diff --git a/.travis.yml b/.travis.yml index 65508237..09eb38fa 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,7 +6,8 @@ branches: only: - master - develop - - feature/issue-175 + - /^feature\/.*$/ + - /^bugfix\/.*$/ before_cache: - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock diff --git a/build.gradle b/build.gradle index accee440..f77ceebb 100644 --- a/build.gradle +++ b/build.gradle @@ -6,20 +6,18 @@ buildscript { } dependencies { classpath "org.grails:grails-gradle-plugin:$grailsVersion" - classpath "org.grails.plugins:hibernate5:7.0.5" - classpath "gradle.plugin.com.github.erdi.webdriver-binaries:webdriver-binaries-gradle-plugin:2.0" - classpath "com.bertramlabs.plugins:asset-pipeline-gradle:3.3.2" - classpath 'org.grails.plugins:database-migration:3.1.0' + classpath "org.grails.plugins:hibernate5:${gormVersion}" + classpath "gradle.plugin.com.github.erdi.webdriver-binaries:webdriver-binaries-gradle-plugin:$webdriverBinariesVersion" + classpath "com.bertramlabs.plugins:asset-pipeline-gradle:3.4.6" + classpath 'org.grails.plugins:database-migration:4.2.0' } } plugins { - id "com.gorylenko.gradle-git-properties" version "2.4.0-rc2" + id "com.gorylenko.gradle-git-properties" version "2.4.1" } - -version "3.1.3" - +version "4.0.0-SNAPSHOT" group "au.org.ala" apply plugin:"eclipse" @@ -31,12 +29,9 @@ apply plugin:"com.bertramlabs.asset-pipeline" apply plugin:"org.grails.grails-gsp" apply plugin:"maven-publish" -bootJar { - enabled = true - classifier = 'exec' -} publishing { + targetCompatibility = 1.11 repositories { maven { name 'Nexus' @@ -49,34 +44,15 @@ publishing { } publications { mavenJar(MavenPublication) { - pom.withXml { - def pomNode = asNode() - pomNode.dependencyManagement.replaceNode {} - - // simply remove dependencies without a version - // version-less dependencies are handled with dependencyManagement - // see https://github.com/spring-gradle-plugins/dependency-management-plugin/issues/8 for more complete solutions - pomNode.dependencies.dependency.findAll { - it.version.text().isEmpty() - }.each { - it.replaceNode {} - } - } - from components.web -// if (bootJar && bootJar.enabled && bootJar.classifier) { -// def repackagedFile = file("$libsDir/$project.name-$project.version-${bootJar.classifier}.jar") -// if (repackagedFile.exists()) { -// artifact(repackagedFile) { -// classifier bootRepackage.classifier -// } -// } else { -// logger.quiet("Spring Boot repackage with classifier specified but file is not present!") -// } -// } + artifact bootWar } } } +bootWar { + launchScript() +} + repositories { mavenLocal() maven { url "https://nexus.ala.org.au/content/groups/public/" } @@ -100,92 +76,88 @@ sourceSets { dependencies { developmentOnly("org.springframework.boot:spring-boot-devtools") - compile "org.springframework.boot:spring-boot-starter-logging" - compile "org.springframework.boot:spring-boot-autoconfigure" - compile "org.grails:grails-core" - compile "org.springframework.boot:spring-boot-starter-actuator" - compile "org.springframework.boot:spring-boot-starter-tomcat" - compile "org.grails:grails-web-boot" - compile "org.grails:grails-logging" - compile "org.grails:grails-plugin-rest" - compile "org.grails:grails-plugin-databinding" - compile "org.grails:grails-plugin-i18n" - compile "org.grails:grails-plugin-services" - compile "org.grails:grails-plugin-url-mappings" - compile "org.grails:grails-plugin-interceptors" - compile "org.grails.plugins:cache" - compile "org.grails.plugins:async" - compile "org.grails.plugins:scaffolding" - compile "org.grails.plugins:events" - compile "org.grails.plugins:hibernate5" - compile "org.hibernate:hibernate-core:5.4.18.Final" - compile "org.grails.plugins:gsp" - - compile "com.opencsv:opencsv:3.7" - compile "io.micronaut:micronaut-http-client" + implementation "org.springframework.boot:spring-boot-starter-logging" + implementation "org.springframework.boot:spring-boot-autoconfigure" + implementation "org.grails:grails-core" + implementation "org.springframework.boot:spring-boot-starter-actuator" + implementation "org.springframework.boot:spring-boot-starter-tomcat" + implementation "org.grails:grails-web-boot" + implementation "org.grails:grails-logging" + implementation "org.grails:grails-plugin-rest" + implementation "org.grails:grails-plugin-databinding" + implementation "org.grails:grails-plugin-i18n" + implementation "org.grails:grails-plugin-services" + implementation "org.grails:grails-plugin-url-mappings" + implementation "org.grails:grails-plugin-interceptors" + implementation "org.grails.plugins:cache" + implementation "org.grails.plugins:async" + implementation "org.grails.plugins:scaffolding" + implementation "org.grails.plugins:events" + implementation "org.grails.plugins:hibernate5" + implementation "org.hibernate:hibernate-core:5.4.18.Final" + implementation "org.grails.plugins:gsp" + + implementation "com.opencsv:opencsv:3.7" + implementation "io.micronaut:micronaut-http-client" compileOnly "io.micronaut:micronaut-inject-groovy" - compile "org.apache.httpcomponents:httpclient:4.5.13" - compile "commons-io:commons-io:2.11.0" + implementation "io.reactivex.rxjava3:rxjava:3.1.6" + implementation "org.apache.httpcomponents:httpclient:4.5.13" + implementation "commons-io:commons-io:2.11.0" // See: https://github.com/AtlasOfLivingAustralia/collectory/issues/84#issuecomment-1070670979 // before updating mysql-connector-java - compile "mysql:mysql-connector-java:8.0.22" - compile "org.grails.plugins:ala-bootstrap3:4.1.0" - compile "au.org.ala.plugins.grails:ala-charts-plugin:2.1.2" - compile "org.grails.plugins:ala-auth:5.1.1" - compile "org.grails.plugins:ala-ws-security-plugin:4.1.2" - compile "org.grails.plugins:ala-ws-plugin:3.1.1" - compile "org.grails.plugins:audit-logging:4.0.3" - compile "org.grails.plugins:external-config:2.0.0" - compile "org.grails.plugins:ala-admin-plugin:2.3.0" - compile 'au.org.ala.plugins:openapi:1.1.0' + implementation "mysql:mysql-connector-java:8.0.22" + implementation "org.grails.plugins:ala-bootstrap3:4.1.0" + implementation "au.org.ala.plugins.grails:ala-charts-plugin:2.3.0" + implementation "org.grails.plugins:ala-auth:$alaSecurityLibsVersion" + implementation "org.grails.plugins:ala-ws-security-plugin:$alaSecurityLibsVersion" + implementation "org.grails.plugins:ala-ws-plugin:$alaSecurityLibsVersion" + implementation "org.grails.plugins:audit-logging:4.0.3" + implementation 'dk.glasius:external-config:3.1.1' + implementation "org.grails.plugins:ala-admin-plugin:2.3.0" + implementation 'au.org.ala.plugins:openapi:1.1.0' console "org.grails:grails-console" profile "org.grails.profiles:web" - runtime "org.glassfish.web:el-impl:2.1.2-b03" - runtime "com.h2database:h2" - runtime "org.apache.tomcat:tomcat-jdbc" - runtime "javax.xml.bind:jaxb-api:2.3.1" - runtime "com.bertramlabs.plugins:asset-pipeline-grails:3.2.4" - testCompile "io.micronaut:micronaut-inject-groovy" - testCompile "org.grails:grails-gorm-testing-support" - testCompile "org.mockito:mockito-core" - testCompile "org.grails:grails-web-testing-support" - testCompile "org.grails.plugins:geb" - testCompile "org.seleniumhq.selenium:selenium-remote-driver:3.141.59" - testCompile "org.seleniumhq.selenium:selenium-api:3.141.59" - testCompile "org.seleniumhq.selenium:selenium-support:3.141.59" - testRuntime "org.seleniumhq.selenium:selenium-chrome-driver:3.141.59" - testRuntime "org.seleniumhq.selenium:selenium-firefox-driver:3.141.59" - compile 'org.grails.plugins:sentry:11.7.25' - // In newer versions use 'implementation' - compile 'org.liquibase:liquibase-core:3.10.3' - compile "org.grails.plugins:database-migration:3.1.0" + runtimeOnly "org.glassfish.web:el-impl:2.1.2-b03" + runtimeOnly "com.h2database:h2" + runtimeOnly "org.apache.tomcat:tomcat-jdbc" + runtimeOnly "javax.xml.bind:jaxb-api:2.3.1" + runtimeOnly "com.bertramlabs.plugins:asset-pipeline-grails:3.4.6" + testImplementation "io.micronaut:micronaut-inject-groovy" + testImplementation "org.grails:grails-gorm-testing-support" + testImplementation "org.mockito:mockito-core" + testImplementation "org.grails:grails-web-testing-support" + testImplementation "org.grails.plugins:geb" + testImplementation "org.seleniumhq.selenium:selenium-remote-driver:$seleniumVersion" + testImplementation "org.seleniumhq.selenium:selenium-api:$seleniumVersion" + testImplementation "org.seleniumhq.selenium:selenium-support:$seleniumVersion" + runtimeOnly "net.sourceforge.htmlunit:htmlunit:2.18" + testImplementation "org.seleniumhq.selenium:selenium-htmlunit-driver:2.47.1" + testImplementation "org.seleniumhq.selenium:selenium-chrome-driver:$seleniumVersion" + testImplementation "org.seleniumhq.selenium:selenium-firefox-driver:$seleniumVersion" + testImplementation "org.seleniumhq.selenium:selenium-safari-driver:$seleniumSafariDriverVersion" + implementation 'org.grails.plugins:sentry:11.7.25' + // db-migration + implementation 'org.liquibase:liquibase-core:4.19.0' + implementation('org.grails.plugins:database-migration:4.2.0') { + // spring-boot-cli exclusion required since Grails5 upgrade to prevent NullPointerException Error: https://github.com/grails/grails-database-migration/issues/268 + exclude module: 'spring-boot-cli' + } } bootRun { ignoreExitValue true jvmArgs( - '-Dspring.output.ansi.enabled=always', - '-noverify', - '-XX:TieredStopAtLevel=1', - '-Xmx1024m') + '-Dspring.output.ansi.enabled=always', + '-noverify', + '-XX:TieredStopAtLevel=1', + '-Xmx2048m') sourceResources sourceSets.main String springProfilesActive = 'spring.profiles.active' systemProperty springProfilesActive, System.getProperty(springProfilesActive) } -tasks.withType(GroovyCompile) { - configure(groovyOptions) { - forkOptions.jvmArgs = ['-Xmx1024m'] - } -} - -webdriverBinaries { - chromedriver '2.45.0' - geckodriver '0.24.0' -} - tasks.withType(Test) { systemProperty "geb.env", System.getProperty('geb.env') systemProperty "geb.build.reportsDir", reporting.file("geb/integrationTest") @@ -193,14 +165,17 @@ tasks.withType(Test) { systemProperty "webdriver.gecko.driver", System.getProperty('webdriver.gecko.driver') } +webdriverBinaries { + chromedriver "$chromeDriverVersion" + geckodriver "$geckodriverVersion" +} assets { minifyJs = true minifyCss = true } -springBoot { - buildInfo() +test { + testLogging.showStandardStreams = true } - diff --git a/gradle.properties b/gradle.properties index 903ab8ca..cb00d8fc 100644 --- a/gradle.properties +++ b/gradle.properties @@ -1,5 +1,13 @@ -grailsVersion=4.1.1 -gorm.version=7.0.8.RELEASE +grailsVersion=5.2.1 +gormVersion=7.2.1 org.gradle.daemon=true org.gradle.parallel=true org.gradle.jvmargs=-Dfile.encoding=UTF-8 -Xmx1024M +gebVersion=2.3 +groovyVersion=3.0.11 +seleniumVersion=3.14.0 +webdriverBinariesVersion=2.6 +chromeDriverVersion=2.45.0 +geckodriverVersion=0.24.0 +seleniumSafariDriverVersion=3.14.0 +alaSecurityLibsVersion=6.0.4 \ No newline at end of file diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index 87b738cb..7454180f 100644 Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 5028f28f..ffed3a25 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-5.6.4-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index af6708ff..1b6c7873 100755 --- a/gradlew +++ b/gradlew @@ -1,78 +1,129 @@ -#!/usr/bin/env sh +#!/bin/sh + +# +# Copyright © 2015-2021 the original 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 -## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# ############################################################################## # Attempt to set APP_HOME + # Resolve links: $0 may be a link -PRG="$0" -# Need this for relative symlinks. -while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac done -SAVED="`pwd`" -cd "`dirname \"$PRG\"`/" >/dev/null -APP_HOME="`pwd -P`" -cd "$SAVED" >/dev/null + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit APP_NAME="Gradle" -APP_BASE_NAME=`basename "$0"` +APP_BASE_NAME=${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" +MAX_FD=maximum warn () { echo "$*" -} +} >&2 die () { echo echo "$*" echo exit 1 -} +} >&2 # OS specific support (must be 'true' or 'false'). cygwin=false msys=false darwin=false nonstop=false -case "`uname`" in - CYGWIN* ) - cygwin=true - ;; - Darwin* ) - darwin=true - ;; - MINGW* ) - msys=true - ;; - NONSTOP* ) - nonstop=true - ;; +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; esac CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + # Determine the Java command to use to start the JVM. if [ -n "$JAVA_HOME" ] ; then if [ -x "$JAVA_HOME/jre/sh/java" ] ; then # IBM's JDK on AIX uses strange locations for the executables - JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACMD=$JAVA_HOME/jre/sh/java else - JAVACMD="$JAVA_HOME/bin/java" + JAVACMD=$JAVA_HOME/bin/java fi if [ ! -x "$JAVACMD" ] ; then die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME @@ -81,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the location of your Java installation." fi else - JAVACMD="java" + JAVACMD=java which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the @@ -89,84 +140,95 @@ location of your Java installation." fi # Increase the maximum file descriptors if we can. -if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then - MAX_FD_LIMIT=`ulimit -H -n` - if [ $? -eq 0 ] ; then - if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then - MAX_FD="$MAX_FD_LIMIT" - fi - ulimit -n $MAX_FD - if [ $? -ne 0 ] ; then - warn "Could not set maximum file descriptor limit: $MAX_FD" - fi - else - warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" - fi +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac fi -# For Darwin, add options to specify how the application appears in the dock -if $darwin; then - GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" -fi +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) -# For Cygwin, switch paths to Windows format before running java -if $cygwin ; then - APP_HOME=`cygpath --path --mixed "$APP_HOME"` - CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` - JAVACMD=`cygpath --unix "$JAVACMD"` - - # We build the pattern for arguments to be converted via cygpath - ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` - SEP="" - for dir in $ROOTDIRSRAW ; do - ROOTDIRS="$ROOTDIRS$SEP$dir" - SEP="|" - done - OURCYGPATTERN="(^($ROOTDIRS))" - # Add a user-defined pattern to the cygpath arguments - if [ "$GRADLE_CYGPATTERN" != "" ] ; then - OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" - fi # Now convert the arguments - kludge to limit ourselves to /bin/sh - i=0 - for arg in "$@" ; do - CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` - CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option - - if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition - eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` - else - eval `echo args$i`="\"$arg\"" + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) fi - i=$((i+1)) + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg done - case $i in - (0) set -- ;; - (1) set -- "$args0" ;; - (2) set -- "$args0" "$args1" ;; - (3) set -- "$args0" "$args1" "$args2" ;; - (4) set -- "$args0" "$args1" "$args2" "$args3" ;; - (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; - (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; - (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; - (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; - (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; - esac fi -# Escape application args -save () { - for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done - echo " " -} -APP_ARGS=$(save "$@") - -# Collect all arguments for the java command, following the shell quoting and substitution rules -eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" - -# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong -if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then - cd "$(dirname "$0")" -fi +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# + +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat index 6d57edc7..ac1b06f9 100755 --- a/gradlew.bat +++ b/gradlew.bat @@ -1,84 +1,89 @@ -@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 Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@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 execute + +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 execute + +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 + +: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 %* + +: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 diff --git a/grails-app/assets/javascripts/application.js b/grails-app/assets/javascripts/application.js index 098f6cd1..8084b6f9 100644 --- a/grails-app/assets/javascripts/application.js +++ b/grails-app/assets/javascripts/application.js @@ -8,5 +8,6 @@ //= require jquery-3.3.1.min //= require jquery.i18n.properties-1.0.9.min //= require jquery.ba-bbq.min +//= require moment-with-locales.min.js //= require datasets.js //= require_self diff --git a/grails-app/assets/javascripts/datasets.js b/grails-app/assets/javascripts/datasets.js index 89e44750..73c20223 100644 --- a/grails-app/assets/javascripts/datasets.js +++ b/grails-app/assets/javascripts/datasets.js @@ -32,6 +32,9 @@ var allResources; /* holds current filtered list */ var resources; +/* holds resources facet for stats */ +var rersourcesStats; + /* list of filters currently in effect - items are {name, value} */ var currentFilters = []; @@ -50,29 +53,50 @@ var biocacheUrl; /* options for all tooltips */ var tooltipOptions = {position:{my: 'left bottom', at: 'center top-10'}, show: {duration: 130, effect:'fade'}, hide: {duration: 200, effect:'fade'}, collision: "fit"}; +function drCount(dr) { + try { + return resourcesStats[0].fieldResult.find((result) => result.fq.includes(dr)).count; + } + catch (e) { + return -1; + } +} + /** load resources and show first page **/ -function loadResources(serverUrl, biocacheRecordsUrl) { +function loadResources(serverUrl, biocacheRecordsUrl, biocacheServicesUrl) { baseUrl = serverUrl; biocacheUrl = biocacheRecordsUrl; - $.getJSON(baseUrl + "/public/condensed.json", function(data) { - allResources = data; - // no filtering at this stage - resources = allResources; - - setStateFromHash(); - updateTotal(); - calculateFacets(); - showFilters(); - resources.sort(comparator); - displayPage(); - wireDownloadLink(); - wireSearchLink(); - - // set up tooltips - // - don't do download link because the title changes and the tooltip app does not update - // - also limit to content to exclude links in header - $('div.collectory-content [title][id!="downloadLink"]'); - }); + + function loadResourcesCondensed() { + $.getJSON(baseUrl + "/public/condensed.json", function (data) { + allResources = data; + // no filtering at this stage + resources = allResources; + + setStateFromHash(); + updateTotal(); + calculateFacets(); + showFilters(); + resources.sort(comparator); + displayPage(); + wireDownloadLink(); + wireSearchLink(); + + // set up tooltips + // - don't do download link because the title changes and the tooltip app does not update + // - also limit to content to exclude links in header + $('div.collectory-content [title][id!="downloadLink"]'); + }); + } + + if (COLLECTORY_CONF.showExtraInfoInDataSetsView) { + $.getJSON(biocacheServicesUrl + "/occurrences/facets?facets=data_resource_uid&pageSize=0&flimit=-1", function(dataStats) { + resourcesStats = dataStats; + loadResourcesCondensed(); + }); + } else { + loadResourcesCondensed(); + } } /*************************************************\ * List display @@ -107,6 +131,14 @@ function appendResource(value) { var $rowB = $('

').appendTo($div); var $rowC = $('