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-rw-r--r--gnu/packages/java.scm176
1 files changed, 176 insertions, 0 deletions
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 7ad0c41268..298874f757 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -59,6 +59,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux) ;alsa
+ #:use-module (gnu packages maths)
#:use-module (gnu packages web)
#:use-module (gnu packages wget)
#:use-module (gnu packages pkg-config)
@@ -2347,6 +2348,181 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
(description "This package provides a parser for command line arguments.")
(license license:asl2.0))))
+(define-public java-cisd-jhdf5
+ (let ((revision 39162)
+ (base-version "14.12.6"))
+ (package
+ (name "java-cisd-jhdf5")
+ (version (string-append base-version "-" (number->string revision)))
+ (source (origin
+ (method svn-fetch)
+ (uri (svn-reference
+ (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+ "jhdf5/tags/release/"
+ (version-major+minor base-version)
+ ".x/" base-version "/jhdf5/"))
+ (revision revision)))
+ (file-name (string-append "java-cisd-jhdf5-" version "-checkout"))
+ (sha256
+ (base32
+ "13i17s2hn0q9drdqvp8csy7770p3hdbh9rp30ihln2ldkfawdmz0"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete included gradle jar
+ (delete-file-recursively "gradle/wrapper")
+ ;; Delete pre-built native libraries
+ (delete-file-recursively "libs")
+ #t))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:make-flags '("-file" "build/build.xml")
+ #:build-target "jar-all"
+ #:test-target "jar-test"
+ #:jdk ,icedtea-8
+ #:phases
+ (modify-phases %standard-phases
+ ;; Don't erase results from the build phase when building tests.
+ (add-after 'unpack 'separate-test-target-from-clean
+ (lambda _
+ (substitute* "build/build.xml"
+ (("\"jar-test\" depends=\"clean, ")
+ "\"jar-test\" depends=\""))
+ #t))
+ (add-after 'unpack 'unpack-build-resources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (copy-recursively (assoc-ref inputs "build-resources")
+ "../build_resources")
+ (delete-file-recursively "../build_resources/lib/")
+ (mkdir-p "../build_resources/lib")
+ ;; Remove dependency on classycle
+ (substitute* "../build_resources/ant/build-common.xml"
+ (("<taskdef name=\"dependency-checker.*") "")
+ (("classname=\"classycle.*") "")
+ (("classpath=\"\\$\\{lib\\}/classycle.*") ""))
+ ;; Remove dependency on svn
+ (substitute* "build/build.xml"
+ (("<build-info.*") "")
+ (("\\$\\{revision.number\\}")
+ ,(number->string revision))
+ (("\\$\\{version.number\\}") ,base-version))
+ #t))
+ (add-after 'unpack-build-resources 'fix-dependencies
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "../build_resources/ant/build-common.xml"
+ (("../libraries/testng/testng-jdk15.jar")
+ (string-append (assoc-ref inputs "java-testng")
+ "/share/java/java-testng.jar")))
+ (substitute* "build/build.xml"
+ (("\\$\\{lib\\}/sis-base/sis-base.jar")
+ (string-append (assoc-ref inputs "java-cisd-base")
+ "/share/java/sis-base.jar"))
+ (("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar")
+ (string-append (assoc-ref inputs "java-cisd-args4j")
+ "/share/java/cisd-args4j.jar"))
+ (("\\$\\{lib\\}/commons-lang/commons-lang.jar")
+ (string-append (assoc-ref inputs "java-commons-lang")
+ "/share/java/commons-lang-"
+ ,(package-version java-commons-lang) ".jar"))
+ (("\\$\\{lib\\}/commons-io/commons-io.jar")
+ (string-append (assoc-ref inputs "java-commons-io")
+ "/share/java/commons-io-"
+ ,(package-version java-commons-io)
+ "-SNAPSHOT.jar"))
+ (("\\$\\{lib\\}/testng/testng-jdk15.jar")
+ (string-append (assoc-ref inputs "java-testng")
+ "/share/java/java-testng.jar"))
+ (("\\$\\{lib\\}/junit4/junit.jar")
+ (string-append (assoc-ref inputs "java-junit")
+ "/share/java/junit.jar"))
+ (("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar")
+ (string-append (assoc-ref inputs "java-hamcrest-core")
+ "/share/java/hamcrest-core.jar")))
+ ;; Remove dependency on ch.rinn.restrictions
+ (with-directory-excursion "source/java/ch/systemsx/cisd/hdf5/"
+ (substitute* '("BitSetConversionUtils.java"
+ "HDF5Utils.java")
+ (("import ch.rinn.restrictions.Private;") "")
+ (("@Private") "")))
+ (with-directory-excursion "sourceTest/java/ch/systemsx/cisd/hdf5/"
+ (substitute* '("BitSetConversionTest.java"
+ "h5ar/HDF5ArchiverTest.java")
+ (("import ch.rinn.restrictions.Friend;") "")
+ (("@Friend.*") ""))
+ ;; Remove leftovers from removing @Friend
+ (substitute* "h5ar/HDF5ArchiverTest.java"
+ (("\\{ HDF5Archiver.class, IdCache.class, LinkRecord.class \\}\\)")
+ "")))
+ #t))
+ (add-before 'configure 'build-native-library
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((jdk (assoc-ref inputs "jdk"))
+ (hdf5 (assoc-ref inputs "hdf5"))
+ (dir ,(match (%current-system)
+ ("i686-linux"
+ "i386-Linux")
+ ((or "armhf-linux" "aarch64-linux")
+ "arm-Linux")
+ ((or "x86_64-linux")
+ "amd64-Linux")
+ (_ "unknown-Linux"))))
+ (with-directory-excursion "source/c"
+ (apply invoke `("gcc" "-shared" "-O3"
+ "-fPIC"
+ "-Wl,--exclude-libs,ALL"
+ ,@(find-files "jhdf5" "\\.c$")
+ ,@(find-files "hdf-java" "\\.c$")
+ ,(string-append "-I" hdf5 "/include")
+ ,(string-append "-I" jdk "/include")
+ ,(string-append "-I" jdk "/include/linux")
+ ,(string-append hdf5 "/lib/libhdf5.a")
+ "-o" "libjhdf5.so" "-lz")))
+ (install-file "source/c/libjhdf5.so"
+ (string-append "libs/native/jhdf5/" dir))
+ #t)))
+ ;; In the "check" phase we only build the test executable.
+ (add-after 'check 'run-tests
+ (lambda _
+ (invoke "java" "-jar" "targets/dist/sis-jhdf5-test.jar")
+ (delete-file "targets/dist/sis-jhdf5-test.jar")
+ #t))
+ (replace 'install
+ (install-jars "targets/dist")))))
+ (inputs
+ `(("java-cisd-base" ,java-cisd-base)
+ ("java-cisd-args4j" ,java-cisd-args4j)
+ ("java-commons-lang" ,java-commons-lang)
+ ("java-commons-io" ,java-commons-io)
+ ("hdf5" ,hdf5)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("jdk" ,icedtea-8)
+ ("java-testng" ,java-testng)
+ ("java-junit" ,java-junit)
+ ("java-jmock" ,java-jmock)
+ ("java-hamcrest-core" ,java-hamcrest-core)
+ ("build-resources"
+ ,(origin
+ (method svn-fetch)
+ (uri (svn-reference
+ (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+ "jhdf5/tags/release/"
+ (version-major+minor base-version)
+ ".x/" base-version
+ "/build_resources/"))
+ (revision revision)))
+ (sha256
+ (base32
+ "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk"))))))
+ (home-page "https://wiki-bsse.ethz.ch/display/JHDF5/")
+ (synopsis "Java binding for HDF5")
+ (description "JHDF5 is a high-level API in Java for reading and writing
+HDF5 files, building on the libraries provided by the HDF Group.")
+ ;; The C sources are under a non-copyleft license, which looks like a
+ ;; variant of the BSD licenses. The whole package is under the ASL2.0.
+ (license (list license:asl2.0
+ (license:non-copyleft "file://source/c/COPYING"))))))
+
(define-public java-classpathx-servletapi
(package
(name "java-classpathx-servletapi")