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 <[email protected]> Sat, 19 Jan 2019 02:52:43 -0800 + [ Gilles Filippini <[email protected]> ] + * Tentative fix to build against json-simple 3 Closes: #960654 + + -- Olivier Sallou <[email protected]> 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 <[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 @@ 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 $$3}') +JSON_SIMPLE_3 = $(shell dpkg --compare-versions '$(JSON_SIMPLE_VERSION)' '>' '3.1.1-1~' && echo yes || echo no) +ifeq (yes,$(JSON_SIMPLE_3)) +JSON_SIMPLE_PACKAGE = com.github.cliftonlabs.json_simple +else +JSON_SIMPLE_PACKAGE = org.json.simple +endif + %: dh $@ --with javahelper @@ -31,6 +39,10 @@ override_dh_auto_configure: sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml override_dh_auto_build: + find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ + -exec sed -i.json-simple \ + -e 's,@JSON_SIMPLE_PACKAGE@,$(JSON_SIMPLE_PACKAGE),' \ + {} \; -print cd biojava-jcolorbrewer && ant jar cd biojava-forester && ant jar cd biojava-core && ant jar @@ -104,6 +116,8 @@ override_dh_clean: rm -rf doc find . -name "*.class" -delete rm -rf buildtest + find . -type f -name \*.java.json-simple \ + -exec sh -c 'file={} && mv $$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 You're receiving this email because of your account on salsa.debian.org.
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