Version 19; also temp fix to use local repo while repo.tranmsartfound…

…ation.org is unavailable

IpaApi/build.gradle

@@ -3,7 +3,7 @@ apply plugin: 'maven'
 apply plugin: 'maven-publish'
 
 group = 'com.ittm_solutions.ipacore'
-version = '16.4-SNAPSHOT'
+version = '19.0-SNAPSHOT'
 
 description = 'IpaApi add-on for SmartR'
 

IpaApi/pom.xml

@@ -2,7 +2,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>com.ittm_solutions.ipacore</groupId>
   <artifactId>IpaApi</artifactId>
-  <version>16.4-SNAPSHOT</version>
+  <version>19.0-SNAPSHOT</version>
   <build>
     <sourceDirectory>src</sourceDirectory>
     <plugins>

Rmodules/RdcRmodulesGrailsPlugin.groovy

@@ -21,7 +21,7 @@ import org.springframework.stereotype.Component
 import org.transmartproject.core.users.User
 
 class RdcRmodulesGrailsPlugin {
-    def version = '16.4-SNAPSHOT'
+    def version = '19.0-SNAPSHOT'
     def grailsVersion = '2.5.4 > *'
     def title = 'R Modules Plugin'
     def author = 'Sai Kumar Munikuntla'

Rmodules/grails-app/conf/BuildConfig.groovy

@@ -31,15 +31,16 @@ grails.project.dependency.resolution = {
         mavenLocal() // Note: use 'grails maven-install' to install required plugins locally
         grailsCentral()
         mavenCentral()
-        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+//        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+        mavenRepo 'http://localhost/content/repositories/public/'
     }
 
     dependencies {
  	compile 'com.google.guava:guava:19.0'
         compile 'net.sf.opencsv:opencsv:2.3'
         compile 'org.mapdb:mapdb:0.9.10'
         compile 'org.rosuda:Rserve:1.7.3'
-	compile 'org.transmartproject:transmart-core-api:16.4-SNAPSHOT'
+	compile 'org.transmartproject:transmart-core-api:19.0-SNAPSHOT'
 //	compile 'com.lowagie:itext:2.0.8' //latest 4.2.2
 //	compile 'org.xhtmlrenderer:core-renderer:R8'
 
@@ -57,7 +58,7 @@ grails.project.dependency.resolution = {
         compile ':quartz:1.0.2'
 	compile ':spring-security-core:2.0.0'
 
-	compile ':transmart-shared:16.4-SNAPSHOT'
+	compile ':transmart-shared:19.0-SNAPSHOT'
 
 	build ':release:3.1.2', ':rest-client-builder:2.1.1', {
 	    export = false

SmartR/grails-app/conf/BuildConfig.groovy

@@ -45,7 +45,8 @@ grails.project.dependency.resolution = {
             grailsCentral()
             mavenLocal()
             mavenCentral()
-            mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+//            mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+            mavenRepo 'http://localhost/content/repositories/public/'
         }
     }
     else {
@@ -61,11 +62,11 @@ grails.project.dependency.resolution = {
 
         compile 'com.google.guava:guava:19.0'
 //	compile 'com.google.guava:guava:16.0-dev-20140115-68c8348'
-        compile 'org.transmartproject:transmart-core-api:16.4-SNAPSHOT'
+        compile 'org.transmartproject:transmart-core-api:19.0-SNAPSHOT'
         //test 'com.jayway.restassured:rest-assured:2.4.1'
 
         runtime 'org.javassist:javassist:3.16.1-GA'
-        runtime 'com.ittm_solutions.ipacore:IpaApi:16.4-SNAPSHOT'
+        runtime 'com.ittm_solutions.ipacore:IpaApi:19.0-SNAPSHOT'
 
 	test 'org.hamcrest:hamcrest-library:1.3'
         test 'org.hamcrest:hamcrest-core:1.3'
@@ -90,10 +91,10 @@ grails.project.dependency.resolution = {
         test ':karma-test-runner:0.2.4'
 
         if (!dm) {
-            runtime ':transmart-core:16.4-SNAPSHOT'
+            runtime ':transmart-core:19.0-SNAPSHOT'
 
-            test ':transmart-core:16.4-SNAPSHOT'
-            test ':transmart-core-db-tests:16.4-SNAPSHOT'
+            test ':transmart-core:19.0-SNAPSHOT'
+            test ':transmart-core-db-tests:19.0-SNAPSHOT'
         }
         else {
             dm.internalDependencies delegate

SmartR/smartRGrailsPlugin.groovy

@@ -14,9 +14,9 @@ class smartRGrailsPlugin {
     public static final String TRANSMART_EXTENSIONS_REGISTRY_BEAN_NAME = 'transmartExtensionsRegistry'
 
     // the plugin version
-    def version = '16.4-SNAPSHOT'
+    def version = '19.0-SNAPSHOT'
     // the version or versions of Grails the plugin is designed for
-    def grailsVersion = '2.3 > *'
+    def grailsVersion = '2.5.4 > *'
     // resources that are excluded from plugin packaging
     def pluginExcludes = [
         'grails-app/views/error.gsp'
@@ -114,7 +114,7 @@ class smartRGrailsPlugin {
 
         if (ctx.containsBean(TRANSMART_EXTENSIONS_REGISTRY_BEAN_NAME)) {
             ctx.getBean(TRANSMART_EXTENSIONS_REGISTRY_BEAN_NAME)
-                    .registerAnalysisTabExtension('smartR', '/SmartR/loadScripts', 'addSmartRPanel')
+                    .registerAnalysisTabExtension('smartR', '/smartR/loadScripts', 'addSmartRPanel')
         }
 
     }

biomart-domain/BiomartDomainGrailsPlugin.groovy

@@ -1,6 +1,6 @@
 class BiomartDomainGrailsPlugin {
     // the plugin version
-    def version = '16.4-SNAPSHOT'
+    def version = '19.0-SNAPSHOT'
     // the version or versions of Grails the plugin is designed for
     def grailsVersion = '2.5,4 > *'
     // the other plugins this plugin depends on

biomart-domain/grails-app/conf/BuildConfig.groovy

@@ -20,14 +20,15 @@ grails.project.dependency.resolution = {
         mavenCentral()
         mavenLocal() // Note: use 'grails maven-install' to install required plugins locally
 
-        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+//        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+        mavenRepo 'http://localhost/content/repositories/public/'
     }
     dependencies {
         // specify dependencies here under either 'build', 'compile', 'runtime', 'test' or 'provided' scopes eg.
         // runtime 'mysql:mysql-connector-java:5.1.13'
     }
     plugins {
-        String tmVersion = '16.4-SNAPSHOT'
+        String tmVersion = '19.0-SNAPSHOT'
 
         compile ':transmart-java:' + tmVersion
 

dalliance-plugin/DalliancePluginGrailsPlugin.groovy

@@ -1,8 +1,8 @@
 class DalliancePluginGrailsPlugin {
     // the plugin version
-    def version = '16.4-SNAPSHOT'
+    def version = '19.0-SNAPSHOT'
     // the version or versions of Grails the plugin is designed for
-    def grailsVersion = '2.3 > *'
+    def grailsVersion = '2.5.4 > *'
     // resources that are excluded from plugin packaging
     def pluginExcludes = [
         'grails-app/views/error.gsp'

folder-management-plugin/FolderManagementGrailsPlugin.groovy

@@ -1,6 +1,6 @@
 class FolderManagementGrailsPlugin {
     // the plugin version
-    def version = '16.4-SNAPSHOT'
+    def version = '19.0-SNAPSHOT'
     // the version or versions of Grails the plugin is designed for
     def grailsVersion = '2.5.4 > *'
     // the other plugins this plugin depends on

folder-management-plugin/grails-app/conf/BuildConfig.groovy

@@ -13,7 +13,8 @@ grails.project.dependency.resolution = {
         mavenLocal()
         grailsCentral()
         mavenCentral()
-        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+//        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+        mavenRepo 'http://localhost/content/repositories/public/'
     }
 
     dependencies {
@@ -31,10 +32,10 @@ grails.project.dependency.resolution = {
 
     plugins {
 	compile ':asset-pipeline:2.14.1.1'
-        compile ':search-domain:16.4-SNAPSHOT'
-	compile ':transmart-core:16.4-SNAPSHOT'
+        compile ':search-domain:19.0-SNAPSHOT'
+	compile ':transmart-core:19.0-SNAPSHOT'
 
-//        compile ':transmart-legacy-db:16.4-SNAPSHOT'
+//        compile ':transmart-legacy-db:19.0-SNAPSHOT'
 //        compile ':spring-security-core:2.0.0'
         compile ':quartz:1.0.2'
 

galaxy-export-plugin/GalaxyExportPluginGrailsPlugin.groovy

@@ -3,9 +3,9 @@ class GalaxyExportPluginGrailsPlugin {
     public static final String TRANSMART_EXTENSIONS_REGISTRY_BEAN_NAME = 'transmartExtensionsRegistry'
 
     // the plugin version
-    def version = '16.4-SNAPSHOT'
+    def version = '19.0-SNAPSHOT'
     // the version or versions of Grails the plugin is designed for
-    def grailsVersion = '2.3 > *'
+    def grailsVersion = '2.5.4 > *'
     // resources that are excluded from plugin packaging
     def pluginExcludes = [
             'grails-app/views/error.gsp'
@@ -57,7 +57,7 @@ Brief summary/description of the plugin.
         if (galaxyEnabled && ctx.containsBean(TRANSMART_EXTENSIONS_REGISTRY_BEAN_NAME)) {
             ctx.getBean(TRANSMART_EXTENSIONS_REGISTRY_BEAN_NAME)
                     .registerAnalysisTabExtension('galaxy-export-plugin',
-                    '/GalaxyExportPlugin/loadScripts', 'addGalaxyPanel', )
+                    '/galaxyExportPlugin/loadScripts', 'addGalaxyPanel', )
         }
     }
 

galaxy-export-plugin/grails-app/conf/BuildConfig.groovy

@@ -17,7 +17,8 @@ grails.project.dependency.resolution = {
         mavenLocal()
         mavenCentral()
 
-        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+//        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+        mavenRepo 'http://localhost/content/repositories/public/'
     }
     dependencies {
         compile 'com.github.jmchilton.blend4j:blend4j:0.1.2' 
@@ -39,8 +40,8 @@ grails.project.dependency.resolution = {
     plugins {
 	compile ':asset-pipeline:2.14.1.1'
 
-        compile ':transmart-legacy-db:16.4-SNAPSHOT'
-        compile ':transmart-shared:16.4-SNAPSHOT'
+        compile ':transmart-legacy-db:19.0-SNAPSHOT'
+        compile ':transmart-shared:19.0-SNAPSHOT'
 
         build ':tomcat:8.0.50'
 	build ':release:3.1.2', ':rest-client-builder:2.1.1', {
@@ -52,7 +53,7 @@ grails.project.dependency.resolution = {
 	// not included in 18.1 beta
 //	runtime ':resources:1.2.14'
 
-        compile ':rdc-rmodules:16.4-SNAPSHOT'
+        compile ':rdc-rmodules:19.0-SNAPSHOT'
     }
 
 

mydas/mydas/build.gradle

@@ -2,7 +2,7 @@ allprojects  {
   apply plugin: 'maven'
 
   group = 'uk.ac.ebi.mydas'
-version = '1.7.0.transmart-16.4-SNAPSHOT'
+  version = '1.7.0.transmart-19.0-SNAPSHOT'
 }
 
 subprojects {

mydas/mydas/example_server_installation/pom.xml

@@ -28,21 +28,21 @@
     <groupId>uk.ac.ebi.mydas.example</groupId>
     <artifactId>mydas_example</artifactId>
     <packaging>war</packaging>
-    <version>1.7.0.transmart-16.4-SNAPSHOT</version>
+    <version>1.7.0.transmart-19.0-SNAPSHOT</version>
     <name>mydas_example Maven Webapp</name>
     <url>http://www.ebi.ac.uk</url>
 
     <parent>
         <groupId>uk.ac.ebi.mydas</groupId>
         <artifactId>mydas_master</artifactId>
-        <version>1.7.0.transmart-16.4-SNAPSHOT</version>
+        <version>1.7.0.transmart-19.0-SNAPSHOT</version>
     </parent>
 
     <dependencies>
         <dependency>
             <groupId>uk.ac.ebi.mydas</groupId>
             <artifactId>mydas</artifactId>
-            <version>1.7.0.transmart-16.4-SNAPSHOT</version>
+            <version>1.7.0.transmart-19.0-SNAPSHOT</version>
         </dependency>
 
         <dependency>

mydas/mydas/pom.xml

@@ -17,7 +17,7 @@
 
     <groupId>uk.ac.ebi.mydas</groupId>
     <artifactId>mydas_master</artifactId>
-    <version>1.7.0.transmart-16.4-SNAPSHOT</version>
+    <version>1.7.0.transmart-19.0-SNAPSHOT</version>
 
     <packaging>pom</packaging>
     <name>mydas_master Maven Webapp</name>
@@ -32,11 +32,18 @@
     </licenses>
 
     <repositories>
+<!--
         <repository>
             <id>repo.transmartfoundation.org</id>
             <name>TranSMART Foundation Maven Public Group</name>
             <url>http://repo.transmartfoundation.org/content/groups/public/</url>
         </repository>
+-->
+        <repository>
+            <id>localhost</id>
+            <name>TranSMART Foundation Maven Public Group</name>
+            <url>http://localhost/groups/public/</url>
+        </repository>
     </repositories>
 
     <description>

mydas/mydas/server_core/pom.xml

@@ -28,12 +28,12 @@
 
     <groupId>uk.ac.ebi.mydas</groupId>
     <artifactId>mydas</artifactId>
-    <version>1.7.0.transmart-16.4-SNAPSHOT</version>
+    <version>1.7.0.transmart-19.0-SNAPSHOT</version>
 
     <parent>
         <groupId>uk.ac.ebi.mydas</groupId>
         <artifactId>mydas_master</artifactId>
-        <version>1.7.0.transmart-16.4-SNAPSHOT</version>
+        <version>1.7.0.transmart-19.0-SNAPSHOT</version>
     </parent>
 
     <packaging>jar</packaging>

search-domain/SearchDomainGrailsPlugin.groovy

@@ -1,5 +1,5 @@
 class SearchDomainGrailsPlugin {
-    def version = '16.4-SNAPSHOT'
+    def version = '19.0-SNAPSHOT'
     def grailsVersion = '2.5.4 > *'
     def title = 'tranSMART SearchApp Domain Objects'
     def author = 'David Newton'

search-domain/grails-app/conf/BuildConfig.groovy

@@ -18,7 +18,8 @@ grails.project.dependency.resolution = {
         grailsCentral()
         mavenCentral()
         mavenLocal() // Note: use 'grails maven-install' to install required plugins locally
-        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+//        mavenRepo 'https://repo.transmartfoundation.org/content/repositories/public/'
+        mavenRepo 'http://localhost/content/repositories/public/'
     }
 
     dependencies {
@@ -28,7 +29,7 @@ grails.project.dependency.resolution = {
     }
 
     plugins {
-        String tmVersion = '16.4-SNAPSHOT'
+        String tmVersion = '19.0-SNAPSHOT'
 
 	compile ':biomart-domain:' + tmVersion
 	compile ':transmart-shared:' + tmVersion

spring-security-auth0/SpringSecurityAuth0GrailsPlugin.groovy

@@ -10,8 +10,8 @@ import org.transmart.plugin.auth0.Auth0Config
 import org.transmart.plugin.auth0.Auth0Service
 
 class SpringSecurityAuth0GrailsPlugin {
-    String version = '16.4-SNAPSHOT'
-    String grailsVersion = '2.3 > *'
+    String version = '19.0-SNAPSHOT'
+    String grailsVersion = '2.5.4 > *'
     String title = 'Spring Security Auth0 Plugin'
     String author = 'Burt Beckwith'
     String authorEmail = '[email protected]'

spring-security-auth0/grails-app/conf/BuildConfig.groovy

@@ -28,7 +28,7 @@ grails.project.dependency.resolution = {
 	compile ':spring-security-core:2.0.0'
 	compile ':cache:1.1.8'
 
-	String tmVersion = '16.4-SNAPSHOT'
+	String tmVersion = '19.0-SNAPSHOT'
 	compile ':search-domain:'    + tmVersion
 	compile ':transmart-core:'   + tmVersion
 	compile ':transmart-custom:' + tmVersion

transmart-batch/build.gradle

@@ -9,7 +9,7 @@ apply plugin: 'codenarc'
 apply plugin: 'maven'
 
 group 'org.transmartproject'
-version '16.4-SNAPSHOT'
+version '19-BETA'
 
 repositories {
     mavenCentral()

transmart-core-api/pom.xml

@@ -6,7 +6,7 @@
     <groupId>org.transmartproject</groupId>
     <artifactId>transmart-core-api</artifactId>
     <name>tranSMART Core API</name>
-    <version>16.4-SNAPSHOT</version>
+    <version>19.0-SNAPSHOT</version>
 
     <build>
         <pluginManagement>
@@ -108,6 +108,7 @@
     </dependencies>
 
     <distributionManagement>
+<!--
         <repository>
             <id>repo.transmartfoundation.org-releases</id>
             <url>https://repo.transmartfoundation.org/content/repositories/releases/</url>
@@ -116,7 +117,16 @@
             <id>repo.transmartfoundation.org-snapshots</id>
             <url>https://repo.transmartfoundation.org/content/repositories/snapshots/</url>
         </snapshotRepository>
+-->
     </distributionManagement>
+        <repository>
+            <id>localhost</id>
+            <url>http://localhost/content/repositories/releases/</url>
+        </repository>
+        <snapshotRepository>
+            <id>localhost</id>
+            <url>http://localhost/content/repositories/snapshots/</url>
+        </snapshotRepository>
 
     <properties>
         <groovyVersion>2.1.0</groovyVersion>