Merge pull request #26 from AtlasOfLivingAustralia/develop

Release 2.1.0 PR

.travis.yml

@@ -1,12 +1,12 @@
-dist: trusty
 language: groovy
 jdk:
-- oraclejdk8
+- oraclejdk11
 sudo: false
 branches:
   only:
   - master
   - develop
+  - feature/oidc-auth
 before_cache:
 - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
 - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
@@ -19,5 +19,6 @@ after_success:
 - '[ "${TRAVIS_PULL_REQUEST}" = "false" ] && travis_retry ./gradlew publish'
 env:
   global:
+  - JAVA_TOOL_OPTIONS=-Dhttps.protocols=TLSv1.2
   - secure: Z6Jfqbjh+XtuJZpVEmBq3ZarQYG2Hb++md9uBKQeWyy23pM7Mh3S3enne3DNs7zyPEUYVr+udUZI5uGyKmjMKZqAgacZZeAtaj4tcJyZPJDzxCTyxzA+BlcYT3/tdmv/9jH4iwolp9CPHGZA69WhlttV9NLg9GBCpElfxi2bs7A=
   - secure: Bl6/Y0aI9Dq3CxZBJgES+M39O62+zkxzI93/6R0g0b7e86i6v5l319Y9fi3PLQ+YsIwJDMMSPvksKOLCk+e0WrizcdF21fDcJlHyO6WrnPoZIHA+dvMJ2AORIbHtBWo5KdczDmWR9/n2UkV6xwRZ0MRZ25bZLy3AsHh/I/5FMPA=

build.gradle

@@ -7,12 +7,12 @@ buildscript {
     dependencies {
         classpath "org.grails:grails-gradle-plugin:$grailsVersion"
         classpath "gradle.plugin.com.github.erdi.webdriver-binaries:webdriver-binaries-gradle-plugin:2.0"
-        // classpath "org.grails.plugins:hibernate5:7.0.4"
         classpath "com.bertramlabs.plugins:asset-pipeline-gradle:3.2.4"
     }
 }
 
-version "2.0.1"
+
+version "2.1-SNAPSHOT"
 group "au.org.ala"
 
 apply plugin:"eclipse"
@@ -24,8 +24,6 @@ apply plugin:"com.bertramlabs.asset-pipeline"
 apply plugin:"org.grails.grails-gsp"
 apply plugin:"maven-publish"
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
 
 repositories {
     mavenLocal()
@@ -82,10 +80,11 @@ dependencies {
     compile 'org.webjars:knockout:3.5.1'
 
     // ALA Plugins
-    compile group: 'org.grails.plugins', name: 'ala-auth', version: '3.2.2'
-    compile group: 'org.grails.plugins', name: 'ala-admin-plugin', version: '2.2'
-    compile group: 'org.grails.plugins', name: 'ala-bootstrap3', version: '3.2.3'
-    compile group: 'au.org.ala.plugins.grails', name: 'images-client-plugin', version: '1.2'
+     compile "org.grails.plugins:ala-auth:5.1.1"
+     compile "org.grails.plugins:ala-admin-plugin:2.3.0"
+     runtime "org.grails.plugins:ala-bootstrap3:4.1.0"
+     compile "au.org.ala.plugins.grails:images-client-plugin:1.4"
+
 }
 
 bootRun {

gradle.properties

@@ -1,5 +1,5 @@
-grailsVersion=4.0.5
+grailsVersion=4.1.1
 gorm.version=7.0.8.RELEASE
 org.gradle.daemon=true
 org.gradle.parallel=true
-org.gradle.jvmargs=-Dfile.encoding=UTF-8 -Xmx1024M
+org.gradle.jvmargs=-Dfile.encoding=UTF-8 -Xmx1024M

gradlew

@@ -1,5 +1,21 @@
 #!/usr/bin/env sh
 
+#
+# Copyright 2015 the original author or authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 ##############################################################################
 ##
 ##  Gradle start up script for UN*X
@@ -28,7 +44,7 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m"'
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
@@ -109,8 +125,8 @@ if $darwin; then
     GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
 fi
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
     APP_HOME=`cygpath --path --mixed "$APP_HOME"`
     CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
     JAVACMD=`cygpath --unix "$JAVACMD"`

gradlew.bat

@@ -1,84 +1,100 @@
-@if "%DEBUG%" == "" @echo off
-@rem ##########################################################################
-@rem
-@rem  Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m"
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto init
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
-
-:end
-@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

grails-app/conf/application.yml

@@ -157,14 +157,24 @@ security:
     cas:
         appServerName:  https://specimens.ala.org.au
         casServerName:   https://auth.ala.org.au
-        uriFilterPattern:   /admin.*,/alaAdmin.*
+        uriFilterPattern:   /admin/*,/alaAdmin/*
+        enabled: false
+    oidc:
+        enabled: true
+        discoveryUri: https://auth-test.ala.org.au/cas/oidc/.well-known
+        scope: openid profile email ala roles
+        clientId: 'change me'
+        secret: 'change me'
+
+headerAndFooter:
+    baseURL: "https://www.ala.org.au/commonui-bs3-2019"
+    version: "2"
+
 skin:
-    layout: main
-    fluidLayout: true
-    orgNameLong: Atlas of Living Australia
+    layout: "ala-main"
+    orgNameLong: "Atlas of Living Australia"
+    orgNameShort: "ALA"
+
 specimenbrowser:
     data:
         url: file:///data/specimenbrowser/config/data.json
-headerAndFooter:
-    baseURL: https://www.ala.org.au/commonui-bs3-2019
-    version: 2

grails-app/views/admin/counts.gsp

@@ -2,7 +2,7 @@
 <!doctype html>
 <html>
     <head>
-        <meta name="layout" content="main"/>
+        <meta name="layout" content="${grailsApplication.config.skin.layout}"/>
         <meta name="breadcrumbs" content="${g.createLink(controller: 'admin', action: 'index')},Admin"/>
         <title>Image Counts - Specimen image browser - Atlas of Living Australia</title>
         <asset:javascript src="admin.js"/>

grails-app/views/admin/index.gsp

@@ -1,7 +1,7 @@
 <!doctype html>
 <html>
 	<head>
-		<meta name="layout" content="main"/>
+		<meta name="layout" content="${grailsApplication.config.skin.layout}"/>
 		<meta name="breadcrumbs" content="${g.createLink(controller: 'view', action: 'homePage')},Specimen Images"/>
 		<title>Admin - Specimen image browser - Atlas of Living Australia</title>
 		<style type="text/css" media="screen">

grails-app/views/browse/index.gsp

@@ -1,7 +1,7 @@
 <%@ page contentType="text/html;charset=UTF-8" %>
 <html>
 <head>
-    <meta name="layout" content="main"/>
+    <meta name="layout" content="${grailsApplication.config.skin.layout}"/>
     <meta name="breadcrumbs" content="${g.createLink(controller: 'view', action: 'homePage')},Specimen Images"/>
     <title>Specimens | Atlas of Living Australia</title>
     <asset:javascript src="browser.js"/>
@@ -60,7 +60,7 @@
             </div>
             <div class="col-md-9">
                 <div class="alert alert-info" data-bind="visible:loadStatus()==='done'">
-                    <span data-bind="text:totalRecords"></span> images are available.
+                    <strong><span data-bind="text:imageList.images().length"></span></strong> image(s) loaded from <strong><span data-bind="text:totalRecords"></span></strong> records
                 </div>
                 <div class="alert alert-warning" data-bind="visible:loadStatus()==='no results'">No images are available for this search.</div>
                 <div class="alert alert-error" data-bind="visible:loadStatus()==='error'">An error occurred.</div>
@@ -132,10 +132,9 @@
             richQuery += allCollectionsFilter;
         }
 
-        var entityNameLookup = new AjaxLauncher(collectoryServicesURL + '/resolveNames/'),
+        var entityNameLookup = new AjaxLauncher(collectoryServicesURL + 'resolveNames/'),
             richQueryUrl = richQuery + "&q=" + (entityUid === '' ? '*:*' : buildQueryString(entityUid)),
             imagesLookup = new AjaxLauncher(urlConcat(biocacheServicesUrl, wsBase + richQueryUrl));
-
         var initialQueryResultsLoaded;
 
         $(window).load(function () {

grails-app/views/error.gsp

@@ -2,7 +2,7 @@
 <html>
 	<head>
 		<title><g:if env="development">Grails Runtime Exception</g:if><g:else>Error</g:else></title>
-		<meta name="layout" content="main">
+		<meta name="layout" content="${grailsApplication.config.skin.layout}"/>
 		<g:if env="development"><link rel="stylesheet" href="${resource(dir: 'css', file: 'errors.css')}" type="text/css"></g:if>
 	</head>
 	<body>

grails-app/views/notFound.gsp

@@ -2,7 +2,7 @@
 <html>
     <head>
         <title>Page Not Found</title>
-        <meta name="layout" content="main">
+        <meta name="layout" content="${grailsApplication.config.skin.layout}"/>
         <g:if env="development"><asset:stylesheet src="errors.css"/></g:if>
     </head>
     <body>