X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=build.gradle;h=d5b39e34fd95c2bcb026dcbab4dd2fee31402a43;hb=dfeb3218d3ffbe36bb289ebfacbe2ed23ba26cc1;hp=a3ca4b8ce4375c758df352ff9fe099c53c58eccd;hpb=d59675fab74acfcb19063b7f0081cb22ef3e4d5e;p=jalview.git
diff --git a/build.gradle b/build.gradle
index a3ca4b8..d5b39e3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -12,13 +12,25 @@ import java.security.MessageDigest
import groovy.transform.ExternalizeMethods
import groovy.util.XmlParser
import groovy.xml.XmlUtil
-
+import com.vladsch.flexmark.util.ast.Node
+import com.vladsch.flexmark.html.HtmlRenderer
+import com.vladsch.flexmark.parser.Parser
+import com.vladsch.flexmark.util.data.MutableDataSet
+import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
+import com.vladsch.flexmark.ext.tables.TablesExtension
+import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
+import com.vladsch.flexmark.ext.autolink.AutolinkExtension
+import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
+import com.vladsch.flexmark.ext.toc.TocExtension
buildscript {
repositories {
mavenCentral()
mavenLocal()
}
+ dependencies {
+ classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
+ }
}
@@ -45,24 +57,13 @@ def string(Object o) {
return o == null ? "" : o.toString()
}
-
-ext {
- jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
- jalviewDirRelativePath = jalviewDir
-
- // local build environment properties
- // can be "projectDir/local.properties"
- def localProps = "${projectDir}/local.properties"
- def propsFile = null;
- if (file(localProps).exists()) {
- propsFile = localProps
+def overrideProperties(String propsFileName, boolean output = false) {
+ if (propsFileName == null) {
+ return
}
- // or "../projectDir_local.properties"
- def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
- if (file(dirLocalProps).exists()) {
- propsFile = dirLocalProps
- }
- if (propsFile != null) {
+ def propsFile = file(propsFileName)
+ if (propsFile != null && propsFile.exists()) {
+ println("Using properties from file '${propsFileName}'")
try {
def p = new Properties()
def localPropsFIS = new FileInputStream(propsFile)
@@ -70,18 +71,43 @@ ext {
localPropsFIS.close()
p.each {
key, val ->
- def oldval = findProperty(key)
- setProperty(key, val)
- if (oldval != null) {
- println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ def oldval
+ if (project.hasProperty(key)) {
+ oldval = project.findProperty(key)
+ project.setProperty(key, val)
+ if (output) {
+ println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+ }
} else {
- println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ ext.setProperty(key, val)
+ if (output) {
+ println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+ }
}
}
} catch (Exception e) {
- System.out.println("Exception reading local.properties")
+ println("Exception reading local.properties")
+ e.printStackTrace()
}
}
+}
+
+ext {
+ jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+ jalviewDirRelativePath = jalviewDir
+
+ getdownChannelName = CHANNEL.toLowerCase()
+ // default to "default". Currently only has different cosmetics for "develop", "release", "default"
+ propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+ // Import channel_properties
+ channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+ channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ overrideProperties(channelGradleProperties, false)
+ // local build environment properties
+ // can be "projectDir/local.properties"
+ overrideProperties("${projectDir}/local.properties", true)
+ // or "../projectDir_local.properties"
+ overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
////
// Import releaseProps from the RELEASE file
@@ -99,7 +125,7 @@ ext {
}
////
// Set JALVIEW_VERSION if it is not already set
- if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
+ if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
JALVIEW_VERSION = releaseProps.get("jalview.version")
}
@@ -155,29 +181,31 @@ ext {
//cloverTestClassesDir = cloverClassesDir
cloverDb = string("${cloverBuildDir}/clover.db")
- resourceClassesDir = useClover ? cloverClassesDir : classesDir
-
testSourceDir = useClover ? cloverTestInstrDir : testDir
testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
buildDist = true
+ buildProperties = null
// the following values might be overridden by the CHANNEL switch
- getdownChannelName = CHANNEL.toLowerCase()
getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
getdownAppDistDir = getdown_app_dir_alt
- buildProperties = string("${resourceDir}/${build_properties_file}")
+ getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
reportRsyncCommand = false
jvlChannelName = CHANNEL.toLowerCase()
install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
- install4jDSStore = "DS_Store-NON-RELEASE"
- install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
+ install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+ install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
install4jInstallerName = "${jalview_name} Non-Release Installer"
install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
install4jExtraScheme = "jalviewx"
+ install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
+ install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
+ install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
+ install4jBackground = string("${install4j_images_dir}/${install4j_background}")
switch (CHANNEL) {
case "BUILD":
@@ -193,12 +221,10 @@ ext {
install4jExtraScheme = "jalviewb"
break
- case "RELEASE":
+ case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
getdownAppDistDir = getdown_app_dir_release
reportRsyncCommand = true
install4jSuffix = ""
- install4jDSStore = "DS_Store"
- install4jDMGBackgroundImage = "jalview_dmg_background.png"
install4jInstallerName = "${jalview_name} Installer"
break
@@ -241,8 +267,6 @@ ext {
JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
install4jSuffix = "Develop"
- install4jDSStore = "DS_Store-DEVELOP"
- install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
install4jExtraScheme = "jalviewd"
install4jInstallerName = "${jalview_name} Develop Installer"
break
@@ -256,8 +280,6 @@ ext {
}
JALVIEW_VERSION = JALVIEW_VERSION+"-test"
install4jSuffix = "Test"
- install4jDSStore = "DS_Store-TEST-RELEASE"
- install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
install4jExtraScheme = "jalviewt"
install4jInstallerName = "${jalview_name} Test Installer"
break
@@ -281,13 +303,11 @@ ext {
}
JALVIEW_VERSION = "TEST"
install4jSuffix = "Test-Local"
- install4jDSStore = "DS_Store-TEST-RELEASE"
- install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
install4jExtraScheme = "jalviewt"
install4jInstallerName = "${jalview_name} Test Installer"
break
- case "LOCAL":
+ case [ "LOCAL", "JALVIEWJS" ]:
JALVIEW_VERSION = "TEST"
getdownAppBase = file(getdownWebsiteDir).toURI().toString()
getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
@@ -301,7 +321,13 @@ ext {
}
// override getdownAppBase if requested
if (findProperty("getdown_appbase_override") != null) {
- getdownAppBase = string(getProperty("getdown_appbase_override"))
+ // revert to LOCAL if empty string
+ if (string(getdown_appbase_override) == "") {
+ getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+ getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+ } else {
+ getdownAppBase = string(getdown_appbase_override)
+ }
println("Overriding getdown appbase with '${getdownAppBase}'")
}
// sanitise file name for jalview launcher file for this channel
@@ -427,12 +453,18 @@ ext {
install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
}
+ resourceBuildDir = string("${buildDir}/resources")
+ resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+ helpBuildDir = string("${resourceBuildDir}/help_build")
+ docBuildDir = string("${resourceBuildDir}/doc_build")
-
+ if (buildProperties == null) {
+ buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
+ }
buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
- helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm")
helpParentDir = string("${jalviewDir}/${help_parent_dir}")
helpSourceDir = string("${helpParentDir}/${help_dir}")
+ helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
@@ -470,16 +502,14 @@ sourceSets {
}
resources {
- srcDirs resourceDir
- srcDirs += helpParentDir
+ srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
}
- jar.destinationDir = file("${jalviewDir}/${package_dir}")
-
compileClasspath = files(sourceSets.main.java.outputDir)
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.main.resources.srcDirs)
}
clover {
@@ -516,6 +546,7 @@ sourceSets {
compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
runtimeClasspath = compileClasspath
+ runtimeClasspath += files(sourceSets.test.resources.srcDirs)
}
}
@@ -536,14 +567,12 @@ eclipse {
classpath {
//defaultOutputDir = sourceSets.main.java.outputDir
- def removeThese = []
- configurations.each{
- if (it.isCanBeResolved()) {
- removeThese += it
+ configurations.each{ c->
+ if (c.isCanBeResolved()) {
+ minusConfigurations += [c]
}
}
- minusConfigurations += removeThese
plusConfigurations = [ ]
file {
@@ -993,89 +1022,182 @@ def getDate(format) {
}
-task createBuildProperties(type: WriteProperties) {
- group = "build"
- description = "Create the ${buildProperties} file"
-
- inputs.dir(sourceDir)
- inputs.dir(resourceDir)
- file(buildProperties).getParentFile().mkdirs()
- outputFile (buildProperties)
- // taking time specific comment out to allow better incremental builds
- comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
- //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
- property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
- property "VERSION", JALVIEW_VERSION
- property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
- outputs.file(outputFile)
-}
-
+def convertMdToHtml (FileTree mdFiles, File cssFile) {
+ MutableDataSet options = new MutableDataSet()
-clean {
- doFirst {
- delete buildProperties
+ def extensions = new ArrayList<>()
+ extensions.add(AnchorLinkExtension.create())
+ extensions.add(AutolinkExtension.create())
+ extensions.add(StrikethroughExtension.create())
+ extensions.add(TaskListExtension.create())
+ extensions.add(TablesExtension.create())
+ extensions.add(TocExtension.create())
+
+ options.set(Parser.EXTENSIONS, extensions)
+
+ // set GFM table parsing options
+ options.set(TablesExtension.WITH_CAPTION, false)
+ options.set(TablesExtension.COLUMN_SPANS, false)
+ options.set(TablesExtension.MIN_HEADER_ROWS, 1)
+ options.set(TablesExtension.MAX_HEADER_ROWS, 1)
+ options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
+ options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
+ options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
+ // GFM anchor links
+ options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
+ options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
+ options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
+ options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "")
+
+ Parser parser = Parser.builder(options).build()
+ HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+
+ mdFiles.each { mdFile ->
+ // add table of contents
+ def mdText = "[TOC]\n"+mdFile.text
+
+ // grab the first top-level title
+ def title = null
+ def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
+ def matcher = mdText =~ titleRegex
+ if (matcher.size() > 0) {
+ // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
+ title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
+ }
+ // or use the filename if none found
+ if (title == null) {
+ title = mdFile.getName()
+ }
+
+ Node document = parser.parse(mdText)
+ String htmlBody = renderer.render(document)
+ def htmlText = '''
+
+
+
+
+
+
+'''
+ htmlText += ((title != null) ? " ${title}" : '' )
+ htmlText += '''
+
+'''
+ htmlText += ((cssFile != null) ? cssFile.text : '')
+ htmlText += '''
+
+'''
+ htmlText += htmlBody
+ htmlText += '''
+
+
+'''
+
+ def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+ def htmlFile = file(htmlFilePath)
+ println("Creating ${htmlFilePath}")
+ htmlFile.text = htmlText
+ }
+}
+
+
+task copyDocs(type: Copy) {
+ def inputDir = "${jalviewDir}/${doc_dir}"
+ def outputDir = "${docBuildDir}/${doc_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
}
-}
-
-
-task cleanBuildingHTML(type: Delete) {
- doFirst {
- delete buildingHTML
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
}
+ into outputDir
+
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
}
-task convertBuildingMD(type: Exec) {
- dependsOn cleanBuildingHTML
- def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
- def css = "${jalviewDir}/${doc_dir}/github.css"
+task convertMdFiles {
+ dependsOn copyDocs
+ def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+ def cssFile = file("${jalviewDir}/${flexmark_css}")
- def pandoc = null
- pandoc_exec.split(",").each {
- if (file(it.trim()).exists()) {
- pandoc = it.trim()
- return true
- }
+ doLast {
+ convertMdToHtml(mdFiles, cssFile)
}
- def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
- if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
- pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
- }
+ inputs.files(mdFiles)
+ inputs.file(cssFile)
- doFirst {
- if (pandoc != null && file(pandoc).exists()) {
- commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
- } else {
- println("Cannot find pandoc. Skipping convert building.md to HTML")
- throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
- }
+ def htmlFiles = []
+ mdFiles.each { mdFile ->
+ def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+ htmlFiles.add(file(htmlFilePath))
}
-
- ignoreExitValue true
-
- inputs.file(buildingMD)
- inputs.file(css)
- outputs.file(buildingHTML)
+ outputs.files(htmlFiles)
}
-task syncDocs(type: Sync) {
- //dependsOn convertBuildingMD
- def syncDir = "${classesDir}/${doc_dir}"
- from fileTree("${jalviewDir}/${doc_dir}")
- into syncDir
+task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${helpBuildDir}/${help_dir}"
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.hs')
+ include('**/*.xml')
+ include('**/*.jhm')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.hs')
+ exclude('**/*.xml')
+ exclude('**/*.jhm')
+ }
+ into outputDir
+ inputs.dir(inputDir)
+ outputs.files(helpFile)
+ outputs.dir(outputDir)
}
-task copyHelp(type: Copy) {
- def inputDir = helpSourceDir
- def outputDir = "${resourceClassesDir}/${help_dir}"
+task copyResources(type: Copy) {
+ group = "build"
+ description = "Copy (and make text substitutions in) the resources dir to the build area"
+
+ def inputDir = resourceDir
+ def outputDir = resourcesBuildDir
from(inputDir) {
- exclude '**/*.gif'
- exclude '**/*.jpg'
- exclude '**/*.png'
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
filter(ReplaceTokens,
beginToken: '$$',
endToken: '$$',
@@ -1086,52 +1208,96 @@ task copyHelp(type: Copy) {
)
}
from(inputDir) {
- include '**/*.gif'
- include '**/*.jpg'
- include '**/*.png'
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
}
into outputDir
inputs.dir(inputDir)
- outputs.files(helpFile)
outputs.dir(outputDir)
}
+task copyChannelResources(type: Copy) {
+ dependsOn copyResources
+ group = "build"
+ description = "Copy the channel resources dir to the build resources area"
+
+ def inputDir = "${channelDir}/${resource_dir}"
+ def outputDir = resourcesBuildDir
+ from inputDir
+ into outputDir
-task syncLib(type: Sync) {
- def syncDir = "${resourceClassesDir}/${libDistDir}"
- from fileTree("${jalviewDir}/${libDistDir}")
- into syncDir
+ inputs.dir(inputDir)
+ outputs.dir(outputDir)
}
+task createBuildProperties(type: WriteProperties) {
+ dependsOn copyResources
+ group = "build"
+ description = "Create the ${buildProperties} file"
+
+ inputs.dir(sourceDir)
+ inputs.dir(resourcesBuildDir)
+ outputFile (buildProperties)
+ // taking time specific comment out to allow better incremental builds
+ comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+ //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+ property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+ property "VERSION", JALVIEW_VERSION
+ property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+ outputs.file(outputFile)
+}
-task syncResources(type: Sync) {
- dependsOn createBuildProperties
- from resourceDir
- include "**/*.*"
- into "${resourceClassesDir}"
- preserve {
- include "**"
- }
+
+task buildIndices(type: JavaExec) {
+ dependsOn copyHelp
+ classpath = sourceSets.main.compileClasspath
+ main = "com.sun.java.help.search.Indexer"
+ workingDir = "${helpBuildDir}/${help_dir}"
+ def argDir = "html"
+ args = [ argDir ]
+ inputs.dir("${workingDir}/${argDir}")
+
+ outputs.dir("${classesDir}/doc")
+ outputs.dir("${classesDir}/help")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+ outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+ outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+ outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+ outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+ outputs.file("${workingDir}/JavaHelpSearch/TMAP")
}
+task buildResources {
+ dependsOn copyResources
+ dependsOn copyChannelResources
+ dependsOn createBuildProperties
+}
task prepare {
- dependsOn syncResources
- dependsOn syncDocs
+ dependsOn buildResources
+ dependsOn copyDocs
dependsOn copyHelp
+ dependsOn convertMdFiles
+ dependsOn buildIndices
}
+compileJava.dependsOn prepare
+run.dependsOn compileJava
+//run.dependsOn prepare
+
+
//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
test {
dependsOn prepare
- //dependsOn compileJava ////? DELETE
if (useClover) {
dependsOn cloverClasses
} else { //?
- dependsOn compileJava //?
+ dependsOn compileJava //?
}
useTestNG() {
@@ -1144,7 +1310,16 @@ test {
maxHeapSize = "1024m"
workingDir = jalviewDir
- //systemProperties 'clover.jar' System.properties.clover.jar
+ def testLaf = project.findProperty("test_laf")
+ if (testLaf != null) {
+ println("Setting Test LaF to '${testLaf}'")
+ systemProperty "laf", testLaf
+ }
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
jvmArgs += additional_compiler_args
@@ -1157,26 +1332,6 @@ test {
}
-task buildIndices(type: JavaExec) {
- dependsOn copyHelp
- classpath = sourceSets.main.compileClasspath
- main = "com.sun.java.help.search.Indexer"
- workingDir = "${classesDir}/${help_dir}"
- def argDir = "html"
- args = [ argDir ]
- inputs.dir("${workingDir}/${argDir}")
-
- outputs.dir("${classesDir}/doc")
- outputs.dir("${classesDir}/help")
- outputs.file("${workingDir}/JavaHelpSearch/DOCS")
- outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
- outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
- outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
- outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
- outputs.file("${workingDir}/JavaHelpSearch/TMAP")
-}
-
-
task compileLinkCheck(type: JavaCompile) {
options.fork = true
classpath = files("${jalviewDir}/${utils_dir}")
@@ -1191,13 +1346,14 @@ task compileLinkCheck(type: JavaCompile) {
task linkCheck(type: JavaExec) {
- dependsOn prepare, compileLinkCheck
+ dependsOn prepare
+ dependsOn compileLinkCheck
def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
classpath = files("${jalviewDir}/${utils_dir}")
main = "HelpLinksChecker"
workingDir = jalviewDir
- args = [ "${classesDir}/${help_dir}", "-nointernet" ]
+ args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
def errFOS = outFOS
@@ -1208,13 +1364,14 @@ task linkCheck(type: JavaExec) {
outFOS,
errorOutput)
- inputs.dir("${classesDir}/${help_dir}")
+ inputs.dir(helpBuildDir)
outputs.file(helpLinksCheckerOutFile)
}
+
// import the pubhtmlhelp target
ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
ant.importBuild "${utils_dir}/publishHelp.xml"
@@ -1226,19 +1383,20 @@ task cleanPackageDir(type: Delete) {
jar {
+ dependsOn prepare
dependsOn linkCheck
- dependsOn buildIndices
- dependsOn createBuildProperties
manifest {
attributes "Main-Class": main_class,
"Permissions": "all-permissions",
- "Application-Name": "Jalview Desktop",
- "Codebase": application_codebase
+ "Application-Name": install4jApplicationName,
+ "Codebase": application_codebase,
+ "Implementation-Version": JALVIEW_VERSION
}
- destinationDir = file("${jalviewDir}/${package_dir}")
- archiveName = rootProject.name+".jar"
+ def outputDir = "${jalviewDir}/${package_dir}"
+ destinationDirectory = file(outputDir)
+ archiveFileName = rootProject.name+".jar"
exclude "cache*/**"
exclude "*.jar"
@@ -1246,8 +1404,11 @@ jar {
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir(classesDir)
- outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
+ inputs.dir(sourceSets.main.java.outputDir)
+ sourceSets.main.resources.srcDirs.each{ dir ->
+ inputs.dir(dir)
+ }
+ outputs.file("${outputDir}/${archiveFileName}")
}
@@ -1259,10 +1420,11 @@ task copyJars(type: Copy) {
// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
task syncJars(type: Sync) {
+ dependsOn jar
from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
into "${jalviewDir}/${package_dir}"
preserve {
- include jar.archiveName
+ include jar.archiveFileName.getOrNull()
}
}
@@ -1286,6 +1448,7 @@ task cleanDist {
dependsOn clean
}
+
shadowJar {
group = "distribution"
description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
@@ -1296,7 +1459,8 @@ shadowJar {
include("*.jar")
}
manifest {
- attributes 'Implementation-Version': JALVIEW_VERSION
+ attributes "Implementation-Version": JALVIEW_VERSION,
+ "Application-Name": install4jApplicationName
}
mainClassName = shadow_jar_main_class
mergeServiceFiles()
@@ -1340,6 +1504,14 @@ task getdownWebsite() {
if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
}
+ if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
+ props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
+ props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
+ props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
+ props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+ props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+ props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
+ }
props.put("getdown_txt_title", jalview_name)
props.put("getdown_txt_ui.name", install4jApplicationName)
@@ -1707,7 +1879,7 @@ task installers(type: com.install4j.gradle.Install4jTask) {
'BUNDLE_ID': install4jBundleId,
'INTERNAL_ID': install4jInternalId,
'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
- 'MACOS_DS_STORE': install4jDSStore,
+ 'MACOS_DMG_DS_STORE': install4jDMGDSStore,
'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
'INSTALLER_NAME': install4jInstallerName,
'INSTALL4J_UTILS_DIR': install4j_utils_dir,
@@ -1724,6 +1896,11 @@ task installers(type: com.install4j.gradle.Install4jTask) {
'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
'EXECUTABLE_NAME': install4jExecutableName,
'EXTRA_SCHEME': install4jExtraScheme,
+ 'MAC_ICONS_FILE': install4jMacIconsFile,
+ 'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
+ 'PNG_ICON_FILE': install4jPngIconFile,
+ 'BACKGROUND': install4jBackground,
+
]
//println("INSTALL4J VARIABLES:")
@@ -1765,16 +1942,11 @@ task sourceDist(type: Tar) {
group "distribution"
description "Create a source .tar.gz file for distribution"
- dependsOn convertBuildingMD
+ dependsOn convertMdFiles
def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
- // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
- try {
- archiveFileName = outputFileName
- } catch (Exception e) {
- archiveName = outputFileName
- }
+ archiveFileName = outputFileName
compression Compression.GZIP
@@ -1864,7 +2036,7 @@ task helppages {
dependsOn copyHelp
dependsOn pubhtmlhelp
- inputs.dir("${classesDir}/${help_dir}")
+ inputs.dir("${helpBuildDir}/${help_dir}")
outputs.dir("${buildDir}/distributions/${help_dir}")
}
@@ -2145,7 +2317,9 @@ task jalviewjsSyncAllLibs (type: Sync) {
task jalviewjsSyncResources (type: Sync) {
- def inputFiles = fileTree(dir: resourceDir)
+ dependsOn buildResources
+
+ def inputFiles = fileTree(dir: resourcesBuildDir)
def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
@@ -2668,11 +2842,7 @@ task jalviewjsSiteTar(type: Tar) {
description "Creates a tar.gz file for the website"
dependsOn jalviewjsBuildSite
def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
- try {
- archiveFileName = outputFilename
- } catch (Exception e) {
- archiveName = outputFilename
- }
+ archiveFileName = outputFilename
compression Compression.GZIP
@@ -2761,10 +2931,25 @@ task jalviewjsIDE_checkJ2sPlugin {
if (eclipseHome == null || ! IN_ECLIPSE) {
throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
}
- def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
- def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
- if (!eclipseJ2sPluginFile.exists()) {
- def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin"
+ def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
+ def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
+ if (altPluginsDir != null && file(altPluginsDir).exists()) {
+ eclipseJ2sPluginDirs += altPluginsDir
+ }
+ def foundPlugin = false
+ def j2sPluginFileName = j2sPluginFile.getName()
+ def eclipseJ2sPlugin
+ def eclipseJ2sPluginFile
+ eclipseJ2sPluginDirs.any { dir ->
+ eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
+ eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+ if (eclipseJ2sPluginFile.exists()) {
+ foundPlugin = true
+ return true
+ }
+ }
+ if (!foundPlugin) {
+ def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
System.err.println(msg)
throw new StopExecutionException(msg)
}
@@ -2782,7 +2967,7 @@ task jalviewjsIDE_checkJ2sPlugin {
System.err.println(msg)
throw new StopExecutionException(msg)
} else {
- def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+ def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
println(msg)
}
}