[med-svn] r18738 - in trunk/packages/logol/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Thu Feb 5 13:44:34 UTC 2015
Author: osallou
Date: 2015-02-05 13:44:33 +0000 (Thu, 05 Feb 2015)
New Revision: 18738
Added:
trunk/packages/logol/trunk/debian/README.Debian
trunk/packages/logol/trunk/debian/patches/remove_drmaa_support
Modified:
trunk/packages/logol/trunk/debian/changelog
trunk/packages/logol/trunk/debian/control
trunk/packages/logol/trunk/debian/patches/series
Log:
create a patch to remove drmaa requirement due to gridengine removal of Jessie
Added: trunk/packages/logol/trunk/debian/README.Debian
===================================================================
--- trunk/packages/logol/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/logol/trunk/debian/README.Debian 2015-02-05 13:44:33 UTC (rev 18738)
@@ -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.
Modified: trunk/packages/logol/trunk/debian/changelog
===================================================================
--- trunk/packages/logol/trunk/debian/changelog 2015-02-05 08:10:52 UTC (rev 18737)
+++ trunk/packages/logol/trunk/debian/changelog 2015-02-05 13:44:33 UTC (rev 18738)
@@ -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 at debian.org> Sun, 01 Feb 2015 08:56:52 +0100
+
logol (1.7.0-1) unstable; urgency=low
* New upstream release
Modified: trunk/packages/logol/trunk/debian/control
===================================================================
--- trunk/packages/logol/trunk/debian/control 2015-02-05 08:10:52 UTC (rev 18737)
+++ trunk/packages/logol/trunk/debian/control 2015-02-05 13:44:33 UTC (rev 18738)
@@ -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.
Added: trunk/packages/logol/trunk/debian/patches/remove_drmaa_support
===================================================================
--- trunk/packages/logol/trunk/debian/patches/remove_drmaa_support (rev 0)
+++ trunk/packages/logol/trunk/debian/patches/remove_drmaa_support 2015-02-05 13:44:33 UTC (rev 18738)
@@ -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 at 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;
+-
+ }
+
+ }
Modified: trunk/packages/logol/trunk/debian/patches/series
===================================================================
--- trunk/packages/logol/trunk/debian/patches/series 2015-02-05 08:10:52 UTC (rev 18737)
+++ trunk/packages/logol/trunk/debian/patches/series 2015-02-05 13:44:33 UTC (rev 18738)
@@ -1,5 +1,6 @@
+remove_drmaa_support
fixLibPath
-fixDrmmato6.2
+#fixDrmmato6.2
setDebianDirs
fix_doc_generation
remove_rubygems_usage
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