[med-svn] [Git][med-team/biojava4-live][master] 2 commits: add patch for bug 960654 to use simplejson >=3
Olivier Sallou
gitlab at salsa.debian.org
Fri May 15 10:21:23 BST 2020
Olivier Sallou pushed to branch master at Debian Med / biojava4-live
Commits:
b488029d by Olivier Sallou at 2020-05-15T09:12:13+00:00
add patch for bug 960654 to use simplejson >=3
- - - - -
522dbf4f by Olivier Sallou at 2020-05-15T09:21:11+00:00
upload fix release
- - - - -
3 changed files:
- debian/changelog
- debian/patches/use_simple_json
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,12 @@
-biojava4-live (4.2.12+dfsg-3) UNRELEASED; urgency=medium
+biojava4-live (4.2.12+dfsg-3) unstable; urgency=medium
- * Team upload.
+ [ Michael R. Crusoe ]
* Don't hardcode openjdk-11 path in debian/rules
- -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 19 Jan 2019 02:52:43 -0800
+ [ Gilles Filippini <pini at debian.org> ]
+ * Tentative fix to build against json-simple 3 Closes: #960654
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 15 May 2020 09:04:30 +0000
biojava4-live (4.2.12+dfsg-2) unstable; urgency=medium
=====================================
debian/patches/use_simple_json
=====================================
@@ -2,24 +2,42 @@ 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/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
-+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+ .
+ [ Gilles Filippini <pini at debian.org> ]
+ Patche updated to migrate away from deprecated json-simple 1.x classes
+ See json-simple 2.0.0 changelog:
+ > * Deprecated JSONParse and JSONValue in favor of Jsoner.
+ > * Deprecated JSONStreamAware and JSONAware in favor of Jsonable.
+ > * Deprecated JSONObject in favor of JsonObject.
+ > * Deprecated JSONArray in favor of JsonArray.
+ .
+ This patch now uses the new json-simple Json* classes. It is compatible
+ with both 2.x and 3.x json-simple releases, with a few ajustments
+ regarding backward incompatible changes in json-simple 3.x:
+ - The package name, changed to com.github.cliftonlabs.json_simple
+ This change is handled using place-holders @JSON_SIMPLE_PACKAGE@ which
+ are substituted at build time by debian/rules.
+ .
+ With this trick the package is compatible with json-simple 2.x and 3.x.
+Last-Updated: 2020-05-15
+Index: biojava4-live-4.2.12+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+===================================================================
+--- biojava4-live-4.2.12+dfsg.orig/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
++++ biojava4-live-4.2.12+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
@@ -20,8 +20,10 @@
*/
package org.biojava.nbio.ws.hmmer;
-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;
++import @JSON_SIMPLE_PACKAGE at .JsonArray;
++import @JSON_SIMPLE_PACKAGE at .JsonObject;
++import @JSON_SIMPLE_PACKAGE at .Jsoner;
+
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-@@ -136,15 +138,13 @@
+@@ -136,15 +138,13 @@ public class RemoteHmmerScan implements
SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
try {
@@ -27,29 +45,29 @@ Last-Updated: 2012-12-02
-
- JSONObject hmresults = json.getJSONObject("results");
-
-+ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
-+ JSONObject hmresults = (JSONObject) json.get("results");
++ JsonObject json= Jsoner.deserialize(result.toString(), (JsonObject) null);
++ JsonObject hmresults = (JsonObject) json.get("results");
- JSONArray hits = hmresults.getJSONArray("hits");
-+ JSONArray hits = (JSONArray) hmresults.get("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);
++ JsonObject hit = (JsonObject) hits.get(i);
HmmerResult hmmResult = new HmmerResult();
-@@ -168,11 +168,11 @@
+@@ -168,11 +168,11 @@ public class RemoteHmmerScan implements
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");
++ 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);
++ JsonObject d = (JsonObject) hmmdomains.get(j);
Integer is_included = getInteger(d.get("is_included"));
if ( is_included == 0) {
continue;
=====================================
debian/rules
=====================================
@@ -8,6 +8,14 @@ export LC_ALL=C.UTF-8
JAVA_HOME=/usr/lib/jvm/default-java
+JSON_SIMPLE_VERSION = $(shell dpkg -l libjson-simple-java | grep '^ii' | awk '{print $$3}')
+JSON_SIMPLE_3 = $(shell dpkg --compare-versions '$(JSON_SIMPLE_VERSION)' '>' '3.1.1-1~' && echo yes || echo no)
+ifeq (yes,$(JSON_SIMPLE_3))
+JSON_SIMPLE_PACKAGE = com.github.cliftonlabs.json_simple
+else
+JSON_SIMPLE_PACKAGE = org.json.simple
+endif
+
%:
dh $@ --with javahelper
@@ -31,6 +39,10 @@ override_dh_auto_configure:
sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml
override_dh_auto_build:
+ find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \
+ -exec sed -i.json-simple \
+ -e 's, at JSON_SIMPLE_PACKAGE@,$(JSON_SIMPLE_PACKAGE),' \
+ {} \; -print
cd biojava-jcolorbrewer && ant jar
cd biojava-forester && ant jar
cd biojava-core && ant jar
@@ -104,6 +116,8 @@ override_dh_clean:
rm -rf doc
find . -name "*.class" -delete
rm -rf buildtest
+ find . -type f -name \*.java.json-simple \
+ -exec sh -c 'file={} && mv $$file $${file%.json-simple}' \; -print
get-orig-source:
debian/get-orig-source
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/bfb41b0a2c0ec58faf4baf2acfb4cb8e0c2ab9aa...522dbf4f55bda13d720da7d3d6464e99dc0b83b3
--
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/bfb41b0a2c0ec58faf4baf2acfb4cb8e0c2ab9aa...522dbf4f55bda13d720da7d3d6464e99dc0b83b3
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