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Commit bdbe6a3b authored by Piotr Gawron's avatar Piotr Gawron
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use vacuum analyze instead of vacuum full (locks on db are not required)

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CHANGELOG
View file @ bdbe6a3b
minerva (16.0.7) stable; urgency=medium
* Bug fix (performance): vacuum cron job could cause deadlock and starvation
of db connections
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 14 Jan 2022 13:00:00 +0200
minerva (16.0.6) stable; urgency=medium
* Bug fix (performance): fetching all bioEntities using plugin API is faster;
reactions and elements are fetched in parallel (#1605)
......
CellDesigner-plugin/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
......@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
......
annotation/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
......@@ -18,7 +18,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- dependency from the MapViewer dao -->
......@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
......@@ -34,13 +34,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Log4J2 -->
......
commons/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
......
converter-CellDesigner/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
......@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Log4J2 -->
......
converter-SBGNML/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
......@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
......
converter-graphics/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
......@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Log4J2-->
......
converter-sbml/pom.xml
View file @ bdbe6a3b
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
......@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Log4J2 -->
......@@ -154,7 +154,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
<scope>test</scope>
</dependency>
......
converter/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>converter</artifactId>
......@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
......
frontend-js/pom.xml
View file @ bdbe6a3b
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
......
model-command/pom.xml
View file @ bdbe6a3b
......@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
......@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
......@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Log4J2-->
......
model/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
......@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Java xml serialization -->
......
pathvisio/pom.xml
View file @ bdbe6a3b
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
......@@ -77,20 +77,20 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Log4J2 -->
......
persist/pom.xml
View file @ bdbe6a3b
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>persist</artifactId>
......@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- apache ftp -->
......
persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
View file @ bdbe6a3b
......@@ -249,7 +249,7 @@ public class DbUtils extends Observable {
public void execute(final Connection connection) throws SQLException {
boolean autoCommit = connection.getAutoCommit();
connection.setAutoCommit(true);
connection.prepareStatement("VACUUM FULL").execute();
connection.prepareStatement("VACUUM ANALYZE").execute();
connection.setAutoCommit(autoCommit);
}
});
......
pom.xml
View file @ bdbe6a3b
......@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
......
rest-api/pom.xml
View file @ bdbe6a3b
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
......@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
......
service/pom.xml
View file @ bdbe6a3b
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>service</artifactId>
......@@ -20,7 +20,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- dependency from the MapViewer dao -->
......@@ -28,47 +28,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>annotation</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-SBGNML</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-sbml</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<!-- Log4J2 -->
......
web/pom.xml
View file @ bdbe6a3b
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</parent>
<artifactId>web</artifactId>
<packaging>war</packaging>
......@@ -33,19 +33,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>rest-api</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
<version>16.0.6</version>
<version>16.0.7</version>
</dependency>
<dependency>
......
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