Merge pull request #2418 from intermine/dev

Release 5.0.6
intermine · Jan 7, 2022 · 21a40f5 · 21a40f5
2 parents b3b328e + 3e248be
commit 21a40f5
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Showing 17 changed files with 35 additions and 30 deletions.
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@ InterMine
 
 Master: [![InterMine CI](https://github.com/intermine/intermine/workflows/InterMine%20CI/badge.svg?branch=master)](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
 Dev: [![InterMine CI](https://github.com/intermine/intermine/workflows/InterMine%20CI/badge.svg?branch=dev)](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
-[![Version](http://img.shields.io/badge/version-5.0.5-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
+[![Version](http://img.shields.io/badge/version-5.0.6-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
 [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE)
 [![Research software impact](http://depsy.org/api/package/pypi/intermine/badge.svg)](http://depsy.org/package/python/intermine)
 [![Conda](https://anaconda.org/anaconda/conda-build/badges/installer/conda.svg)](https://anaconda.org/bioconda/intermine)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -7,6 +7,11 @@
  * information or http://www.gnu.org/copyleft/lesser.html.
  *
  */
+InterMine 5.0.6 (Dicember 2021)
+
+#2414 - Upgraded psi lib version (thanks @asherpasha)
+#2416 - Log4j upgraded to 2.17.1 (thanks @asherpasha)
+
 InterMine 5.0.5 (Dicember 2021)
 
 #2411 - Log4j-1x compatibility upgrade (thanks @asherpasha)

diff --git a/bio/build.gradle b/bio/build.gradle
@@ -1,6 +1,6 @@
 subprojects {
     group = 'org.intermine'
-    version = '5.0.5'
+    version = '5.0.6'
 
     apply plugin: "java"
     apply plugin: "maven"

diff --git a/bio/gradle.properties b/bio/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.5
-systemProp.bioVersion=5.0.5
+systemProp.imVersion=5.0.6
+systemProp.bioVersion=5.0.6
 
 # some unit tests need additional classes that aren't in the core model.
 # we use flymine's model. don't touch!

diff --git a/bio/postprocess-test/build.gradle b/bio/postprocess-test/build.gradle
@@ -17,7 +17,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.5'
+    version = '5.0.6'
 
     apply plugin: 'java'
     apply plugin: 'maven'

diff --git a/bio/postprocess-test/gradle.properties b/bio/postprocess-test/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.5
-systemProp.bioVersion=5.0.5
+systemProp.imVersion=5.0.6
+systemProp.bioVersion=5.0.6
 
 systemProp.flymineVersion=4.0.0
 

diff --git a/bio/postprocess/build.gradle b/bio/postprocess/build.gradle
@@ -16,7 +16,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.5'
+    version = '5.0.6'
 
     apply plugin: 'java'
     apply plugin: 'maven'

diff --git a/bio/postprocess/gradle.properties b/bio/postprocess/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.5
-systemProp.bioVersion=5.0.5
+systemProp.imVersion=5.0.6
+systemProp.bioVersion=5.0.6
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
 

diff --git a/bio/sources/build.gradle b/bio/sources/build.gradle
@@ -16,7 +16,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.5'
+    version = '5.0.6'
 
     apply plugin: 'java'
     apply plugin: 'maven'
@@ -42,7 +42,7 @@ subprojects {
     }
 
     dependencies {
-        compile group: 'org.apache.logging.log4j', name: 'log4j-1.2-api', version: '2.17.0'
+        compile group: 'org.apache.logging.log4j', name: 'log4j-1.2-api', version: '2.17.1'
         compile group: 'org.intermine', name: 'bio-core', version: System.getProperty("bioVersion"), transitive: false
         compile group : "org.intermine", name: "intermine-resources", version: System.getProperty("imVersion") // log4j
         compile group: 'commons-collections', name: 'commons-collections', version: '3.2'

diff --git a/bio/sources/gradle.properties b/bio/sources/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.5
-systemProp.bioVersion=5.0.5
+systemProp.imVersion=5.0.6
+systemProp.bioVersion=5.0.6
 
 # some unit tests need additional classes that aren't in the core model.
 # we use flymine's model. don't touch!

diff --git a/bio/webapp/build.gradle b/bio/webapp/build.gradle
@@ -34,10 +34,10 @@ dependencies {
 
     compile (project(':bio-tools')) { transitive = false }
     compile group: "org.intermine", name: "intermine-jbrowse-endpoint", version: System.getProperty("imVersion")
-    compile group: 'psidev.psi.mi.jami.bridges', name: 'bridges-core', version: '3.0.0'
-    compile group: 'psidev.psi.mi.jami.bridges', name: 'jami-ols', version: '3.0.0'
-    compile group: 'psidev.psi.mi.jami', name: 'jami-core', version: '3.0.0'
-    compile group: 'psidev.psi.mi.jami', name: 'jami-interactionviewer-json', version: '3.0.0'
+    compile group: 'psidev.psi.mi.jami.bridges', name: 'bridges-core', version: '3.2.12'
+    compile group: 'psidev.psi.mi.jami.bridges', name: 'jami-ols', version: '3.2.12'
+    compile group: 'psidev.psi.mi.jami', name: 'jami-core', version: '3.2.12'
+    compile group: 'psidev.psi.mi.jami', name: 'jami-interactionviewer-json', version: '3.2.12'
     compile group: "org.biojava", name: "biojava-core", version: "4.2.0"
     compile group: "org.biojava", name: "biojava-genome", version: "4.2.0"
     compile group: "org.biojava", name: "biojava-ontology", version: "4.2.0"

diff --git a/intermine/build.gradle b/intermine/build.gradle
@@ -1,6 +1,6 @@
 subprojects {
     group = 'org.intermine'
-    version '5.0.5'
+    version '5.0.6'
 
     apply plugin: "java"
     apply plugin: "maven"
@@ -22,16 +22,16 @@ subprojects {
     configurations {
         all {
             resolutionStrategy {
-                force 'org.apache.logging.log4j:log4j-1.2-api:2.17.0'
+                force 'org.apache.logging.log4j:log4j-1.2-api:2.17.1'
             }
         }
     }
 
     if (it.name != 'intermine-resources') {
         dependencies {
             compile group: 'ant', name: 'ant', version: '1.6.5'
-            compile group: 'org.apache.logging.log4j', name: 'log4j-1.2-api', version: '2.17.0'
-            compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j-impl', version: '2.17.0'
+            compile group: 'org.apache.logging.log4j', name: 'log4j-1.2-api', version: '2.17.1'
+            compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j-impl', version: '2.17.1'
             testCompile group: 'junit', name: 'junit', version: '4.8.2'
         }
 

diff --git a/intermine/gradle.properties b/intermine/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.5
-systemProp.bioVersion=5.0.5
+systemProp.imVersion=5.0.6
+systemProp.bioVersion=5.0.6
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
 

diff --git a/intermine/webapp/src/main/java/org/intermine/web/logic/Constants.java b/intermine/webapp/src/main/java/org/intermine/web/logic/Constants.java
@@ -226,7 +226,7 @@ private Constants() {
     /**
      * Current version of the InterMine code
      */
-    public static final String INTERMINE_VERSION = "5.0.5";
+    public static final String INTERMINE_VERSION = "5.0.6";
 
     /**
      * Key for a Map from class name to Boolean.TRUE for all classes in the model that do not have

diff --git a/plugin/build.gradle b/plugin/build.gradle
@@ -4,7 +4,7 @@ apply plugin: 'maven'
 apply plugin: 'signing'
 
 group 'org.intermine'
-version '5.0.5'
+version '5.0.6'
 
 sourceCompatibility = 1.8
 

diff --git a/plugin/gradle.properties b/plugin/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.5
-systemProp.bioVersion=5.0.5
+systemProp.imVersion=5.0.6
+systemProp.bioVersion=5.0.6
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
 

diff --git a/testmine/build.gradle b/testmine/build.gradle
@@ -1,5 +1,5 @@
 ext {
-    imVersion = "5.0.5"
+    imVersion = "5.0.6"
     taskGroup = "InterMine"
     minePropertyFileName = "testmodel.properties"
     minePropertyFile = "${System.env.HOME}/.intermine/$minePropertyFileName"
@@ -28,7 +28,7 @@ subprojects {
 
     dependencies {
         compile group: 'ant', name: 'ant', version: '1.6.5'
-        compile group: 'org.apache.logging.log4j', name: 'log4j-1.2-api', version: '2.17.0'
+        compile group: 'org.apache.logging.log4j', name: 'log4j-1.2-api', version: '2.17.1'
         commonResources group: "org.intermine", name: "intermine-resources", version: imVersion
     }