diff --git a/CHANGELOG b/CHANGELOG
index 493a5fbd27a4164acabd1f07d47e3f9178a7a1d8..f96dba83806fbfd4aa90b7f5d08ebe73756873a9 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,8 @@
+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)
diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml
index 8f07c889ecf60659b46f4e50cd5a8f1767dbb438..6508b076a65158401be488979a4c2b46f01cfdff 100644
--- a/CellDesigner-plugin/pom.xml
+++ b/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>
diff --git a/annotation/pom.xml b/annotation/pom.xml
index a4cc3d91cbc366443584e87f85500f7bdfd5e297..67b6180d20da47b708d2aa5037f43b6d52cf2b37 100644
--- a/annotation/pom.xml
+++ b/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 -->
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorImpl.java
index 26ccb290800c8e632942e9afad1ec921746c7757..e00d05a9bdc5e32800304b9248c04ed6b386c7c7 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorImpl.java
+++ b/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;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
index fdd94a21df47de804eca15a861d79efb37ba3a44..d0741fdf9ca83ebc3c6355559ef69b15c3304dfc 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
@@ -1,17 +1,5 @@
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
diff --git a/commons/pom.xml b/commons/pom.xml
index ddef5cdbb7a574bf4820c9a96fc1f7d706ad8b84..e6f14fcc11859fefee1f8d900d4d2998cfd81d5f 100644
--- a/commons/pom.xml
+++ b/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>
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 8f6e65f0f971038e6ca25e0c614142b7f80170b3..f7928409ef236f9587074927e5be3b79dd4b76c1 100644
--- a/converter-CellDesigner/pom.xml
+++ b/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 -->
diff --git a/converter-SBGNML/pom.xml b/converter-SBGNML/pom.xml
index e7c66bcda74245f5f4d6ffdc39ca6d195df549c4..d2afce40115f512de33a34b2cd155a299e654d66 100644
--- a/converter-SBGNML/pom.xml
+++ b/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>
diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml
index 8b77ca66a71978b529dd1dc3d25da35b7c2d81f9..2f6013be71d07073e782a06b9ea8eb311d3602a2 100644
--- a/converter-graphics/pom.xml
+++ b/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 -->
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index de6b7d476d01a6160547504e06f9bc41e5861122..9c20cb13815a7cb5e638e54644fe213c54e7f89a 100644
--- a/converter-sbml/pom.xml
+++ b/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>
diff --git a/converter/pom.xml b/converter/pom.xml
index d69a4b09124d420ae78e9a8943b584d9a5c8bbae..131e80d7249d91d60446302b150ff13cdb41f738 100644
--- a/converter/pom.xml
+++ b/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>
diff --git a/frontend-js/pom.xml b/frontend-js/pom.xml
index 5bd97ae4414f22baa716e9c02e26cd8f7c88236e..ec5d8e0a1fd000caea4df38eb5a21c1700e2d4b8 100644
--- a/frontend-js/pom.xml
+++ b/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>
diff --git a/model-command/pom.xml b/model-command/pom.xml
index 0bb694f02687ab670477188c538472b74c1781ca..c59505c996603cb0452cbe2186ace3a9902403bc 100644
--- a/model-command/pom.xml
+++ b/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-->
diff --git a/model/pom.xml b/model/pom.xml
index e5f15286b35ad29e78b435022f993bc668804e8f..ac6d49db43e964d0d820db4b6c8f8b024916187b 100644
--- a/model/pom.xml
+++ b/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 -->
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index 97ea99b0d414c5d16b5b4b64755fb78878610a0b..e0bb5e020f268a70fabe8d2ec52bae7f8152f099 100644
--- a/pathvisio/pom.xml
+++ b/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 -->
diff --git a/persist/pom.xml b/persist/pom.xml
index b7b4648513e72b72eac0b3221c837da62b60ddc3..ab652879069b04c879d0113dd5b102b568e4a0da 100644
--- a/persist/pom.xml
+++ b/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 -->
diff --git a/pom.xml b/pom.xml
index 3b26d9816004063629dda49cc28d8a9e39fc55cb..84aa63f6e139d5eee0c2e507b8bf51ded992a48e 100644
--- a/pom.xml
+++ b/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>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index 426d2b9dbd316e57391d6ed5b763e64ea6a04d69..ca69ab18bd95921aa64e7922fd17bf4fc691c268 100644
--- a/rest-api/pom.xml
+++ b/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>
diff --git a/service/pom.xml b/service/pom.xml
index d2b62f9cf1ef27f7340ea4747ddb5e36721e72ed..f18dfa8796b8255173cba04a9dc5e49926ca0fab 100644
--- a/service/pom.xml
+++ b/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 -->
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java b/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java
index c12eced06e5763f9fac5bf94da87eb18a41a2b03..d8d715af1455901dd8d410f916666eadb8befd28 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/MinervaJobService.java
@@ -1,32 +1,5 @@
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;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 986a755f28c646a1236f5dd599c0ee308a8ce89f..7f5decb95b9ec68d675d5d1568966ab83cac02fc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -398,18 +398,18 @@ public class ProjectService implements IProjectService {
}
}
- @Override
public Project createProject(final CreateProjectParams params) {
Project project2 = self.getProjectByProjectId(params.getProjectId());
if (project2 == null) {
- logger.error("Project with given id does not exist: " + params.getProjectId());
+ logger.error("Project with given id does not exist: {}", params.getProjectId());
return null;
}
+ //noinspection MismatchedReadAndWriteOfArray
double[] outOfMemoryBuffer;
MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
try {
UploadedFileEntry file = fileService.getById(params.getProjectFileId());
- logger.debug("Running: " + params.getProjectId() + "; fileId=" + params.getProjectFileId());
+ logger.debug("Running: {}; fileId={}", params.getProjectId(), params.getProjectFileId());
outOfMemoryBuffer = new double[OUT_OF_MEMORY_BACKUP_BUFFER_SIZE];
for (int i = 0; i < OUT_OF_MEMORY_BACKUP_BUFFER_SIZE; i++) {
outOfMemoryBuffer[i] = Math.random() * OUT_OF_MEMORY_BACKUP_BUFFER_SIZE;
@@ -432,14 +432,14 @@ public class ProjectService implements IProjectService {
if (params.isCacheModel()) {
self.cacheData(params.getProjectId());
} else {
- self.createRefreshDrugInfoJobs(params.getProjectId());
- self.createRefreshChemicalInfoJobs(params.getProjectId());
- self.createRefreshMiRnaInfoJobs(params.getProjectId());
+ createRefreshDrugInfoJobs(params.getProjectId());
+ createRefreshChemicalInfoJobs(params.getProjectId());
+ createRefreshMiRnaInfoJobs(params.getProjectId());
}
- self.createRefreshMiriamInfoJobs(params.getProjectId());
+ createRefreshMiriamInfoJobs(params.getProjectId());
self.updateProjectStatus(params.getProjectId(), ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS);
- if (params.getNotifyEmail() != null && !params.getNotifyEmail().equals("")) {
+ if (params.getNotifyEmail() != null && !params.getNotifyEmail().isEmpty()) {
try {
sendSuccesfullEmail(params);
} catch (MessagingException e) {
@@ -447,13 +447,13 @@ public class ProjectService implements IProjectService {
}
}
- logger.info("Project " + params.getProjectId() + " created successfully.");
+ logger.info("Project {} created successfully.", params.getProjectId());
} catch (PersistenceException e) {
outOfMemoryBuffer = null;
logger.error("Problem with database", e);
self.projectFailure(params.getProjectId(), ProjectLogEntryType.DATABASE_PROBLEM,
"Problem with uploading to database. "
- + "You might violated some unhandled constraints or you run out of memory. Underlaying eror:\n"
+ + "You might violated some unhandled constraints or you run out of memory. Underlying error:\n"
+ e.getMessage() + "\nMore information can be found in log file.",
e);
} catch (OutOfMemoryError oome) {
@@ -492,69 +492,42 @@ public class ProjectService implements IProjectService {
}
- @Override
public void createRefreshMiriamInfoJobs(final String projectId) {
- Project project = self.getProjectByProjectId(projectId, true);
- for (ModelData model : project.getModels()) {
- for (Element bioEntity : model.getElements()) {
- for (MiriamData md : bioEntity.getMiriamData()) {
- minervaJobService.addJob(createRefreshMiriamInfoJob(md));
- }
- }
- for (Reaction bioEntity : model.getReactions()) {
- for (MiriamData md : bioEntity.getMiriamData()) {
- minervaJobService.addJob(createRefreshMiriamInfoJob(md));
- }
- }
- for (MiriamData md : model.getMiriamData()) {
- minervaJobService.addJob(createRefreshMiriamInfoJob(md));
- }
+ for (MiriamData miriamData : self.getMiriamForProject(projectId)) {
+ minervaJobService.addJob(createRefreshMiriamInfoJob(miriamData));
}
}
- @Override
public void createRefreshDrugInfoJobs(final String projectId) {
- Project project = self.getProjectByProjectId(projectId, true);
- Set<MiriamData> set = new HashSet<>();
- for (ModelData model : project.getModels()) {
- for (Element bioEntity : model.getElements()) {
- set.addAll(bioEntity.getMiriamData());
- }
- for (Reaction bioEntity : model.getReactions()) {
- set.addAll(bioEntity.getMiriamData());
- }
- }
- for (MiriamData miriamData : set) {
+ for (MiriamData miriamData : self.getMiriamForProject(projectId)) {
minervaJobService.addJob(createRefreshDrugInfoJob(miriamData));
}
}
- @Override
public void createRefreshChemicalInfoJobs(final String projectId) {
Project project = self.getProjectByProjectId(projectId, true);
MiriamData disease = project.getDisease();
if (disease != null) {
-
- Set<MiriamData> set = new HashSet<>();
- for (ModelData model : project.getModels()) {
- for (Element bioEntity : model.getElements()) {
- set.addAll(bioEntity.getMiriamData());
- }
- for (Reaction bioEntity : model.getReactions()) {
- set.addAll(bioEntity.getMiriamData());
- }
- }
- for (MiriamData miriamData : set) {
+ for (MiriamData miriamData : self.getMiriamForProject(projectId)) {
minervaJobService.addJob(createRefreshChemicalInfoJob(miriamData, disease));
}
}
}
- @Override
public void createRefreshMiRnaInfoJobs(final String projectId) {
+ for (MiriamData miriamData : self.getMiriamForProject(projectId)) {
+ minervaJobService.addJob(createRefreshMiRnaInfoJob(miriamData));
+ }
+ }
+
+ @Override
+ public Set<MiriamData> getMiriamForProject(final String projectId) {
Project project = self.getProjectByProjectId(projectId, true);
Set<MiriamData> set = new HashSet<>();
+
for (ModelData model : project.getModels()) {
+ set.addAll(model.getMiriamData());
+
for (Element bioEntity : model.getElements()) {
set.addAll(bioEntity.getMiriamData());
}
@@ -562,9 +535,7 @@ public class ProjectService implements IProjectService {
set.addAll(bioEntity.getMiriamData());
}
}
- for (MiriamData miriamData : set) {
- minervaJobService.addJob(createRefreshMiRnaInfoJob(miriamData));
- }
+ return set;
}
private MinervaJob createRefreshDrugInfoJob(final MiriamData md) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index d6bb975def0c468a690790efba2682fe9acaac83..3bebb31582068fd70545a6f6ee1d88fe6b912f35 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -1,11 +1,5 @@
package lcsb.mapviewer.services.interfaces;
-import java.io.IOException;
-import java.util.List;
-import java.util.Set;
-
-import org.springframework.transaction.annotation.Transactional;
-
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -17,28 +11,31 @@ import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.job.MinervaJob;
import lcsb.mapviewer.model.job.MinervaJobExecutor;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.ProjectBackground;
import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
import lcsb.mapviewer.services.ObjectNotFoundException;
import lcsb.mapviewer.services.utils.CreateProjectParams;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Set;
/**
* Service that manages projects.
- *
+ *
* @author Piotr Gawron
- *
*/
public interface IProjectService extends MinervaJobExecutor {
/**
- * Returns a project with a give {@link Project#projectId project identifier}.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return project with an identifier given as parameter. Null if such project
- * doesn't exist.
+ * Returns a project with a give {@link Project#getProjectId() project identifier}.
+ *
+ * @param projectId {@link Project#getProjectId()} project identifier}
+ * @return project with an identifier given as parameter. Null if such project doesn't exist.
*/
@Transactional
Project getProjectByProjectId(final String projectId);
@@ -47,19 +44,17 @@ public interface IProjectService extends MinervaJobExecutor {
Project getProjectByProjectId(final String projectId, final boolean initializeLazy);
/**
- * Checks if project with a given {@link Project#projectId identifier} exists.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return <code>true</code> if the project with the given name exists,
- * <code>false</code> otherwise
+ * Checks if project with a given {@link Project#getProjectId() identifier} exists.
+ *
+ * @param projectId {@link Project#getProjectId()} project identifier}
+ * @return <code>true</code> if the project with the given name exists, <code>false</code> otherwise
*/
@Transactional
boolean projectExists(final String projectId);
/**
* Returns list of all projects.
- *
+ *
* @return list of all projects.
*/
@Transactional
@@ -70,30 +65,24 @@ public interface IProjectService extends MinervaJobExecutor {
/**
* Removes project from the system.
- *
- * @param project
- * object to remove
+ *
+ * @param project object to remove
*/
@Transactional
MinervaJob submitRemoveProjectJob(final Project project);
/**
* Creates project using give parameters. See {@link CreateProjectParams}.
- *
- * @param params
- * information about project to create
+ *
+ * @param params information about project to create
*/
@Transactional
MinervaJob submitCreateProjectJob(final CreateProjectParams params) throws SecurityException;
- @Transactional
- Project createProject(final CreateProjectParams params) throws SecurityException;
-
/**
* Method that updates information about raw {@link Project} object.
- *
- * @param project
- * project to update
+ *
+ * @param project project to update
*/
@Transactional
void updateProject(final Project project);
@@ -148,14 +137,10 @@ public interface IProjectService extends MinervaJobExecutor {
/**
* This method creates set of images for the model backgrounds.
*
- * @param params
- * configuration parameters including set of backgrounds to generate
- * @throws IOException
- * thrown when there are problems with generating files
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- * @throws CommandExecutionException
- * thrown when one of the files describing backgrounds is invalid
+ * @param params configuration parameters including set of backgrounds to generate
+ * @throws IOException thrown when there are problems with generating files
+ * @throws DrawingException thrown when there was a problem with drawing a map
+ * @throws CommandExecutionException thrown when one of the files describing backgrounds is invalid
*/
@Transactional
void createImages(CreateProjectParams params) throws IOException, DrawingException, CommandExecutionException;
@@ -166,12 +151,9 @@ public interface IProjectService extends MinervaJobExecutor {
/**
* Sends email about unsuccessful project creation.
*
- * @param projectName
- * name of the project
- * @param email
- * email where we want to send information
- * @param e
- * exception that caused problem
+ * @param projectName name of the project
+ * @param email email where we want to send information
+ * @param e exception that caused problem
*/
@Transactional
void sendUnsuccesfullEmail(String projectName, String email, Throwable e);
@@ -179,12 +161,9 @@ public interface IProjectService extends MinervaJobExecutor {
/**
* Updates status of the generating project.
*
- * @param projectId
- * project that is generated
- * @param status
- * what is the current status
- * @param progress
- * what is the progress
+ * @param projectId project that is generated
+ * @param status what is the current status
+ * @param progress what is the progress
*/
@Transactional
void updateProjectStatus(String projectId, ProjectStatus status, double progress);
@@ -192,9 +171,6 @@ public interface IProjectService extends MinervaJobExecutor {
@Transactional
void addLogEntries(String projectId, Set<ProjectLogEntry> createLogEntries);
- @Transactional
- void createRefreshMiriamInfoJobs(String projectId);
-
@Transactional
void submitArchiveProjectJob(String projectId);
@@ -207,12 +183,6 @@ public interface IProjectService extends MinervaJobExecutor {
void reviveBackgrounds(String projectId);
@Transactional
- void createRefreshDrugInfoJobs(String projectId);
-
- @Transactional
- void createRefreshChemicalInfoJobs(String projectId);
-
- @Transactional
- void createRefreshMiRnaInfoJobs(String projectId);
+ Set<MiriamData> getMiriamForProject(String projectId);
}
diff --git a/web/pom.xml b/web/pom.xml
index bb9c1becabe3029bcb157cc01fbc18a34b177535..e9856a891bf0dc654162832ac162bfe8f3853b98 100644
--- a/web/pom.xml
+++ b/web/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>web</artifactId>
<packaging>jar</packaging>
@@ -36,19 +36,19 @@
<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>rest-api</artifactId>
- <version>17.1.0</version>
+ <version>17.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
- <version>17.1.0</version>
+ <version>17.1.1</version>
</dependency>
<dependency>