From 822609bdeb91d490fcbf11f64d85a00a3d405588 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Thu, 14 Mar 2024 09:15:30 +0100
Subject: [PATCH] always refresh links in newly added miriam
---
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 +++++++++---------
.../services/impl/ProjectService.java | 3 +--
web/pom.xml | 8 ++++----
19 files changed, 67 insertions(+), 62 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 6a5feaa4ff..ef1639edd0 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,9 @@
+minerva (17.0.0~beta.6) unstable; urgency=medium
+ * Bug fix (regression): when caching data on project upload annotation links
+ were not present (#2012)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Mar 2024 10:00:00 +0200
+
minerva (17.0.0~beta.5) unstable; urgency=medium
* Small improvement (regression): additional info about archive/revive
project action (#1971)
diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml
index 4af37e4b5c..05f57537de 100644
--- a/CellDesigner-plugin/pom.xml
+++ b/CellDesigner-plugin/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
diff --git a/annotation/pom.xml b/annotation/pom.xml
index dd5846141d..05f358520a 100644
--- a/annotation/pom.xml
+++ b/annotation/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</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>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Log4J2 -->
diff --git a/commons/pom.xml b/commons/pom.xml
index 6a7a76f724..d7c3aa904d 100644
--- a/commons/pom.xml
+++ b/commons/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 42146cad94..a7ec50143f 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-SBGNML/pom.xml b/converter-SBGNML/pom.xml
index 745e3e3310..084fbab222 100644
--- a/converter-SBGNML/pom.xml
+++ b/converter-SBGNML/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml
index 5e2c828080..d62cb10b52 100644
--- a/converter-graphics/pom.xml
+++ b/converter-graphics/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index d4134d7a8b..f3159fe05f 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Log4J2 -->
@@ -167,7 +167,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
<scope>test</scope>
</dependency>
diff --git a/converter/pom.xml b/converter/pom.xml
index 1461e781c8..c208389009 100644
--- a/converter/pom.xml
+++ b/converter/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
diff --git a/frontend-js/pom.xml b/frontend-js/pom.xml
index a321af8e8a..93019aa996 100644
--- a/frontend-js/pom.xml
+++ b/frontend-js/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
diff --git a/model-command/pom.xml b/model-command/pom.xml
index 111638e549..14cab75758 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Log4J2-->
diff --git a/model/pom.xml b/model/pom.xml
index 9f98485334..1692eb32df 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Java xml serialization -->
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index 1a86ce03bd..74d4dffc93 100644
--- a/pathvisio/pom.xml
+++ b/pathvisio/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
@@ -77,26 +77,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Log4J2 -->
diff --git a/persist/pom.xml b/persist/pom.xml
index 1a7672fe2a..317c5dc023 100644
--- a/persist/pom.xml
+++ b/persist/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>persist</artifactId>
@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Hibernate -->
diff --git a/pom.xml b/pom.xml
index 30e2f5f599..6deebb69db 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index f31b282757..4adae49b7d 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
diff --git a/service/pom.xml b/service/pom.xml
index 0c1f1a12eb..0c2f4e033a 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>service</artifactId>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,47 +27,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>annotation</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-SBGNML</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-sbml</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<!-- Log4J2 -->
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 bb4178cd83..92c1309a8d 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -432,9 +432,8 @@ public class ProjectService implements IProjectService {
if (params.isCacheModel()) {
self.cacheData(params.getProjectId());
- } else {
- self.createRefreshMiriamInfoJobs(params.getProjectId());
}
+ self.createRefreshMiriamInfoJobs(params.getProjectId());
self.updateProjectStatus(params.getProjectId(), ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS);
if (params.getNotifyEmail() != null && !params.getNotifyEmail().equals("")) {
diff --git a/web/pom.xml b/web/pom.xml
index a965995928..c0ebbb3c9e 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</parent>
<artifactId>web</artifactId>
<packaging>jar</packaging>
@@ -36,19 +36,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>rest-api</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
- <version>17.0.0~beta.5</version>
+ <version>17.0.0~beta.6</version>
</dependency>
<dependency>
--
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