X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=df1f5cd00d1092ec11c9d438e6fc1e0beac96fbc;hb=9ba4d4c0690650d114a7a772b902596f05daaa46;hp=84b84e74217bc4f908865c90d9a49e581e743acf;hpb=0361b476db64be2e75318999b2cbe2c8f2e26296;p=jalview.git diff --git a/build.gradle b/build.gradle index 84b84e7..df1f5cd 100644 --- a/build.gradle +++ b/build.gradle @@ -10,6 +10,11 @@ import org.gradle.plugins.ide.eclipse.model.Output import org.gradle.plugins.ide.eclipse.model.Library import java.security.MessageDigest import java.util.regex.Matcher +import java.util.concurrent.Executors +import java.util.concurrent.Future +import java.util.concurrent.ScheduledExecutorService +import java.util.concurrent.TimeUnit +import java.nio.file.Path import groovy.transform.ExternalizeMethods import groovy.util.XmlParser import groovy.xml.XmlUtil @@ -48,9 +53,9 @@ plugins { id 'application' id 'eclipse' id "com.diffplug.gradle.spotless" version "3.28.0" - id 'com.github.johnrengelman.shadow' version '4.0.3' + id 'com.github.johnrengelman.shadow' version '6.0.0' id 'com.install4j.gradle' version '10.0.3' - id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree + id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree id 'com.palantir.git-version' version '0.13.0' apply false } @@ -67,39 +72,48 @@ def string(Object o) { return o == null ? "" : o.toString() } -def overrideProperties(String propsFileName, boolean output = false) { - if (propsFileName == null) { - return - } +def Properties readPropertiesFile(String propsFileName) { + def p = null def propsFile = file(propsFileName) if (propsFile != null && propsFile.exists()) { println("Using properties from file '${propsFileName}'") try { - def p = new Properties() + p = new Properties() def localPropsFIS = new FileInputStream(propsFile) p.load(localPropsFIS) localPropsFIS.close() - p.each { - key, val -> - def oldval - if (project.hasProperty(key)) { - oldval = project.findProperty(key) - project.setProperty(key, val) - if (output) { - println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'") - } - } else { - ext.setProperty(key, val) - if (output) { - println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'") - } - } - } } catch (Exception e) { - println("Exception reading local.properties") + println("Exception reading properties file '${propsFileName}'") e.printStackTrace() } } + return p +} + +def overrideProperties(String propsFileName, boolean output = false) { + if (propsFileName == null) { + return + } + def propsFile = file(propsFileName) + if (propsFile != null && propsFile.exists()) { + println("Using properties from file '${propsFileName}'") + def p = readPropertiesFile(propsFileName) + p.each { key, 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 { + ext.setProperty(key, val) + if (output) { + println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'") + } + } + } + } } ext { @@ -118,12 +132,14 @@ ext { channelDir = string("${jalviewDir}/${channel_properties_dir}/${channelDirName}") channelGradleProperties = string("${channelDir}/channel_gradle.properties") channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}") + localProperties = "local.properties" + localEclipseProperties = "local_eclipse.properties" overrideProperties(channelGradleProperties, false) // local build environment properties // can be "projectDir/local.properties" - overrideProperties("${projectDir}/local.properties", true) + overrideProperties("${projectDir}/${localProperties}", true) // or "../projectDir_local.properties" - overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true) + overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_${localProperties}", true) //// // Import releaseProps from the RELEASE file @@ -555,11 +571,12 @@ ext { if (IN_ECLIPSE) { jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir) } else { - jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js") + jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/sitejs") } - jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib") - jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs") - jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core") + jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/lib") + jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/swingjs") + jalviewjsTransferSiteMergeDir = string("${jalviewjsBuildDir}/merge/${jalviewjs_site_dir}") + jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}/core") jalviewjsJalviewCoreHtmlFile = string("") jalviewjsJalviewCoreName = string(jalviewjs_core_name) jalviewjsCoreClasslists = [] @@ -568,11 +585,19 @@ ext { jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}") jalviewjsJ2sProps = null jalviewjsJ2sPlugin = jalviewjs_j2s_plugin + jalviewjsStderrLaunchFilename = "${jalviewjsSiteDir}/"+(file(jalviewjs_stderr_launch).getName()) + closureCompilerJar = "${jalviewDir}/${jalviewjs_closure_compiler}" + eclipseWorkspace = null eclipseBinary = string("") eclipseVersion = string("") + eclipseProductVersion = string("") eclipseDebug = false + + jalviewjsChromiumUserDir = "${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}" + jalviewjsChromiumProfileDir = "${ext.jalviewjsChromiumUserDir}/${jalviewjs_chromium_profile_name}" + // ENDEXT } @@ -770,6 +795,20 @@ eclipse { } } } + // local eclipse settings + def localEclipsePropertiesFile = file("${jalviewDirAbsolutePath}/${localEclipseProperties}") + if (localEclipsePropertiesFile.exists()) { + def eclipse_prefs = new Properties() + def ins2 = new FileInputStream(localEclipsePropertiesFile) + println("Loading Eclipse Preferences from '${localEclipsePropertiesFile}'") + eclipse_prefs.load(ins2) + ins2.close() + eclipse_prefs.forEach { t, v -> + props.putAt(t, v) + } + } else { + println("No local Eclipse Preferences file '${localEclipsePropertiesFile}'") + } } } @@ -1064,7 +1103,7 @@ compileJava { // JBP->BS should the print statement in doFirst refer to compile_target_compatibility ? sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args + options.compilerArgs += additional_compiler_args options.encoding = "UTF-8" doFirst { print ("Setting target compatibility to "+compile_target_compatibility+"\n") @@ -1076,7 +1115,7 @@ compileJava { compileTestJava { sourceCompatibility = compile_source_compatibility targetCompatibility = compile_target_compatibility - options.compilerArgs = additional_compiler_args + options.compilerArgs += additional_compiler_args doFirst { print ("Setting target compatibility to "+targetCompatibility+"\n") } @@ -1732,36 +1771,142 @@ task prepare { compileJava.dependsOn prepare run.dependsOn compileJava -//run.dependsOn prepare +compileTestJava.dependsOn compileJava + -//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir test { - dependsOn prepare + group = "Verification" + description = "Runs all testTaskN tasks)" if (useClover) { dependsOn cloverClasses - } else { //? - dependsOn compileJava //? + } else { //? + dependsOn testClasses + } + + // not running tests in this task + exclude "**/*" +} +/* testTask0 is the main test task */ +task testTask0(type: Test) { + group = "Verification" + description = "The main test task. Runs all non-testTaskN-labelled tests (unless excluded)" + useTestNG() { + includeGroups testng_groups.split(",") + excludeGroups testng_excluded_groups.split(",") + tasks.withType(Test).matching {it.name.startsWith("testTask") && it.name != name}.all {t -> excludeGroups t.name} + preserveOrder true + useDefaultListeners=true } +} +/* separated tests */ +task testTask1(type: Test) { + group = "Verification" + description = "Tests that need to be isolated from the main test run" useTestNG() { - includeGroups testng_groups - excludeGroups testng_excluded_groups + includeGroups name + excludeGroups testng_excluded_groups.split(",") preserveOrder true useDefaultListeners=true } +} - maxHeapSize = "4096m" - jvmArgs '-Xmx4096m', '-Xms4096m' +task testTask2(type: Test) { + group = "Verification" + description = "Tests that need to be isolated from the main test run" + useTestNG() { + includeGroups name + excludeGroups testng_excluded_groups.split(",") + preserveOrder true + useDefaultListeners=true + } +} +task testTask3(type: Test) { + group = "Verification" + description = "Tests that need to be isolated from the main test run" + useTestNG() { + includeGroups name + excludeGroups testng_excluded_groups.split(",") + preserveOrder true + useDefaultListeners=true + } +} -/* delete these! - maxParallelForks = 1 - forkEvery = 1 - failFast = true - jvmArgs '-Xmx2048m', '-Xms2048m' +/* insert more testTaskNs here -- change N to next digit or other string */ +/* +task testTaskN(type: Test) { + group = "Verification" + description = "Tests that need to be isolated from the main test run" + useTestNG() { + includeGroups name + excludeGroups testng_excluded_groups.split(",") + preserveOrder true + useDefaultListeners=true + } +} */ +/* + * adapted from https://medium.com/@wasyl/pretty-tests-summary-in-gradle-744804dd676c + * to summarise test results from all Test tasks + */ +/* START of test tasks results summary */ +import groovy.time.TimeCategory +import org.gradle.api.tasks.testing.logging.TestExceptionFormat +import org.gradle.api.tasks.testing.logging.TestLogEvent +rootProject.ext.testsResults = [] // Container for tests summaries + +tasks.withType(Test).matching {t -> t.getName().startsWith("testTask")}.all { testTask -> + + // from original test task + if (useClover) { + dependsOn cloverClasses + } else { //? + dependsOn testClasses //? + } + + // run main tests first + if (!testTask.name.equals("testTask0")) + testTask.mustRunAfter "testTask0" + + testTask.testLogging { logging -> + events TestLogEvent.FAILED +// TestLogEvent.SKIPPED, +// TestLogEvent.STANDARD_OUT, +// TestLogEvent.STANDARD_ERROR + + exceptionFormat TestExceptionFormat.FULL + showExceptions true + showCauses true + showStackTraces true + if (test_output) { + showStandardStreams true + } + info.events = [ TestLogEvent.FAILED ] + } + + if (OperatingSystem.current().isMacOsX()) { + testTask.systemProperty "apple.awt.UIElement", "true" + testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true" + } + + + ignoreFailures = true // Always try to run all tests for all modules + + afterSuite { desc, result -> + if (desc.parent) + return // Only summarize results for whole modules + + def resultsInfo = [testTask.project.name, testTask.name, result, TimeCategory.minus(new Date(result.endTime), new Date(result.startTime)), testTask.reports.html.entryPoint] + + rootProject.ext.testsResults.add(resultsInfo) + } + + // from original test task + maxHeapSize = "1024m" + workingDir = jalviewDir def testLaf = project.findProperty("test_laf") if (testLaf != null) { @@ -1778,11 +1923,143 @@ test { jvmArgs += additional_compiler_args doFirst { + // this is not perfect yet -- we should only add the commandLineIncludePatterns to the + // testTasks that include the tests, and exclude all from the others. + // get --test argument + filter.commandLineIncludePatterns = test.filter.commandLineIncludePatterns + // do something with testTask.getCandidateClassFiles() to see if the test should silently finish because of the + // commandLineIncludePatterns not matching anything. Instead we are doing setFailOnNoMatchingTests(false) below + + if (useClover) { println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover") } } + + + /* don't fail on no matching tests (so --tests will run across all testTasks) */ + testTask.filter.setFailOnNoMatchingTests(false) + + /* ensure the "test" task dependsOn all the testTasks */ + test.dependsOn testTask +} + +gradle.buildFinished { + def allResults = rootProject.ext.testsResults + + if (!allResults.isEmpty()) { + printResults allResults + allResults.each {r -> + if (r[2].resultType == TestResult.ResultType.FAILURE) + throw new GradleException("Failed tests!") + } + } +} + +private static String colString(styler, col, colour, text) { + return col?"${styler[colour](text)}":text +} + +private static String getSummaryLine(s, pn, tn, rt, rc, rs, rf, rsk, t, col) { + def colour = 'black' + def text = rt + def nocol = false + if (rc == 0) { + text = "-----" + nocol = true + } else { + switch(rt) { + case TestResult.ResultType.SUCCESS: + colour = 'green' + break; + case TestResult.ResultType.FAILURE: + colour = 'red' + break; + default: + nocol = true + break; + } + } + StringBuilder sb = new StringBuilder() + sb.append("${pn}") + if (tn != null) + sb.append(":${tn}") + sb.append(" results: ") + sb.append(colString(s, col && !nocol, colour, text)) + sb.append(" (") + sb.append("${rc} tests, ") + sb.append(colString(s, col && rs > 0, 'green', rs)) + sb.append(" successes, ") + sb.append(colString(s, col && rf > 0, 'red', rf)) + sb.append(" failures, ") + sb.append("${rsk} skipped) in ${t}") + return sb.toString() +} + +private static void printResults(allResults) { + + // styler from https://stackoverflow.com/a/56139852 + def styler = 'black red green yellow blue magenta cyan white'.split().toList().withIndex(30).collectEntries { key, val -> [(key) : { "\033[${val}m${it}\033[0m" }] } + + def maxLength = 0 + def failedTests = false + def summaryLines = [] + def totalcount = 0 + def totalsuccess = 0 + def totalfail = 0 + def totalskip = 0 + def totaltime = TimeCategory.getSeconds(0) + // sort on project name then task name + allResults.sort {a, b -> a[0] == b[0]? a[1]<=>b[1]:a[0] <=> b[0]}.each { + def projectName = it[0] + def taskName = it[1] + def result = it[2] + def time = it[3] + def report = it[4] + def summaryCol = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, true) + def summaryPlain = getSummaryLine(styler, projectName, taskName, result.resultType, result.testCount, result.successfulTestCount, result.failedTestCount, result.skippedTestCount, time, false) + def reportLine = "Report file: ${report}" + def ls = summaryPlain.length() + def lr = reportLine.length() + def m = [ls, lr].max() + if (m > maxLength) + maxLength = m + def info = [ls, summaryCol, reportLine] + summaryLines.add(info) + failedTests |= result.resultType == TestResult.ResultType.FAILURE + totalcount += result.testCount + totalsuccess += result.successfulTestCount + totalfail += result.failedTestCount + totalskip += result.skippedTestCount + totaltime += time + } + def totalSummaryCol = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, true) + def totalSummaryPlain = getSummaryLine(styler, "OVERALL", "", failedTests?TestResult.ResultType.FAILURE:TestResult.ResultType.SUCCESS, totalcount, totalsuccess, totalfail, totalskip, totaltime, false) + def tls = totalSummaryPlain.length() + if (tls > maxLength) + maxLength = tls + def info = [tls, totalSummaryCol, null] + summaryLines.add(info) + + def allSummaries = [] + for(sInfo : summaryLines) { + def ls = sInfo[0] + def summary = sInfo[1] + def report = sInfo[2] + + StringBuilder sb = new StringBuilder() + sb.append("│" + summary + " " * (maxLength - ls) + "│") + if (report != null) { + sb.append("\n│" + report + " " * (maxLength - report.length()) + "│") + } + allSummaries += sb.toString() + } + + println "┌${"${"─" * maxLength}"}┐" + println allSummaries.join("\n├${"${"─" * maxLength}"}┤\n") + println "└${"${"─" * maxLength}"}┘" } +/* END of test tasks results summary */ task compileLinkCheck(type: JavaCompile) { @@ -1903,22 +2180,56 @@ task cleanDist { } +task launcherJar(type: Jar) { + manifest { + attributes ( + "Main-Class": shadow_jar_main_class, + "Implementation-Version": JALVIEW_VERSION, + "Application-Name": applicationName + ) + } +} + shadowJar { group = "distribution" description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar" if (buildDist) { dependsOn makeDist } - from ("${jalviewDir}/${libDistDir}") { - include("*.jar") - } + + def jarFiles = fileTree(dir: "${jalviewDir}/${libDistDir}", include: "*.jar", exclude: "regex.jar").getFiles() + def groovyJars = jarFiles.findAll {it1 -> file(it1).getName().startsWith("groovy-swing")} + def otherJars = jarFiles.findAll {it2 -> !file(it2).getName().startsWith("groovy-swing")} + from groovyJars + from otherJars + manifest { - attributes "Implementation-Version": JALVIEW_VERSION, - "Application-Name": applicationName + // shadowJar manifest must inheritFrom another Jar task. Can't set attributes here. + inheritFrom(project.tasks.launcherJar.manifest) + } + // we need to include the groovy-swing Include-Package for it to run in the shadowJar + doFirst { + def jarFileManifests = [] + groovyJars.each { jarFile -> + def mf = zipTree(jarFile).getFiles().find { it.getName().equals("MANIFEST.MF") } + if (mf != null) { + jarFileManifests += mf + } + } + manifest { + from (jarFileManifests) { + eachEntry { details -> + if (!details.key.equals("Import-Package")) { + details.exclude() + } + } + } + } } duplicatesStrategy "INCLUDE" + // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead mainClassName = shadow_jar_main_class mergeServiceFiles() classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION @@ -1972,9 +2283,9 @@ task getdownImages() { dependsOn getdownImagesProcess } -task getdownWebsite() { +task getdownWebsiteBuild() { group = "distribution" - description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer" + description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer. No digest is created." dependsOn getdownImages if (buildDist) { @@ -2026,8 +2337,8 @@ task getdownWebsite() { props.put("getdown_txt_ui.instant_background_image", "${getdownImagesBuildDir}/${getdown_instant_background_image}") props.put("getdown_txt_ui.error_background", "${getdownImagesBuildDir}/${getdown_error_background}") props.put("getdown_txt_ui.progress_image", "${getdownImagesBuildDir}/${getdown_progress_image}") - props.put("getdown_txt_ui.icon", "${getdownImagesBuildDir}/${getdown_icon}") - props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesBuildDir}/${getdown_mac_dock_icon}") + props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}") + props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}") } props.put("getdown_txt_title", jalview_name) @@ -2086,7 +2397,7 @@ task getdownWebsite() { from s into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}" } - getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}" + getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${script}" } } @@ -2228,7 +2539,9 @@ task getdownDigestDir(type: JavaExec) { task getdownDigest(type: JavaExec) { group = "distribution" description = "Digest the getdown website folder" - dependsOn getdownWebsite + + dependsOn getdownWebsiteBuild + doFirst { classpath = files(getdownLauncher) } @@ -2261,12 +2574,19 @@ task getdown() { } } +task getdownWebsite { + group = "distribution" + description = "A task to create the whole getdown channel website dir including digest file" + + dependsOn getdownWebsiteBuild + dependsOn getdownDigest +} task getdownArchiveBuild() { group = "distribution" description = "Put files in the archive dir to go on the website" - dependsOn getdownWebsite + dependsOn getdownWebsiteBuild def v = "v${JALVIEW_VERSION_UNDERSCORES}" def vDir = "${getdownArchiveDir}/${v}" @@ -2576,6 +2896,7 @@ task installerFiles(type: com.install4j.gradle.Install4jTask) { 'WRAPPER_LINK': getdownWrapperLink, 'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script, 'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script, + 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script, 'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir, 'INSTALLER_NAME': install4jInstallerName, 'INSTALL4J_UTILS_DIR': install4j_utils_dir, @@ -2775,6 +3096,7 @@ task sourceDist(type: Tar) { into project.name def EXCLUDE_FILES=[ + "dist/*", "build/*", "bin/*", "test-output/", @@ -2954,12 +3276,14 @@ task jalviewjsEnableAltFileProperty(type: WriteProperties) { task jalviewjsSetEclipseWorkspace { def propKey = "jalviewjs_eclipse_workspace" def propVal = null + // see if jalviewjs_eclipse_workspace is set by a property if (project.hasProperty(propKey)) { propVal = project.getProperty(propKey) if (propVal.startsWith("~/")) { propVal = System.getProperty("user.home") + propVal.substring(1) } } + // else look for an existing build/jalviewjs/eclipse_workspace_location file def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}" def propsFile = file(propsFileName) def eclipseWsDir = propVal @@ -3008,13 +3332,14 @@ task jalviewjsSetEclipseWorkspace { } //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date - outputs.file(propsFileName) - outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() } + //outputs.file(propsFileName) // don't want this to be deleted because of falsely "stale" task + outputs.upToDateWhen { eclipseWorkspace.exists() && (propsFile.exists() || !writeProps) } } task jalviewjsEclipsePaths { - def eclipseProduct + def eclipseProductFile + def eclipseSetupLog def eclipseRoot = jalviewjs_eclipse_root if (eclipseRoot.startsWith("~/")) { @@ -3023,32 +3348,49 @@ task jalviewjsEclipsePaths { if (OperatingSystem.current().isMacOsX()) { eclipseRoot += "/Eclipse.app" eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse" - eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" + eclipseProductFile = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" + eclipseSetupLog = "${eclipseRoot}/Contents/Eclipse/configuration/org.eclipse.oomph.setup/setup.log" } else if (OperatingSystem.current().isWindows()) { // check these paths!! if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" } eclipseBinary = "${eclipseRoot}/eclipse.exe" - eclipseProduct = "${eclipseRoot}/.eclipseproduct" + eclipseProductFile = "${eclipseRoot}/.eclipseproduct" + eclipseSetupLog = "${eclipseRoot}/configuration/org.eclipse.oomph.setup/setup.log" } else { // linux or unix if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" -println("eclipseDir exists") } eclipseBinary = "${eclipseRoot}/eclipse" - eclipseProduct = "${eclipseRoot}/.eclipseproduct" + eclipseProductFile = "${eclipseRoot}/.eclipseproduct" + eclipseSetupLog = "${eclipseRoot}/configuration/org.eclipse.oomph.setup/setup.log" } - eclipseVersion = "4.13" // default + eclipseVersion = "unknown" // default def assumedVersion = true - if (file(eclipseProduct).exists()) { - def fis = new FileInputStream(eclipseProduct) + if (file(eclipseProductFile).exists()) { + def fis = new FileInputStream(eclipseProductFile) def props = new Properties() props.load(fis) eclipseVersion = props.getProperty("version") fis.close() assumedVersion = false } + if (file(eclipseSetupLog).exists()) { + def productRegex = /(?m)^\[[^\]]+\]\s+Product\s+(org\.eclipse.\S*)/ + int lineCount = 0 + file(eclipseSetupLog).eachLine { String line -> + def matcher = line =~ productRegex + if (matcher.size() > 0) { + eclipseProductVersion = matcher[0][1] + return true + } + if (lineCount >= 100) { + return true + } + lineCount++ + } + } def propKey = "eclipse_debug" eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true")) @@ -3064,6 +3406,9 @@ println("eclipseDir exists") if (!assumedVersion) { println("ECLIPSE VERSION=${eclipseVersion}") + if (eclipseProductVersion.length() != 0) { + println("ECLIPSE PRODUCT=${eclipseProductVersion}") + } } } } @@ -3123,41 +3468,37 @@ jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse */ -task jalviewjsTransferUnzipSwingJs { - def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}" - - doLast { - copy { - from zipTree(file_zip) - into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" - } - } +task jalviewjsTransferUnzipSwingJs(type: Copy) { + def swingJsZipFile = "${jalviewDir}/${jalviewjs_swingjs_zip}" + from zipTree( "${jalviewDir}/${jalviewjs_swingjs_zip}" ) + into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" - inputs.file file_zip - outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}" + inputs.file swingJsZipFile } -task jalviewjsTransferUnzipLib { - def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip") +task jalviewjsTransferUnzipLib(type: Copy) { + def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip").sort() - doLast { - zipFiles.each { file_zip -> - copy { - from zipTree(file_zip) - into "${jalviewDir}/${jalviewjsTransferSiteLibDir}" + zipFiles.each { file_zip -> + from zipTree(file_zip) + + // The following replace() is needed due to a mismatch in Jmol calls to + // colorPtToFFRGB$javajs_util_T3d when only colorPtToFFRGB$javajs_util_T3 is defined + // in the SwingJS.zip (github or the one distributed with JSmol) + if (file_zip.getName().startsWith("Jmol-SwingJS")) { + filter { line -> + def l = "" + while(!line.equals(l)) { + line = line.replace('colorPtToFFRGB$javajs_util_T3d', 'colorPtToFFRGB$javajs_util_T3') + l = line + } + return line } } - } - - inputs.files zipFiles - outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}" -} - -task jalviewjsTransferUnzipAllLibs { - dependsOn jalviewjsTransferUnzipSwingJs - dependsOn jalviewjsTransferUnzipLib + } + into "${jalviewDir}/${jalviewjsTransferSiteLibDir}" } @@ -3186,7 +3527,6 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { if (! IN_ECLIPSE) { inputs.properties(jalviewjsJ2sProps) - outputs.file(jalviewjsJ2sAltSettingsFileName) } } @@ -3198,46 +3538,81 @@ task jalviewjsEclipseSetup { } -task jalviewjsSyncAllLibs (type: Sync) { - dependsOn jalviewjsTransferUnzipAllLibs - def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}") - inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") +task jalviewjsSyncLibs (type: Sync) { + dependsOn jalviewjsTransferUnzipLib + dependsOn jalviewjsTransferUnzipSwingJs + + def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteLibDir}") + def inputFiles = fileTree(dir: inputDir) def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" from inputFiles into outputDir def outputFiles = [] - rename { filename -> - outputFiles += "${outputDir}/${filename}" - null + inputFiles.each{ file -> + def rfile = inputDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputDir}/${rfile}") + outputFiles += "${ofile}" } preserve { - include "**" + include "**/*" + } + + duplicatesStrategy "EXCLUDE" + + outputs.files outputFiles + inputs.files inputFiles +} + +task jalviewjsSyncSwingJS (type: Sync) { + dependsOn jalviewjsTransferUnzipSwingJs + mustRunAfter jalviewjsSyncLibs + + def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}") + def inputFiles = fileTree(dir: inputDir) + def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" + + from inputFiles + into outputDir + def outputFiles = [] + inputFiles.each{ file -> + def rfile = inputDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputDir}/${rfile}") + outputFiles += "${ofile}" + } + preserve { + include "**/*" } - // should this be exclude really ? duplicatesStrategy "INCLUDE" outputs.files outputFiles inputs.files inputFiles } +task jalviewjsSyncAllLibs { + dependsOn jalviewjsSyncLibs + dependsOn jalviewjsSyncSwingJS +} + task jalviewjsSyncResources (type: Sync) { dependsOn buildResources - def inputFiles = fileTree(dir: resourcesBuildDir) + def inputDir = file(resourcesBuildDir) + def inputFiles = fileTree(dir: inputDir) def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" from inputFiles into outputDir def outputFiles = [] - rename { filename -> - outputFiles += "${outputDir}/${filename}" - null + inputFiles.each{ file -> + def rfile = inputDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputDir}/${rfile}") + outputFiles += "${ofile}" } preserve { - include "**" + include "**/*" } outputs.files outputFiles inputs.files inputFiles @@ -3245,19 +3620,22 @@ task jalviewjsSyncResources (type: Sync) { task jalviewjsSyncSiteResources (type: Sync) { - def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}") + def inputDir = file("${jalviewDir}/${jalviewjs_site_resource_dir}") + def inputFiles = fileTree(dir: inputDir) def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" from inputFiles into outputDir def outputFiles = [] - rename { filename -> - outputFiles += "${outputDir}/${filename}" - null + inputFiles.each{ file -> + def rfile = inputDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputDir}/${rfile}") + outputFiles += "${ofile}" } preserve { - include "**" + include "**/*" } + outputs.files outputFiles inputs.files inputFiles } @@ -3265,19 +3643,24 @@ task jalviewjsSyncSiteResources (type: Sync) { task jalviewjsSyncBuildProperties (type: Sync) { dependsOn createBuildProperties - def inputFiles = [file(buildProperties)] + + def f = file(buildProperties) + def inputDir = f.getParentFile() + def inputFiles = [f] def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" from inputFiles into outputDir def outputFiles = [] - rename { filename -> - outputFiles += "${outputDir}/${filename}" - null + inputFiles.each{ file -> + def rfile = inputDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputDir}/${rfile}") + outputFiles += "${ofile}" } preserve { - include "**" + include "**/*" } + outputs.files outputFiles inputs.files inputFiles } @@ -3299,7 +3682,8 @@ task jalviewjsProjectImport(type: Exec) { } //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" - def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview" + def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/${eclipse_project_name}" + executable(eclipseBinary) args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath]) if (eclipseDebug) { @@ -3309,19 +3693,22 @@ task jalviewjsProjectImport(type: Exec) { if (!IN_ECLIPSE) { args += [ "-D${j2sHeadlessBuildProperty}=true" ] args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ] + inputs.file("${jalviewjsJ2sAltSettingsFileName}") } - inputs.file("${jalviewDir}/.project") - outputs.upToDateWhen { - file(projdir).exists() - } + outputs.upToDateWhen( { + if (IN_ECLIPSE) { + return true + } + def projDirExists = file(projdir).exists() + return projDirExists + } ) } - +// jalviewjs_eclipse_workspace_location_file task jalviewjsTranspile(type: Exec) { - dependsOn jalviewjsEclipseSetup dependsOn jalviewjsProjectImport - dependsOn jalviewjsEclipsePaths + if (!IN_ECLIPSE) { dependsOn jalviewjsEnableAltFileProperty } @@ -3356,11 +3743,12 @@ task jalviewjsTranspile(type: Exec) { def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}" def logOutFile = file(logOutFileName) logOutFile.createNewFile() - logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} -BINARY: ${eclipseBinary} -VERSION: ${eclipseVersion} -WORKSPACE: ${eclipseWorkspace} -DEBUG: ${eclipseDebug} + def info = """ROOT: ${jalviewjs_eclipse_root} +ECLIPSE BINARY: ${eclipseBinary} +ECLIPSE VERSION: ${eclipseVersion} +ECLIPSE PRODUCT: ${eclipseProductVersion} +ECLIPSE WORKSPACE: ${eclipseWorkspace} +ECLIPSE DEBUG: ${eclipseDebug} ---- """ def logOutFOS = new FileOutputStream(logOutFile, true) // true == append @@ -3386,12 +3774,58 @@ DEBUG: ${eclipseDebug} logErrFOS, stderr) } + standardOutput.write(string(info).getBytes("UTF-8")) } doLast { - if (stdout.toString().contains("Error processing ")) { + def transpileError = false + def j2sIsActive = false + def j2sBuildStarting = false + def compilingLines = 0 + def j2sBuildingJavascript = false + def j2sBuildingJavascriptRegex = /(?m)^J2S building JavaScript for (\d+) files/ + def numFiles = 0 + def transpilingLines = 0 + stdout.toString().eachLine { String line -> + if (line.startsWith("J2S isActive true")) { + j2sIsActive = true + } + if (line.startsWith("J2S buildStarting")) { + j2sBuildStarting = true + } + if (line =~ / Compiling /) { + compilingLines++ + } + if (!j2sBuildingJavascript) { + def matcher = line =~ j2sBuildingJavascriptRegex + if (matcher.size() > 0) { + numFiles = Integer.valueOf(matcher[0][1]) + j2sBuildingJavascript = true + } + } + if (line.startsWith("J2S transpiling ")) { + transpilingLines++ + } + if (line.contains("Error processing ")) { + transpileError = true + } + } + + println("J2S IS ACTIVE=${j2sIsActive}") + println("J2S BUILD STARTING=${j2sBuildStarting}") + println("J2S BUILDING JAVASCRIPT=${j2sBuildingJavascript}") + println("NUM FILES=${numFiles}") + println("COMPILING LINES=${compilingLines}") + println("TRANSPILING LINES=${transpilingLines}") + println("TRANSPILE ERROR=${transpileError}") + + if (!j2sIsActive + || transpileError + || (j2sBuildStarting && transpilingLines == 0) + || (transpilingLines < compilingLines) + || (transpilingLines != numFiles) + ) { // j2s did not complete transpile - //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") if (jalviewjs_ignore_transpile_errors.equals("true")) { println("IGNORING TRANSPILE ERRORS") println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'") @@ -3401,9 +3835,127 @@ DEBUG: ${eclipseDebug} } } + if (IN_ECLIPSE) { + inputs.file(jalviewjsJ2sSettingsFileName) + } else { + inputs.file(jalviewjsJ2sAltSettingsFileName) + } inputs.dir("${jalviewDir}/${sourceDir}") - outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}") - outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } ) + + def inputJavaDir = file("${jalviewDir}/${sourceDir}") + def inputJavaFiles = fileTree(dir: inputJavaDir) + def outputJsDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}" + def outputJsFiles = [] + inputJavaFiles.each{ file -> + def rfile = inputJavaDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputJsDir}/${rfile}") + def ofilenamejs = ofile.getPath() + if (ofilenamejs.endsWith(".java")) { + ofilenamejs = ofilenamejs.substring(0,ofilenamejs.length()-4)+"js" + } + outputJsFiles += "${ofilenamejs}" + } + + outputs.files outputJsFiles + outputs.file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}") +} + + +task jalviewjsTransferSiteMergeSiteJsDir (type: Copy) { + dependsOn jalviewjsTranspile + + def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteJsDir}") + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}" + into outputDir + from { + def inputFiles = fileTree(dir: inputDir) + return inputFiles + } + + includeEmptyDirs = false + exclude "**/*.html" + exclude "**/*.htm" + + // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite) + duplicatesStrategy "INCLUDE" + + // SiteJs files should take priority and write over existing files if different + // so we define the output files + outputs.upToDateWhen( + { + def transpiledFiles = jalviewjsTransferSiteMergeSiteJsDir.getOutputs().getFiles() + def inputFiles = fileTree(dir: inputDir) + if (inputFiles.size() < transpiledFiles.size()) { + return false + } + def retVal = ! inputFiles.any { file -> + def rfile = inputDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputDir}/${rfile}") + if (!ofile.exists() || ofile.lastModified() < file.lastModified()) { + return true // this is NOTted to false + } + } + + return retVal + } + ) + + inputs.files jalviewjsTranspile +} + +task jalviewjsTransferSiteMergeLibDir (type: Copy) { + dependsOn jalviewjsTransferUnzipLib + + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}" + + // This takes the outputs of jalviewjsTransferUnzipLib + from jalviewjsTransferUnzipLib + into outputDir + + includeEmptyDirs = false + exclude "**/*.html" + exclude "**/*.htm" + + // don't overwrite files in the destination + // Note, this closure gets run at run stage not config stage + eachFile { + if (it.getRelativePath().getFile(file(outputDir)).exists()) { + it.exclude() + } + } + + duplicatesStrategy "INCLUDE" +} + +task jalviewjsTransferSiteMergeSwingJsDir (type: Copy) { + dependsOn jalviewjsTransferUnzipSwingJs + + def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}" + + // This takes the outputs of jalviewjsTransferUnzipSwingJs + from jalviewjsTransferUnzipSwingJs + into outputDir + + includeEmptyDirs = false + exclude "**/*.html" + exclude "**/*.htm" + + // DO overwrite files in the destination + + // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite) + duplicatesStrategy "INCLUDE" +} + +// we run after SiteJs and exclude overwriting files +jalviewjsTransferSiteMergeLibDir.mustRunAfter jalviewjsTransferSiteMergeSiteJsDir +jalviewjsTransferSiteMergeLibDir.mustRunAfter jalviewjsTransferSiteMergeSwingJsDir +// we run this last, overwriting files from sitejs and lib, to ensure a consistent SwingJS +jalviewjsTransferSiteMergeSwingJsDir.mustRunAfter jalviewjsTransferSiteMergeSiteJsDir + +task jalviewjsTransferSiteMergeDirs { + dependsOn jalviewjsTransferSiteMergeLibDir + dependsOn jalviewjsTransferSiteMergeSwingJsDir + dependsOn jalviewjsTransferSiteMergeSiteJsDir } @@ -3421,6 +3973,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin def coreTop = file(prefixFile) def coreBottom = file(suffixFile) + def missingFiles = [] coreFile.getParentFile().mkdirs() coreFile.createNewFile() coreFile.write( coreTop.getText("UTF-8") ) @@ -3434,6 +3987,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin msg = "...file '"+f.getPath()+"' does not exist, skipping" println(msg) logOutFile.append(msg+"\n") + missingFiles += f } } coreFile.append( coreBottom.getText("UTF-8") ) @@ -3445,11 +3999,11 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin def logErrFOS = logOutFOS javaexec { - classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"]) + classpath = files([closureCompilerJar]) main = "com.google.javascript.jscomp.CommandLineRunner" jvmArgs = [ "-Dfile.encoding=UTF-8" ] - args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ] - maxHeapSize = "2g" + args = [ "--compilation_level", jalviewjs_closure_compiler_optimization_level, "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ] + maxHeapSize = "4g" msg = "\nRunning '"+commandLine.join(' ')+"'\n" println(msg) @@ -3476,21 +4030,25 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin } } msg = "--" + if (missingFiles.size() > 0) { + msg += "\n!!! These files were listed but missing:\n" + missingFiles.each { file -> msg += "!!! " + file.getPath() + "\n" } + msg = "--" + } println(msg) logOutFile.append(msg+"\n") } -task jalviewjsBuildAllCores { +task jalviewjsBuildCore { group "JalviewJS" description "Build the core js lib closures listed in the classlists dir" - dependsOn jalviewjsTranspile - dependsOn jalviewjsTransferUnzipSwingJs + dependsOn jalviewjsTransferSiteMergeDirs - def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}" - def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}" - def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}" - def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}" + def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}" + def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}" + def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}" + def jsDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_js_subdir}" def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core" def prefixFile = "${jsDir}/core/coretop2.js" def suffixFile = "${jsDir}/core/corebottom2.js" @@ -3509,8 +4067,7 @@ task jalviewjsBuildAllCores { ] } - // _jmol and _jalview cores. Add any other peculiar classlist.txt files here - //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ] + // _jalview core classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ] jalviewjsCoreClasslists = [] @@ -3551,65 +4108,18 @@ task jalviewjsBuildAllCores { outputs.file(zjsfile) } - // _stevesoft core. add any cores without a classlist here (and the inputs and outputs) - def stevesoftClasslistName = "_stevesoft" - def stevesoftClasslist = [ - 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js", - 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js", - 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"), - 'name': stevesoftClasslistName - ] - jalviewjsCoreClasslists += stevesoftClasslist - inputs.files(stevesoftClasslist['list']) - outputs.file(stevesoftClasslist['jsfile']) - outputs.file(stevesoftClasslist['zjsfile']) - - // _all core - def allClasslistName = "_all" - def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js") - allJsFiles += fileTree( - dir: libJ2sDir, - include: "**/*.js", - excludes: [ - // these exlusions are files that the closure-compiler produces errors for. Should fix them - "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js", - "**/org/jmol/export/JSExporter.js" - ] - ) - allJsFiles += fileTree( - dir: swingJ2sDir, - include: "**/*.js", - excludes: [ - // these exlusions are files that the closure-compiler produces errors for. Should fix them - "**/sun/misc/Unsafe.js", - "**/swingjs/jquery/jquery-editable-select.js", - "**/swingjs/jquery/j2sComboBox.js", - "**/sun/misc/FloatingDecimal.js" - ] - ) - def allClasslist = [ - 'jsfile': "${outputDir}/core${allClasslistName}.js", - 'zjsfile': "${outputDir}/core${allClasslistName}.z.js", - 'list': allJsFiles, - 'name': allClasslistName - ] - // not including this version of "all" core at the moment - //jalviewjsCoreClasslists += allClasslist - inputs.files(allClasslist['list']) - outputs.file(allClasslist['jsfile']) - outputs.file(allClasslist['zjsfile']) - doFirst { def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}") logOutFile.getParentFile().mkdirs() logOutFile.createNewFile() - logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n") + logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildCore\n----\n") jalviewjsCoreClasslists.each { jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true")) } } + inputs.file(closureCompilerJar) } @@ -3639,7 +4149,8 @@ def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inpu task jalviewjsPublishCoreTemplates { - dependsOn jalviewjsBuildAllCores + dependsOn jalviewjsBuildCore + def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}" def inputFile = file(inputFileName) def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}" @@ -3662,29 +4173,43 @@ task jalviewjsPublishCoreTemplates { task jalviewjsSyncCore (type: Sync) { - dependsOn jalviewjsBuildAllCores + dependsOn jalviewjsBuildCore dependsOn jalviewjsPublishCoreTemplates - def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}") + + def inputDir = file("${jalviewDir}/${jalviewjsTransferSiteCoreDir}") + def inputFiles = fileTree(dir: inputDir) def outputDir = "${jalviewDir}/${jalviewjsSiteDir}" from inputFiles into outputDir def outputFiles = [] - rename { filename -> - outputFiles += "${outputDir}/${filename}" - null + inputFiles.each{ file -> + def rfile = inputDir.toPath().relativize(file.toPath()) + def ofile = new File("${outputDir}/${rfile}") + outputFiles += "${ofile}" } preserve { - include "**" + include "**/*" } + outputs.files outputFiles inputs.files inputFiles } // this Copy version of TransferSiteJs will delete anything else in the target dir +task jalviewjsCopyTransferSiteMergeDir(type: Copy) { + dependsOn jalviewjsTransferSiteMergeDirs + + from "${jalviewDir}/${jalviewjsTransferSiteMergeDir}" + into "${jalviewDir}/${jalviewjsSiteDir}" +} + + +// this Copy version of TransferSiteJs will delete anything else in the target dir task jalviewjsCopyTransferSiteJs(type: Copy) { dependsOn jalviewjsTranspile + from "${jalviewDir}/${jalviewjsTransferSiteJsDir}" into "${jalviewDir}/${jalviewjsSiteDir}" } @@ -3696,7 +4221,7 @@ task jalviewjsSyncTransferSiteJs(type: Sync) { include "**/*.*" into "${jalviewDir}/${jalviewjsSiteDir}" preserve { - include "**" + include "**/*" } } @@ -3715,7 +4240,7 @@ jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs task jalviewjsPrepareSite { group "JalviewJS" description "Prepares the website folder including unzipping files and copying resources" - dependsOn jalviewjsSyncAllLibs + //dependsOn jalviewjsSyncAllLibs // now using jalviewjsCopyTransferSiteMergeDir dependsOn jalviewjsSyncResources dependsOn jalviewjsSyncSiteResources dependsOn jalviewjsSyncBuildProperties @@ -3726,7 +4251,7 @@ task jalviewjsPrepareSite { task jalviewjsBuildSite { group "JalviewJS" description "Builds the whole website including transpiled code" - dependsOn jalviewjsCopyTransferSiteJs + dependsOn jalviewjsCopyTransferSiteMergeDir dependsOn jalviewjsPrepareSite } @@ -3989,9 +4514,165 @@ task eclipseAutoBuildTask { } +task jalviewjsCopyStderrLaunchFile(type: Copy) { + from file(jalviewjs_stderr_launch) + into jalviewjsSiteDir + + inputs.file jalviewjs_stderr_launch + outputs.file jalviewjsStderrLaunchFilename +} + +task cleanJalviewjsChromiumUserDir { + doFirst { + delete jalviewjsChromiumUserDir + } + outputs.dir jalviewjsChromiumUserDir + // always run when depended on + outputs.upToDateWhen { !file(jalviewjsChromiumUserDir).exists() } +} + +task jalviewjsChromiumProfile { + dependsOn cleanJalviewjsChromiumUserDir + mustRunAfter cleanJalviewjsChromiumUserDir + + def firstRun = file("${jalviewjsChromiumUserDir}/First Run") + + doFirst { + mkdir jalviewjsChromiumProfileDir + firstRun.text = "" + } + outputs.file firstRun +} + +task jalviewjsLaunchTest { + group "Test" + description "Check JalviewJS opens in a browser" + dependsOn jalviewjsBuildSite + dependsOn jalviewjsCopyStderrLaunchFile + dependsOn jalviewjsChromiumProfile + + def macOS = OperatingSystem.current().isMacOsX() + def chromiumBinary = macOS ? jalviewjs_macos_chromium_binary : jalviewjs_chromium_binary + if (chromiumBinary.startsWith("~/")) { + chromiumBinary = System.getProperty("user.home") + chromiumBinary.substring(1) + } + + def stdout + def stderr + doFirst { + def timeoutms = Integer.valueOf(jalviewjs_chromium_overall_timeout) * 1000 + + def binary = file(chromiumBinary) + if (!binary.exists()) { + throw new StopExecutionException("Could not find chromium binary '${chromiumBinary}'. Cannot run task ${name}.") + } + stdout = new ByteArrayOutputStream() + stderr = new ByteArrayOutputStream() + def execStdout + def execStderr + if (jalviewjs_j2s_to_console.equals("true")) { + execStdout = new org.apache.tools.ant.util.TeeOutputStream( + stdout, + System.out) + execStderr = new org.apache.tools.ant.util.TeeOutputStream( + stderr, + System.err) + } else { + execStdout = stdout + execStderr = stderr + } + // macOS seems okay now with timeout arguments + def execArgs = [ + "--virtual-time-budget=${timeoutms}", + "--timeout=${timeoutms}", + ] + execArgs += [ + "--no-sandbox", // --no-sandbox IS USED BY THE THORIUM APPIMAGE ON THE BUILDSERVER + "--headless=new", + "--disable-gpu", + "--user-data-dir=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_chromium_user_dir}", + "--profile-directory=${jalviewjs_chromium_profile_name}", + "--allow-file-access-from-files", + "--enable-logging=stderr", + "file://${jalviewDirAbsolutePath}/${jalviewjsStderrLaunchFilename}" + ] + + java.lang.Runnable runChrome = () -> { + exec { + standardOutput = execStdout + errorOutput = execStderr + executable(chromiumBinary) + args(execArgs) + println "COMMAND: '"+commandLine.join(" ")+"'" + } + } + + if (macOS) { + // we create our own timeout executor as --timeout doesn't work on macOS + ScheduledExecutorService executor = Executors.newScheduledThreadPool(3); + + Future f1 = executor.submit( runChrome ) + + def noChangeBytes = 0 + def noChangeIterations = 0 + executor.scheduleAtFixedRate( + () -> { + String stderrString = stderr.toString() + // shutdown the task if we have a success string + if (stderrString.contains(jalviewjs_desktop_init_string)) { + f1.cancel(true) + Thread.sleep(100) + executor.shutdownNow() + } else + // if no change in stderr for 10s then also end + if (noChangeIterations >= jalviewjs_chromium_idle_timeout) { + executor.shutdownNow() + } + if (stderrString.length() == noChangeBytes) { + noChangeIterations++ + } else { + noChangeBytes = stderrString.length() + noChangeIterations = 0 + } + }, + 200, 200, TimeUnit.MILLISECONDS) + + executor.schedule(new Runnable(){ + public void run(){ + f1.cancel(true) + executor.shutdownNow() + } + }, timeoutms, TimeUnit.MILLISECONDS) + + executor.awaitTermination(timeoutms+200, TimeUnit.MILLISECONDS) + f1.cancel(true) + executor.shutdownNow() + } else { + // just run chrome and rely on --virtual-time-budget and --timeout + runChrome.run() + } + + } + + doLast { + def found = false + stderr.toString().eachLine { line -> + if (line.contains(jalviewjs_desktop_init_string)) { + println("Found line '"+line+"'") + found = true + return + } + } + if (!found) { + throw new GradleException("Could not find evidence of Desktop launch in JalviewJS.") + } + } +} + + task jalviewjs { group "JalviewJS" - description "Build the site" + description "Build the JalviewJS site and run the launch test" dependsOn jalviewjsBuildSite + dependsOn jalviewjsLaunchTest } -