cytoscape: bump java-overlay version to 2.7, fix swingx dep.

1 files changed, 144 insertions, 0 deletions

diff --git a/sci-biology/cytoscape/cytoscape-2.7.0.ebuild b/sci-biology/cytoscape/cytoscape-2.7.0.ebuild
new file mode 100644
index 0000000..8f77943
--- /dev/null
+++ b/sci-biology/cytoscape/cytoscape-2.7.0.ebuild
@@ -0,0 +1,144 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+EANT_ANT_TASKS="jakarta-regexp-1.4 batik-1.7 xalan xsdlib relaxng-datatype jaxb-2"
+EANT_GENTOO_CLASSPATH="swing-layout-1,stax-ex,xmlstreambuffer,sjsxp,concurrent-util,jsr173,jsr181,jsr250,saaj-api,fastinfoset,junit,batik-1.7,freehep-graphicsio-svg,freehep-util,freehep-xml,freehep-export,freehep-graphicsio,freehep-graphicsio-java,freehep-swing,freehep-graphicsio-ps,freehep-io,freehep-graphics2d,freehep-misc-deps,itext,swingx-0.9,piccolo2d,tclib"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+inherit versionator java-pkg-2 java-ant-2 eutils
+
+MY_PV=$(replace_all_version_separators '_')
+
+DESCRIPTION="A visualization platform for molecular interaction networks"
+HOMEPAGE="http://www.cytoscape.org/"
+SRC_URI="http://chianti.ucsd.edu/Cyto-${MY_PV}/cytoscapeSource-v${PV}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/swing-layout:1
+	dev-java/stax-ex
+	dev-java/xmlstreambuffer
+	dev-java/sjsxp
+	dev-java/concurrent-util
+	dev-java/jsr173
+	dev-java/jsr181
+	dev-java/jsr250
+	java-virtuals/saaj-api
+	dev-java/fastinfoset
+	dev-java/itext
+	dev-java/jdom:1.0
+	dev-java/junit
+	dev-java/colt
+	dev-java/javahelp
+	>=dev-java/swingx-0.9.5
+	>=dev-java/l2fprod-common-7.3-r1
+	dev-java/tclib
+	dev-java/piccolo2d
+	~dev-java/biojava-1.6
+	dev-java/freehep-graphicsio-java
+	dev-java/freehep-graphicsio-ps
+	dev-java/freehep-graphicsio-svg
+	dev-java/freehep-xml
+	dev-java/jgoodies-looks:2.0"
+#	dev-java/jaxb dev-java/javahelp
+DEPEND=">=virtual/jdk-1.6
+	dev-java/jakarta-regexp:1.4
+	>=dev-java/batik-1.7-r1
+	dev-java/xalan
+	dev-java/xsdlib
+	dev-java/relaxng-datatype
+	${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+	${COMMON_DEPS}"
+
+S="${WORKDIR}"
+
+java_prepare() {
+	einfo "Removing bundled jars..."
+	find -name 'stax-ex.jar' -print -delete
+	find -name 'saaj.jar' -print -delete
+	find -name 'streambuffer.jar' -print -delete
+	find -name 'sjsxp.jar' -print -delete
+	find -name 'concurrent.jar' -print -delete
+	find -name 'jsr*.jar' -print -delete
+	find -name 'FastInfoset.jar' -print -delete
+	find -name 'jaxws-*.jar' -print -delete
+	find -name 'http.jar' -print -delete
+	find -name 'activation.jar' -print -delete
+	find -name 'glf.jar' -print -delete
+	find -name 'freehep*.jar' -print -delete
+	find -name 'itext*.jar' -print -delete
+	find -name 'swingx*.jar' -print -delete
+	find -name 'piccolo*.jar' -print -delete
+	find -name 'jnlp.jar' -print -delete
+#	find -name 'wizard.jar' -print -delete
+#	find -name 'jaxb*.jar' -print -delete
+#	find -name 'swingunit.jar' -print -delete
+
+	cd extra-jars
+	find -name '*.jar' -print -delete
+	cd "${S}"
+
+	cd lib
+	find -name 'colt.jar' -print -delete
+	java-pkg_jar-from colt
+	find -name 'jhall.jar' -print -delete
+	java-pkg_jar-from javahelp
+	find -name 'looks-*.jar' -print -delete
+	java-pkg_jar-from jgoodies-looks-2.0
+	find -name 'jdom*.jar' -print -delete
+	java-pkg_jar-from jdom-1.0
+	find -name 'junit.jar' -print -delete
+	java-pkg_jar-from junit
+	find -name 'l2fprod-common*.jar' -print -delete
+	java-pkg_jar-from l2fprod-common
+	find -name 'swing-layout*.jar' -print -delete
+	java-pkg_jar-from swing-layout-1
+	find -name 'biojava*.jar' -print -delete
+	java-pkg_jar-from biojava
+	find -name 'tclib.jar' -print -delete
+	cd "${S}"
+
+	cd lib/build-libs
+	find -name 'batik*.jar' -print -delete
+	java-pkg_jar-from batik-1.7
+	find -name 'jakarta*.jar' -print -delete
+	java-pkg_jar-from jakarta-regexp-1.4
+	find -name 'xalan*.jar' -print -delete
+	java-pkg_jar-from xalan
+	find -name 'xsdlib*.jar' -print -delete
+	java-pkg_jar-from xsdlib
+	find -name 'relaxngDatatype.jar' -print -delete
+	java-pkg_jar-from relaxng-datatype
+	cd "${S}"
+
+	# Skip the jalopy ant build target (produces access violations)
+	perl -i -ne 'print unless /taskdef.*name="jalopy"/../<\/target>/' build.xml || die
+
+	# TODO: HACK. Rip out the rasterize task because of batik incompatibility
+	perl -i -ne 'print unless /taskdef.*name="rasterize"/../<\/taskdef>/' build.xml || die
+	perl -i -ne 'print unless /^\s*<rasterize/../^\s*dest=.*>/' build.xml || die
+}
+
+src_install() {
+	java-pkg_dojar cytoscape.jar
+	java-pkg_dojar lib/*.jar
+	java-pkg_jarinto /usr/share/${PN}/plugins
+	java-pkg_dojar plugins/core/*.jar
+
+	# replacement for resources/bin/cytoscape.sh
+	java-pkg_dolauncher cytoscape.sh --main cytoscape.CyMain \
+		--java_args '-Dswing.aatext=true -Xss5M -Xmx512M' \
+		--pkg_args '-p '/usr/share/${PN}/plugins' \"$@\"'
+	insinto /usr/share/pixmaps
+	newins images/icon100.png cytoscape.png
+	make_desktop_entry cytoscape.sh Cytoscape /usr/share/pixmaps/cytoscape.png
+
+	dodoc docs/pdf/manual.pdf
+}