gnu: Move Java compression packages to new module.

* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable.
(java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz):
Move these variables from here...
* gnu/packages/java-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module
references.

1 files changed, 1 insertions, 279 deletions

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index b2b4488683..029d11ef21 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -45,7 +45,6 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
-  #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
@@ -59,7 +58,6 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages java)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-check)
@@ -1265,7 +1263,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
 100% bigger.")
     (license license:asl2.0)))
 
-(define bitshuffle-for-snappy
+(define-public bitshuffle-for-snappy
   (package
     (inherit bitshuffle)
     (name "bitshuffle-for-snappy")
@@ -1302,245 +1300,6 @@ install: libbitshuffle.so
     (inputs '())
     (native-inputs '())))
 
-(define-public java-snappy
-  (package
-    (name "java-snappy")
-    (version "1.1.7.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/xerial/snappy-java/archive/"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1p557vdv006ysgxbpp83krmq0066k46108vyiyka69w8i4i8rbbm"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "snappy.jar"
-       #:source-dir "src/main/java"
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'remove-binaries
-           (lambda _
-             (delete-file "lib/org/xerial/snappy/OSInfo.class")
-             (delete-file-recursively "src/main/resources/org/xerial/snappy/native")
-             #t))
-         (add-before 'build 'build-jni
-           (lambda _
-             ;; Rebuild one of the binaries we removed earlier
-             (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java"
-                      "-d" "lib")
-             ;; Link to the dynamic bitshuffle and snappy, not the static ones
-             (substitute* "Makefile.common"
-               (("-shared")
-                "-shared -lbitshuffle -lsnappy"))
-             (substitute* "Makefile"
-               ;; Don't try to use git, don't download bitshuffle source
-               ;; and don't build it.
-               (("\\$\\(SNAPPY_GIT_UNPACKED\\) ")
-                "")
-               ((": \\$\\(SNAPPY_GIT_UNPACKED\\)")
-                ":")
-               (("\\$\\(BITSHUFFLE_UNPACKED\\) ")
-                "")
-               ((": \\$\\(SNAPPY_SOURCE_CONFIGURED\\)") ":")
-               ;; What we actually want to build
-               (("SNAPPY_OBJ:=.*")
-                "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, \
-                 SnappyNative.o BitShuffleNative.o)\n")
-               ;; Since we removed the directory structure in "native" during
-               ;; the previous phase, we need to recreate it.
-               (("NAME\\): \\$\\(SNAPPY_OBJ\\)")
-                "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)"))
-             ;; Finally we can run the Makefile to build the dynamic library.
-             ;; Use the -nocmake target to avoid a dependency on cmake,
-             ;; which in turn requires the "git_unpacked" directory.
-             (invoke "make" "native-nocmake")))
-         ;; Once we have built the shared library, we need to place it in the
-         ;; "build" directory so it can be added to the jar file.
-         (add-after 'build-jni 'copy-jni
-           (lambda _
-             (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")
-             #t))
-         (add-before 'check 'fix-failing
-           (lambda _
-             (with-directory-excursion "src/test/java/org/xerial/snappy"
-               ;; This package assumes maven build, which puts results in "target".
-               ;; We put them in "build" instead, so fix that.
-               (substitute* "SnappyLoaderTest.java"
-                 (("target/classes") "build/classes"))
-               ;; This requires Hadoop, which is not in Guix yet.
-               (delete-file "SnappyHadoopCompatibleOutputStreamTest.java"))
-             #t)))))
-    (inputs
-     `(("osgi-framework" ,java-osgi-framework)))
-    (propagated-inputs
-     `(("bitshuffle" ,bitshuffle-for-snappy)
-       ("snappy" ,snappy)))
-    (native-inputs
-     `(("junit" ,java-junit)
-       ("hamcrest" ,java-hamcrest-core)
-       ("xerial-core" ,java-xerial-core)
-       ("classworlds" ,java-plexus-classworlds)
-       ("commons-lang" ,java-commons-lang)
-       ("commons-io" ,java-commons-io)
-       ("perl" ,perl)))
-    (home-page "https://github.com/xerial/snappy-java")
-    (synopsis "Compression/decompression algorithm in Java")
-    (description "Snappy-java is a Java port of snappy, a fast C++
-compressor/decompressor.")
-    (license license:asl2.0)))
-
-(define-public java-snappy-1
-  (package
-    (inherit java-snappy)
-    (version "1.0.3-rc3")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/xerial/snappy-java/archive/"
-                                  "snappy-java-" version ".tar.gz"))
-              (sha256
-               (base32
-                "08hsxlqidiqck0q57fshwyv3ynyxy18vmhrai9fyc8mz17m7gsa3"))))
-    (arguments
-     `(#:jar-name "snappy.jar"
-       #:source-dir "src/main/java"
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'remove-binaries
-           (lambda _
-             (delete-file "lib/org/xerial/snappy/OSInfo.class")
-             (delete-file-recursively "src/main/resources/org/xerial/snappy/native")
-             #t))
-         (add-before 'build 'build-jni
-           (lambda _
-             ;; Rebuild one of the binaries we removed earlier
-             (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java"
-                      "-d" "lib")
-             ;; Link to the dynamic snappy, not the static ones
-             (substitute* "Makefile.common"
-               (("-shared") "-shared -lsnappy"))
-             (substitute* "Makefile"
-               ;; Don't download the sources here.
-               (("\\$\\(SNAPPY_UNPACKED\\) ") "")
-               ((": \\$\\(SNAPPY_UNPACKED\\) ") ":")
-               ;; What we actually want to build
-               (("SNAPPY_OBJ:=.*")
-                "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, SnappyNative.o)\n")
-               ;; Since we removed the directory structure in "native" during
-               ;; the previous phase, we need to recreate it.
-               (("NAME\\): \\$\\(SNAPPY_OBJ\\)")
-                "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)"))
-             ;; Finally we can run the Makefile to build the dynamic library.
-             (invoke "make" "native")))
-         ;; Once we have built the shared library, we need to place it in the
-         ;; "build" directory so it can be added to the jar file.
-         (add-after 'build-jni 'copy-jni
-           (lambda _
-             (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")
-             #t))
-         (add-before 'check 'fix-tests
-           (lambda _
-             (mkdir-p "src/test/resources/org/xerial/snappy/")
-             (copy-recursively "src/test/java/org/xerial/snappy/testdata"
-                               "src/test/resources/org/xerial/snappy/testdata")
-             (install-file "src/test/java/org/xerial/snappy/alice29.txt"
-                           "src/test/resources/org/xerial/snappy/")
-             #t)))))))
-
-(define-public java-iq80-snappy
-  (package
-    (name "java-iq80-snappy")
-    (version "0.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/dain/snappy/archive/snappy-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "0rb3zhci7w9wzd65lfnk7p3ip0n6gb58a9qpx8n7r0231gahyamf"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "iq80-snappy.jar"
-       #:source-dir "src/main/java"
-       #:test-dir "src/test"
-       #:jdk ,icedtea-8
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (define (test class)
-               (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
-                                                   ":build/classes"
-                                                   ":build/test-classes")
-                       "-Dtest.resources.dir=src/test/resources"
-                       "org.testng.TestNG" "-testclass"
-                       class))
-             (invoke "ant" "compile-tests")
-             (test "org.iq80.snappy.SnappyFramedStreamTest")
-             (test "org.iq80.snappy.SnappyStreamTest")
-             #t))
-         (add-before 'build 'remove-hadoop-dependency
-           (lambda _
-             ;; We don't have hadoop
-             (delete-file "src/main/java/org/iq80/snappy/HadoopSnappyCodec.java")
-             (delete-file "src/test/java/org/iq80/snappy/TestHadoopSnappyCodec.java")
-             #t)))))
-    (home-page "https://github.com/dain/snappy")
-    (native-inputs
-     `(("guava" ,java-guava)
-       ("java-snappy" ,java-snappy)
-       ("hamcrest" ,java-hamcrest-core)
-       ("testng" ,java-testng)))
-    (synopsis "Java port of the Snappy (de)compressor")
-    (description
-     "Iq80-snappy is a port of the Snappy compressor and decompressor rewritten
-in pure Java.  This compression code produces a byte-for-byte exact copy of the
-output created by the original C++ code, and is extremely fast.")
-    (license license:asl2.0)))
-
-(define-public java-jbzip2
-  (package
-    (name "java-jbzip2")
-    (version "0.9.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://storage.googleapis.com/"
-                                  "google-code-archive-source/v2/"
-                                  "code.google.com/jbzip2/"
-                                  "source-archive.zip"))
-              (file-name (string-append name "-" version ".zip"))
-              (sha256
-               (base32
-                "0ncmhlqmrfmj96nqf6p77b9ws35lcfsvpfxzwxi2asissc83z1l3"))))
-    (build-system ant-build-system)
-    (native-inputs
-     `(("unzip" ,unzip)
-       ("java-junit" ,java-junit)))
-    (arguments
-     `(#:tests? #f                      ; no tests
-       #:jar-name "jbzip2.jar"
-       #:source-dir "tags/release-0.9.1/src"
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-encoding-problems
-           (lambda _
-             ;; Some of the files we're patching are
-             ;; ISO-8859-1-encoded, so choose it as the default
-             ;; encoding so the byte encoding is preserved.
-             (with-fluids ((%default-port-encoding #f))
-               (substitute* "tags/release-0.9.1/src/org/itadaki/bzip2/HuffmanAllocator.java"
-                 (("Milidi.") "Milidiu")))
-             #t)))))
-    (home-page "https://code.google.com/archive/p/jbzip2/")
-    (synopsis "Java bzip2 compression/decompression library")
-    (description "Jbzip2 is a Java bzip2 compression/decompression library.
-It can be used as a replacement for the Apache @code{CBZip2InputStream} /
-@code{CBZip2OutputStream} classes.")
-    (license license:expat)))
-
 (define-public p7zip
   (package
     (name "p7zip")
@@ -2099,43 +1858,6 @@ without having to worry how it does so, or use different interfaces for each
 type by using either Perl modules, or command-line tools on your system.")
     (license license:perl-license)))
 
-(define-public java-tukaani-xz
-  (package
-    (name "java-tukaani-xz")
-    (version "1.6")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://tukaani.org/xz/xz-java-" version ".zip"))
-              (sha256
-               (base32
-                "1z3p1ri1gvl07inxn0agx44ck8n7wrzfmvkz8nbq3njn8r9wba8x"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:tests? #f; no tests
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'chdir
-           (lambda _
-             ;; Our build system enters the first directory in the archive, but
-             ;; the package is not contained in a subdirectory
-             (chdir "..")
-             #t))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             ;; Do we want to install *Demo.jar?
-             (install-file "build/jar/xz.jar"
-                           (string-append
-                             (assoc-ref outputs "out")
-                             "/share/java/xz.jar"))
-             #t)))))
-    (native-inputs
-     `(("unzip" ,unzip)))
-    (home-page "https://tukaani.org")
-    (synopsis "XZ in Java")
-    (description "Tukaani-xz is an implementation of xz compression/decompression
-algorithms in Java.")
-    (license license:public-domain)))
-
 (define-public lunzip
   (package
     (name "lunzip")