id 'java'
id 'application'
id 'eclipse'
- id "com.diffplug.gradle.spotless" version "3.28.0"
- id 'com.github.johnrengelman.shadow' version '4.0.3'
+ id "com.diffplug.spotless" version "6.18.0" //.gradle.spotless" "3.28.0"
+ id 'com.github.johnrengelman.shadow' version '8.1.1' // was 4.0.3
id 'com.install4j.gradle' version '9.0.6'
- id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
+ id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
id 'com.palantir.git-version' version '0.13.0' apply false
}
if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
JALVIEW_VERSION = releaseProps.get("jalview.version")
}
+ println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
// this property set when running Eclipse headlessly
j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
testDir = string("${jalviewDir}/${bareTestSourceDir}")
classesDir = string("${jalviewDir}/${classes_dir}")
+ destinationDirectory = file(classesDir)
// clover
useClover = clover.equals("true")
main {
java {
srcDirs sourceDir
- outputDir = file(classesDir)
+ destinationDirectory = file(classesDir)
}
resources {
srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
}
- compileClasspath = files(sourceSets.main.java.outputDir)
+ compileClasspath = files(sourceSets.main.java.destinationDirectory)
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
runtimeClasspath = compileClasspath
clover {
java {
srcDirs cloverInstrDir
- outputDir = cloverClassesDir
+ destinationDirectory = cloverClassesDir
}
resources {
srcDirs = sourceSets.main.resources.srcDirs
}
- compileClasspath = files( sourceSets.clover.java.outputDir )
+ compileClasspath = files( sourceSets.clover.java.destinationDirectory )
//compileClasspath += files( testClassesDir )
compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
test {
java {
srcDirs testSourceDir
- outputDir = file(testClassesDir)
+ destinationDirectory = file(testClassesDir)
}
resources {
srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
}
- compileClasspath = files( sourceSets.test.java.outputDir )
+ compileClasspath = files( sourceSets.test.java.destinationDirectory )
compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
}
classpath {
- //defaultOutputDir = sourceSets.main.java.outputDir
+ //defaultOutputDir = sourceSets.main.java.destinationDirectory
configurations.each{ c->
if (c.isCanBeResolved()) {
minusConfigurations += [c]
HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
- //don't want to add outputDir as eclipse is using its own output dir in bin/main
+ //don't want to add destinationDirectory as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath, especially if they don't exist
return false // groovy "continue" in .any closure
}
sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
- //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+ //no longer want to add destinationDirectory as eclipse is using its own output dir in bin/main
if (it.isDirectory() || ! it.exists()) {
// don't add dirs to classpath
return false // groovy "continue" in .any closure
clean {
doFirst {
- delete sourceSets.main.java.outputDir
+ delete sourceSets.main.java.destinationDirectory
}
}
cleanTest {
dependsOn cleanClover
doFirst {
- delete sourceSets.test.java.outputDir
+ delete sourceSets.test.java.destinationDirectory
}
}
task copyDocs(type: Copy) {
def inputDir = "${jalviewDir}/${doc_dir}"
- def outputDir = "${docBuildDir}/${doc_dir}"
+ def destinationDirectory = "${docBuildDir}/${doc_dir}"
from(inputDir) {
include('**/*.txt')
include('**/*.md')
exclude('**/*.html')
exclude('**/*.xml')
}
- into outputDir
+ into destinationDirectory
inputs.dir(inputDir)
- outputs.dir(outputDir)
+ outputs.dir(destinationDirectory)
}
}
+def hugoTemplateSubstitutions(String input, Map extras=null) {
+ def replacements = [
+ DATE: getDate("yyyy-MM-dd"),
+ CHANNEL: propertiesChannelName,
+ APPLICATION_NAME: applicationName,
+ GIT_HASH: gitHash,
+ GIT_BRANCH: gitBranch,
+ VERSION: JALVIEW_VERSION,
+ JAVA_VERSION: JAVA_VERSION,
+ VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
+ DRAFT: "false",
+ JVL_HEADER: ""
+ ]
+ def output = input
+ if (extras != null) {
+ extras.each{ k, v ->
+ output = output.replaceAll("__${k}__", ((v == null)?"":v))
+ }
+ }
+ replacements.each{ k, v ->
+ output = output.replaceAll("__${k}__", ((v == null)?"":v))
+ }
+ return output
+}
+
+def mdFileComponents(File mdFile, def dateOnly=false) {
+ def map = [:]
+ def content = ""
+ if (mdFile.exists()) {
+ def inFrontMatter = false
+ def firstLine = true
+ mdFile.eachLine { line ->
+ if (line.matches("---")) {
+ def prev = inFrontMatter
+ inFrontMatter = firstLine
+ if (inFrontMatter != prev)
+ return false
+ }
+ if (inFrontMatter) {
+ def m = null
+ if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
+ map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
+ } else if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
+ map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
+ } else if (m == line =~ /^channel:\s*(\S+)/) {
+ map["channel"] = m[0][1]
+ } else if (m == line =~ /^version:\s*(\S+)/) {
+ map["version"] = m[0][1]
+ } else if (m == line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
+ map[ m[0][1] ] = m[0][2]
+ }
+ if (dateOnly && map["date"] != null) {
+ return false
+ }
+ } else {
+ if (dateOnly)
+ return false
+ content += line+"\n"
+ }
+ firstLine = false
+ }
+ }
+ return dateOnly ? map["date"] : [map, content]
+}
+
+task hugoTemplates {
+ group "website"
+ description "Create partially populated md pages for hugo website build"
+
+ def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
+ def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
+ def templateFiles = fileTree(dir: hugoTemplatesDir)
+ def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
+ def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
+ def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
+ def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
+
+ doFirst {
+ // specific release template for version archive
+ def changes = ""
+ def whatsnew = null
+ def givenDate = null
+ def givenChannel = null
+ def givenVersion = null
+ if (CHANNEL == "RELEASE") {
+ def (map, content) = mdFileComponents(releaseMdFile)
+ givenDate = map.date
+ givenChannel = map.channel
+ givenVersion = map.version
+ changes = content
+ if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
+ throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
+ }
+
+ if (whatsnewMdFile.exists())
+ whatsnew = whatsnewMdFile.text
+ }
+
+ def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
+ def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
+
+ def changesHugo = null
+ if (changes != null) {
+ changesHugo = '<div class="release_notes">\n\n'
+ def inSection = false
+ changes.eachLine { line ->
+ def m = null
+ if (m == line =~ /^##([^#].*)$/) {
+ if (inSection) {
+ changesHugo += "</div>\n\n"
+ }
+ def section = m[0][1].trim()
+ section = section.toLowerCase()
+ section = section.replaceAll(/ +/, "_")
+ section = section.replaceAll(/[^a-z0-9_\-]/, "")
+ changesHugo += "<div class=\"${section}\">\n\n"
+ inSection = true
+ } else if (m == line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
+ def comment = m[0][2].trim()
+ if (comment != "") {
+ comment = comment.replaceAll('"', """)
+ def issuekeys = []
+ comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
+ def newline = m[0][1]
+ if (comment.trim() != "")
+ newline += "{{<comment>}}${comment}{{</comment>}} "
+ newline += m[0][3].trim()
+ if (issuekeys.size() > 0)
+ newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
+ if (m[0][4] != null)
+ newline += m[0][4]
+ line = newline
+ }
+ }
+ changesHugo += line+"\n"
+ }
+ if (inSection) {
+ changesHugo += "\n</div>\n\n"
+ }
+ changesHugo += '</div>'
+ }
+
+ templateFiles.each{ templateFile ->
+ def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
+ def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
+ def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
+
+ def outPathName = string("${hugoBuildDir}/$newRelPathName")
+
+ copy {
+ from templateFile
+ rename(templateFile.getName(), newFileName)
+ into outPathName
+ }
+
+ def newFile = file("${outPathName}/${newFileName}".toString())
+ def content = newFile.text
+ newFile.text = hugoTemplateSubstitutions(content,
+ [
+ WHATSNEW: whatsnew,
+ CHANGES: changesHugo,
+ DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
+ DRAFT: givenDate == null ? "true" : "false",
+ JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
+ JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
+ ]
+ )
+ }
+
+ }
+
+ inputs.file(oldJvlFile)
+ inputs.dir(hugoTemplatesDir)
+ inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
+ inputs.property("CHANNEL", { CHANNEL })
+}
+
+def getMdDate(File mdFile) {
+ return mdFileComponents(mdFile, true)
+}
+
+def getMdSections(String content) {
+ def sections = [:]
+ def sectionContent = ""
+ def sectionName = null
+ content.eachLine { line ->
+ def m = null
+ if (m == line =~ /^##([^#].*)$/) {
+ if (sectionName != null) {
+ sections[sectionName] = sectionContent
+ sectionName = null
+ sectionContent = ""
+ }
+ sectionName = m[0][1].trim()
+ sectionName = sectionName.toLowerCase()
+ sectionName = sectionName.replaceAll(/ +/, "_")
+ sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
+ } else if (sectionName != null) {
+ sectionContent += line+"\n"
+ }
+ }
+ if (sectionContent != null) {
+ sections[sectionName] = sectionContent
+ }
+ return sections
+}
+
+
task copyHelp(type: Copy) {
def inputDir = helpSourceDir
- def outputDir = "${helpBuildDir}/${help_dir}"
+ def destinationDirectory = "${helpBuildDir}/${help_dir}"
from(inputDir) {
include('**/*.txt')
include('**/*.md')
exclude('**/*.xml')
exclude('**/*.jhm')
}
- into outputDir
+ into destinationDirectory
inputs.dir(inputDir)
outputs.files(helpFile)
- outputs.dir(outputDir)
+ outputs.dir(destinationDirectory)
}
-task copyResources(type: Copy) {
- group = "build"
- description = "Copy (and make text substitutions in) the resources dir to the build area"
+/*
+task releasesTemplates {
+ group "help"
+ description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
- def inputDir = resourceDir
- def outputDir = resourcesBuildDir
- from(inputDir) {
- include('**/*.txt')
- include('**/*.md')
- include('**/*.html')
- include('**/*.xml')
- filter(ReplaceTokens,
- beginToken: '$$',
- endToken: '$$',
- tokens: [
- 'Version-Rel': JALVIEW_VERSION,
- 'Year-Rel': getDate("yyyy")
- ]
- )
- }
- from(inputDir) {
- exclude('**/*.txt')
- exclude('**/*.md')
- exclude('**/*.html')
- exclude('**/*.xml')
- }
- into outputDir
+ dependsOn copyHelp
- inputs.dir(inputDir)
- outputs.dir(outputDir)
-}
+ def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
+ def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
+ def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
+ def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
+ def releasesMdDir = "${jalviewDir}/${releases_dir}"
+ def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
-task copyChannelResources(type: Copy) {
- dependsOn copyResources
- group = "build"
- description = "Copy the channel resources dir to the build resources area"
+ doFirst {
+ def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
+ def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
- def inputDir = "${channelDir}/${resource_dir}"
- def outputDir = resourcesBuildDir
- from inputDir
- into outputDir
+ if (CHANNEL == "RELEASE") {
+ if (!releaseMdFile.exists()) {
+ throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
+ }
+ if (!whatsnewMdFile.exists()) {
+ throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
+ }
+ }
- inputs.dir(inputDir)
- outputs.dir(outputDir)
-}
+ def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
+ def releaseFilesDates = releaseFiles.collectEntries {
+ [(it): getMdDate(it)]
+ }
+ releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
-task createBuildProperties(type: WriteProperties) {
- dependsOn copyResources
- group = "build"
- description = "Create the ${buildProperties} file"
-
- inputs.dir(sourceDir)
+ def releasesTemplate = releasesTemplateFile.text
+ def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
+ def versionTemplate = m[0][1]
+
+ MutableDataSet options = new MutableDataSet()
+
+ def extensions = new ArrayList<>()
+ options.set(Parser.EXTENSIONS, extensions)
+ options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
+
+ Parser parser = Parser.builder(options).build()
+ HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+
+ def actualVersions = releaseFiles.collect { rf ->
+ def (rfMap, rfContent) = mdFileComponents(rf)
+ return rfMap.version
+ }
+ def versionsHtml = ""
+ def linkedVersions = []
+ releaseFiles.reverse().each { rFile ->
+ def (rMap, rContent) = mdFileComponents(rFile)
+
+ def versionLink = ""
+ def partialVersion = ""
+ def firstPart = true
+ rMap.version.split("\\.").each { part ->
+ def displayPart = ( firstPart ? "" : "." ) + part
+ partialVersion += displayPart
+ if (
+ linkedVersions.contains(partialVersion)
+ || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
+ ) {
+ versionLink += displayPart
+ } else {
+ versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
+ linkedVersions += partialVersion
+ }
+ firstPart = false
+ }
+ def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
+
+ def lm = null
+ def rContentProcessed = ""
+ rContent.eachLine { line ->
+ if (lm == line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
+ line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
+ } else if (lm == line =~ /^###([^#]+.*)$/) {
+ line = "_${lm[0][1].trim()}_"
+ }
+ rContentProcessed += line + "\n"
+ }
+
+ def rContentSections = getMdSections(rContentProcessed)
+ def rVersion = versionTemplate
+ if (rVersion != "") {
+ def rNewFeatures = rContentSections["new_features"]
+ def rIssuesResolved = rContentSections["issues_resolved"]
+ Node newFeaturesNode = parser.parse(rNewFeatures)
+ String newFeaturesHtml = renderer.render(newFeaturesNode)
+ Node issuesResolvedNode = parser.parse(rIssuesResolved)
+ String issuesResolvedHtml = renderer.render(issuesResolvedNode)
+ rVersion = hugoTemplateSubstitutions(rVersion,
+ [
+ VERSION: rMap.version,
+ VERSION_LINK: versionLink,
+ DISPLAY_DATE: displayDate,
+ NEW_FEATURES: newFeaturesHtml,
+ ISSUES_RESOLVED: issuesResolvedHtml
+ ]
+ )
+ versionsHtml += rVersion
+ }
+ }
+
+ releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
+ releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
+ releasesHtmlFile.text = releasesTemplate
+
+ if (whatsnewMdFile.exists()) {
+ def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
+ def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
+ Node whatsnewNode = parser.parse(whatsnewMd)
+ String whatsnewHtml = renderer.render(whatsnewNode)
+ whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
+ whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
+ [
+ VERSION: JALVIEW_VERSION,
+ DISPLAY_DATE: wnDisplayDate
+ ]
+ )
+ } else if (gradle.taskGraph.hasTask(":linkCheck")) {
+ whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
+ }
+
+ }
+
+ inputs.file(releasesTemplateFile)
+ inputs.file(whatsnewTemplateFile)
+ inputs.dir(releasesMdDir)
+ inputs.dir(whatsnewMdDir)
+ outputs.file(releasesHtmlFile)
+ outputs.file(whatsnewHtmlFile)
+}
+
+*/
+
+task copyResources(type: Copy) {
+ group = "build"
+ description = "Copy (and make text substitutions in) the resources dir to the build area"
+
+ def inputDir = resourceDir
+ def destinationDirectory = resourcesBuildDir
+ from(inputDir) {
+ include('**/*.txt')
+ include('**/*.md')
+ include('**/*.html')
+ include('**/*.xml')
+ filter(ReplaceTokens,
+ beginToken: '$$',
+ endToken: '$$',
+ tokens: [
+ 'Version-Rel': JALVIEW_VERSION,
+ 'Year-Rel': getDate("yyyy")
+ ]
+ )
+ }
+ from(inputDir) {
+ exclude('**/*.txt')
+ exclude('**/*.md')
+ exclude('**/*.html')
+ exclude('**/*.xml')
+ }
+ into destinationDirectory
+
+ inputs.dir(inputDir)
+ outputs.dir(destinationDirectory)
+}
+
+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 destinationDirectory = resourcesBuildDir
+ from inputDir
+ into destinationDirectory
+
+ inputs.dir(inputDir)
+ outputs.dir(destinationDirectory)
+}
+
+task createBuildProperties(type: WriteProperties) {
+ dependsOn copyResources
+ dependsOn copyChannelResources
+ group = "build"
+ description = "Create the ${buildProperties} file"
+
+ inputs.dir(sourceDir)
inputs.dir(resourcesBuildDir)
outputFile (buildProperties)
// taking time specific comment out to allow better incremental builds
property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
property "VERSION", JALVIEW_VERSION
property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+ property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION
if (getdownSetAppBaseProperty) {
property "GETDOWNAPPBASE", getdownAppBase
property "GETDOWNAPPDISTDIR", getdownAppDistDir
task buildIndices(type: JavaExec) {
dependsOn copyHelp
+ //dependsOn releasesTemplates
classpath = sourceSets.main.compileClasspath
main = "com.sun.java.help.search.Indexer"
workingDir = "${helpBuildDir}/${help_dir}"
dependsOn buildResources
dependsOn copyDocs
dependsOn copyHelp
+ //dependsOn releasesTemplates
dependsOn convertMdFiles
dependsOn buildIndices
}
+// random block of dependencies
compileJava.dependsOn prepare
run.dependsOn compileJava
//run.dependsOn prepare
+compileTestJava.dependsOn compileJava //
+compileTestJava.dependsOn buildIndices //
+processResources.dependsOn copyChannelResources //
+processResources.dependsOn copyResources //
+processResources.dependsOn createBuildProperties //
+processResources.dependsOn copyDocs //
+processResources.dependsOn convertMdFiles //
+processResources.dependsOn copyHelp //
+processResources.dependsOn buildIndices //
//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
}
+/*
task compileLinkCheck(type: JavaCompile) {
options.fork = true
classpath = files("${jalviewDir}/${utils_dir}")
def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
classpath = files("${jalviewDir}/${utils_dir}")
main = "HelpLinksChecker"
- workingDir = jalviewDir
+ workingDir = "${helpBuildDir}"
args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
inputs.dir(helpBuildDir)
outputs.file(helpLinksCheckerOutFile)
}
+*/
// import the pubhtmlhelp target
}
}
+// block of dependencies
+//compileTestJava.dependsOn compileLinkCheck //
+//copyChannelResources.dependsOn compileLinkCheck //
+//convertMdFiles.dependsOn compileLinkCheck //
jar {
dependsOn prepare
- dependsOn linkCheck
+ dependsOn //linkCheck
manifest {
attributes "Main-Class": main_class,
"Implementation-Version": JALVIEW_VERSION
}
- def outputDir = "${jalviewDir}/${package_dir}"
- destinationDirectory = file(outputDir)
+ def destinationDirectory = "${jalviewDir}/${package_dir}"
+ destinationDirectory = file(destinationDirectory)
archiveFileName = rootProject.name+".jar"
duplicatesStrategy "EXCLUDE"
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir(sourceSets.main.java.outputDir)
+ inputs.dir(sourceSets.main.java.destinationDirectory)
sourceSets.main.resources.srcDirs.each{ dir ->
inputs.dir(dir)
}
- outputs.file("${outputDir}/${archiveFileName}")
+ outputs.file("${destinationDirectory}/${archiveFileName}")
}
mainClassName = shadow_jar_main_class
mergeServiceFiles()
- classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+ archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
}
}
}
-def hugoTemplateSubstitutions(String input, Map extras=null) {
- def replacements = [
- DATE: getDate("yyyy-MM-dd"),
- CHANNEL: propertiesChannelName,
- APPLICATION_NAME: applicationName,
- GIT_HASH: gitHash,
- GIT_BRANCH: gitBranch,
- VERSION: JALVIEW_VERSION,
- JAVA_VERSION: JAVA_VERSION,
- VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
- DRAFT: "false",
- JVL_HEADER: ""
- ]
- def output = input
- if (extras != null) {
- extras.each{ k, v ->
- output = output.replaceAll("__${k}__", ((v == null)?"":v))
- }
- }
- replacements.each{ k, v ->
- output = output.replaceAll("__${k}__", ((v == null)?"":v))
- }
- return output
-}
-
-def mdFileComponents(File mdFile, def dateOnly=false) {
- def map = [:]
- def content = ""
- if (mdFile.exists()) {
- def inFrontMatter = false
- def firstLine = true
- mdFile.eachLine { line ->
- if (line.matches("---")) {
- def prev = inFrontMatter
- inFrontMatter = firstLine
- if (inFrontMatter != prev)
- return false
- }
- if (inFrontMatter) {
- def m = null
- if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
- map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
- } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
- map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
- } else if (m = line =~ /^channel:\s*(\S+)/) {
- map["channel"] = m[0][1]
- } else if (m = line =~ /^version:\s*(\S+)/) {
- map["version"] = m[0][1]
- } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
- map[ m[0][1] ] = m[0][2]
- }
- if (dateOnly && map["date"] != null) {
- return false
- }
- } else {
- if (dateOnly)
- return false
- content += line+"\n"
- }
- firstLine = false
- }
- }
- return dateOnly ? map["date"] : [map, content]
-}
-
-task hugoTemplates {
- group "website"
- description "Create partially populated md pages for hugo website build"
-
- def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
- def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
- def templateFiles = fileTree(dir: hugoTemplatesDir)
- def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
- def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
- def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
- def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
-
- doFirst {
- // specific release template for version archive
- def changes = ""
- def whatsnew = null
- def givenDate = null
- def givenChannel = null
- def givenVersion = null
- if (CHANNEL == "RELEASE") {
- def (map, content) = mdFileComponents(releaseMdFile)
- givenDate = map.date
- givenChannel = map.channel
- givenVersion = map.version
- changes = content
- if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
- throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
- }
-
- if (whatsnewMdFile.exists())
- whatsnew = whatsnewMdFile.text
- }
-
- def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
- def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
-
- def changesHugo = null
- if (changes != null) {
- changesHugo = '<div class="release_notes">\n\n'
- def inSection = false
- changes.eachLine { line ->
- def m = null
- if (m = line =~ /^##([^#].*)$/) {
- if (inSection) {
- changesHugo += "</div>\n\n"
- }
- def section = m[0][1].trim()
- section = section.toLowerCase()
- section = section.replaceAll(/ +/, "_")
- section = section.replaceAll(/[^a-z0-9_\-]/, "")
- changesHugo += "<div class=\"${section}\">\n\n"
- inSection = true
- } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
- def comment = m[0][2].trim()
- if (comment != "") {
- comment = comment.replaceAll('"', """)
- def issuekeys = []
- comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
- def newline = m[0][1]
- if (comment.trim() != "")
- newline += "{{<comment>}}${comment}{{</comment>}} "
- newline += m[0][3].trim()
- if (issuekeys.size() > 0)
- newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
- if (m[0][4] != null)
- newline += m[0][4]
- line = newline
- }
- }
- changesHugo += line+"\n"
- }
- if (inSection) {
- changesHugo += "\n</div>\n\n"
- }
- changesHugo += '</div>'
- }
-
- templateFiles.each{ templateFile ->
- def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
- def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
- def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
-
- def outPathName = string("${hugoBuildDir}/$newRelPathName")
-
- copy {
- from templateFile
- rename(templateFile.getName(), newFileName)
- into outPathName
- }
-
- def newFile = file("${outPathName}/${newFileName}".toString())
- def content = newFile.text
- newFile.text = hugoTemplateSubstitutions(content,
- [
- WHATSNEW: whatsnew,
- CHANGES: changesHugo,
- DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
- DRAFT: givenDate == null ? "true" : "false",
- JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
- JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
- ]
- )
- }
-
- }
-
- inputs.file(oldJvlFile)
- inputs.dir(hugoTemplatesDir)
- inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
- inputs.property("CHANNEL", { CHANNEL })
-}
-
-def getMdDate(File mdFile) {
- return mdFileComponents(mdFile, true)
-}
-
-def getMdSections(String content) {
- def sections = [:]
- def sectionContent = ""
- def sectionName = null
- content.eachLine { line ->
- def m = null
- if (m = line =~ /^##([^#].*)$/) {
- if (sectionName != null) {
- sections[sectionName] = sectionContent
- sectionName = null
- sectionContent = ""
- }
- sectionName = m[0][1].trim()
- sectionName = sectionName.toLowerCase()
- sectionName = sectionName.replaceAll(/ +/, "_")
- sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
- } else if (sectionName != null) {
- sectionContent += line+"\n"
- }
- }
- if (sectionContent != null) {
- sections[sectionName] = sectionContent
- }
- return sections
-}
-
-task releasesTemplates {
- def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
- def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
- def releasesHtmlFile = file("${helpSourceDir}/${releases_html}")
- def whatsnewHtmlFile = file("${helpSourceDir}/${whatsnew_html}")
- def releasesMdDir = "${jalviewDir}/${releases_dir}"
- def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
-
- doFirst {
- def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
- def releaseFilesDates = releaseFiles.collectEntries {
- [(it): getMdDate(it)]
- }
- releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
-
- def releasesTemplate = releasesTemplateFile.text
- def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
- def versionTemplate = m[0][1]
-
- MutableDataSet options = new MutableDataSet()
-
- def extensions = new ArrayList<>()
- options.set(Parser.EXTENSIONS, extensions)
- options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
-
- Parser parser = Parser.builder(options).build()
- HtmlRenderer renderer = HtmlRenderer.builder(options).build()
-
- def actualVersions = releaseFiles.collect { rf ->
- def (rfMap, rfContent) = mdFileComponents(rf)
- return rfMap.version
- }
- def versionsHtml = ""
- def linkedVersions = []
- releaseFiles.reverse().each { rFile ->
- def (rMap, rContent) = mdFileComponents(rFile)
-
- def versionLink = ""
- def partialVersion = ""
- def firstPart = true
- rMap.version.split("\\.").each { part ->
- def displayPart = ( firstPart ? "" : "." ) + part
- partialVersion += displayPart
- if (
- linkedVersions.contains(partialVersion)
- || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
- ) {
- versionLink += displayPart
- } else {
- versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
- linkedVersions += partialVersion
- }
- firstPart = false
- }
- def displayDate = releaseFilesDates[rFile].format("d MMMMM yyyy")
-
- def rContentSections = getMdSections(rContent)
- def rVersion = versionTemplate
- if (rVersion != "") {
- Node newFeaturesNode = parser.parse(rContentSections["new_features"])
- String newFeaturesHtml = renderer.render(newFeaturesNode)
- Node issuesResolvedNode = parser.parse(rContentSections["issues_resolved"])
- String issuesResolvedHtml = renderer.render(issuesResolvedNode)
- rVersion = hugoTemplateSubstitutions(rVersion,
- [
- VERSION: rMap.version,
- VERSION_LINK: versionLink,
- DISPLAY_DATE: displayDate,
- NEW_FEATURES: newFeaturesHtml,
- ISSUES_RESOLVED: issuesResolvedHtml
- ]
- )
- versionsHtml += rVersion
- }
- }
-
- releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
- releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
- releasesHtmlFile.text = releasesTemplate
- }
-
- inputs.file(releasesTemplateFile)
- inputs.file(whatsnewTemplateFile)
- inputs.dir(releasesMdDir)
- inputs.dir(whatsnewMdDir)
- outputs.file(releasesHtmlFile)
- outputs.file(whatsnewHtmlFile)
-}
-
-
task helppages {
+ group "help"
+ description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
+
dependsOn copyHelp
dependsOn pubhtmlhelp
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
- def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
from inputFiles
- into outputDir
+ into destinationDirectory
}
dependsOn jalviewjsTransferUnzipAllLibs
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
- into outputDir
+ into destinationDirectory
def outputFiles = []
rename { filename ->
- outputFiles += "${outputDir}/${filename}"
+ outputFiles += "${destinationDirectory}/${filename}"
null
}
preserve {
dependsOn buildResources
def inputFiles = fileTree(dir: resourcesBuildDir)
- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
- into outputDir
+ into destinationDirectory
def outputFiles = []
rename { filename ->
- outputFiles += "${outputDir}/${filename}"
+ outputFiles += "${destinationDirectory}/${filename}"
null
}
preserve {
task jalviewjsSyncSiteResources (type: Sync) {
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
- into outputDir
+ into destinationDirectory
def outputFiles = []
rename { filename ->
- outputFiles += "${outputDir}/${filename}"
+ outputFiles += "${destinationDirectory}/${filename}"
null
}
preserve {
task jalviewjsSyncBuildProperties (type: Sync) {
dependsOn createBuildProperties
def inputFiles = [file(buildProperties)]
- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
from inputFiles
- into outputDir
+ into destinationDirectory
def outputFiles = []
rename { filename ->
- outputFiles += "${outputDir}/${filename}"
+ outputFiles += "${destinationDirectory}/${filename}"
null
}
preserve {
def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
def prefixFile = "${jsDir}/core/coretop2.js"
def suffixFile = "${jsDir}/core/corebottom2.js"
}
def list = fileTree(dir: j2sDir, includes: filelist)
- def jsfile = "${outputDir}/core${name}.js"
- def zjsfile = "${outputDir}/core${name}.z.js"
+ def jsfile = "${destinationDirectory}/core${name}.js"
+ def zjsfile = "${destinationDirectory}/core${name}.z.js"
jalviewjsCoreClasslists += [
'jsfile': jsfile,
// _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
def stevesoftClasslistName = "_stevesoft"
def stevesoftClasslist = [
- 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
- 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+ 'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js",
+ 'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js",
'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
'name': stevesoftClasslistName
]
]
)
def allClasslist = [
- 'jsfile': "${outputDir}/core${allClasslistName}.js",
- 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+ 'jsfile': "${destinationDirectory}/core${allClasslistName}.js",
+ 'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js",
'list': allJsFiles,
'name': allClasslistName
]
dependsOn jalviewjsBuildAllCores
def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
def inputFile = file(inputFileName)
- def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
def outputFiles = []
jalviewjsCoreClasslists.each { cl ->
- def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+ def outputFile = "${destinationDirectory}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
cl['outputfile'] = outputFile
outputFiles += outputFile
}
dependsOn jalviewjsBuildAllCores
dependsOn jalviewjsPublishCoreTemplates
def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
- def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+ def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
from inputFiles
- into outputDir
+ into destinationDirectory
def outputFiles = []
rename { filename ->
- outputFiles += "${outputDir}/${filename}"
+ outputFiles += "${destinationDirectory}/${filename}"
null
}
preserve {
git://source.jalview.org / jalview.git / blobdiff