.gitignore

@@ -2,3 +2,7 @@
 /test-output
 /bin
 /build
+/.gradle
+.classpath
+.project
+.settings/

build.gradle

@@ -4,7 +4,7 @@ group='sis'
 
 dependencies {
     compile 'apache:commons-io:+',
-            'apache:commons-lang:+',
+            'apache:commons-lang3:+',
             'testng:testng:+',
             'rinn:restrictions:+'
 } 
@@ -24,6 +24,7 @@ sourceSets {
 }
 
 jar {
+    archiveName "${project.group}-base-${version}.jar"
     manifest {
         attributes 'Main-Class': 'ch.systemsx.cisd.base.BuildAndEnvironmentInfo'
     }
@@ -35,13 +36,21 @@ jar {
     from fileTree("libs/")
 }
 
+sourcesJar {
+    archiveName "${project.group}-base-${version}-sources.jar"
+}
+
 task standaloneTestJar(type: Jar, dependsOn: [classes, testClasses]) {
-    archiveName "${project.group}-base-test.jar"
+    archiveName "${project.group}-base-${version}-tests.jar"
     from files(sourceSets.main.output.classesDir)
     from files(sourceSets.main.output.resourcesDir)
     from files(sourceSets.test.output.classesDir)
     from files("libs")
  
+    from('targets/dist') {
+        include 'BUILD*INFO'
+    }    
+
     from {configurations.testRuntime.collect {zipTree(it)}}
  
     manifest {
@@ -49,13 +58,16 @@ task standaloneTestJar(type: Jar, dependsOn: [classes, testClasses]) {
     }
 }
 
-task javadocZip(type: Zip, dependsOn: javadoc) {
-    archiveName "${project.group}-base-javadoc.zip"
+task javadocZip(type: Jar, dependsOn: javadoc) {
+    archiveName "${project.group}-base-${version}-javadoc.jar"
+    baseName "${project.group}-base-javadoc"
     from javadoc.destinationDir
 }
 
 task distributionZip(type: Zip, dependsOn: [jar, sourcesJar, javadocZip, standaloneTestJar]) {
-    baseName = "${project.group}-base"
+    def ver = project.ext.versionNumber.startsWith('SNAPSHOT') ? "${version}" : ""
+    def myVersion = project.ext.versionNumber.startsWith('SNAPSHOT') ? "${project.ext.versionNumber}-${project.ext.revisionNumber}" : project.ext.versionNumber
+    archiveName "${project.group}-base-${myVersion}.zip"
     from ('dist') {
         into "${project.group}-base"
     }
@@ -66,12 +78,10 @@ task distributionZip(type: Zip, dependsOn: [jar, sourcesJar, javadocZip, standal
 
     from (jar.archivePath) {
         into "${project.group}-base/lib"
-        rename '(.*)', "${project.group}-base.jar"
     }
     
     from (sourcesJar.archivePath) {
         into "${project.group}-base/src"
-        rename '(.*)', "${project.group}-base-src.jar"
     }
     
     from (standaloneTestJar.archivePath) {

debian/changelog

-libsis-base-java (18.08~pre+git20180810.9248fca+dfsg-1) UNRELEASED; urgency=medium
+libsis-base-java (18.08.0+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream Git checkout
   * Upstream moved to Gitlab
@@ -8,7 +8,7 @@ libsis-base-java (18.08~pre+git20180810.9248fca+dfsg-1) UNRELEASED; urgency=medi
   * Drop now unneeded get-orig-source target
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.2.0
-  TODO: Run time test failure: testGetLinkInfoRegularFile
+  * Build-Depends: s/libcommons-lang-java/libcommons-lang3-java/
 
  -- Andreas Tille <tille@debian.org>  Tue, 14 Aug 2018 09:31:05 +0200
 

debian/control

@@ -8,7 +8,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11),
                default-jdk,
                javahelper,
-               libcommons-lang-java,
+               libcommons-lang3-java,
                libcommons-io-java,
                testng,
                libtool,

debian/patches/fix_tests.patch

@@ -4,7 +4,7 @@ Forwarded: no
 Author: Olivier Sallou <osallou@debian.org>
 --- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
 +++ b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-@@ -164,14 +164,14 @@
+@@ -165,14 +165,14 @@ public class UnixTests extends AbstractF
          { "requires_unix" })
      public void testGetUid()
      {
@@ -21,7 +21,7 @@ Author: Olivier Sallou <osallou@debian.org>
          assertEquals(Unix.getUid(), Unix.getEuid());
      }
  
-@@ -179,14 +179,14 @@
+@@ -180,14 +180,14 @@ public class UnixTests extends AbstractF
          { "requires_unix" })
      public void testGetGid()
      {

debian/patches/remove_ch_rinn_imports.patch

@@ -5,7 +5,7 @@ Forwarded: no
 Last-Updated: 2015-08-21
 --- a/source/java/ch/systemsx/cisd/base/unix/Unix.java
 +++ b/source/java/ch/systemsx/cisd/base/unix/Unix.java
-@@ -19,7 +19,6 @@
+@@ -19,7 +19,6 @@ package ch.systemsx.cisd.base.unix;
  import java.io.File;
  import java.io.IOException;
  
@@ -13,7 +13,7 @@ Last-Updated: 2015-08-21
  import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
  import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
  import ch.systemsx.cisd.base.utilities.NativeLibraryUtilities;
-@@ -415,13 +414,11 @@
+@@ -415,13 +414,11 @@ public final class Unix
  
      private static native String strerror();
  
@@ -29,7 +29,7 @@ Last-Updated: 2015-08-21
          try
 --- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
 +++ b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-@@ -24,7 +24,6 @@
+@@ -25,7 +25,6 @@ import java.nio.charset.Charset;
  import org.apache.commons.io.FileUtils;
  import org.testng.annotations.Test;
  
@@ -37,7 +37,7 @@ Last-Updated: 2015-08-21
  import ch.systemsx.cisd.base.BuildAndEnvironmentInfo;
  import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
  import ch.systemsx.cisd.base.unix.Unix.Group;
-@@ -36,7 +35,6 @@
+@@ -37,7 +36,6 @@ import ch.systemsx.cisd.base.unix.Unix.S
   * 
   * @author Bernd Rinn
   */

debian/patches/skip_testGetLinkInfoDirectory.patch

@@ -19,7 +19,7 @@ Forwarded-Upstream: Bernd Rinn <brinn@ethz.ch>
 
 --- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
 +++ b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-@@ -78,7 +78,7 @@ public class UnixTests extends AbstractF
+@@ -79,7 +79,7 @@ public class UnixTests extends AbstractF
      }
  
      @Test(groups =

debian/rules

@@ -3,7 +3,7 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-export CLASSPATH=/usr/share/java/commons-lang.jar:/usr/share/java/commons-io.jar:/usr/share/java/testng.jar
+export CLASSPATH=/usr/share/java/commons-lang3.jar:/usr/share/java/commons-io.jar:/usr/share/java/testng.jar
 
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 

debian/watch

 version=4
 
-opts="mode=git,pretty=18.08~pre+git%cd.%h,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-    https://sissource.ethz.ch/sispub/base.git HEAD
-
-# The versioning is <year>.<month>.<patch level>. So the next release will be
-# something like 18.09.0 or 18.10.0. If you call the pre-release 18.08, you will
-# be fine
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://sissource.ethz.ch/sispub/base/tags .*archive/18.08.0/base@ANY_VERSION@@ARCHIVE_EXT@

gradle/wrapper/gradle-wrapper.properties

-#Tue Jun 13 15:27:00 CEST 2017
+#Fri Aug 17 11:54:01 CEST 2018
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=http\://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/3.5/gradle-3.5-all.zip
+distributionUrl=http\://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/4.9/gradle-4.9-all.zip

javaproject.gradle

@@ -53,10 +53,6 @@ buildscript {
     apply from: './repository.gradle'
     
     repositories repositoryConfig
-    
-    dependencies {
-        classpath 'cisd:cisd-ant-tasks:+'
-    }
 }
 
 repositories repositoryConfig
@@ -93,36 +89,14 @@ def execute_working_dir(command, arguments, working_dir) {
     }
 }
 
-ext.svnCommand = 'svn'
-
-def isSvnProject() {
-   return new java.io.File(projectDir, ".svn").isDirectory() || new java.io.File(projectDir, "../.svn").isDirectory() 
-}
-
 def isGitProject() {
    return new java.io.File(projectDir, ".git").isDirectory() || new java.io.File(projectDir, "../.git").isDirectory() 
 }
 
-def executeSVN(arguments) {
-    arguments.add(0, '--non-interactive')
-    return execute(svnCommand, arguments)
-}
-
 def calculateCleanFlag() {
-    return 'clean'
-    for (childProject in project.childProjects.values()) {
-        if (childProject.cleanFlag == 'dirty') {
-            return 'dirty'
-        }
-    }
-    def isSvn = isSvnProject()
-    if (isSvn) {
-        def output = executeSVN(['status', '../' + project.name])
-        def lines = output.findAll({ (it.startsWith('?') || it.trim().isEmpty()) == false})
-        return lines.isEmpty() ? 'clean' : 'dirty'
-    } else if (isGitProject()) {
+    if (isGitProject()) {
         def output = execute_working_dir('git', ['status', '--porcelain'], '../' + project.name)
-        return output.length == 0 ? 'clean' : 'dirty'
+        return (output.length == 0 || (output.length ==1 && output[0].length() == 0)) ? 'clean' : 'dirty'
     } else {
     	return 'dirty'
     }
@@ -133,23 +107,13 @@ def findMaximum(lines, key) {
 }
 
 def calculateBuildInfo() {
-    if (isSvnProject()) {
-        def output = executeSVN(['info', '-R', '../' + project.name])
-        def maxRevisionNumber = findMaximum(output, 'Revision:')
-        project.ext.revisionNumber = findMaximum(output, 'Last Changed Rev:')
-        if (maxRevisionNumber < project.ext.revisionNumber) {
-            throw new GradleException("Maximum revision ($maxRevisionNumber) is less than the maximum "
-                      + "last changed revision ($project.ext.revisionNumber).")
-        }
-        project.ext.versionNumber = 'SNAPSHOT'
-        def url = output.findAll({ it.startsWith('URL:')})[0].split('URL:')[1].trim()
-        if (url.contains('/trunk') == false) {
-            def pathElements = url.split('/')
-            project.ext.versionNumber = 'libraries' == pathElements[-2] ? pathElements[-3] : pathElements[-2]
-        }
-    } else if (isGitProject()) {
-        def gitlogoutput = execute_working_dir('git', ['log', '-1', '--format=%at'], '../' + project.name)
-        project.ext.revisionNumber = Integer.parseInt(gitlogoutput[0])
+    if (isGitProject()) {
+        def gitlogoutput = execute_working_dir('git', ['log', '-1', '--format=%at-%H'], '../' + project.name)
+        def rev = gitlogoutput[0].split("-")
+        project.ext.revisionNumber = Integer.parseInt(rev[0])
+        def commitHash = rev[1]
+        def date = new java.text.SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssX").format(new Date(revisionNumber * 1000L))
+        project.ext.revisionInfo = "${commitHash} [${date}]"
         def tag = 'git tag -l --points-at HEAD'.execute().text.trim()
         if (tag == null || tag.isEmpty()) {
             project.ext.versionNumber = 'SNAPSHOT'
@@ -159,22 +123,15 @@ def calculateBuildInfo() {
            project.ext.versionNumber = tag
         }
     } else {
+        project.ext.revisionInfo = '?'
         project.ext.revisionNumber = 1
         project.ext.versionNumber = 'SNAPSHOT'
     }
 
-    for (childProject in project.childProjects.values()) {
-        project.ext.revisionNumber = Math.max(project.ext.revisionNumber, childProject.revisionNumber)
-        if (project.ext.versionNumber != childProject.versionNumber) {
-            throw new GradleException("Inconsistent version numbers: "
-                        + "${project.name} at version ${project.ext.versionNumber} but "
-                        + "${childProject.name} at version ${childProject.versionNumber}.") 
-        } 
-    }
-    version = "${project.ext.versionNumber}-r${project.ext.revisionNumber}"
-    project.ext.revisionForPublication = project.ext.versionNumber.startsWith('SNAPSHOT') ? "r${project.ext.revisionNumber}" : project.ext.versionNumber
+    version = project.ext.versionNumber.startsWith('SNAPSHOT') ? "${project.ext.revisionNumber}" : project.ext.versionNumber
+    project.ext.revisionForPublication = project.ext.versionNumber.startsWith('SNAPSHOT') ? "${project.ext.revisionNumber}" : project.ext.versionNumber
     project.ext.cleanFlag = calculateCleanFlag()
-    def buildInfo = "${project.ext.versionNumber}:${project.ext.revisionNumber}:${project.ext.cleanFlag}"
+    def buildInfo = "${project.ext.versionNumber}::${project.ext.revisionInfo}::${project.ext.cleanFlag}"
     println "BUILD INFO for $project: $buildInfo"
     def targetsDist = 'targets/dist'
     def distFolder = new File("${project.projectDir}/$targetsDist")
@@ -255,17 +212,6 @@ compileJava {
     }
 }
 
-compileTestJava {
-    options.encoding = 'utf-8'
-    options.fork = true
-    doFirst {
-        options.forkOptions.with {
-            executable = 'java'
-            jvmArgs = createJvmArgs()
-        }
-    }
-}
-
 def createJvmArgs() {
     def args = ['-cp', configurations.ecj.asPath, 'org.eclipse.jdt.internal.compiler.batch.Main', '-nowarn']
     return args

source/c/unix.c

 /*
- * Copyright 2008 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

source/java/ch/systemsx/cisd/base/BuildAndEnvironmentInfo.java

 /*
- * Copyright 2009 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

source/java/ch/systemsx/cisd/base/annotation/JsonObject.java

 /*
- * Copyright 2012 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

source/java/ch/systemsx/cisd/base/convert/NativeArrayEncoding.java

 /*
- * Copyright 2010 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

source/java/ch/systemsx/cisd/base/convert/NativeTaggedArray.java

 /*
- * Copyright 2010 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

source/java/ch/systemsx/cisd/base/exceptions/CheckedExceptionTunnel.java

 /*
- * Copyright 2007 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

source/java/ch/systemsx/cisd/base/exceptions/IErrorStrategy.java

 /*
- * Copyright 2012 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

source/java/ch/systemsx/cisd/base/exceptions/IOExceptionUnchecked.java

 /*
- * Copyright 2008 ETH Zuerich, CISD
+ * Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.