diff options
Diffstat (limited to 'gnu/packages/java.scm')
| -rw-r--r-- | gnu/packages/java.scm | 491 |
1 files changed, 488 insertions, 3 deletions
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 0f8c04e8ba..5cc4a56f81 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) @@ -2084,6 +2085,444 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n" (native-inputs `(("unzip" ,unzip))))) +(define-public java-cisd-base + (let ((revision 38938) + (base-version "14.12.0")) + (package + (name "java-cisd-base") + (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/" + "base/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/base/")) + (revision revision))) + (file-name (string-append "java-cisd-base-" version "-checkout")) + (sha256 + (base32 + "1i5adyf7nzclb0wydgwa1az04qliid8035vpahaandmkmigbnxiy")) + (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") + #:test-target "jar-test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "build-resources") + "../build_resources") + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/testng/testng-jdk15.jar") + (string-append (assoc-ref inputs "java-testng") + "/share/java/java-testng.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")) + ;; Remove dependency on svn + (("<build-info.*") "") + (("\\$\\{revision.number\\}") + ,(number->string revision)) + (("\\$\\{version.number\\}") ,base-version)) + ;; Remove dependency on classycle + (substitute* "../build_resources/ant/build-common.xml" + (("<taskdef name=\"dependency-checker.*") "") + (("classname=\"classycle.*") "") + (("classpath=\"\\$\\{lib\\}/classycle.*") "")) + #t)) + ;; A few tests fail because of the lack of a proper /etc/groups and + ;; /etc/passwd file in the build container. + (add-after 'unpack 'disable-broken-tests + (lambda _ + (substitute* "sourceTest/java/ch/systemsx/cisd/base/AllTests.java" + (("Unix.isOperational\\(\\)") "false")) + #t)) + ;; These decorators are almost useless and pull in an unpackaged + ;; dependency. + (add-after 'unpack 'remove-useless-decorators + (lambda _ + (substitute* "source/java/ch/systemsx/cisd/base/unix/Unix.java" + (("@Private") "") + (("import ch.rinn.restrictions.Private;") "")) + (substitute* "sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java" + (("@Friend.*") "") + (("import ch.rinn.restrictions.Friend;") "")) + #t)) + (add-before 'configure 'build-native-code + (lambda* (#:key inputs #:allow-other-keys) + (let ((jdk (assoc-ref inputs "jdk")) + (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" + (invoke "gcc" "-shared" "-O3" "-fPIC" "unix.c" + (string-append "-I" jdk "/include") + (string-append "-I" jdk "/include/linux") + "-o" "libunix.so") + (invoke "gcc" "-shared" "-O3" "-fPIC" + "-DMACHINE_BYTE_ORDER=1" + "copyCommon.c" + "copyByteChar.c" + "copyByteDouble.c" + "copyByteFloat.c" + "copyByteInt.c" + "copyByteLong.c" + "copyByteShort.c" + (string-append "-I" jdk "/include") + (string-append "-I" jdk "/include/linux") + "-o" "libnativedata.so")) + (install-file "source/c/libunix.so" + (string-append "libs/native/unix/" dir)) + (install-file "source/c/libnativedata.so" + (string-append "libs/native/nativedata/" dir)) + #t))) + ;; In the "check" phase we only build the test executable. + (add-after 'check 'run-tests + (lambda _ + (invoke "java" "-jar" "targets/dist/sis-base-test.jar") + (delete-file "targets/dist/sis-base-test.jar") + #t)) + (replace 'install (install-jars "targets/dist"))))) + (native-inputs + `(("jdk" ,icedtea-8) + ("java-commons-lang" ,java-commons-lang) + ("java-commons-io" ,java-commons-io) + ("java-testng" ,java-testng) + ("build-resources" + ,(origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "base/tags/release/" + (version-major+minor base-version) + ".x/" base-version + "/build_resources/")) + (revision revision))) + (sha256 + (base32 + "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk")))))) + (home-page "http://svnsis.ethz.ch") + (synopsis "Utility classes for libraries from ETH Zurich") + (description "This library supplies some utility classes needed for +libraries from the SIS division at ETH Zurich like jHDF5.") + ;; 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-cisd-args4j + (let ((revision 39162) + (base-version "9.11.2")) + (package + (name "java-cisd-args4j") + (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/" + "args4j/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/args4j/")) + (revision revision))) + (file-name (string-append "java-cisd-args4j-" version "-checkout")) + (sha256 + (base32 + "0hhqznjaivq7ips7mkwas78z42s6djsm20rrs7g1zd59rcsakxn2")))) + (build-system ant-build-system) + (arguments + `(#:make-flags '("-file" "build/build.xml") + #:tests? #f ; there are no tests + ;; There are weird build failures with JDK8, such as: "The type + ;; java.io.ObjectInputStream cannot be resolved. It is indirectly + ;; referenced from required .class files" + #:jdk ,icedtea-7 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform) + (sxml xpath)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "../build_resources") + (invoke "tar" "xf" (assoc-ref inputs "build-resources") + "-C" "../build_resources" + "--strip-components=1") + (mkdir-p "../build_resources/lib") + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + ;; FIXME: There should be a more convenient abstraction for + ;; editing XML files. + (with-directory-excursion "../build_resources/ant/" + (chmod "build-common.xml" #o664) + (call-with-output-file "build-common.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build-common.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove dependency on classycle and custom ant tasks + (taskdef . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) kids))) + (if (or (member "build-info" name) + (member "dependency-checker" name) + (member "build-java-subprojects" name) + (member "project-classpath" name)) + '() ; skip + `(,tag ,@kids))))) + (typedef . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) kids))) + (if (member "recursive-jar" name) + '() ; skip + `(,tag ,@kids))))) + (build-java-subprojects . ,(lambda _ '())) + ;; Ignore everything else + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build-common.xml.new" "build-common.xml")) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/cisd-base/cisd-base.jar") + (string-append (assoc-ref inputs "java-cisd-base") + "/share/java/sis-base.jar")) + ;; Remove dependency on svn + (("<build-info.*") "") + (("\\$\\{revision.number\\}") + ,(number->string revision)) + (("\\$\\{version.number\\}") ,base-version) + ;; Don't use custom ant tasks. + (("recursive-jar") "jar") + (("<project-classpath.*") "")) + #t)) + (replace 'install (install-jars "targets/dist"))))) + (inputs + `(("java-cisd-base" ,java-cisd-base))) + (native-inputs + `(("ecj" ,java-ecj-3.5) + ("build-resources" + ,(origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "args4j/tags/release/" + (version-major+minor base-version) + ".x/" base-version + "/build_resources/")) + (revision revision))) + (sha256 + (base32 + "056cam4k8pll7ass31sy6gwn8g8719njc41yf4l02b0342nilkyf")) + (modules '((guix build utils))) + ;; Delete bundled pre-built jars. + (snippet + '(begin (delete-file-recursively "lib/") #t)))))) + (home-page "http://svnsis.ethz.ch") + (synopsis "Command line parser library") + (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") @@ -5584,7 +6023,9 @@ tree walking, and translation.") version ".tar.gz")) (sha256 (base32 - "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m")))) + "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m")) + (patches + (search-patches "antlr3-3_3-fix-java8-compilation.patch")))) (arguments `(#:jar-name (string-append ,name "-" ,version ".jar") #:source-dir (string-join '("tool/src/main/java" @@ -5674,7 +6115,9 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;")) version ".tar.gz")) (sha256 (base32 - "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z")))) + "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z")) + (patches + (search-patches "antlr3-3_1-fix-java8-compilation.patch")))) (arguments `(#:jar-name (string-append "antlr3-" ,version ".jar") #:source-dir "src:runtime/Java/src" @@ -6537,7 +6980,8 @@ it manages project dependencies, gives diffs jars, and much more.") ;; packaging. It uses the version referenced in pom.xml. We replace ;; it with our own version. (substitute* "src/test/java/org/ops4j/pax/tinybundles/bnd/BndTest.java" - (("2.4.0.201411031534") "3.4.0"))))))) + (("[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*") + ,(package-version java-aqute-bndlib)))))))) (inputs `(("lang" ,java-ops4j-base-lang) ("io" ,java-ops4j-base-io) @@ -8853,3 +9297,44 @@ against expected outcomes.") ("java-junit" ,java-junit))) (native-inputs `(("java-mockito-1" ,java-mockito-1))))) + +(define-public java-openchart2 + (package + (name "java-openchart2") + (version "1.4.3") + (source (origin + (method url-fetch) + (uri (string-append "http://download.approximatrix.com/openchart2/" + "openchart2-" version ".source.zip")) + (sha256 + (base32 + "1xq96zm5r02n1blja0072jmmsifmxc40lbyfbnmcnr6mw42frh4g")))) + (build-system ant-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-junit-errors + (lambda _ + (with-directory-excursion "unittest/src/com/approximatrix/charting/" + (substitute* '("coordsystem/ticklocator/NumericXTickLocatorTest.java" + "coordsystem/ticklocator/NumericYTickLocatorTest.java" + "coordsystem/ticklocator/ObjectXTickLocatorTest.java" + "model/DefaultChartDataModelConstraintsTest.java" + "model/MultiScatterDataModelConstraintsTest.java" + "model/threedimensional/DotPlotDataModelConstraintsTest.java") + (("(assertEquals[^;]+);" before _) + (string-append (string-drop-right before 2) ", 1E-6);")))) + #t)) + (replace 'install (install-jars "."))))) + (native-inputs + `(("unzip" ,unzip) + ("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://approximatrix.com/products/openchart2/") + (synopsis "Simple plotting for Java") + (description "Openchart2 provides a simple, yet powerful, interface for +Java programmers to create two-dimensional charts and plots. The library +features an assortment of graph styles, including advanced scatter plots, bar +graphs, and pie charts.") + (license license:lgpl2.1+))) |