X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=9161ed25e7b8c46ef5127f4dee20c14c1182a798;hb=254e54378f7545b2fdba83794625ebda03cb52d2;hp=d89f3edaaf21f77ce7f675a4393e85457cd3ca34;hpb=ce916cd46bbe1ec0446d8672b7341f5af7471b6e;p=jalview.git diff --git a/build.gradle b/build.gradle index d89f3ed..9161ed2 100644 --- a/build.gradle +++ b/build.gradle @@ -45,10 +45,10 @@ plugins { 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 } @@ -138,6 +138,7 @@ ext { if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) { JALVIEW_VERSION = releaseProps.get("jalview.version") } + println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'") // this property set when running Eclipse headlessly j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild") @@ -182,6 +183,7 @@ ext { testDir = string("${jalviewDir}/${bareTestSourceDir}") classesDir = string("${jalviewDir}/${classes_dir}") + destinationDirectory = file(classesDir) // clover useClover = clover.equals("true") @@ -546,14 +548,14 @@ sourceSets { main { java { srcDirs sourceDir - outputDir = file(classesDir) + destinationDirectory = file(classesDir) } resources { srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ] } - compileClasspath = files(sourceSets.main.java.outputDir) + compileClasspath = files(sourceSets.main.java.destinationDirectory) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath @@ -563,14 +565,14 @@ sourceSets { clover { java { srcDirs cloverInstrDir - outputDir = cloverClassesDir + destinationDirectory = cloverClassesDir } resources { srcDirs = sourceSets.main.resources.srcDirs } - compileClasspath = files( sourceSets.clover.java.outputDir ) + compileClasspath = files( sourceSets.clover.java.destinationDirectory ) //compileClasspath += files( testClassesDir ) compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"]) @@ -582,14 +584,14 @@ sourceSets { test { java { srcDirs testSourceDir - outputDir = file(testClassesDir) + destinationDirectory = file(testClassesDir) } resources { srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs } - compileClasspath = files( sourceSets.test.java.outputDir ) + compileClasspath = files( sourceSets.test.java.destinationDirectory ) compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"]) @@ -614,7 +616,7 @@ eclipse { } classpath { - //defaultOutputDir = sourceSets.main.java.outputDir + //defaultOutputDir = sourceSets.main.java.destinationDirectory configurations.each{ c-> if (c.isCanBeResolved()) { minusConfigurations += [c] @@ -653,7 +655,7 @@ eclipse { HashMap alreadyAddedLibPath = new HashMap<>(); sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any { - //don't want to add outputDir as eclipse is using its own output dir in bin/main + //don't want to add destinationDirectory as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath, especially if they don't exist return false // groovy "continue" in .any closure @@ -673,7 +675,7 @@ eclipse { } sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any { - //no longer want to add outputDir as eclipse is using its own output dir in bin/main + //no longer want to add destinationDirectory as eclipse is using its own output dir in bin/main if (it.isDirectory() || ! it.exists()) { // don't add dirs to classpath return false // groovy "continue" in .any closure @@ -1050,7 +1052,7 @@ compileTestJava { clean { doFirst { - delete sourceSets.main.java.outputDir + delete sourceSets.main.java.destinationDirectory } } @@ -1058,7 +1060,7 @@ clean { cleanTest { dependsOn cleanClover doFirst { - delete sourceSets.test.java.outputDir + delete sourceSets.test.java.destinationDirectory } } @@ -1150,7 +1152,7 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) { task copyDocs(type: Copy) { def inputDir = "${jalviewDir}/${doc_dir}" - def outputDir = "${docBuildDir}/${doc_dir}" + def destinationDirectory = "${docBuildDir}/${doc_dir}" from(inputDir) { include('**/*.txt') include('**/*.md') @@ -1171,10 +1173,10 @@ task copyDocs(type: Copy) { exclude('**/*.html') exclude('**/*.xml') } - into outputDir + into destinationDirectory inputs.dir(inputDir) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } @@ -1199,9 +1201,217 @@ task convertMdFiles { } +def hugoTemplateSubstitutions(String input, Map extras=null) { + def replacements = [ + DATE: getDate("yyyy-MM-dd"), + CHANNEL: propertiesChannelName, + APPLICATION_NAME: applicationName, + GIT_HASH: gitHash, + GIT_BRANCH: gitBranch, + VERSION: JALVIEW_VERSION, + JAVA_VERSION: JAVA_VERSION, + VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES, + DRAFT: "false", + JVL_HEADER: "" + ] + def output = input + if (extras != null) { + extras.each{ k, v -> + output = output.replaceAll("__${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 = '
\n\n' + def inSection = false + changes.eachLine { line -> + def m = null + if (m == line =~ /^##([^#].*)$/) { + if (inSection) { + changesHugo += "
\n\n" + } + def section = m[0][1].trim() + section = section.toLowerCase() + section = section.replaceAll(/ +/, "_") + section = section.replaceAll(/[^a-z0-9_\-]/, "") + changesHugo += "
\n\n" + inSection = true + } else if (m == line =~ /^(\s*-\s*)(.*?)()?\s*$/) { + 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 += "{{}}${comment}{{}} " + newline += m[0][3].trim() + if (issuekeys.size() > 0) + newline += " {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}" + if (m[0][4] != null) + newline += m[0][4] + line = newline + } + } + changesHugo += line+"\n" + } + if (inSection) { + changesHugo += "\n
\n\n" + } + changesHugo += '' + } + + templateFiles.each{ templateFile -> + def newFileName = string(hugoTemplateSubstitutions(templateFile.getName())) + def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent() + def newRelPathName = hugoTemplateSubstitutions( relPath.toString() ) + + def outPathName = string("${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') @@ -1226,20 +1436,159 @@ task copyHelp(type: Copy) { exclude('**/*.xml') exclude('**/*.jhm') } - into outputDir + into destinationDirectory inputs.dir(inputDir) outputs.files(helpFile) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } +/* +task releasesTemplates { + group "help" + description "Recreate whatsNew.html and releases.html from markdown files and templates in help" + + dependsOn copyHelp + + 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}" + + doFirst { + def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md") + def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md") + + if (CHANNEL == "RELEASE") { + if (!releaseMdFile.exists()) { + throw new GradleException("File ${releaseMdFile} must be created for RELEASE") + } + if (!whatsnewMdFile.exists()) { + throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE") + } + } + + def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md") + def releaseFilesDates = releaseFiles.collectEntries { + [(it): getMdDate(it)] + } + releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) } + + def releasesTemplate = releasesTemplateFile.text + def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/ + def versionTemplate = m[0][1] + + MutableDataSet options = new MutableDataSet() + + def extensions = new ArrayList<>() + options.set(Parser.EXTENSIONS, extensions) + options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true) + + Parser parser = Parser.builder(options).build() + HtmlRenderer renderer = HtmlRenderer.builder(options).build() + + def actualVersions = releaseFiles.collect { rf -> + def (rfMap, rfContent) = mdFileComponents(rf) + return rfMap.version + } + def versionsHtml = "" + def linkedVersions = [] + releaseFiles.reverse().each { rFile -> + def (rMap, rContent) = mdFileComponents(rFile) + + def versionLink = "" + def partialVersion = "" + def firstPart = true + rMap.version.split("\\.").each { part -> + def displayPart = ( firstPart ? "" : "." ) + part + partialVersion += displayPart + if ( + linkedVersions.contains(partialVersion) + || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version ) + ) { + versionLink += displayPart + } else { + versionLink += "${displayPart}" + 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 outputDir = resourcesBuildDir + def destinationDirectory = resourcesBuildDir from(inputDir) { include('**/*.txt') include('**/*.md') @@ -1260,10 +1609,10 @@ task copyResources(type: Copy) { exclude('**/*.html') exclude('**/*.xml') } - into outputDir + into destinationDirectory inputs.dir(inputDir) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } task copyChannelResources(type: Copy) { @@ -1272,16 +1621,17 @@ task copyChannelResources(type: Copy) { description = "Copy the channel resources dir to the build resources area" def inputDir = "${channelDir}/${resource_dir}" - def outputDir = resourcesBuildDir + def destinationDirectory = resourcesBuildDir from inputDir - into outputDir + into destinationDirectory inputs.dir(inputDir) - outputs.dir(outputDir) + outputs.dir(destinationDirectory) } task createBuildProperties(type: WriteProperties) { dependsOn copyResources + dependsOn copyChannelResources group = "build" description = "Create the ${buildProperties} file" @@ -1294,6 +1644,7 @@ task createBuildProperties(type: WriteProperties) { property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy") property "VERSION", JALVIEW_VERSION property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]" + property "JAVA_COMPILE_VERSION", JAVA_INTEGER_VERSION if (getdownSetAppBaseProperty) { property "GETDOWNAPPBASE", getdownAppBase property "GETDOWNAPPDISTDIR", getdownAppDistDir @@ -1304,6 +1655,7 @@ task createBuildProperties(type: WriteProperties) { task buildIndices(type: JavaExec) { dependsOn copyHelp + //dependsOn releasesTemplates classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" workingDir = "${helpBuildDir}/${help_dir}" @@ -1331,14 +1683,25 @@ task prepare { 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 $jalviewDir @@ -1383,6 +1746,7 @@ test { } +/* task compileLinkCheck(type: JavaCompile) { options.fork = true classpath = files("${jalviewDir}/${utils_dir}") @@ -1403,7 +1767,7 @@ task linkCheck(type: JavaExec) { def helpLinksCheckerOutFile = file("${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 @@ -1417,6 +1781,7 @@ task linkCheck(type: JavaExec) { inputs.dir(helpBuildDir) outputs.file(helpLinksCheckerOutFile) } +*/ // import the pubhtmlhelp target @@ -1431,10 +1796,14 @@ task cleanPackageDir(type: Delete) { } } +// 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, @@ -1444,8 +1813,8 @@ jar { "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" @@ -1456,11 +1825,11 @@ jar { 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}") } @@ -1519,7 +1888,7 @@ shadowJar { mainClassName = shadow_jar_main_class mergeServiceFiles() - classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION + archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION minimize() } @@ -2388,241 +2757,10 @@ task dataInstallersJson { } } -def hugoTemplateSubstitutions(String input) { - def output = input - output = output.replaceAll("__DATE__", getDate("yyyy-MM-dd")) - output = output.replaceAll("__CHANNEL__", propertiesChannelName) - output = output.replaceAll("__APPLICATION_NAME__", applicationName) - output = output.replaceAll("__GIT_HASH__", gitHash) - output = output.replaceAll("__GIT_BRANCH__", gitBranch) - output = output.replaceAll("__VERSION__", JALVIEW_VERSION) - output = output.replaceAll("__JAVA_VERSION__", JAVA_VERSION) - output = output.replaceAll("__VERSION_UNDERSCORES__", JALVIEW_VERSION_UNDERSCORES) - return output -} - -def ulToList(Element ul, int indent) { - def list = "" - ul.children().each { e -> - if (e.tagName().toLowerCase() == "ul") { - list = list.stripTrailing() + "\n" - list += ulToList(e, indent+1) - } else if (e.tagName().toLowerCase() == "li") { - def issues = [] - def issuesText = "" - def mdItem = " " * indent + "- " - e.childNodes().any {n -> - if (n.nodeName().equals("#comment")) { - mdItem += "{{}}${n.getData()}{{}} " - issuesText = n.getData().trim() - issues = n.getData().trim().split(/[,\s]+/).findAll { it.startsWith("JAL-") } - return true - } - } - def safeText = issuesText.replaceAll('"', '\"') - def joinedIssues = issues.join(",") - def issuesLink = (issues.size() > 0) ? - " {{< jal issue=\"${joinedIssues}\" alt=\"${safeText}\" >}}" - : "" - def addedIssues = false - e.childNodes().each { node -> - if (node.nodeName().toLowerCase() == "ul") { - // add issues link before sub list if it's last - if (node.nextSibling() == null) { - mdItem += "${issuesLink}" - addedIssues = true - } - mdItem = mdItem.stripTrailing() + "\n" - mdItem += ulToList(node, indent+1) - } else if (node.nodeName() == "#text") { - mdItem += node.text() - } else if (node.nodeName().toLowerCase() == "strong") { - mdItem += "**${node.text()}**" - } else if (node.nodeName().toLowerCase() == "em") { - // if (true || (node.text().length() > 50 && node.text().count(" ") > 10) || (!node.nextSibling().text().startsWith("\\s*\\n"))) { - mdItem += "*${node.text()}*" - // } else { - // mdItem += "### "+node.text() - // } - } else if (node.nodeName().toLowerCase() == "br") { - mdItem += "
\n" - } else if (node.nodeName().toLowerCase() == "a") { - mdItem += "[${node.text()}](${node.attr('href')})" - } - } - if (!addedIssues) { - mdItem += issuesLink - } - list += mdItem.stripTrailing()+"\n" - } else if (e.tagName().toLowerCase() == "div") { - e.children().each { eee -> - list += ulToList(eee, indent) - } - } else if (e.tagName().toLowerCase() == "strong") { - list += "**${e.text()}**" - } else if (e.tagName().toLowerCase() == "em") { - if (e.text().length() > 50 && e.text().count(" ") > 20) { - list += "*${e.text()}*" - } else { - list += "\n\n### ${e.text()}\n\n" - } - } - } - return list -} - -task hugoTemplates { - group "website" - description "Create partially populated md pages for hugo website build" - - def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}") - def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}" - def templateFiles = fileTree(dir: hugoTemplatesDir) - - doFirst { - // specific release template for version archive - def summary = "${applicationName} ${JALVIEW_VERSION}" - def changes = "" - def oldDate = null - if (CHANNEL == "RELEASE") { - def releasesHtmlFile = file("${helpSourceDir}/${releases_html}") - //HTMLPARSE - def html = releasesHtmlFile.text - def doc = Jsoup.parse(html) - def table = doc.select("table").first() - def headings = table.select("tr").first().select("th").collect { it.text() } - def releaseRow = null - def trs = table.select("tr") - trs.any { tr -> - def tds = tr.select("td") - if (tds.size() == 0) - return false - def releaseTd = tds.first() - if (releaseTd.text().startsWith("${JALVIEW_VERSION} ")) { - releaseRow = tr - return true - } - } - - if (releaseRow != null && headings != null && headings.size() == 3) { - def releaseTd = releaseRow.select("td").first() - def spaceIndex = releaseTd.text().indexOf(" ") - if (spaceIndex >= 0) { - oldDate = new Date().parse("dd/MM/yyyy", releaseTd.text().substring(spaceIndex+1)) - } - def releaseCells = releaseRow.select("td") - if (releaseCells.size() == 3) { - def title1 = headings[1] - def title2 = headings[2] - - def lastDotIndex = JALVIEW_VERSION.lastIndexOf(".") - if (lastDotIndex > 0) { - try { - def patchRelease = JALVIEW_VERSION.substring(lastDotIndex+1) as Integer - def patchReleaseString = null - if (patchRelease == 0) { - patchReleaseString = "first minor" - } else if (patchRelease == 1) { - patchReleaseString = "first patch" - } else if (patchRelease == 2) { - patchReleaseString = "second patch" - } else if (patchRelease == 3) { - patchReleaseString = "third patch" - } else if (patchRelease == 4) { - patchReleaseString = "fourth patch" - } else if (patchRelease == 5) { - patchReleaseString = "fifth patch" - } else if (patchRelease == 6) { - patchReleaseString = "sixth patch" - } else if (patchRelease == 7) { - patchReleaseString = "seventh patch" - } else if (patchRelease > 13 && (patchRelease % 10 == 1)) { - patchReleaseString += "st" - } else if (patchRelease > 13 && (patchRelease % 10 == 2)) { - patchReleaseString += "nd" - } else if (patchRelease > 13 && (patchRelease % 10 == 3)) { - patchReleaseString += "rd" - } else if (patchRelease != null) { - patchReleaseString += "th" - } - summary += (patchReleaseString != null) ? " is the ${patchReleaseString} release in the ${JALVIEW_VERSION.substring(0,lastDotIndex)} series." : "" - } catch(Exception e) { - summary = "" - } - } - - [1,2].each { col -> - def colChanges = "" - if (headings[col] != null && headings[col].size() > 0) { - releaseCells[col].children().each { e -> - if (e.tagName().toLowerCase() == "ul" || e.tagName().toLowerCase() == "div") { - if (colChanges != "") { - colChanges = colChanges.stripTrailing() + "\n" - } - colChanges += ulToList(e, 0) - } else if (e.tagName().toLowerCase() == "em") { - colChanges += "\n\n### ${e.text()}\n\n" - } - } - } - if (colChanges != "") { - def className = headings[col].replaceAll(" ","_").toLowerCase().replaceAll("[^_a-z]","") - changes += "
\n\n## ${headings[col]}\n\n${colChanges}\n
\n\n" - } - } - - if (changes != "") { - changes = "
\n\n${changes}\n\n
" - } - } - } - } - - templateFiles.each{ templateFile -> - def newFileName = string(hugoTemplateSubstitutions(templateFile.getName())) - def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent() - def newRelPathName = hugoTemplateSubstitutions( relPath.toString() ) - - def outPathName = string("${hugoBuildDir}/$newRelPathName") - - copy { - from templateFile - rename(templateFile.getName(), newFileName) - into outPathName - } - - def newFile = file("${outPathName}/${newFileName}".toString()) - def content = newFile.text - // summary in version archive release pages only appears from 2.10.2b2 onwards - if (oldDate.format("yyyy") as Integer >= 2019 || JALVIEW_VERSION.startsWith("2.10")) { - def summaryFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md") - if (summaryFile.exists()) { - summary = summaryFile.text - } else { - summary = "" - } - content = content.replaceAll("__SUMMARY__", summary) - } else { - content = content.replaceAll("__SUMMARY__", "") - } - content = content.replaceAll("__CHANGES__", changes) - if (oldDate != null) { - if (oldDate[java.util.Calendar.YEAR] < 90) { - oldDate[java.util.Calendar.YEAR] += 2000 - } - content = content.replaceAll("__DATE__", oldDate.format("yyyy-MM-dd")) - } - newFile.text = hugoTemplateSubstitutions(content) - } - } - - inputs.dir(hugoTemplatesDir) - inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION }) - inputs.property("CHANNEL", { CHANNEL }) -} - - task helppages { + group "help" + description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'." + dependsOn copyHelp dependsOn pubhtmlhelp @@ -2805,10 +2943,10 @@ task jalviewjsEclipseCopyDropins(type: Copy) { 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 } @@ -2916,13 +3054,13 @@ task jalviewjsSyncAllLibs (type: Sync) { 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 { @@ -2941,13 +3079,13 @@ task jalviewjsSyncResources (type: Sync) { 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 { @@ -2960,13 +3098,13 @@ task jalviewjsSyncResources (type: Sync) { 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 { @@ -2980,13 +3118,13 @@ task jalviewjsSyncSiteResources (type: Sync) { 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 { @@ -3205,7 +3343,7 @@ task jalviewjsBuildAllCores { 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 = "${jsDir}/core/corebottom2.js" @@ -3249,8 +3387,8 @@ task jalviewjsBuildAllCores { } def list = fileTree(dir: j2sDir, includes: filelist) - def jsfile = "${outputDir}/core${name}.js" - def zjsfile = "${outputDir}/core${name}.z.js" + def jsfile = "${destinationDirectory}/core${name}.js" + def zjsfile = "${destinationDirectory}/core${name}.z.js" jalviewjsCoreClasslists += [ 'jsfile': jsfile, @@ -3268,8 +3406,8 @@ task jalviewjsBuildAllCores { // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) def stevesoftClasslistName = "_stevesoft" def stevesoftClasslist = [ - 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js", - 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js", + 'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js", + 'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js", 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"), 'name': stevesoftClasslistName ] @@ -3302,8 +3440,8 @@ task jalviewjsBuildAllCores { ] ) def allClasslist = [ - 'jsfile': "${outputDir}/core${allClasslistName}.js", - 'zjsfile': "${outputDir}/core${allClasslistName}.z.js", + 'jsfile': "${destinationDirectory}/core${allClasslistName}.js", + 'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js", 'list': allJsFiles, 'name': allClasslistName ] @@ -3356,11 +3494,11 @@ task jalviewjsPublishCoreTemplates { dependsOn jalviewjsBuildAllCores def inputFileName = "${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}_${cl.name}.html" cl['outputfile'] = outputFile outputFiles += outputFile } @@ -3379,13 +3517,13 @@ task jalviewjsSyncCore (type: Sync) { dependsOn jalviewjsBuildAllCores dependsOn jalviewjsPublishCoreTemplates def inputFiles = fileTree(dir: "${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 {