From 5b0762e3dc0a6f9f782ec367353c6c408faa5d7b Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 24 Oct 2019 10:46:29 +0100
Subject: [PATCH] JAL-3210 Fixed cleaning tasks.

---
 build.gradle      |   81 ++++++++++++++++++++++++++++++++++++-----------------
 gradle.properties |    4 +--
 2 files changed, 57 insertions(+), 28 deletions(-)

diff --git a/build.gradle b/build.gradle
index c7d2311..63665a9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -509,12 +509,16 @@ compileCloverJava {
 }
 
 clean {
-  delete sourceSets.main.java.outputDir
+  doFirst {
+    delete sourceSets.main.java.outputDir
+  }
 }
 
 cleanTest {
-  delete sourceSets.test.java.outputDir
-  delete cloverInstrDir
+  doFirst {
+    delete sourceSets.test.java.outputDir
+    delete cloverInstrDir
+  }
 }
 
 // format is a string like date.format("dd MMMM yyyy")
@@ -560,12 +564,14 @@ task createBuildProperties(type: WriteProperties) {
 }
 
 def buildingHTML = "$jalviewDir/$docDir/building.html"
-task deleteBuildingHTML(type: Delete) {
-  delete buildingHTML
+task cleanBuildingHTML(type: Delete) {
+  doFirst {
+    delete buildingHTML
+  }
 }
 
 task convertBuildingMD(type: Exec) {
-  dependsOn deleteBuildingHTML
+  dependsOn cleanBuildingHTML
   def buildingMD = "$jalviewDir/$docDir/building.md"
   def css = "$jalviewDir/$docDir/github.css"
 
@@ -597,8 +603,11 @@ task convertBuildingMD(type: Exec) {
   inputs.file(css)
   outputs.file(buildingHTML)
 }
+
 clean {
-  delete buildingHTML
+  doFirst {
+    delete buildingHTML
+  }
 }
 
 task syncDocs(type: Sync) {
@@ -736,7 +745,9 @@ ant.importBuild "$utilsDir/publishHelp.xml"
 
 
 task cleanPackageDir(type: Delete) {
-  delete fileTree("$jalviewDir/$packageDir").include("*.jar")
+  doFirst {
+    delete fileTree("$jalviewDir/$packageDir").include("*.jar")
+  }
 }
 
 jar {
@@ -820,10 +831,6 @@ task getdownWebsite() {
     dependsOn makeDist
   }
 
-	// clean the getdown website and files dir before creating getdown folders
-	delete project.ext.getdownWebsiteDir
-	delete project.ext.getdownFilesDir
-
   def getdownWebsiteResourceFilenames = []
   def getdownTextString = ""
   def getdownResourceDir = project.ext.getdownResourceDir
@@ -831,6 +838,10 @@ task getdownWebsite() {
   def getdownResourceFilenames = []
 
   doFirst {
+    // clean the getdown website and files dir before creating getdown folders
+    delete project.ext.getdownWebsiteDir
+    delete project.ext.getdownFilesDir
+
     copy {
       from buildProperties
       rename(buildPropertiesFile, getdown_build_properties)
@@ -1027,8 +1038,10 @@ task getdown() {
 }
 
 clean {
-  delete project.ext.getdownWebsiteDir
-  delete project.ext.getdownFilesDir
+  doFirst {
+    delete project.ext.getdownWebsiteDir
+    delete project.ext.getdownFilesDir
+  }
 }
 
 install4j {
@@ -1144,7 +1157,9 @@ task installers(type: com.install4j.gradle.Install4jTask) {
 }
 
 clean {
-  delete install4jConf
+  doFirst {
+    delete install4jConf
+  }
 }
 
 task sourceDist (type: Tar) {
@@ -1347,7 +1362,7 @@ task jalviewjsEclipsePaths {
   } 
 }
 
-task jalviewjsEclipseCopyDropins {
+task OLDjalviewjsEclipseCopyDropins {
   dependsOn jalviewjsEclipsePaths
   def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+fromDropinsDir, include: "*.jar")
   def outputDir = eclipseDropinsDir
@@ -1368,6 +1383,12 @@ task jalviewjsEclipseCopyDropins {
   }
 }
 
+// this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
+task jalviewjsEclipseCopyDropins(type: Copy) {
+  from fromDropinsDir
+  into eclipseDropinsDir
+}
+
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   dependsOn jalviewjsSitePath
   outputFile (jalviewDir+"/"+jalviewjs_j2s_settings)
@@ -1388,6 +1409,7 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
       property(siteDirProperty,jalviewjsTransferSiteDir)
     }
   }
+  inputs.properties(props.findAll( { k, v -> k.startsWith("j2s.") } ))
   outputs.file(outputFile)
 }
 
@@ -1429,13 +1451,17 @@ task jalviewjsCopySiteResources (type: Copy) {
   inputs.files inputFiles
 }
 
-task jalviewjsTotalClean {
+task cleanJalviewjsAll {
   group "JalviewJS"
-  description "Delete everything to do with JalviewJS build"
-  //delete jalviewjsBuildDir
-  delete jalviewDir+"/"+eclipse_bin_dir
-  delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
-  delete jalviewDir+"/"+jalviewjs_j2s_settings
+  description "Delete all configuration and build artifacts to do with JalviewJS build"
+  dependsOn cleanJalviewjsSite
+  
+  doFirst {
+    delete jalviewjsBuildDir
+    delete jalviewDir+"/"+eclipse_bin_dir
+    delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
+    delete jalviewDir+"/"+jalviewjs_j2s_settings
+  }
 }
 
 task jalviewjsProjectImport(type: Exec) {
@@ -1507,6 +1533,7 @@ task jalviewjsTranspile(type: Exec) {
   inputs.dir(sourceDir)
   outputs.dir(eclipse_bin_dir+"/main")
   outputs.dir(jalviewjsTransferSiteDir)
+  outputs.upToDateWhen { file("${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
 
 }
 
@@ -1536,9 +1563,11 @@ task jalviewjsBuildSite {
   dependsOn jalviewjsPrepareSite
 }
 
-task jalviewjsSiteClean {
-  //delete jalviewjsTransferSiteDir
-  //delete jalviewjsSiteDir
+task cleanJalviewjsSite {
+  doFirst {
+    delete jalviewjsTransferSiteDir
+    delete jalviewjsSiteDir
+  }
 }
 
 task jalviewjsSiteTar(type: Tar) {
@@ -1625,7 +1654,7 @@ task jalviewjsIDEBuildSite {
 task jalviewjsIDESiteClean {
   group "JalviewJS in Eclipse"
   description "Deletes the Eclipse transpiled site"
-  dependsOn jalviewjsSiteClean
+  dependsOn cleanJalviewjsSite
 }
 
 task jalviewjsIDEServer {
diff --git a/gradle.properties b/gradle.properties
index b0c4113..c035a59 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -167,8 +167,8 @@ j2s.compiler.status = enable
 #j2s.log.methods.declared = j2s_methods_declared.log
 #j2s.log.methods.called = j2s_methods_called.log
 #a semicolon-separated list of package-level file paths to be excluded
-j2s.excluded.paths = test;testng;util
-j2s.include.tests = true
+#j2s.excluded.paths = test;testng;util
+#j2s.include.tests = true
 #j2s.testing = null
 #j2s.compiler.nonqualified.packages = null
 #j2s.compiler.nonqualified.classes = null
-- 
1.7.10.2