Bug#778665: unblock: logol/1.7.0-2
Logol package is affected by gridengine RC bug and removal request from Jessie (gridengine is RC buggy and effectively unmaintained , see the discussion in #776131).
This patch release removes the dependency on libdrmaa-java waiting for reintroduction in backports of gridengine. At this time, logol will put back support and will "follow" in backports.
There is no other modification.
Debidiff is attached to mail.
diff -Nru logol-1.7.0/debian/changelog logol-1.7.0/debian/changelog
--- logol-1.7.0/debian/changelog 2014-05-21 21:26:35.000000000 +0200
+++ logol-1.7.0/debian/changelog 2015-02-05 15:24:35.000000000 +0100
@@ -1,3 +1,12 @@
+logol (1.7.0-2) unstable; urgency=medium
+
+ * d/control,d/patches/remove_drmaa_support: Remove libdrmaa-java dependency
+ due to gridengine removal from Jessie (#776131).
+ d/series: remove drmaa patch
+ d/README.Debian: explain non drmaa support of this release
+
+ -- Olivier Sallou <osallou@debian.org> Sun, 01 Feb 2015 08:56:52 +0100
+
logol (1.7.0-1.1) unstable; urgency=high
* Non-maintainer upload.
diff -Nru logol-1.7.0/debian/control logol-1.7.0/debian/control
--- logol-1.7.0/debian/control 2014-04-18 13:38:41.000000000 +0200
+++ logol-1.7.0/debian/control 2015-02-01 09:00:22.000000000 +0100
@@ -7,13 +7,14 @@
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/logol/
Build-Depends: debhelper (>= 8.0.0),default-jdk (>= 1:1.6),ant,ruby,
gawk, swi-prolog (>=6.4.1-3),
- libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
+ libbiojava-java, antlr3, libcommons-cli-java,
libcommons-collections3-java, libcommons-configuration-java,
libcommons-lang-java, libcommons-logging-java, libxalan2-java,
libxerces2-java, junit4, libgnumail-java,
liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht,
libncursesw5-dev, ant-optional,
cassiopee, ruby-cassiopee
+#libdrmaa-java removed from Jessie, to be reintroduced.
Standards-Version: 3.9.5
Homepage: http://logol.genouest.org
@@ -21,11 +22,12 @@
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java7-runtime,
ruby, gawk,
- libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
+ libbiojava-java, antlr3, libcommons-cli-java,
libcommons-collections3-java, libcommons-configuration-java,
libcommons-lang-java, libcommons-logging-java, libxalan2-java,
libxerces2-java, libgnumail-java, liblog4j1.2-java,
cassiopee, logol-bin
+#libdrmaa-java removed from Jessie, to be reintroduced.
Suggests: ruby-cassiopee (>=0.1.12)
Description: Pattern matching tool using Logol language
Logol is a pattern matching tool using the Logol language.
diff -Nru logol-1.7.0/debian/patches/remove_drmaa_support logol-1.7.0/debian/patches/remove_drmaa_support
--- logol-1.7.0/debian/patches/remove_drmaa_support 1970-01-01 01:00:00.000000000 +0100
+++ logol-1.7.0/debian/patches/remove_drmaa_support 2015-02-01 09:10:24.000000000 +0100
@@ -0,0 +1,166 @@
+Subject: libdrmaa-java removed from Debian (gridengine)
+Description: DRMAA job submission needs a Java drmaa library.
+ libdrmaa-java has been removed from Debian, bug: 776131.
+ This patch removes DRMAA related code waiting for library
+ reintroduction.
+ Logol will work on local mode only.
+Author: Olivier Sallou <osallou@debian.org>
+Last-Updated: 2015-02-01
+--- a/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
++++ b/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
+@@ -230,7 +230,6 @@
+ options.addOption("h",false,"get usage");
+
+ options.addOption("s", true, "sequence database");
+- options.addOption("sge", false, "use SGE");
+ options.addOption("local", false, "use local system");
+ options.addOption("dna", false, "analyse dna, is default");
+ options.addOption("rna", false, "analyse rna");
+@@ -290,7 +289,6 @@
+ usageOptions.addOption("s", true, "sequence database");
+ usageOptions.addOption("g", true, "grammar file to analyse");
+ usageOptions.addOption("m", true, "model file to analyse");
+- usageOptions.addOption("sge", false, "use SGE");
+ usageOptions.addOption("local", false, "use local system");
+ usageOptions.addOption("dna", false, "analyse dna, is default");
+ usageOptions.addOption("rna", false, "analyse rna");
+@@ -355,11 +353,6 @@
+ type=LOCAL;
+ jobmngr = (JobManager) new LocalJobManager();
+ }
+- if( cmd.hasOption( "sge" ) ) {
+- logger.info("Using sge system");
+- type=SGE;
+- jobmngr = (JobManager) new SGEJobManager();
+- }
+ if( cmd.hasOption( "dna" ) ) {
+ format=1;
+ }
+--- a/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
++++ b/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
+@@ -5,10 +5,6 @@
+ import java.util.Vector;
+
+ import org.apache.log4j.Logger;
+-import org.ggf.drmaa.DrmaaException;
+-import org.ggf.drmaa.JobTemplate;
+-import org.ggf.drmaa.Session;
+-import org.ggf.drmaa.SessionFactory;
+ import org.irisa.genouest.logol.Constants;
+
+ /*
+@@ -18,111 +14,30 @@
+
+ private static final Logger logger = Logger.getLogger(org.irisa.genouest.logol.dispatcher.SGEJobManager.class);
+
+- private static String OS = System.getProperty("os.name").toLowerCase();
+-
+-
+- Vector<String> jobs = new Vector<String>();
+- Vector<String> jobsOutput = new Vector<String>();
+- Vector<String> jobsArgs = new Vector<String>();
+- Vector<String> jobIds = new Vector<String>();
+-
+- String arguments = "";
+-
+- static SessionFactory factory = null;
+- static Session session=null;
+-
+-
+- String jobId = null;
+-
+- String installPath=null;
+-
+ UUID uID = null;
+
+ public SGEJobManager() {
+- logger.info("Init DRM communication");
+- if(factory==null) {
+- factory = SessionFactory.getFactory();
+- }
+- if(session==null) {
+- session = factory.getSession();
+- }
+- if(session==null) {
+- logger.error(" Drm session could not open");
+- }
+- logger.info("DRM system: "+session.getDrmSystem());
+- try {
+- session.init("");
+- } catch (DrmaaException e) {
+- logger.error("Could not init the DRM session: "+e.getMessage());
+- }
++ logger.error("DRMAA not supported, libdrmaa-java not available in Debian");
+ }
+
+ public int addJob(String sequence, String output,String jobArgs) {
+- jobs.add(sequence);
+- jobsArgs.add(jobArgs);
+- jobsOutput.add(output);
+ return 0;
+ }
+
+ public int runJobs(String nativeSpecifications) {
+- JobTemplate jt;
+- for(int i=0;i<jobs.size();i++) {
+- try {
+- jt = session.createJobTemplate();
+- if(nativeSpecifications!=null) {
+- jt.setNativeSpecification(nativeSpecifications);
+- }
+-
+- jt.setJobName("LogolMatch");
+-
+- String out = jobsOutput.get(i);
+- // Redirect DRM streams
+- jt.setOutputPath(":" + out+".out");
+- jt.setErrorPath(":" + out + ".err");
+- if(OS.startsWith("win")) {
+- jt.setArgs(new String[] {installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.rb", arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
+- jt.setRemoteCommand("ruby");
+- }
+- else {
+- jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
+- jt.setRemoteCommand(installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.sh");
+- }
+- jobId = session.runJob(jt);
+- logger.info("Executing job: "+jobId);
+- jobIds.add(jobId);
+- session.deleteJobTemplate(jt);
+- } catch (DrmaaException e) {
+- logger.error("Error during job submission: "+e.getMessage());
+- return -1;
+- }
+- }
+-
+-
++ logger.error("DRMAA not supported, libdrmaa-java not available in Debian");
+ return 0;
+ }
+
+ public int waitForJobsOver() {
+-
+- try {
+- session.synchronize(jobIds, Session.TIMEOUT_WAIT_FOREVER, true);
+- session.exit();
+- } catch (DrmaaException e) {
+- logger.error("Error during job submission: "+e.getMessage());
+- }
+- logger.info("Each sequence in bank resulted in a specific result file.");
+- for(int i=0;i<jobs.size();i++) {
+- logger.debug("Result file is available in work directory : "+jobsOutput.get(i));
+- }
++ logger.error("DRMAA not supported, libdrmaa-java not available in Debian");
+ return 0;
+ }
+
+ public void setJobArgs(String args) {
+- arguments=args;
+ }
+
+ public void setInstallPath(String installDir) {
+- installPath = installDir;
+-
+ }
+
+ }
diff -Nru logol-1.7.0/debian/patches/series logol-1.7.0/debian/patches/series
--- logol-1.7.0/debian/patches/series 2014-04-18 12:34:29.000000000 +0200
+++ logol-1.7.0/debian/patches/series 2015-02-01 09:07:30.000000000 +0100
@@ -1,5 +1,6 @@
+remove_drmaa_support
fixLibPath
-fixDrmmato6.2
+#fixDrmmato6.2
setDebianDirs
fix_doc_generation
remove_rubygems_usage
diff -Nru logol-1.7.0/debian/README.Debian logol-1.7.0/debian/README.Debian
--- logol-1.7.0/debian/README.Debian 1970-01-01 01:00:00.000000000 +0100
+++ logol-1.7.0/debian/README.Debian 2015-02-05 14:29:57.000000000 +0100
@@ -0,0 +1,5 @@
+Current release in Debian has removed DRMAA support due to gridengine removal of Jessie.
+
+When libdrmma-java is reintroduced, drmaa support will be set back in logol.
+
+This release will work in local mode only.
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