gnu: ant/java8: Rename to ant.

* gnu/packages/java.scm (ant): Rename to...
(ant/java7): ...this.
(ant/java8): Rename to...
(ant): ...this.
(java-qdox-1.12, java-jarjar, java-hamcrest-core, java-hamcrest-parent-pom)
(java-junit, java-org-ow2-parent-pom-1.3, java-asm-bootstrap): Rename
inputs accordingly.
* gnu/packages/axoloti.scm: Rename accordingly.
* gnu/packages/bioinformatics.scm: idem.
* gnu/packages/groovy.scm: idem.
* gnu/packages/java-maths.scm: idem.
* guix/build-system/ant.scm: idem.

Change-Id: I9d79ce8e351862747420fc2a58301b7f61212293

gnu/packages/axoloti.scm

@@ -341,7 +341,7 @@ runtime.")
        ("java-jgit" ,java-jgit-4.2)
        ("axoloti-runtime" ,axoloti-runtime)))
     (native-inputs
-     (list ant zip ; for repacking the jar
+     (list ant/java7 zip ; for repacking the jar
            unzip))
     (description
      "The Axoloti patcher offers a “patcher” environment similar to Pure Data
@@ -647,7 +647,7 @@ This package provides the runtime.")
        ("java-slf4j-api" ,java-slf4j-api)
        ("ksoloti-runtime" ,ksoloti-runtime)))
     (native-inputs
-     (list ant zip                      ;for repacking the jar
+     (list ant/java7 zip                      ;for repacking the jar
            unzip))
     (description
      "Ksoloti is an environment for generating and processing digital audio.

gnu/packages/bioinformatics.scm

@@ -9283,7 +9283,7 @@ VCF.")
        ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
        #:tests? #f
        #:jdk ,icedtea-8
-       #:ant ,ant/java8
+       #:ant ,ant
        ;; This is only used for tests.
        #:make-flags
        (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
@@ -9353,11 +9353,10 @@ VCF.")
      (list java-snappy-1
            java-commons-jexl-2
            java-cofoja
-           ant/java8                    ;for bzip2 support at runtime
+           ant                          ;for bzip2 support at runtime
            zlib))
     (native-inputs
      `(("ant-apache-bcel" ,ant-apache-bcel)
-       ("ant-junit" ,ant-junit)
        ("java-testng" ,java-testng)
        ("java-commons-bcel" ,java-commons-bcel)
        ("java-jcommander" ,java-jcommander)

gnu/packages/groovy.scm

@@ -412,7 +412,7 @@ similar to javadoc."))))
       (inherit base)
       (arguments
        `(;#:tests? #f;Requires spock-framework which is a circular dependency
-         #:ant ,ant/java8; ant is actually a dependency of this package, and we need 1.10
+         #:ant ,ant; ant is actually a dependency of this package, and we need 1.10
          ,@(substitute-keyword-arguments arguments
              ((#:phases phases)
               `(modify-phases ,phases
@@ -431,8 +431,7 @@ similar to javadoc."))))
          ("java-asm-analysis" ,java-asm-analysis-8)
          ,@(package-inputs base)))
       (native-inputs
-       `(("ant-junit" ,ant-junit)
-         ("groovy-bootstrap" ,groovy-bootstrap)
+       `(("groovy-bootstrap" ,groovy-bootstrap)
          ("groovy-xml" ,groovy-xml)
          ("groovy-test" ,groovy-test)
          ("groovy-tests-bootstrap" ,groovy-tests-bootstrap)

gnu/packages/java-maths.scm

@@ -75,7 +75,7 @@
     (inputs
      (list openblas))
     (native-inputs
-     `(("ant" ,ant)
+     `(("ant" ,ant/java7)
        ("ruby" ,ruby)                   ; for configure script
        ("gfortran" ,gfortran)
        ("jdk" ,icedtea "jdk")))

gnu/packages/java.scm

@@ -1964,8 +1964,7 @@ OpenJDK.")
     (home-page "https://www.jetbrains.com/")
     (license license:gpl2+)))
 
-
-(define-public ant/java8
+(define-public ant
   (package
     (name "ant")
     (version "1.10.15")
@@ -1980,15 +1979,12 @@ OpenJDK.")
               (snippet
                '(begin
                   (for-each delete-file
-                            (find-files "lib/optional" "\\.jar$"))
-                  #t))))
-    (build-system gnu-build-system)
+                            (find-files "lib/optional" "\\.jar$"))))))
+    (build-system ant-build-system)
     (arguments
      (list
-      #:modules '((srfi srfi-1)
-                  (guix build gnu-build-system)
-                  (guix build utils))
-      #:tests? #f                       ;no "check" target
+      #:ant ant/java7
+      #:test-target "test"
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'remove-scripts
@@ -1998,11 +1994,100 @@ OpenJDK.")
               (for-each delete-file
                         (find-files "src/script"
                                     "(.*\\.(bat|cmd)|runant.*|antRun.*)"))))
+          (add-after 'unpack 'link-test-dependencies
+            (lambda* (#:key inputs #:allow-other-keys)
+              (for-each (lambda (file)
+                          (symlink file
+                                   (string-append "lib/optional/"
+                                                  (basename file))))
+                        (append
+                          (find-files (assoc-ref inputs "java-hamcrest-core")
+                                      "\\.jar$")
+                          (find-files (assoc-ref inputs "java-hamcrest-library")
+                                      "\\.jar$")
+                          (find-files (assoc-ref inputs "java-junit")
+                                      "\\.jar$")))))
+          (add-before 'build 'fix-test-failures
+            (lambda _
+              ;; Failure because the directory does not exist
+              (substitute* "src/etc/testcases/taskdefs/exec/exec-with-redirector.xml"
+                (("/usr/bin") (getcwd)))
+              ;; Failure because it cannot read root's name in the build
+              ;; container
+              (delete-file "src/tests/junit/org/apache/tools/ant/types/selectors/OwnedBySelectorTest.java")
+              ;; Cause timestamp issue when trying to rollback time by a few
+              ;; seconds.
+              (for-each (lambda (file) (utime file 5000))
+                        (find-files "src/etc/testcases/taskdefs" "" #:directories? #t))))
           (delete 'bootstrap)
           (delete 'configure)
           (replace 'build
             (lambda* (#:key inputs #:allow-other-keys)
               (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+              (invoke "bash" "bootstrap.sh"
+                      (string-append "-Ddist.dir=" #$output))))
+          (add-after 'build 'fix-executables-paths
+            (lambda* (#:key inputs #:allow-other-keys)
+              (wrap-script (string-append #$output "/bin/ant")
+                `("PATH" suffix
+                  (,(dirname (search-input-file inputs "/bin/sed"))
+                   ,(dirname (search-input-file inputs "/bin/uname"))
+                   ,(dirname (search-input-file inputs "/bin/which")))))
+              (patch-shebang
+               (string-append #$output "/bin/complete-ant-cmd.pl")
+               (list (dirname (search-input-file inputs "/bin/perl"))))))
+          (delete 'install))))
+    (inputs
+     (list coreutils-minimal
+           guile-3.0/pinned
+           java-hamcrest-core
+           java-hamcrest-library
+           java-junit
+           perl
+           sed
+           which))
+    (home-page "https://ant.apache.org")
+    (synopsis "Build tool for Java")
+    (description
+     "Ant is a platform-independent build tool for Java.  It is similar to
+make but is implemented using the Java language, requires the Java platform,
+and is best suited to building Java projects.  Ant uses XML to describe the
+build process and its dependencies, whereas Make uses Makefile format.")
+    (license license:asl2.0)))
+
+;; The 1.9.x series is the last that can be built with GCJ.  The 1.10.x series
+;; requires Java 8.
+(define-public ant/java7
+  (package
+    (name "ant")
+    (version "1.9.15")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://apache/ant/source/apache-ant-"
+                                  version "-src.tar.gz"))
+              (sha256
+               (base32
+                "1xy30f1w5gaqk6g3f0vw7ygix4rb6032qkcw42y4z8wd9jihgygd"))))
+    (build-system gnu-build-system)
+    (arguments
+      `(#:modules ((srfi srfi-1)
+                   (guix build gnu-build-system)
+                   (guix build utils))
+        #:tests? #f                  ; no "check" target
+        #:phases
+        (modify-phases %standard-phases
+          (delete 'bootstrap)
+          (delete 'configure)
+          (add-after 'unpack 'remove-scripts
+            ;; Remove bat / cmd scripts for DOS as well as the antRun and runant
+            ;; wrappers.
+            (lambda _
+              (for-each delete-file
+                        (find-files "src/script"
+                                    "(.*\\.(bat|cmd)|runant.*|antRun.*)"))))
+          (replace 'build
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
 
               ;; Disable tests to avoid dependency on hamcrest-core, which needs
               ;; Ant to build.  This is necessary in addition to disabling the
@@ -2011,9 +2096,10 @@ OpenJDK.")
               (substitute* "build.xml"
                 (("depends=\"jars,test-jar") "depends=\"jars"))
               (invoke "bash" "bootstrap.sh"
-                      (string-append "-Ddist.dir=" #$output))))
+                      (string-append "-Ddist.dir="
+                                     (assoc-ref outputs "out")))))
           (add-after 'build 'strip-jar-timestamps ;based on ant-build-system
-            (lambda _
+            (lambda* (#:key outputs #:allow-other-keys)
               (define (repack-archive jar)
                 (let* ((dir (mkdtemp "jar-contents.XXXXXX"))
                        (manifest (string-append dir "/META-INF/MANIFESTS.MF")))
@@ -2039,11 +2125,11 @@ OpenJDK.")
                       (apply invoke command)))))
               (for-each repack-archive
                         (find-files
-                         (string-append #$output "/lib")
+                         (string-append (assoc-ref %outputs "out") "/lib")
                          "\\.jar$"))))
           (delete 'install))))
     (native-inputs
-     `(("jdk" ,icedtea-8 "jdk")
+     `(("jdk" ,icedtea-7 "jdk")
        ("zip" ,zip)
        ("unzip" ,unzip)))
     (home-page "https://ant.apache.org")
@@ -2055,131 +2141,12 @@ and is best suited to building Java projects.  Ant uses XML to describe the
 build process and its dependencies, whereas Make uses Makefile format.")
     (license license:asl2.0)))
 
-;; The 1.9.x series is the last that can be built with GCJ.  The 1.10.x series
-;; requires Java 8.
-(define-public ant
-  (package (inherit ant/java8)
-    (version "1.9.15")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://apache/ant/source/apache-ant-"
-                                  version "-src.tar.gz"))
-              (sha256
-               (base32
-                "1xy30f1w5gaqk6g3f0vw7ygix4rb6032qkcw42y4z8wd9jihgygd"))))
-    ;; XXX: we do this to avoid a rebuild.  This mess will be cleaned up
-    ;; later.
-    (arguments
-     (substitute-keyword-arguments
-         `(#:modules ((srfi srfi-1)
-                      (guix build gnu-build-system)
-                      (guix build utils))
-           #:tests? #f                  ; no "check" target
-           #:phases
-           (modify-phases %standard-phases
-             (delete 'bootstrap)
-             (delete 'configure)
-             (add-before 'build 'define-java-environment-variables
-               (lambda* (#:key inputs #:allow-other-keys)
-                 ;; First, set environment variables (eases debugging on -K).
-                 (setenv "JAVA_HOME" (assoc-ref inputs "jamvm"))
-                 (setenv "JAVACMD" (search-input-file inputs "/bin/jamvm"))
-                 (setenv "JAVAC" (search-input-file inputs "/bin/jikes"))
-                 (setenv "CLASSPATH" (search-input-file inputs "/lib/rt.jar"))))
-             (replace 'build
-               (lambda* (#:key inputs outputs #:allow-other-keys)
-                 ;; Ant complains if this file doesn't exist.
-                 (setenv "HOME" "/tmp")
-                 (with-output-to-file "/tmp/.ant.properties"
-                   (lambda _ (display "")))
-
-                 ;; Use jikes instead of javac for <javac ...> tags in build.xml
-                 (setenv "ANT_OPTS" "-Dbuild.compiler=jikes")
-
-                 ;; jikes produces lots of warnings, but they are not very
-                 ;; interesting, so we silence them.
-                 (setenv "$BOOTJAVAC_OPTS" "-nowarn")
-
-                 ;; Without these JamVM options the build may freeze.
-                 (substitute* "bootstrap.sh"
-                   (("^\"\\$\\{JAVACMD\\}\" " m)
-                    ,@(if (string-prefix? "armhf" (or (%current-system)
-                                                      (%current-target-system)))
-                          `((string-append m "-Xnocompact "))
-                          `((string-append m "-Xnocompact -Xnoinlining ")))))
-
-                 ;; Disable tests because we are bootstrapping and thus don't have
-                 ;; any of the dependencies required to build and run the tests.
-                 (substitute* "build.xml"
-                   (("depends=\"jars,test-jar\"") "depends=\"jars\""))
-                 (invoke "bash" "bootstrap.sh"
-                         (string-append "-Ddist.dir="
-                                        (assoc-ref outputs "out")))))
-             (add-after 'build 'strip-jar-timestamps ;based on ant-build-system
-               (lambda* (#:key outputs #:allow-other-keys)
-                 (define (repack-archive jar)
-                   (let* ((dir (mkdtemp "jar-contents.XXXXXX"))
-                          (manifest (string-append dir "/META-INF/MANIFESTS.MF")))
-                     (with-directory-excursion dir
-                       (invoke "unzip" jar))
-                     (delete-file jar)
-                     ;; XXX: copied from (gnu build install)
-                     (for-each (lambda (file)
-                                 (let ((s (lstat file)))
-                                   (unless (eq? (stat:type s) 'symlink)
-                                     (utime file  0 0 0 0))))
-                               (find-files dir #:directories? #t))
-                     ;; It is important that the manifest appears first.
-                     (with-directory-excursion dir
-                       (let* ((files (find-files "." ".*" #:directories? #t))
-                              ;; To ensure that the reference scanner can
-                              ;; detect all store references in the jars
-                              ;; we disable compression with the "-0" option.
-                              (command (if (file-exists? manifest)
-                                           `("zip" "-0" "-X" ,jar ,manifest
-                                             ,@files)
-                                           `("zip" "-0" "-X" ,jar ,@files))))
-                         (apply invoke command)))))
-                 (for-each repack-archive
-                           (find-files
-                            (string-append (assoc-ref %outputs "out") "/lib")
-                            "\\.jar$"))))
-             (delete 'install)))
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (delete 'define-java-environment-variables)
-           (add-after 'unpack 'remove-scripts
-             ;; Remove bat / cmd scripts for DOS as well as the antRun and runant
-             ;; wrappers.
-             (lambda _
-               (for-each delete-file
-                         (find-files "src/script"
-                                     "(.*\\.(bat|cmd)|runant.*|antRun.*)"))
-               #t))
-           (replace 'build
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
-
-               ;; Disable tests to avoid dependency on hamcrest-core, which needs
-               ;; Ant to build.  This is necessary in addition to disabling the
-               ;; "check" phase, because the dependency on "test-jar" would always
-               ;; result in the tests to be run.
-               (substitute* "build.xml"
-                 (("depends=\"jars,test-jar") "depends=\"jars"))
-               (invoke "bash" "bootstrap.sh"
-                       (string-append "-Ddist.dir="
-                                      (assoc-ref outputs "out")))))))))
-    (native-inputs
-     `(("jdk" ,icedtea-7 "jdk")
-       ("zip" ,zip)
-       ("unzip" ,unzip)))))
-
 (define-public ant-apache-bcel
   (package
-    (inherit ant/java8)
+    (inherit ant)
     (name "ant-apache-bcel")
     (arguments
-     (substitute-keyword-arguments (package-arguments ant/java8)
+     (substitute-keyword-arguments (package-arguments ant)
        ((#:phases phases)
         #~(modify-phases #$phases
             (add-after 'unpack 'link-bcel
@@ -2200,37 +2167,11 @@ build process and its dependencies, whereas Make uses Makefile format.")
                   (delete-file-recursively bin)
                   (delete-file-recursively lib))))))))
     (inputs
-     (modify-inputs (package-inputs ant/java8)
+     (modify-inputs (package-inputs ant)
        (prepend java-commons-bcel)))))
 
-(define-public ant-junit
-  (package
-    (inherit ant/java8)
-    (name "ant-junit")
-    (arguments
-     (substitute-keyword-arguments (package-arguments ant/java8)
-       ((#:phases phases)
-        #~(modify-phases #$phases
-            (add-after 'unpack 'link-junit
-              (lambda* (#:key inputs #:allow-other-keys)
-                (for-each (lambda (file)
-                            (symlink file
-                                     (string-append "lib/optional/"
-                                                    (basename file))))
-                          (find-files (assoc-ref inputs "java-junit")
-                                      "\\.jar$"))))
-            (add-after 'build 'install
-              (lambda _
-                (let ((share (string-append #$output "/share/java"))
-                      (bin   (string-append #$output "/bin"))
-                      (lib   (string-append #$output "/lib")))
-                  (mkdir-p share)
-                  (install-file (string-append lib "/ant-junit.jar") share)
-                  (delete-file-recursively bin)
-                  (delete-file-recursively lib))))))))
-    (inputs
-     (modify-inputs (package-inputs ant/java8)
-       (prepend java-junit)))))
+(define-deprecated-package ant-junit
+  ant)
 
 (define-public libantlr3c
   (package
@@ -3337,6 +3278,9 @@ is implemented.")
      `(;; Tests require junit
        #:tests? #f
        #:jar-name "qdox.jar"
+       ;; Explicitely use an ant version that includes the junit tasks, since
+       ;; it is a dependency of junit.
+       #:ant ,ant/java7
        #:phases
        (modify-phases %standard-phases
          (replace 'unpack
@@ -3445,6 +3389,9 @@ documentation tools.")
      `(;; Tests require junit, which ultimately depends on this package.
        #:tests? #f
        #:build-target "jar"
+       ;; Explicitely use an ant version that includes the junit tasks, since
+       ;; it is a dependency of junit.
+       #:ant ,ant/java7
        #:phases
        (modify-phases %standard-phases
          (add-before 'build 'do-not-use-bundled-asm
@@ -3543,6 +3490,9 @@ testing frameworks, mocking libraries and UI validation rules.")
     (build-system ant-build-system)
     (arguments
      `(#:tests? #f ; Tests require junit
+       ;; Explicitely use an ant version that includes the junit tasks, since
+       ;; it is a dependency of junit.
+       #:ant ,ant/java7
        #:modules ((guix build ant-build-system)
                   (guix build java-utils)
                   (guix build utils)
@@ -3628,6 +3578,9 @@ testing frameworks, mocking libraries and UI validation rules.")
     (native-inputs '())
     (arguments
      `(#:tests? #f
+       ;; Explicitely use an ant version that includes the junit tasks, since
+       ;; it is a dependency of junit.
+       #:ant ,ant/java7
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -3669,7 +3622,7 @@ testing frameworks, mocking libraries and UI validation rules.")
 (define-public java-junit
   (package
     (name "java-junit")
-    (version "4.12")
+    (version "4.13.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3678,7 +3631,7 @@ testing frameworks, mocking libraries and UI validation rules.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1j8avi91px1z8rjc89cfikwrvfifdmmsarwiyrcnr59ynvpz0v8h"))
+                "1r7k4zzscc8019np3is3bzfigw8fxd6s3259cbhzzh02q6d5p9h3"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -3690,6 +3643,9 @@ testing frameworks, mocking libraries and UI validation rules.")
      `(#:jar-name "junit.jar"
        #:source-dir "src/main/java"
        #:test-dir "src/test"
+       ;; Explicitely use an ant version that includes the junit tasks, so
+       ;; we can run the tests.
+       #:ant ,ant/java7
        #:test-exclude (list "**/SimpleTest.java" "**/StackTracesTest.java"
                             "**/RuleChainTest.java" "**/TestWatchmanTest.java")
        #:phases
@@ -3730,7 +3686,13 @@ sharing common test data, and test runners for running tests.")
      `(#:jar-name "junitparams.jar"
        #:source-dir "src/main/java"
        #:test-dir "src/test"
-       #:test-exclude (list "**/SuperclassTest.java")))
+       #:test-exclude (list
+                        ;; Abstract class: no tests
+                        "**/SuperclassTest.java"
+                        ;; Incompatible tests with junit 4.13.2
+                        "**/BeforeAfterClassTest.java"
+                        "**/FilterableTest.java"
+                        "**/RulesTest.java")))
     (inputs
      (list java-junit))
     (native-inputs
@@ -5199,6 +5161,9 @@ complex transformations and code analysis tools.")
     (build-system ant-build-system)
     (arguments
      `(#:tests? #f
+       ;; Explicitely use an ant version that includes the junit tasks, since
+       ;; it is a dependency of junit.
+       #:ant ,ant/java7
        #:phases
        (modify-phases %standard-phases
          (delete 'unpack)
@@ -5220,6 +5185,9 @@ including java-asm.")
     (properties '((hidden? . #t)))
     (arguments
      (substitute-keyword-arguments (package-arguments java-asm)
+       ;; Explicitely use an ant version that includes the junit tasks, since
+       ;; it is a dependency of junit.
+       ((#:ant _ ant/java7) ant/java7)
        ((#:tests? _) #f)))
     (native-inputs `())))