Author: osallou
Date: 2012-05-30 09:52:44 +0000 (Wed, 30 May 2012)
New Revision: 11102
Added:
trunk/packages/biojava3/biojava3-live/trunk/debian/patches/use_simple_json
Modified:
trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
trunk/packages/biojava3/biojava3-live/trunk/debian/control
trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3.0-java.jlibs
trunk/packages/biojava3/biojava3-live/trunk/debian/patches/series
trunk/packages/biojava3/biojava3-live/trunk/debian/rules
Log:
use simple_json instead of json.org lib
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
2012-05-30 09:45:20 UTC (rev 11101)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
2012-05-30 09:52:44 UTC (rev 11102)
@@ -21,7 +21,7 @@
<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
${lib.dir}/hamcrest.jar"/>
+ <property name="class.path" value="${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}">
@@ -34,6 +34,7 @@
<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"/>
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/control
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/control 2012-05-30
09:45:20 UTC (rev 11101)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/control 2012-05-30
09:52:44 UTC (rev 11102)
@@ -8,7 +8,7 @@
libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
libcommons-cli-java, libguava-java (>= 11.0.1),
openjdk-6-jdk | sun-java6-jdk, junit4,javahelper (>=0.25), libjgrapht-java,
- ant-optional, jmol-applet, icedtea-netx, libhamcrest-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/
@@ -23,7 +23,8 @@
libcommons-dbcp-java (>= 1.1),
libhsqldb-java,
libbytecode-java,
- jmol-applet, icedtea-netx
+ 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
@@ -38,6 +39,7 @@
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
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
2012-05-30 09:45:20 UTC (rev 11101)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
2012-05-30 09:52:44 UTC (rev 11102)
@@ -26,6 +26,7 @@
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 ..
Modified:
trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3.0-java.jlibs
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3.0-java.jlibs
2012-05-30 09:45:20 UTC (rev 11101)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/libbiojava3.0-java.jlibs
2012-05-30 09:52:44 UTC (rev 11102)
@@ -9,3 +9,4 @@
dist/biojava3-structure-gui.jar
dist/biojava3-modfinder.jar
dist/biojava3-protein-disorder.jar
+dist/biojava3-ws.jar
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/patches/series
2012-05-30 09:45:20 UTC (rev 11101)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/patches/series
2012-05-30 09:52:44 UTC (rev 11102)
@@ -1 +1,2 @@
+use_simple_json
fix_code_to_support_latest_jmol
Added:
trunk/packages/biojava3/biojava3-live/trunk/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/patches/use_simple_json
(rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/patches/use_simple_json
2012-05-30 09:52:44 UTC (rev 11102)
@@ -0,0 +1,56 @@
+Subject: use simple_json library
+Author: Olivier Sallou <[email protected]>
+Description: json.org library is not "free", use simple_json
+ library and update according to API
+Last-Updated: 30/05/12
+
+--- 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) {
Modified: trunk/packages/biojava3/biojava3-live/trunk/debian/rules
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/rules 2012-05-30
09:45:20 UTC (rev 11101)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/rules 2012-05-30
09:52:44 UTC (rev 11102)
@@ -36,7 +36,7 @@
cd biojava3-structure-gui && ant jar
cd biojava3-modfinder && ant jar
cd biojava3-protein-disorder && ant jar
- #cd biojava3-ws && ant jar
+ cd biojava3-ws && ant jar
# make doc
rm -rf biojavadoc
mkdir biojavadoc
@@ -59,7 +59,7 @@
# Requires remote access and tmp directory write access
#cd biojava3-structure && ant test
cd biojava3-structure-gui && ant test
- #cd biojava3-ws && ant test
+ cd biojava3-ws && ant test
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