Your message dated Fri, 15 May 2020 09:49:00 +0000
with message-id <[email protected]>
and subject line Bug#960654: fixed in biojava4-live 4.2.12+dfsg-3
has caused the Debian Bug report #960654,
regarding src:biojava4-live: Please add support to build against
libjson-simple-java >= 3
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
960654: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960654
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:biojava4-live
Version: 4.2.12+dfsg-2
Severity: normal
Tags: patch
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hi,
I'd like to transition json-simple 3.1.1 to unstable, but biojava4-live is a
blocker since it builds against libjson-simple-java << 3 only.
The json-simple classes used by biojava4-live were deprecated in version 2.0.0
[1]. There were removed in versions 3.x [2].
[1] https://github.com/cliftonlabs/json-simple/blob/json-simple-2.0.0/README.txt
[2] https://github.com/cliftonlabs/json-simple/blob/json-simple-3.0.1/CHANGELOG
Please find attached a patch proposal to use the current json-simple classes.
I've tested that the package builds correctly against libjson-simple-java
version 2.3.0-1 from unstable and version 3.1.1-1~exp2 currently in
experimental, and the build time test cases report no errors.
Thanks in advance for considering.
_g.
- -- System Information:
Debian Release: buster/sid
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.6.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8),
LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
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diff -Nru biojava4-live-4.2.12+dfsg/debian/changelog
biojava4-live-4.2.12+dfsg/debian/changelog
--- biojava4-live-4.2.12+dfsg/debian/changelog 2019-01-18 20:47:46.000000000
+0100
+++ biojava4-live-4.2.12+dfsg/debian/changelog 2020-05-15 08:50:46.000000000
+0200
@@ -1,3 +1,10 @@
+biojava4-live (4.2.12+dfsg-2.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Tentative fix to build against json-simple 3
+
+ -- Gilles Filippini <[email protected]> Fri, 15 May 2020 08:50:46 +0200
+
biojava4-live (4.2.12+dfsg-2) unstable; urgency=medium
* Team upload.
diff -Nru biojava4-live-4.2.12+dfsg/debian/patches/use_simple_json
biojava4-live-4.2.12+dfsg/debian/patches/use_simple_json
--- biojava4-live-4.2.12+dfsg/debian/patches/use_simple_json 2019-01-18
15:58:37.000000000 +0100
+++ biojava4-live-4.2.12+dfsg/debian/patches/use_simple_json 2020-05-15
08:50:46.000000000 +0200
@@ -2,24 +2,42 @@
Author: Olivier Sallou <[email protected]>
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 <[email protected]> ]
+ 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 @[email protected];
++import @[email protected];
++import @[email protected];
+
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 @@
-
- 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;
diff -Nru biojava4-live-4.2.12+dfsg/debian/rules
biojava4-live-4.2.12+dfsg/debian/rules
--- biojava4-live-4.2.12+dfsg/debian/rules 2019-01-18 18:13:50.000000000
+0100
+++ biojava4-live-4.2.12+dfsg/debian/rules 2020-05-15 08:50:46.000000000
+0200
@@ -8,6 +8,14 @@
JAVA_HOME=/usr/lib/jvm/default-java
+JSON_SIMPLE_VERSION = $(shell dpkg -l libjson-simple-java | grep '^ii' | awk
'{print $$3}')
+JSON_SIMPLE_3 = $(shell dpkg --compare-versions '$(JSON_SIMPLE_VERSION)' '>'
'3.1.1-1~' && echo yes || echo no)
+ifeq (yes,$(JSON_SIMPLE_3))
+JSON_SIMPLE_PACKAGE = com.github.cliftonlabs.json_simple
+else
+JSON_SIMPLE_PACKAGE = org.json.simple
+endif
+
%:
dh $@ --with javahelper
@@ -31,6 +39,10 @@
sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml >
biojava-jcolorbrewer/build.xml
override_dh_auto_build:
+ find . -type f -name \*.java -exec grep -q 'import
@JSON_SIMPLE_PACKAGE@' {} \; \
+ -exec sed -i.json-simple \
+ -e 's,@JSON_SIMPLE_PACKAGE@,$(JSON_SIMPLE_PACKAGE),' \
+ {} \; -print
cd biojava-jcolorbrewer && ant jar
cd biojava-forester && ant jar
cd biojava-core && ant jar
@@ -102,6 +114,8 @@
rm -rf doc
find . -name "*.class" -delete
rm -rf buildtest
+ find . -type f -name \*.java.json-simple \
+ -exec sh -c 'file={} && mv $$file $${file%.json-simple}' \; -print
get-orig-source:
debian/get-orig-source
--- End Message ---
--- Begin Message ---
Source: biojava4-live
Source-Version: 4.2.12+dfsg-3
Done: Olivier Sallou <[email protected]>
We believe that the bug you reported is fixed in the latest version of
biojava4-live, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <[email protected]> (supplier of updated biojava4-live package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 15 May 2020 09:04:30 +0000
Source: biojava4-live
Binary: libbiojava4-java libbiojava4-java-doc libbiojava4.0-java
Architecture: source all
Version: 4.2.12+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Olivier Sallou <[email protected]>
Description:
libbiojava4-java - Java API to biological data and applications (default
version)
libbiojava4-java-doc - [Biology] Documentation for BioJava
libbiojava4.0-java - Java API to biological data and applications (version 4)
Closes: 960654
Changes:
biojava4-live (4.2.12+dfsg-3) unstable; urgency=medium
.
[ Michael R. Crusoe ]
* Don't hardcode openjdk-11 path in debian/rules
.
[ Gilles Filippini <[email protected]> ]
* Tentative fix to build against json-simple 3 Closes: #960654
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