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 20:47:46.0
+0100
+++ biojava4-live-4.2.12+dfsg/debian/changelog 2020-05-15 08:50:46.0
+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 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_json2019-01-18
15:58:37.0 +0100
+++ biojava4-live-4.2.12+dfsg/debian/patches/use_simple_json2020-05-15
08:50:46.0 +0200
@@ -2,24 +2,42 @@
Author: Olivier Sallou
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 ]
+ 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@.JsonArray;
++import @JSON_SIMPLE_PACKAGE@.JsonObject;
++import @JSON_SIMPLE_PACKAGE@.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 results = new TreeSet();
try {
@@ -27,29 +45,29 @@
-
- JSONObject hmresults = json.getJSONObject("results");
-
-+ JSONObject
