From: pvtroshin Date: Tue, 28 Jun 2011 15:30:02 +0000 (+0000) Subject: Clean database & small changes X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a0fab8b5a5e691130d39e4075bbaf70c957891e3;p=jabaws.git Clean database & small changes git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4363 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/ExecutionStatistic/db.lck b/ExecutionStatistic/db.lck deleted file mode 100644 index f130523..0000000 Binary files a/ExecutionStatistic/db.lck and /dev/null differ diff --git a/ExecutionStatistic/log/log.ctrl b/ExecutionStatistic/log/log.ctrl index 65a47ac..30411c9 100644 Binary files a/ExecutionStatistic/log/log.ctrl and b/ExecutionStatistic/log/log.ctrl differ diff --git a/ExecutionStatistic/log/log1.dat b/ExecutionStatistic/log/log1.dat deleted file mode 100644 index fcb2616..0000000 Binary files a/ExecutionStatistic/log/log1.dat and /dev/null differ diff --git a/ExecutionStatistic/log/log10.dat b/ExecutionStatistic/log/log10.dat new file mode 100644 index 0000000..e98a2ea Binary files /dev/null and b/ExecutionStatistic/log/log10.dat differ diff --git a/ExecutionStatistic/log/logmirror.ctrl b/ExecutionStatistic/log/logmirror.ctrl index 65a47ac..30411c9 100644 Binary files a/ExecutionStatistic/log/logmirror.ctrl and b/ExecutionStatistic/log/logmirror.ctrl differ diff --git a/ExecutionStatistic/seg0/c101.dat b/ExecutionStatistic/seg0/c101.dat index 5c46cc6..f0ccb2a 100644 Binary files a/ExecutionStatistic/seg0/c101.dat and b/ExecutionStatistic/seg0/c101.dat differ diff --git a/ExecutionStatistic/seg0/c111.dat b/ExecutionStatistic/seg0/c111.dat index 7af9ca7..bffd45f 100644 Binary files a/ExecutionStatistic/seg0/c111.dat and b/ExecutionStatistic/seg0/c111.dat differ diff --git a/ExecutionStatistic/seg0/c121.dat b/ExecutionStatistic/seg0/c121.dat index d93c0aa..a6d633f 100644 Binary files a/ExecutionStatistic/seg0/c121.dat and b/ExecutionStatistic/seg0/c121.dat differ diff --git 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differ diff --git a/ExecutionStatistic/seg0/c470.dat b/ExecutionStatistic/seg0/c470.dat index d3f4f68..7d279d4 100644 Binary files a/ExecutionStatistic/seg0/c470.dat and b/ExecutionStatistic/seg0/c470.dat differ diff --git a/ExecutionStatistic/seg0/c481.dat b/ExecutionStatistic/seg0/c481.dat index 805cd49..4c84aa8 100644 Binary files a/ExecutionStatistic/seg0/c481.dat and b/ExecutionStatistic/seg0/c481.dat differ diff --git a/ExecutionStatistic/seg0/c51.dat b/ExecutionStatistic/seg0/c51.dat index e53479c..2517f7d 100644 Binary files a/ExecutionStatistic/seg0/c51.dat and b/ExecutionStatistic/seg0/c51.dat differ diff --git a/ExecutionStatistic/seg0/c60.dat b/ExecutionStatistic/seg0/c60.dat index 2a44ef5..67cb3bb 100644 Binary files a/ExecutionStatistic/seg0/c60.dat and b/ExecutionStatistic/seg0/c60.dat differ diff --git a/ExecutionStatistic/seg0/c71.dat b/ExecutionStatistic/seg0/c71.dat index 30e364f..f434890 100644 Binary files a/ExecutionStatistic/seg0/c71.dat and b/ExecutionStatistic/seg0/c71.dat differ diff --git a/ExecutionStatistic/seg0/c81.dat b/ExecutionStatistic/seg0/c81.dat index 0e56d11..fe6fde9 100644 Binary files a/ExecutionStatistic/seg0/c81.dat and b/ExecutionStatistic/seg0/c81.dat differ diff --git a/ExecutionStatistic/seg0/c90.dat b/ExecutionStatistic/seg0/c90.dat index a174a91..28670cb 100644 Binary files a/ExecutionStatistic/seg0/c90.dat and b/ExecutionStatistic/seg0/c90.dat differ diff --git a/ExecutionStatistic/seg0/ca1.dat b/ExecutionStatistic/seg0/ca1.dat index 5bb75b8..48db09c 100644 Binary files a/ExecutionStatistic/seg0/ca1.dat and b/ExecutionStatistic/seg0/ca1.dat differ diff --git a/ExecutionStatistic/seg0/cb1.dat b/ExecutionStatistic/seg0/cb1.dat index c988f78..3c2a7a8 100644 Binary files a/ExecutionStatistic/seg0/cb1.dat and b/ExecutionStatistic/seg0/cb1.dat differ diff --git a/ExecutionStatistic/seg0/cf0.dat b/ExecutionStatistic/seg0/cf0.dat index 0adbb10..b11079e 100644 Binary files a/ExecutionStatistic/seg0/cf0.dat and b/ExecutionStatistic/seg0/cf0.dat differ diff --git a/TODO.txt b/TODO.txt index 5d66c70..2d86534 100644 --- a/TODO.txt +++ b/TODO.txt @@ -1,3 +1,7 @@ +Help information? +statistics - result files +Check progress tracking on large sequence. + Add more detailed tests for webservices? ? ideally should introduce native Mac support (and maybe abandon native windows support in diff --git a/build.xml b/build.xml index 27a2cf9..de21ce4 100644 --- a/build.xml +++ b/build.xml @@ -346,7 +346,8 @@ - + Cleaning Statistics database + @@ -370,7 +371,7 @@ --> - + Preparing a war file without binaries diff --git a/conf/Executable.properties b/conf/Executable.properties index f345f86..f97b168 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -119,3 +119,4 @@ aacon.parameters.file=conf/settings/AAConParameters.xml aacon.presets.file=conf/settings/AAConPresets.xml #aacon.limits.file=conf/settings/AAConLimits.xml #aacon.cluster.cpunum=4 +#aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 diff --git a/testsrc/testdata/ExecutionStatistic/db.lck b/testsrc/testdata/ExecutionStatistic/db.lck new file mode 100644 index 0000000..80917e0 Binary files /dev/null and b/testsrc/testdata/ExecutionStatistic/db.lck differ diff --git a/testsrc/testdata/ExecutionStatistic/log/log.ctrl b/testsrc/testdata/ExecutionStatistic/log/log.ctrl index 0719b95..4cef4fc 100644 Binary files a/testsrc/testdata/ExecutionStatistic/log/log.ctrl and b/testsrc/testdata/ExecutionStatistic/log/log.ctrl differ diff --git a/testsrc/testdata/ExecutionStatistic/log/log3.dat b/testsrc/testdata/ExecutionStatistic/log/log3.dat index 1637373..018b50e 100644 Binary files a/testsrc/testdata/ExecutionStatistic/log/log3.dat and b/testsrc/testdata/ExecutionStatistic/log/log3.dat differ diff --git a/testsrc/testdata/ExecutionStatistic/log/logmirror.ctrl b/testsrc/testdata/ExecutionStatistic/log/logmirror.ctrl index 0719b95..4cef4fc 100644 Binary files a/testsrc/testdata/ExecutionStatistic/log/logmirror.ctrl and b/testsrc/testdata/ExecutionStatistic/log/logmirror.ctrl differ diff --git a/testsrc/testdata/ExecutionStatistic/seg0/c470.dat b/testsrc/testdata/ExecutionStatistic/seg0/c470.dat index 557e924..fbc3b98 100644 Binary files a/testsrc/testdata/ExecutionStatistic/seg0/c470.dat and b/testsrc/testdata/ExecutionStatistic/seg0/c470.dat differ diff --git a/webservices/compbio/stat/collector/StatDB.java b/webservices/compbio/stat/collector/StatDB.java index 08b99f9..f9f5e1a 100644 --- a/webservices/compbio/stat/collector/StatDB.java +++ b/webservices/compbio/stat/collector/StatDB.java @@ -338,9 +338,15 @@ public class StatDB { log.info("Database shut down normally"); } } - public static void main(String[] args) throws SQLException { + public static void main(String[] args) { // This is called from Ant cleanStatTable task - clearStatTable(); + try { + clearStatTable(); + shutdownDBServer(); + } catch (SQLException e) { + System.err.println("Fails to clean up JABAWS stat database!"); + e.printStackTrace(); + } // new StatDB().createStatTable(); // insertData(null); /* diff --git a/website/index.html b/website/index.html index 2e71035..52826d9 100644 --- a/website/index.html +++ b/website/index.html @@ -33,11 +33,12 @@ page Manual Download Contact Us + Usage stats Barton Group
-

JABAWS

+

JABAWS 2

JABAWS:MSA is free software which provides five web services for multiple sequence alignment: Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS conveniently packaged to run on your local computer, server or cluster.