[med-svn] r12588 - in trunk/packages/biojava3/tags: . 3.0.5-1/debian 3.0.5-1/debian/patches
olivier sallou
osallou-guest at alioth.debian.org
Wed Dec 5 09:42:08 UTC 2012
Author: osallou-guest
Date: 2012-12-05 09:42:07 +0000 (Wed, 05 Dec 2012)
New Revision: 12588
Added:
trunk/packages/biojava3/tags/3.0.5-1/
trunk/packages/biojava3/tags/3.0.5-1/debian/build.xml
trunk/packages/biojava3/tags/3.0.5-1/debian/changelog
trunk/packages/biojava3/tags/3.0.5-1/debian/control
trunk/packages/biojava3/tags/3.0.5-1/debian/get-orig-source
trunk/packages/biojava3/tags/3.0.5-1/debian/patches/fix_ascii_characters_mapping
trunk/packages/biojava3/tags/3.0.5-1/debian/patches/series
trunk/packages/biojava3/tags/3.0.5-1/debian/patches/use_simple_json
Removed:
trunk/packages/biojava3/tags/3.0.5-1/debian/build.xml
trunk/packages/biojava3/tags/3.0.5-1/debian/changelog
trunk/packages/biojava3/tags/3.0.5-1/debian/control
trunk/packages/biojava3/tags/3.0.5-1/debian/get-orig-source
trunk/packages/biojava3/tags/3.0.5-1/debian/patches/fix_ascii_character_issue
trunk/packages/biojava3/tags/3.0.5-1/debian/patches/series
trunk/packages/biojava3/tags/3.0.5-1/debian/patches/use_simple_json
Log:
[svn-buildpackage] Tagging biojava3-live 3.0.5-1
Deleted: trunk/packages/biojava3/tags/3.0.5-1/debian/build.xml
===================================================================
--- trunk/packages/biojava3/trunk/debian/build.xml 2012-12-02 18:09:59 UTC (rev 12581)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/build.xml 2012-12-05 09:42:07 UTC (rev 12588)
@@ -1,113 +0,0 @@
-<?xml version="1.0" ?>
-<project name="BJLIB" default="jar" basedir=".">
- <!-- Directory structure -->
- <property name="build.dir" location="../build/BJLIB"/>
- <property name="test.dir" location="../buildtest/BJLIB"/>
- <property name="dist.dir" location="../dist"/>
- <property name="src.dir" location="src/main/java"/>
- <property name="resources.dir" location="src/main/resources"/>
- <property name="test.src.dir" location="src/test/java"/>
- <property name="test.resources.dir" location="src/test/resources"/>
- <property name="lib.dir" location="/usr/share/java"/>
- <property name="docs.dir" location="../javadoc"/>
- <property name="docs.lib.dir" location="../doc/BJLIB"/>
- <property name="class.dir" location="${build.dir}/classes"/>
- <property name="test.class.dir" location="${test.dir}/classes"/>
-
- <property name="project.name" value="biojava"/>
- <property name="debug" value="true"/>
- <property name="optimized" value="true"/>
- <property name="project.version" value="1.8.2"/>
- <property environment="env"/>
- <property name="project.jarfile.name" value="BJLIB.jar"/>
-
- <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar"/>
-
- <path id="compile.classpath">
- <fileset dir="${lib.dir}">
- <include name="commons-cli.jar"/>
- <include name="commons-collections.jar"/>
- <include name="commons-dbcp.jar"/>
- <include name="commons-pool.jar"/>
- <include name="junit4.jar"/>
- <include name="guava.jar"/>
- <include name="jgrapht0.8.jar"/>
- <include name="Jmol.jar"/>
- <include name="hamcrest.jar"/>
- <include name="json_simple.jar"/>
- </fileset>
- <fileset dir="${dist.dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="/usr/share/icedtea-web">
- <include name="netx.jar"/>
- </fileset>
- </path>
-
-
- <target name="clean">
- <echo level="info">Cleaning build directories</echo>
- <delete verbose="true" includeEmptyDirs="true">
- <fileset dir="${build.dir}" includes="**"/>
- <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
- </delete>
- </target>
-
- <target name="javadocs">
- <mkdir dir="${docs.dir}"/>
- <mkdir dir="${docs.lib.dir}"/>
- <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*">
- <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
- </javadoc>
- </target>
-
- <target name="compile">
- <mkdir dir="${class.dir}"/>
- <mkdir dir="${dist.dir}"/>
- <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
- </javac>
- <copy todir="${class.dir}" failonerror="false">
- <fileset dir="${resources.dir}"/>
- </copy>
- </target>
-
- <target name="compile-test">
- <mkdir dir="${test.class.dir}"/>
- <javac srcdir="${test.src.dir}" destdir="${test.class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true">
- </javac>
- <copy todir="${test.class.dir}" failonerror="false">
- <fileset dir="${test.resources.dir}"/>
- </copy>
- <copy todir="${test.class.dir}" failonerror="false">
- <fileset dir="${src.dir}"/>
- </copy>
- </target>
-
- <path id="test.classpath">
- <path refid="compile.classpath"/>
- <pathelement location="${test.class.dir}" />
- </path>
-
- <target name="test" depends="compile-test">
- <junit haltonfailure="yes" printsummary="yes">
- <classpath refid="test.classpath"/>
- <formatter type="plain" usefile="false" />
- <batchtest>
- <fileset dir="${test.class.dir}" includes="**/*Test.class" excludes="**/Abstract*.class" />
- </batchtest>
- </junit>
- </target>
-
- <target name="jar" depends="compile">
- <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
- <manifest>
- <attribute name="Built-By" value="Debian-Med team"/>
- <attribute name="Class-Path" value="${class.path}"/>
- <attribute name="Specification-Title" value="BioJava"/>
- <attribute name="Specification-Version" value="${project.version}"/>
- </manifest>
- </jar>
- </target>
-
-</project>
-
Copied: trunk/packages/biojava3/tags/3.0.5-1/debian/build.xml (from rev 12584, trunk/packages/biojava3/trunk/debian/build.xml)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-1/debian/build.xml (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/build.xml 2012-12-05 09:42:07 UTC (rev 12588)
@@ -0,0 +1,116 @@
+<?xml version="1.0" ?>
+<project name="BJLIB" default="jar" basedir=".">
+ <!-- Directory structure -->
+ <property name="build.dir" location="../build/BJLIB"/>
+ <property name="test.dir" location="../buildtest/BJLIB"/>
+ <property name="dist.dir" location="../dist"/>
+ <property name="src.dir" location="src/main/java"/>
+ <property name="resources.dir" location="src/main/resources"/>
+ <property name="test.src.dir" location="src/test/java"/>
+ <property name="test.resources.dir" location="src/test/resources"/>
+ <property name="lib.dir" location="/usr/share/java"/>
+ <property name="docs.dir" location="../javadoc"/>
+ <property name="docs.lib.dir" location="../doc/BJLIB"/>
+ <property name="class.dir" location="${build.dir}/classes"/>
+ <property name="test.class.dir" location="${test.dir}/classes"/>
+
+ <property name="project.name" value="biojava"/>
+ <property name="debug" value="true"/>
+ <property name="optimized" value="true"/>
+ <property name="project.version" value="1.8.2"/>
+ <property environment="env"/>
+ <property name="project.jarfile.name" value="BJLIB.jar"/>
+
+ <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar"/>
+
+ <path id="compile.classpath">
+ <fileset dir="${lib.dir}">
+ <include name="commons-cli.jar"/>
+ <include name="commons-collections.jar"/>
+ <include name="commons-dbcp.jar"/>
+ <include name="commons-pool.jar"/>
+ <include name="commons-codec.jar"/>
+ <include name="itext5.jar"/>
+ <include name="Jmol.jar"/>
+ <include name="junit4.jar"/>
+ <include name="guava.jar"/>
+ <include name="jgrapht0.8.jar"/>
+ <include name="JmolApplet.jar"/>
+ <include name="hamcrest.jar"/>
+ <include name="json_simple.jar"/>
+ </fileset>
+ <fileset dir="${dist.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="/usr/share/icedtea-web">
+ <include name="netx.jar"/>
+ </fileset>
+ </path>
+
+
+ <target name="clean">
+ <echo level="info">Cleaning build directories</echo>
+ <delete verbose="true" includeEmptyDirs="true">
+ <fileset dir="${build.dir}" includes="**"/>
+ <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
+ </delete>
+ </target>
+
+ <target name="javadocs">
+ <mkdir dir="${docs.dir}"/>
+ <mkdir dir="${docs.lib.dir}"/>
+ <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*">
+ <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
+ </javadoc>
+ </target>
+
+ <target name="compile">
+ <mkdir dir="${class.dir}"/>
+ <mkdir dir="${dist.dir}"/>
+ <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
+ </javac>
+ <copy todir="${class.dir}" failonerror="false">
+ <fileset dir="${resources.dir}"/>
+ </copy>
+ </target>
+
+ <target name="compile-test">
+ <mkdir dir="${test.class.dir}"/>
+ <javac srcdir="${test.src.dir}" destdir="${test.class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true">
+ </javac>
+ <copy todir="${test.class.dir}" failonerror="false">
+ <fileset dir="${test.resources.dir}"/>
+ </copy>
+ <copy todir="${test.class.dir}" failonerror="false">
+ <fileset dir="${src.dir}"/>
+ </copy>
+ </target>
+
+ <path id="test.classpath">
+ <path refid="compile.classpath"/>
+ <pathelement location="${test.class.dir}" />
+ </path>
+
+ <target name="test" depends="compile-test">
+ <junit haltonfailure="yes" printsummary="yes">
+ <classpath refid="test.classpath"/>
+ <formatter type="plain" usefile="false" />
+ <batchtest>
+ <fileset dir="${test.class.dir}" includes="**/*Test.class" excludes="**/Abstract*.class" />
+ </batchtest>
+ </junit>
+ </target>
+
+ <target name="jar" depends="compile">
+ <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
+ <manifest>
+ <attribute name="Built-By" value="Debian-Med team"/>
+ <attribute name="Class-Path" value="${class.path}"/>
+ <attribute name="Specification-Title" value="BioJava"/>
+ <attribute name="Specification-Version" value="${project.version}"/>
+ </manifest>
+ </jar>
+ </target>
+
+</project>
+
Deleted: trunk/packages/biojava3/tags/3.0.5-1/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog 2012-12-02 18:09:59 UTC (rev 12581)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/changelog 2012-12-05 09:42:07 UTC (rev 12588)
@@ -1,15 +0,0 @@
-biojava3-live (3.0.4-2) unstable; urgency=low
-
- [ Olivier Sallou ]
- Patch from James Page <james.page at ubuntu.com> (Closes: #683513).
- * Transition to use default java implementation:
- - d/control: Use default-jdk (>= 1:1.6) instead of openjdk-6-jdk
- for package build.
-
- -- Olivier Sallou <osallou at debian.org> Wed, 01 Aug 2012 15:45:32 +0200
-
-biojava3-live (3.0.4-1) unstable; urgency=low
-
- * Initial release (Closes: #674265)
-
- -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Copied: trunk/packages/biojava3/tags/3.0.5-1/debian/changelog (from rev 12587, trunk/packages/biojava3/trunk/debian/changelog)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-1/debian/changelog (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/changelog 2012-12-05 09:42:07 UTC (rev 12588)
@@ -0,0 +1,22 @@
+biojava3-live (3.0.5-1) unstable; urgency=low
+
+ * New upstream release
+ * Use forester 1.005
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 02 Dec 2012 22:35:09 +0100
+
+biojava3-live (3.0.4-2) unstable; urgency=low
+
+ [ Olivier Sallou ]
+ Patch from James Page <james.page at ubuntu.com> (Closes: #683513).
+ * Transition to use default java implementation:
+ - d/control: Use default-jdk (>= 1:1.6) instead of openjdk-6-jdk
+ for package build.
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 01 Aug 2012 15:45:32 +0200
+
+biojava3-live (3.0.4-1) unstable; urgency=low
+
+ * Initial release (Closes: #674265)
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Deleted: trunk/packages/biojava3/tags/3.0.5-1/debian/control
===================================================================
--- trunk/packages/biojava3/trunk/debian/control 2012-12-02 18:09:59 UTC (rev 12581)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/control 2012-12-05 09:42:07 UTC (rev 12588)
@@ -1,72 +0,0 @@
-Source: biojava3-live
-Section: java
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Olivier Sallou <osallou at debian.org>
-Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
- libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
- libcommons-cli-java, libguava-java (>= 11.0.1),
- default-jdk (>= 1:1.6), junit4,javahelper (>=0.25), libjgrapht-java,
- ant-optional, jmol-applet, icedtea-netx, libhamcrest-java, libjson-simple-java
-Build-Depends: debhelper (>= 9), ant
-Standards-Version: 3.9.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/biojava3/trunk/
-Homepage: http://www.biojava.org
-
-Package: libbiojava3.0-java
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends},
- libcommons-pool-java (>= 1.1),
- libcommons-collections-java (>= 2.1),
- libcommons-dbcp-java (>= 1.1),
- libhsqldb-java,
- libbytecode-java,
- jmol-applet, icedtea-netx,
- libjson-simple-java
-Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
-Description: Java API to biological data and applications (version 3)
- This package presents the Open Source Java API to biological databases
- and a series of mostly sequence-based algorithms.
- .
- BioJava is an open-source project dedicated to providing a Java framework
- for processing biological data. It includes objects for manipulating
- sequences, file parsers, server support, access to BioSQL
- and Ensembl databases, and powerful analysis and statistical routines
- including a dynamic programming toolkit.
-
-Package: libbiojava3-java
-Architecture: all
-Depends: libbiojava3.0-java, ${misc:Depends}
-Provides: libbiojava3-java
-Description: Java API to biological data and applications (default version)
- BioJava is an open-source project dedicated to providing a Java framework
- for processing biological data. It includes objects for manipulating
- sequences, file parsers, server support, access to BioSQL
- and Ensembl databases, and powerful analysis and statistical routines
- including a dynamic programming toolkit.
- .
- BioJava is provided by a vibrant community which meets annually at
- the Bioinformatics Open Source Conference (BOSC) that traditionally
- accompanies the Intelligent Systems in Molecular Biology (ISMB)
- meeting. Much like BioPerl, the employment of this library is valuable
- for everybody active in the field because of the many tricks of the
- trade one learns just by communicating on the mailing list.
- .
- This is a wrapper package which should enable smooth upgrades to new
- versions.
-
-Package: libbiojava3-java-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends}
-Recommends: konqueror|html-browser
-Suggests: libbiojava3-java-demos, libbiojava3-java
-Description: [Biology] Documentation for BioJava
- BioJava is an open-source project dedicated to providing a Java framework
- for processing biological data.
- .
- This package contains the HTML documentation describing the API of BioJava
- which was generated automatically by JavaDoc.
-
Copied: trunk/packages/biojava3/tags/3.0.5-1/debian/control (from rev 12585, trunk/packages/biojava3/trunk/debian/control)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-1/debian/control (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/control 2012-12-05 09:42:07 UTC (rev 12588)
@@ -0,0 +1,76 @@
+Source: biojava3-live
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
+ libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-cli-java, libguava-java (>= 11.0.1),
+ libcommons-codec-java, libitext5-java, libjmol-java,
+ default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
+ ant-optional, icedtea-netx, libhamcrest-java, libjson-simple-java
+Build-Depends: debhelper (>= 9), ant
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/biojava3/trunk/
+Homepage: http://www.biojava.org
+
+Package: libbiojava3.0-java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libcommons-pool-java (>= 1.1),
+ libcommons-collections-java (>= 2.1),
+ libcommons-dbcp-java (>= 1.1),
+ libhsqldb-java,
+ libbytecode-java,
+ icedtea-netx,
+ libjson-simple-java,
+ libcommons-codec-java,
+ libitext5-java,
+ libjmol-java
+Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
+Description: Java API to biological data and applications (version 3)
+ This package presents the Open Source Java API to biological databases
+ and a series of mostly sequence-based algorithms.
+ .
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+
+Package: libbiojava3-java
+Architecture: all
+Depends: libbiojava3.0-java, ${misc:Depends}
+Provides: libbiojava3-java
+Description: Java API to biological data and applications (default version)
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+ .
+ BioJava is provided by a vibrant community which meets annually at
+ the Bioinformatics Open Source Conference (BOSC) that traditionally
+ accompanies the Intelligent Systems in Molecular Biology (ISMB)
+ meeting. Much like BioPerl, the employment of this library is valuable
+ for everybody active in the field because of the many tricks of the
+ trade one learns just by communicating on the mailing list.
+ .
+ This is a wrapper package which should enable smooth upgrades to new
+ versions.
+
+Package: libbiojava3-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: konqueror|html-browser
+Suggests: libbiojava3-java-demos, libbiojava3-java
+Description: [Biology] Documentation for BioJava
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data.
+ .
+ This package contains the HTML documentation describing the API of BioJava
+ which was generated automatically by JavaDoc.
+
Deleted: trunk/packages/biojava3/tags/3.0.5-1/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/trunk/debian/get-orig-source 2012-12-02 18:09:59 UTC (rev 12581)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/get-orig-source 2012-12-05 09:42:07 UTC (rev 12588)
@@ -1,37 +0,0 @@
-#!/bin/bash
-
-set -e
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --verbose --force-download --no-symlink |
- grep "Newest version on remote site is .* local version is .*" |
- head -n 1 |
- sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
-
-mkdir -p ../tarballs
-
-cd ../tarballs
-#biojava-3.0.4-all.tar.gz
-UTAR="biojava-${VERSION}-all.tar.gz"
-mv ../${UTAR} .
-tar -xzf ${UTAR}
-
-mv bj${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
-
-cd $PKG-${VERSION}.orig
- rm -rf target
- rm -rf biojava3*/target
-
-mkdir -p biojava3-forester/src/main/java
-cd biojava3-forester/src/main/java
- wget http://www.biojava.org/download/maven/org/forester/0.955/forester-0.955-sources.jar
- jar xf forester-0.955-sources.jar
- find . -name *.class | xargs rm -f
-cd ../../../..
-cd ..
-
-BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig
-rm -rf ${PKG}-${VERSION}.orig
-
-rm ${UTAR}
-
Copied: trunk/packages/biojava3/tags/3.0.5-1/debian/get-orig-source (from rev 12584, trunk/packages/biojava3/trunk/debian/get-orig-source)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-1/debian/get-orig-source (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/get-orig-source 2012-12-05 09:42:07 UTC (rev 12588)
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download --no-symlink |
+ grep "Newest version on remote site is .* local version is .*" |
+ head -n 1 |
+ sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+
+cd ../tarballs
+#biojava-3.0.4-all.tar.gz
+UTAR="biojava-${VERSION}-all.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv bj${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
+
+cd $PKG-${VERSION}.orig
+ rm -rf target
+ rm -rf biojava3*/target
+
+mkdir -p biojava3-forester/src/main/java
+cd biojava3-forester/src/main/java
+ wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar
+ jar xf forester-1.005-sources-1.005.jar
+ find . -name *.class | xargs rm -f
+cd ../../../..
+cd ..
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig
+rm -rf ${PKG}-${VERSION}.orig
+
+rm ${UTAR}
+
Deleted: trunk/packages/biojava3/tags/3.0.5-1/debian/patches/fix_ascii_character_issue
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue 2012-12-02 18:09:59 UTC (rev 12581)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/patches/fix_ascii_character_issue 2012-12-05 09:42:07 UTC (rev 12588)
@@ -1,16 +0,0 @@
-Subject: ASCII error in pbuilder
-Description: unmappable character for encoding ASCII
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2012-05-31
-
---- a/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
-+++ b/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
-@@ -44,7 +44,7 @@
- /**
- * Method for access REST
- * @param query
-- * service name¡¢method name and parameter for exection rest
-+ * service name method name and parameter for exection rest
- * @return
- * execution result
- * @throws IOException
Copied: trunk/packages/biojava3/tags/3.0.5-1/debian/patches/fix_ascii_characters_mapping (from rev 12587, trunk/packages/biojava3/trunk/debian/patches/fix_ascii_characters_mapping)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-1/debian/patches/fix_ascii_characters_mapping (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/patches/fix_ascii_characters_mapping 2012-12-05 09:42:07 UTC (rev 12588)
@@ -0,0 +1,17 @@
+Subject: ASCII error in pbuilder
+Description: unmappable character for encoding ASCII
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2012-12-05
+Forwarded: yes
+Bug: http://code.google.com/p/forester/issues/detail?id=1
+--- a/biojava3-forester/src/main/java/org/forester/test/Test.java
++++ b/biojava3-forester/src/main/java/org/forester/test/Test.java
+@@ -1310,7 +1310,7 @@
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
+- .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
++ .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489-493." ) ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
Deleted: trunk/packages/biojava3/tags/3.0.5-1/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series 2012-12-02 18:09:59 UTC (rev 12581)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/patches/series 2012-12-05 09:42:07 UTC (rev 12588)
@@ -1,3 +0,0 @@
-use_simple_json
-fix_code_to_support_latest_jmol
-fix_ascii_character_issue
Copied: trunk/packages/biojava3/tags/3.0.5-1/debian/patches/series (from rev 12587, trunk/packages/biojava3/trunk/debian/patches/series)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-1/debian/patches/series (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/patches/series 2012-12-05 09:42:07 UTC (rev 12588)
@@ -0,0 +1,3 @@
+use_simple_json
+fix_code_to_support_latest_jmol
+fix_ascii_characters_mapping
Deleted: trunk/packages/biojava3/tags/3.0.5-1/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/use_simple_json 2012-12-02 18:09:59 UTC (rev 12581)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/patches/use_simple_json 2012-12-05 09:42:07 UTC (rev 12588)
@@ -1,56 +0,0 @@
-Subject: use simple_json library
-Author: Olivier Sallou <osallou at debian.org>
-Description: json.org library is not "free", use simple_json
- library and update according to API
-Last-Updated: 2012-05-30
-
---- a/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
-+++ b/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
-@@ -13,8 +13,9 @@
- import java.util.TreeSet;
-
- import org.biojava3.core.sequence.ProteinSequence;
--import org.json.JSONArray;
--import org.json.JSONObject;
-+import org.json.simple.JSONArray;
-+import org.json.simple.JSONObject;
-+import org.json.simple.JSONValue;
-
-
- /** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
-@@ -102,15 +103,14 @@
-
- SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
- try {
-- JSONObject json = new JSONObject(result.toString());
-+ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
-+ JSONObject hmresults = (JSONObject) json.get("results");
-
-- JSONObject hmresults = json.getJSONObject("results");
-
-+ JSONArray hits = (JSONArray) hmresults.get("hits");
-
-- JSONArray hits = hmresults.getJSONArray("hits");
--
-- for(int i =0 ; i < hits.length() ; i++){
-- JSONObject hit = hits.getJSONObject(i);
-+ for(int i =0 ; i < hits.size() ; i++){
-+ JSONObject hit = (JSONObject) hits.get(i);
- //System.out.println("hit: "+ hit);
-
- HmmerResult hmmResult = new HmmerResult();
-@@ -125,11 +125,11 @@
- hmmResult.setPvalue((Double)hit.get("pvalue"));
- hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
-
-- JSONArray hmmdomains = hit.getJSONArray("domains");
-+ JSONArray hmmdomains = (JSONArray) hit.get("domains");
-
- SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
-- for ( int j= 0 ; j < hmmdomains.length() ; j++){
-- JSONObject d = hmmdomains.getJSONObject(j);
-+ for ( int j= 0 ; j < hmmdomains.size() ; j++){
-+ JSONObject d = (JSONObject) hmmdomains.get(j);
- //System.out.println(d);
- Integer is_reported = getInteger(d.get("is_reported"));
- if ( is_reported != 1) {
Copied: trunk/packages/biojava3/tags/3.0.5-1/debian/patches/use_simple_json (from rev 12582, trunk/packages/biojava3/trunk/debian/patches/use_simple_json)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-1/debian/patches/use_simple_json (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-1/debian/patches/use_simple_json 2012-12-05 09:42:07 UTC (rev 12588)
@@ -0,0 +1,54 @@
+Subject: use simple_json library
+Author: Olivier Sallou <osallou at debian.org>
+Description: json.org library is not "free", use simple_json
+ library and update according to API
+Last-Updated: 2012-12-02
+
+--- a/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
++++ b/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java
+@@ -13,8 +13,9 @@
+ import java.util.TreeSet;
+
+ import org.biojava3.core.sequence.ProteinSequence;
+-import net.sf.json.JSONArray;
+-import net.sf.json.JSONObject;
++import org.json.simple.JSONArray;
++import org.json.simple.JSONObject;
++import org.json.simple.JSONValue;
+
+
+ /** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
+@@ -102,15 +103,13 @@
+
+ SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
+ try {
+- JSONObject json = JSONObject.fromObject(result.toString());
++ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
++ JSONObject hmresults = (JSONObject) json.get("results");
+
+- JSONObject hmresults = json.getJSONObject("results");
+-
+-
+- JSONArray hits = hmresults.getJSONArray("hits");
++ JSONArray hits = (JSONArray) hmresults.get("hits");
+
+ for(int i =0 ; i < hits.size() ; i++){
+- JSONObject hit = hits.getJSONObject(i);
++ JSONObject hit = (JSONObject) hits.get(i);
+ //System.out.println("hit: "+ hit);
+
+ HmmerResult hmmResult = new HmmerResult();
+@@ -134,11 +133,11 @@
+ hmmResult.setPvalue((Double)hit.get("pvalue"));
+ hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
+
+- JSONArray hmmdomains = hit.getJSONArray("domains");
++ JSONArray hmmdomains = (JSONArray) hit.get("domains");
+
+ SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
+ for ( int j= 0 ; j < hmmdomains.size() ; j++){
+- JSONObject d = hmmdomains.getJSONObject(j);
++ JSONObject d = (JSONObject) hmmdomains.get(j);
+ //System.out.println(d);
+ Integer is_reported = getInteger(d.get("is_reported"));
+ if ( is_reported != 1) {
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