[med-svn] r17930 - in trunk/packages/biojava3/tags: . 3.1.0+dfsg-1/debian 3.1.0+dfsg-1/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Wed Sep 3 06:17:34 UTC 2014
Author: osallou
Date: 2014-09-03 06:17:33 +0000 (Wed, 03 Sep 2014)
New Revision: 17930
Added:
trunk/packages/biojava3/tags/3.1.0+dfsg-1/
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/README.source
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/changelog
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/control
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/get-orig-source
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/java8_compatibility.patch
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/series
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/skip_network_related_tests
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/use_simple_json
Removed:
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/README.source
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/changelog
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/control
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/get-orig-source
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/series
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/skip_network_related_tests
trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/use_simple_json
Log:
[svn-buildpackage] Tagging biojava3-live 3.1.0+dfsg-1
Deleted: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/README.source
===================================================================
--- trunk/packages/biojava3/trunk/debian/README.source 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/README.source 2014-09-03 06:17:33 UTC (rev 17930)
@@ -1,13 +0,0 @@
-biojava for Debian
-------------------
-
-Biojava3 uses the forester library version 0.955. The source version is hosted in Biojava repo only and does not
-match any release available in forester web site. To manage, a specific biojava3-forester library is created.
-The get-orig-source embeds this library version in the code. Future releases are expected to refer to forester code/release
- and forester code embedding should not be needed anymore.
-
-json.org dependency is replaced by json-simple with a patch for biojava3-ws. Future release will use json-lib
-
-Some tests are skipped due to errors dependending on context (nfs dirs), remote access required....
-
-
Copied: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/README.source (from rev 17680, trunk/packages/biojava3/trunk/debian/README.source)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/README.source (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/README.source 2014-09-03 06:17:33 UTC (rev 17930)
@@ -0,0 +1,14 @@
+biojava for Debian
+------------------
+
+Biojava3 uses the forester library version 0.955.
+The source version is hosted in Biojava repo only and does not
+match any release available in forester web site. To manage,
+a specific biojava3-forester library is created.
+
+The get-orig-source embeds this library version in the code.
+
+json.org dependency is replaced by json-simple with a patch for biojava3-ws.
+Future release will use json-lib
+
+Some tests are skipped due to errors dependending on context (nfs dirs), remote access required....
Deleted: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/changelog 2014-09-03 06:17:33 UTC (rev 17930)
@@ -1,57 +0,0 @@
-biojava3-live (3.0.7+dfsg-3) unstable; urgency=medium
-
- * d/control, d/build.xml: replace dependency to libcommons-collections3-java
- (Closes: #744208).
-
- -- Olivier Sallou <osallou at debian.org> Mon, 12 May 2014 09:39:08 +0200
-
-biojava3-live (3.0.7+dfsg-2) unstable; urgency=medium
-
- * d/build.xml, d/control: change deps jar file name(Closes: #747781).
-
- -- Olivier Sallou <osallou at debian.org> Mon, 12 May 2014 09:31:04 +0200
-
-biojava3-live (3.0.7+dfsg-1) unstable; urgency=low
-
- * New upstream release
- * Use Standards 3.9.5
-
- [debian/watch]: use new upstream GitHub repository
-
- -- Olivier Sallou <osallou at debian.org> Tue, 18 Jun 2013 14:40:39 +0200
-
-biojava3-live (3.0.5-3) unstable; urgency=low
-
- * Fix issue wit itext5 >= 5.4.1 related to API change (Closes: #712359)
- * debian/build.xml: fork junit tests
-
- -- Olivier Sallou <osallou at debian.org> Tue, 18 Jun 2013 12:53:24 +0200
-
-biojava3-live (3.0.5-2) unstable; urgency=low
-
- * Remove tests needing network access (Closes: #696947)
-
- -- Olivier Sallou <osallou at debian.org> Thu, 03 Jan 2013 11:08:51 +0100
-
-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
Copied: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/changelog (from rev 17929, trunk/packages/biojava3/trunk/debian/changelog)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/changelog (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/changelog 2014-09-03 06:17:33 UTC (rev 17930)
@@ -0,0 +1,72 @@
+biojava3-live (3.1.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 03 Sep 2014 07:57:21 +0200
+
+biojava3-live (3.0.8+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+ * Patch to fix Java 8 compatiblity (Closes: #745085).
+ Thanks to Emmanuel Bourg <ebourg at apache.org>.
+ * Remove patch to use log4j, not needed anymore.
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 10 Aug 2014 23:51:14 +0200
+
+biojava3-live (3.0.7+dfsg-3) unstable; urgency=medium
+
+ * d/control, d/build.xml: replace dependency to libcommons-collections3-java
+ (Closes: #744208).
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 12 May 2014 09:39:08 +0200
+
+biojava3-live (3.0.7+dfsg-2) unstable; urgency=medium
+
+ * d/build.xml, d/control: change deps jar file name(Closes: #747781).
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 12 May 2014 09:31:04 +0200
+
+biojava3-live (3.0.7+dfsg-1) unstable; urgency=low
+
+ * New upstream release
+ * Use Standards 3.9.5
+
+ [debian/watch]: use new upstream GitHub repository
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 18 Jun 2013 14:40:39 +0200
+
+biojava3-live (3.0.5-3) unstable; urgency=low
+
+ * Fix issue wit itext5 >= 5.4.1 related to API change (Closes: #712359)
+ * debian/build.xml: fork junit tests
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 18 Jun 2013 12:53:24 +0200
+
+biojava3-live (3.0.5-2) unstable; urgency=low
+
+ * Remove tests needing network access (Closes: #696947)
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 03 Jan 2013 11:08:51 +0100
+
+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/3.1.0+dfsg-1/debian/control
===================================================================
--- trunk/packages/biojava3/trunk/debian/control 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/control 2014-09-03 06:17:33 UTC (rev 17930)
@@ -1,80 +0,0 @@
-Source: biojava3-live
-Section: java
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
-Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
- libcommons-collections3-java, libcommons-pool-java (>= 1.1),
- libcommons-logging-java,
- libcommons-cli-java, libguava-java (>= 11.0.1),
- libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java,
- default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
- ant-optional, icedtea-netx, libhamcrest-java,
- libjson-simple-java (>=1.1.1),
- liblog4j1.2-java
-Build-Depends: debhelper (>= 9), ant
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava3/trunk/
-Vcs-Svn: svn://anonscm.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-collections3-java,
- libcommons-dbcp-java (>= 1.1),
- libcommons-logging-java,
- libhsqldb-java,
- libbytecode-java,
- icedtea-netx,
- libjson-simple-java,
- libcommons-codec-java,
- libitext5-java (>= 5.4.1),
- libjmol-java,
- liblog4j1.2-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/3.1.0+dfsg-1/debian/control (from rev 17928, trunk/packages/biojava3/trunk/debian/control)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/control (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/control 2014-09-03 06:17:33 UTC (rev 17930)
@@ -0,0 +1,81 @@
+Source: biojava3-live
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
+ libcommons-collections3-java, libcommons-pool-java (>= 1.1),
+ libcommons-logging-java,
+ libcommons-cli-java, libguava-java (>= 17.0),
+ libcommons-codec-java, libitext5-java (>= 5.4.1), libjmol-java,
+ default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
+ ant-optional, icedtea-netx, libhamcrest-java,
+ libjson-simple-java (>=1.1.1),
+ liblog4j1.2-java
+Build-Depends: debhelper (>= 9), ant
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava3/trunk/
+Vcs-Svn: svn://anonscm.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-collections3-java,
+ libcommons-dbcp-java (>= 1.1),
+ libcommons-logging-java,
+ libhsqldb-java,
+ libbytecode-java,
+ icedtea-netx,
+ libjson-simple-java,
+ libcommons-codec-java,
+ libitext5-java (>= 5.4.1),
+ libjmol-java,
+ liblog4j1.2-java,
+ libguava-java (>= 17.0)
+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/3.1.0+dfsg-1/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/trunk/debian/get-orig-source 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/get-orig-source 2014-09-03 06:17:33 UTC (rev 17930)
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-set -e
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --verbose --force-download |
- 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-3.0.7.tar.gz
-UTAR="biojava-${VERSION}.tar.gz"
-mv ../${UTAR} .
-tar -xzf ${UTAR}
-
-mv biojava-biojava-${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
- rm -f resources/*.jar
- rm forester-1.005-sources-1.005.jar
-cd ../../../..
-cd ..
-
-BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}.orig
-rm -rf ${PKG}-${VERSION}.orig
-
-rm ${UTAR}
-
Copied: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/get-orig-source (from rev 17679, trunk/packages/biojava3/trunk/debian/get-orig-source)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/get-orig-source (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/get-orig-source 2014-09-03 06:17:33 UTC (rev 17930)
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download |
+ 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-3.0.7.tar.gz
+UTAR="biojava-${VERSION}.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv biojava-biojava-${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
+ wget http://www.biojava.org/download/maven/org/forester/forester-lgpl/1.005/forester-lgpl-1.005-sources.jar
+ #jar xf forester-1.005-sources-1.005.jar
+ jar xf forester-lgpl-1.005-sources.jar
+ find . -name *.class | xargs rm -f
+ rm -f resources/*.jar
+ rm forester-lgpl-1.005-sources.jar
+ #rm forester-1.005-sources-1.005.jar
+cd ../../../..
+cd ..
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}.orig
+rm -rf ${PKG}-${VERSION}.orig
+
+rm ${UTAR}
+
Copied: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/java8_compatibility.patch (from rev 17679, trunk/packages/biojava3/trunk/debian/patches/java8_compatibility.patch)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/java8_compatibility.patch (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/java8_compatibility.patch 2014-09-03 06:17:33 UTC (rev 17930)
@@ -0,0 +1,13 @@
+Description: Fix a test failure with Java 8
+Author: Emmanuel Bourg <ebourg at apache.org>
+Forwarded: no
+--- a/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
++++ b/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
+@@ -108,7 +108,7 @@
+ this.circular = circular;
+ this.betweenCompounds = betweenCompounds;
+ this.accession = accession;
+- this.subLocations = Collections.unmodifiableList(subLocations);
++ this.subLocations = subLocations != null ? Collections.unmodifiableList(subLocations) : Collections.<Location>emptyList();
+ assertLocation();
+ }
Deleted: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/series 2014-09-03 06:17:33 UTC (rev 17930)
@@ -1,5 +0,0 @@
-use_simple_json
-fix_ascii_characters_mapping
-skip_network_related_tests
-fix_itext_class_updates
-fix_uselog4j1
Copied: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/series (from rev 17679, trunk/packages/biojava3/trunk/debian/patches/series)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/series (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/series 2014-09-03 06:17:33 UTC (rev 17930)
@@ -0,0 +1,5 @@
+use_simple_json
+fix_ascii_characters_mapping
+skip_network_related_tests
+fix_itext_class_updates
+java8_compatibility.patch
Deleted: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/skip_network_related_tests 2014-09-03 06:17:33 UTC (rev 17930)
@@ -1,52 +0,0 @@
-Author: Olivier Sallou <osallou at debian/org>
-Last-Updated: 2013-01-03
-Subject: Some tests use network access
-Description: Remove tests requiring external
- network access
-Forwarded: yes
-Bug: https://redmine.open-bio.org/issues/3402
---- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
-+++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
-@@ -40,20 +40,7 @@
-
- public void testUniprot(String uniprotID) throws Exception{
-
-- ProteinSequence seq = getUniprot(uniprotID);
--
-- AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
--
--/* for (AminoAcidCompound compound : seq) {
-- System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
-- }
-- */
-- compoundSet.verifySequence(seq);
--
--
--
-- float[] values = Jronn.getDisorderScores(seq);
--
-+ // Skip network related tests
-
- }
-
---- a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
-+++ b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
-@@ -56,17 +56,7 @@
- * Method 1: With the GenbankProxySequenceReader
- */
- //Try with the GenbankProxySequenceReader
-- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
-- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
-- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
-- System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" + proteinSequence.getSequenceAsString().substring(0, 10) + "...");
--
-- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-- = new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
-- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
-- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
-- System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" + dnaSequence.getSequenceAsString().substring(0, 10) + "...");
-+ // Skipping it due to network requirements
- /*
- * Method 2: With the GenbankReaderHelper
- */
Copied: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/skip_network_related_tests (from rev 17679, trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/skip_network_related_tests (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/skip_network_related_tests 2014-09-03 06:17:33 UTC (rev 17930)
@@ -0,0 +1,52 @@
+Author: Olivier Sallou <osallou at debian/org>
+Last-Updated: 2013-01-03
+Subject: Some tests use network access
+Description: Remove tests requiring external
+ network access
+Forwarded: yes
+Bug: https://redmine.open-bio.org/issues/3402
+--- a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
++++ b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
+@@ -56,17 +56,7 @@
+ * Method 1: With the GenbankProxySequenceReader
+ */
+ //Try with the GenbankProxySequenceReader
+- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
+- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
+- System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" + proteinSequence.getSequenceAsString().substring(0, 10) + "...");
+-
+- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
+- = new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
+- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
+- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
+- System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" + dnaSequence.getSequenceAsString().substring(0, 10) + "...");
++ // Skipping it due to network requirements
+ /*
+ * Method 2: With the GenbankReaderHelper
+ */
+--- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
++++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
+@@ -43,21 +43,6 @@
+
+ public void testUniprot(String uniprotID) throws Exception{
+
+- ProteinSequence seq = getUniprot(uniprotID);
+-
+- AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+-
+-/* for (AminoAcidCompound compound : seq) {
+- System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
+- }
+- */
+- compoundSet.verifySequence(seq);
+-
+-
+-
+- @SuppressWarnings("unused")
+- float[] values = Jronn.getDisorderScores(seq);
+-
+
+ }
+
Deleted: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/use_simple_json 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/use_simple_json 2014-09-03 06:17:33 UTC (rev 17930)
@@ -1,54 +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: 2012-12-02
-
---- 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) {
Copied: trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/use_simple_json (from rev 17679, trunk/packages/biojava3/trunk/debian/patches/use_simple_json)
===================================================================
--- trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/use_simple_json (rev 0)
+++ trunk/packages/biojava3/tags/3.1.0+dfsg-1/debian/patches/use_simple_json 2014-09-03 06:17:33 UTC (rev 17930)
@@ -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.
+@@ -103,15 +104,13 @@
+
+ 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();
+@@ -135,11 +134,11 @@
+ 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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