From c2b201719b6e5e79ede13aec951797ccb45aa96d Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 21 Feb 2023 13:03:27 +0100
Subject: [PATCH] disable assistive technology
---
CHANGELOG | 6 ++++++
CellDesigner-plugin/pom.xml | 8 ++++----
annotation/pom.xml | 10 +++++-----
commons/pom.xml | 2 +-
converter-CellDesigner/pom.xml | 6 +++---
converter-SBGNML/pom.xml | 10 +++++-----
converter-graphics/pom.xml | 6 +++---
converter-sbml/pom.xml | 12 ++++++------
converter/pom.xml | 4 ++--
frontend-js/pom.xml | 2 +-
model-command/pom.xml | 6 +++---
model/pom.xml | 4 ++--
pathvisio/pom.xml | 10 +++++-----
persist/pom.xml | 4 ++--
pom.xml | 2 +-
rest-api/pom.xml | 8 ++++----
service/pom.xml | 18 +++++++++---------
web/pom.xml | 8 ++++----
.../mapviewer/web/bean/utils/StartupBean.java | 10 ++++++++--
.../web/bean/utils/StartupBeanTest.java | 9 +++++++++
20 files changed, 83 insertions(+), 62 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 6396225075..da3aa61496 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,9 @@
+minerva (16.2.12) stable; urgency=medium
+ * Bug fix: Java Assistive Technology caused randomly issues with map upload
+ (#1681)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Tue, 21 Feb 2023 12:00:00 +0200
+
minerva (16.2.11) stable; urgency=medium
* Bug fix: there was a race condition in very rare situations when exporting
to CellDesigner (#1728)
diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml
index 0aa7df3bde..620e4fc471 100644
--- a/CellDesigner-plugin/pom.xml
+++ b/CellDesigner-plugin/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
diff --git a/annotation/pom.xml b/annotation/pom.xml
index 16273cc907..0e1adeacc3 100644
--- a/annotation/pom.xml
+++ b/annotation/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
@@ -18,7 +18,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</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>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Log4J2 -->
diff --git a/commons/pom.xml b/commons/pom.xml
index 0d3d0fa7c5..8861d9be2a 100644
--- a/commons/pom.xml
+++ b/commons/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index fc594b9a92..7f2e12d313 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-SBGNML/pom.xml b/converter-SBGNML/pom.xml
index 7cff1d1201..3e3759d6d8 100644
--- a/converter-SBGNML/pom.xml
+++ b/converter-SBGNML/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml
index 0d7bc42bd0..a8019de598 100644
--- a/converter-graphics/pom.xml
+++ b/converter-graphics/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Log4J2-->
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index 0acc79025f..5ec00d5305 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Log4J2 -->
@@ -154,7 +154,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
<scope>test</scope>
</dependency>
diff --git a/converter/pom.xml b/converter/pom.xml
index 71e533b585..85c9f8b463 100644
--- a/converter/pom.xml
+++ b/converter/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
diff --git a/frontend-js/pom.xml b/frontend-js/pom.xml
index 423d34421a..3d2079030a 100644
--- a/frontend-js/pom.xml
+++ b/frontend-js/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
diff --git a/model-command/pom.xml b/model-command/pom.xml
index f80bae4f15..57ca5b8851 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Log4J2-->
diff --git a/model/pom.xml b/model/pom.xml
index 472e57dd5e..a74fd3bcd2 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Java xml serialization -->
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index 276c227eff..cd3c568279 100644
--- a/pathvisio/pom.xml
+++ b/pathvisio/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
@@ -77,26 +77,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Log4J2 -->
diff --git a/persist/pom.xml b/persist/pom.xml
index 30b28e1c17..5a2ed526a0 100644
--- a/persist/pom.xml
+++ b/persist/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>persist</artifactId>
@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- apache ftp -->
diff --git a/pom.xml b/pom.xml
index 697c5a5b89..80f0278047 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index 2494bb621d..01af0f2cc3 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
diff --git a/service/pom.xml b/service/pom.xml
index 99a82a0600..0fe1d0257c 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>service</artifactId>
@@ -20,7 +20,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -28,47 +28,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>annotation</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-SBGNML</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-sbml</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<!-- Log4J2 -->
diff --git a/web/pom.xml b/web/pom.xml
index ccee3ef4e5..7a2ee3cc87 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</parent>
<artifactId>web</artifactId>
<packaging>war</packaging>
@@ -31,19 +31,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>rest-api</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
- <version>16.2.11</version>
+ <version>16.2.12</version>
</dependency>
<dependency>
diff --git a/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
index c97fe36a56..e14f6c6266 100644
--- a/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
+++ b/web/src/main/java/lcsb/mapviewer/web/bean/utils/StartupBean.java
@@ -3,6 +3,7 @@ package lcsb.mapviewer.web.bean.utils;
import java.io.File;
import java.io.IOException;
import java.sql.SQLException;
+import java.util.Properties;
import javax.annotation.PostConstruct;
import javax.servlet.ServletContext;
@@ -69,6 +70,7 @@ public class StartupBean {
modifyXFrameDomain();
modifyCorsDomain();
setSessionLength();
+ disableAssistiveTechnologies();
removeInterruptedReferenceGenomeDownloads();
logger.debug("Application startup script ends");
}
@@ -141,8 +143,8 @@ public class StartupBean {
}
/**
- * Set {@link ProjectStatus#FAIL} statuses to projects that were uploading
- * when application was shutdown.
+ * Set {@link ProjectStatus#FAIL} statuses to projects that were uploading when
+ * application was shutdown.
*/
private void setInterruptedProjectsStatuses() {
try {
@@ -165,4 +167,8 @@ public class StartupBean {
}
}
+ private void disableAssistiveTechnologies() {
+ Properties props = System.getProperties();
+ props.setProperty("javax.accessibility.assistive_technologies", "");
+ }
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/bean/utils/StartupBeanTest.java b/web/src/test/java/lcsb/mapviewer/web/bean/utils/StartupBeanTest.java
index 59d17c6519..039bc86d28 100644
--- a/web/src/test/java/lcsb/mapviewer/web/bean/utils/StartupBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/bean/utils/StartupBeanTest.java
@@ -1,6 +1,9 @@
package lcsb.mapviewer.web.bean.utils;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+
+import java.util.Properties;
import org.junit.After;
import org.junit.Before;
@@ -53,4 +56,10 @@ public class StartupBeanTest extends ControllerIntegrationTest {
assertEquals(0, super.getErrorLogs().size());
}
+ @Test
+ public void testAssistiveTechnologies() {
+ Properties props = System.getProperties();
+ assertNotEquals(props.getProperty("javax.accessibility.assistive_technologies"), "org.GNOME.Accessibility.AtkWrapper");
+ }
+
}
--
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