownloader webPageDownloader = new WebPageDownloader();
 
   @Before
   public void setUp() {
@@ -88,15 +87,15 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
 
     tairAnnotator.annotateElement(protein);
 
-    int cntUniProts = 0;
+    int countUniprot = 0;
 
     for (final MiriamData md : protein.getMiriamData()) {
       if (md.getDataType().equals(MiriamType.UNIPROT)) {
-        cntUniProts++;
+        countUniprot++;
       }
     }
 
-    assertTrue("No UNIPROT annotation extracted from TAIR annotator", cntUniProts > 1);
+    assertTrue("No UNIPROT annotation extracted from TAIR annotator", countUniprot > 1);
   }
 
   @Test
@@ -140,13 +139,13 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
 
   @Test
   public void testTairToUniprotFromKEGG() throws Exception {
-    // TAIR Loci comming from annotators should be ignored by TAIR (only TAIR
+    // TAIR Loci coming from annotators should be ignored by TAIR (only TAIR
     // LOCI provided by the human annotator should be considered)
     Species protein = new GenericProtein("id");
     protein.setName("bla");
     protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "2200427", KeggAnnotator.class));
     tairAnnotator.annotateElement(protein);
-    assertTrue(protein.getMiriamData().size() == 1);
+    assertEquals(1, protein.getMiriamData().size());
   }
 
   @Test

commons/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>commons</artifactId>
 	<name>Mapviewer commons</name>

converter-CellDesigner/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>converter-CellDesigner</artifactId>
 	<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->

converter-SBGNML/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>converter-SBGNML</artifactId>
 
@@ -20,26 +20,26 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 			<scope>test</scope>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>

converter-graphics/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>converter-graphics</artifactId>
 	<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->

converter-sbml/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>converter-sbml</artifactId>
 	<name>converter-sbml</name>
@@ -40,22 +40,22 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->
@@ -167,7 +167,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 			<scope>test</scope>
 		</dependency>
 

converter/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>lcsb.mapviewer</groupId>
     <artifactId>parent</artifactId>
-    <version>17.1.0</version>
+    <version>17.1.1</version>
   </parent>
   
   <artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
       <artifactId>model</artifactId>
-      <version>17.1.0</version>
+      <version>17.1.1</version>
     </dependency>
 		<dependency>
 			<groupId>xerces</groupId>

frontend-js/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>frontend-js</artifactId>
 	<name>frontend-js</name>

model-command/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <groupId>lcsb.mapviewer</groupId>
     <artifactId>parent</artifactId>
-    <version>17.1.0</version>
+    <version>17.1.1</version>
   </parent>
   <artifactId>model-command</artifactId>
   <name>Model commands</name>
@@ -16,7 +16,7 @@
 		<dependency>
     	<groupId>lcsb.mapviewer</groupId>
       <artifactId>model</artifactId>
-      <version>17.1.0</version>
+      <version>17.1.1</version>
     </dependency>
     
 
@@ -24,7 +24,7 @@
 		<dependency>
       <groupId>lcsb.mapviewer</groupId>
       <artifactId>converter-CellDesigner</artifactId>
-      <version>17.1.0</version>
+      <version>17.1.1</version>
     </dependency>
 
 		<!-- Log4J2-->

model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>model</artifactId>
 	<name>model MapViewer</name>
@@ -15,7 +15,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>commons</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Java xml serialization -->

pathvisio/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>pathvisio</artifactId>
 	<name>Pathvisio plugin</name>
@@ -77,26 +77,26 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
 			<scope>test</scope>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->

persist/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 
 	<artifactId>persist</artifactId>
@@ -26,7 +26,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Hibernate -->

pom.xml

@@ -6,7 +6,7 @@
 
 	<groupId>lcsb.mapviewer</groupId>
 	<artifactId>parent</artifactId>
-	<version>17.1.0</version>
+	<version>17.1.1</version>
 	<packaging>pom</packaging>
 
     <name>parent MapViewer</name>

rest-api/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 	<artifactId>rest-api</artifactId>
 	<name>rest-api</name>
@@ -19,19 +19,19 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>service</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>pathvisio</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>

service/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>17.1.0</version>
+		<version>17.1.1</version>
 	</parent>
 
 	<artifactId>service</artifactId>
@@ -20,7 +20,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer dao -->
@@ -28,47 +28,47 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>annotation</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer cell designer parser -->
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer SBGN-ML parser -->
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-SBGNML</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer graphics converter -->
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- dependency from the SBML parser -->
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-sbml</artifactId>
-			<version>17.1.0</version>
+			<version>17.1.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->

service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java

 package lcsb.mapviewer.services.impl;
 
-import java.sql.SQLException;
-import java.util.Calendar;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.ScheduledThreadPoolExecutor;
-import java.util.concurrent.ThreadFactory;
-
-import javax.annotation.PostConstruct;
-
-import org.apache.commons.lang3.exception.ExceptionUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.springframework.beans.BeansException;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.SpringApplication;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.ApplicationContextAware;
-import org.springframework.jdbc.datasource.init.ScriptException;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
 import lcsb.mapviewer.annotation.cache.CacheQueryMinervaJob;
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.common.MinervaConfigurationHolder;
@@ -41,13 +14,38 @@ import lcsb.mapviewer.persist.CustomDatabasePopulator;
 import lcsb.mapviewer.persist.dao.MinervaJobDao;
 import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
 import lcsb.mapviewer.services.interfaces.IMinervaJobService;
+import org.apache.commons.lang3.exception.ExceptionUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.beans.BeansException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.SpringApplication;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.jdbc.datasource.init.ScriptException;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+import javax.annotation.PostConstruct;
+import java.sql.SQLException;
+import java.util.Calendar;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ScheduledThreadPoolExecutor;
+import java.util.concurrent.ThreadFactory;
 
 @Service
 public class MinervaJobService implements IMinervaJobService, ApplicationContextAware {
 
   private ApplicationContext context;
 
-  private Logger logger = LogManager.getLogger();
+  private final Logger logger = LogManager.getLogger();
 
   private MinervaJobDao minervaJobDao;
 
@@ -72,7 +70,7 @@ public class MinervaJobService implements IMinervaJobService, ApplicationContext
 
   @Autowired
   public MinervaJobService(final MinervaJobDao minervaJobDao, final GeneralCacheInterface cache, final CacheTypeDao cacheTypeDao,
-      final CustomDatabasePopulator flyway, final MinervaConfigurationHolder configurationHolder) {
+                           final CustomDatabasePopulator flyway, final MinervaConfigurationHolder configurationHolder) {
     this.minervaJobDao = minervaJobDao;
     this.cache = cache;
     this.cacheTypeDao = cacheTypeDao;