From 1c8cbe10ed2f25b3b36620a13d16e8cb96f6523f Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Fri, 3 Jun 2011 12:59:24 +0000 Subject: [PATCH] exclude cancelled jobs from incomplete git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4214 e3abac25-378b-4346-85de-24260fe3988d --- TODO.txt | 11 ++++++++--- build.xml | 7 +++++++ conf/Engine.cluster.properties | 4 ++-- statpages/MonthlySummary.jsp | 2 +- statpages/Statistics.jsp | 2 +- testsrc/compbio/metadata/AllTestSuit.java | 2 +- webservices/compbio/stat/collector/StatDB.java | 2 +- webservices/compbio/stat/collector/StatProcessor.java | 2 +- 8 files changed, 22 insertions(+), 10 deletions(-) diff --git a/TODO.txt b/TODO.txt index ca89290..539954e 100644 --- a/TODO.txt +++ b/TODO.txt @@ -1,16 +1,21 @@ TODO: +Registry 1 week +webservices - 1 week +client - 1 week +docs - 1 week Cluster stats: + +cancelled should not be reported as incomplete! -Remove hyperlinks from tasks which workdirs were removed -graph generation -user documentation (do not forget how to enable follow symlinks!) -use the same name for output for different executables - -clean stat db task before packing web app - -pack web apps with stat db + +ant task to clean up clean stat db task before packing web app + +pack web apps with stat db (NOT TESTED!) +change input size bites +add help info for each column in the detailed job list table +replace default -1 with ? - -delete and re-import the database to fix clustal input staff + +delete and re-import the database to fix clustal input staff add to help text: To disable a web service remove it from WEB-INF/sun-jaxws.xml descriptor diff --git a/build.xml b/build.xml index fc99421..412a049 100644 --- a/build.xml +++ b/build.xml @@ -330,6 +330,12 @@ + + + + + + @@ -370,6 +376,7 @@ + diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties index b0bfdad..344858b 100644 --- a/conf/Engine.cluster.properties +++ b/conf/Engine.cluster.properties @@ -12,8 +12,8 @@ engine.cluster.enable=true # to the job folders if this path is within JABA web application. # JABAWS statistic application just assume that the last name in the path is the # application folder in the root of JABAWS web application. -#cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout - +# cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout +cluster.tmp.directory=/homes/pvtroshin/workspace/jaba2/jobsout # Enable/disable cluster statistics collector cluster.stat.collector.enable=false diff --git a/statpages/MonthlySummary.jsp b/statpages/MonthlySummary.jsp index 4e3bbea..d69db5a 100644 --- a/statpages/MonthlySummary.jsp +++ b/statpages/MonthlySummary.jsp @@ -64,7 +64,7 @@ For each month the table contains the following information.
  • The period of time for which statistics is displayed. For example Jan 2011 means period of time from the first of January to the 31 of January.
  • Total - the total number of jobs accepted by JABAWS
    • -
  • Incomplete - the number of jobs for which the result file was not found or was empty
    • +
  • Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled
  • Cancelled - the number of jobs cancelled by the user
  • Abandoned - the number of jobs which result(s) were not collected
    • diff --git a/statpages/Statistics.jsp b/statpages/Statistics.jsp index 752d047..8026e53 100644 --- a/statpages/Statistics.jsp +++ b/statpages/Statistics.jsp @@ -41,7 +41,7 @@ time specified in the title.

    Each table contains the following information for each web service
    • Total - the total number of jobs accepted by a particular JABA service
      • -
    • Incomplete - the number of jobs for which the result file was not found or was empty
      • +
    • Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled
    • Cancelled - the number of jobs cancelled by the user
    • Abandoned - the number of jobs which result(s) were not collected
    diff --git a/testsrc/compbio/metadata/AllTestSuit.java b/testsrc/compbio/metadata/AllTestSuit.java index 24ca11d..c359d28 100644 --- a/testsrc/compbio/metadata/AllTestSuit.java +++ b/testsrc/compbio/metadata/AllTestSuit.java @@ -70,7 +70,7 @@ public class AllTestSuit { // For cluster execution paths MUST BE ABSOLUTE as cluster hosts will not be // able to access the task otherwise public static final String OUTPUT_DIR_ABSOLUTE = AllTestSuit.CURRENT_DIRECTORY - + File.separator + "jobsout" + File.separator; + + File.separator + "local_jobsout" + File.separator; public static final String RUNNER_TEST_LOGGER = "RunnerLogger"; diff --git a/webservices/compbio/stat/collector/StatDB.java b/webservices/compbio/stat/collector/StatDB.java index 2b7b66b..98b6fda 100644 --- a/webservices/compbio/stat/collector/StatDB.java +++ b/webservices/compbio/stat/collector/StatDB.java @@ -205,7 +205,7 @@ public class StatDB { public int getIncompleteCount(Timestamp from, Timestamp to) throws SQLException { // !js.hasResult() - String incompleteQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and resultsize<=0 "; + String incompleteQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and resultsize<=0 and isCancelled=0"; return getIntResult(from, to, incompleteQuery); } diff --git a/webservices/compbio/stat/collector/StatProcessor.java b/webservices/compbio/stat/collector/StatProcessor.java index fdd832e..d4dbf78 100644 --- a/webservices/compbio/stat/collector/StatProcessor.java +++ b/webservices/compbio/stat/collector/StatProcessor.java @@ -136,7 +136,7 @@ public class StatProcessor { public List getIncompleteJobs() { List aJobs = new ArrayList(); for (JobStat js : stats) { - if (!js.hasResult()) { + if (!js.hasResult() && !js.getIsCancelled()) { aJobs.add(js); } } -- 1.7.10.2