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"
+ }
}
id 'com.github.johnrengelman.shadow' version '4.0.3'
id 'com.install4j.gradle' version '8.0.4'
id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+ id 'com.palantir.git-version' version '0.12.3'
}
repositories {
cloverBuildDir = "${buildDir}/clover"
cloverInstrDir = file("${cloverBuildDir}/clover-instr")
cloverClassesDir = file("${cloverBuildDir}/clover-classes")
- cloverReportDir = file("${buildDir}/reports")
+ cloverReportDir = file("${buildDir}/reports/clover")
cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
//cloverTestClassesDir = cloverClassesDir
modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
modules_runtimeClasspath = modules_compileClasspath
*/
- gitHash = string("")
- gitBranch = string("")
+ def details = versionDetails()
+ gitHash = details.gitHash
+ gitBranch = details.branchName
println("Using a ${CHANNEL} profile.")
task cleanClover {
doFirst {
delete cloverBuildDir
+ delete cloverReportDir
}
}
file(cloverDb).exists()
}
- def cloverHtmlDir = "${cloverReportDir}/clover"
+ def cloverHtmlDir = cloverReportDir
inputs.dir cloverClassesDir
outputs.dir cloverHtmlDir
file(cloverDb).exists()
}
- def cloverXmlFile = "${cloverReportDir}/clover/clover.xml"
+ def cloverXmlFile = "${cloverReportDir}/clover.xml"
inputs.dir cloverClassesDir
outputs.file cloverXmlFile
}
-task setGitVals {
- def hashStdOut = new ByteArrayOutputStream()
- exec {
- commandLine "git", "rev-parse", "--short", "HEAD"
- standardOutput = hashStdOut
- ignoreExitValue true
- }
-
- def branchStdOut = new ByteArrayOutputStream()
- exec {
- commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
- standardOutput = branchStdOut
- ignoreExitValue true
- }
-
- gitHash = hashStdOut.toString().trim()
- gitBranch = branchStdOut.toString().trim()
-
- outputs.upToDateWhen { false }
-}
-
-
task createBuildProperties(type: WriteProperties) {
group = "build"
description = "Create the ${buildProperties} file"
- dependsOn setGitVals
inputs.dir(sourceDir)
inputs.dir(resourceDir)
file(buildProperties).getParentFile().mkdirs()
}
-task convertBuildingMD(type: Exec) {
+def convertMdToHtml (FileTree mdFiles, File cssFile) {
+ MutableDataSet options = new MutableDataSet()
+
+ 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, "<span class=\"octicon octicon-link\"></span>")
+
+ 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 = '''<html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <meta http-equiv="Content-Style-Type" content="text/css" />
+ <meta name="generator" content="flexmark" />
+'''
+ htmlText += ((title != null) ? " <title>${title}</title>" : '' )
+ htmlText += '''
+ <style type="text/css">code{white-space: pre;}</style>
+'''
+ htmlText += ((cssFile != null) ? cssFile.text : '')
+ htmlText += '''</head>
+ <body>
+'''
+ htmlText += htmlBody
+ htmlText += '''
+ </body>
+</html>
+'''
+
+ def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+ def htmlFile = file(htmlFilePath)
+ htmlFile.text = htmlText
+ }
+}
+
+
+task convertMdFiles {
dependsOn cleanBuildingHTML
- def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
- def css = "${jalviewDir}/${doc_dir}/github.css"
+ def mdFiles = fileTree(dir: "${jalviewDir}/${doc_dir}", include: "*.md")
+ def cssFile = file("${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
+ dependsOn convertMdFiles
def syncDir = "${classesDir}/${doc_dir}"
from fileTree("${jalviewDir}/${doc_dir}")
into syncDir
-
}
shadowJar {
group = "distribution"
+ description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
if (buildDist) {
dependsOn makeDist
}
task installers(type: com.install4j.gradle.Install4jTask) {
group = "distribution"
description = "Create the install4j installers"
- dependsOn setGitVals
dependsOn getdown
dependsOn copyInstall4jTemplate
task sourceDist(type: Tar) {
+ group "distribution"
+ description "Create a source .tar.gz file for distribution"
+ 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]
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 '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
System.err.println(msg)
throw new StopExecutionException(msg)
}
System.err.println(msg)
throw new StopExecutionException(msg)
} else {
- def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+ def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
println(msg)
}
}
description "Sync libs and resources to site dir, but not closure cores"
dependsOn jalviewjsIDE_SyncSiteAll
- dependsOn cleanJalviewjsTransferSite
+ //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
}
git://source.jalview.org / jalview.git / blobdiff