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 (file)
index f130523..0000000
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diff --git a/ExecutionStatistic/log/log.ctrl b/ExecutionStatistic/log/log.ctrl
index 65a47ac..30411c9 100644 (file)
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diff --git a/ExecutionStatistic/log/log1.dat b/ExecutionStatistic/log/log1.dat
deleted file mode 100644 (file)
index fcb2616..0000000
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diff --git a/ExecutionStatistic/log/log10.dat b/ExecutionStatistic/log/log10.dat
new file mode 100644 (file)
index 0000000..e98a2ea
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diff --git a/ExecutionStatistic/log/logmirror.ctrl b/ExecutionStatistic/log/logmirror.ctrl
index 65a47ac..30411c9 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c101.dat b/ExecutionStatistic/seg0/c101.dat
index 5c46cc6..f0ccb2a 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c111.dat b/ExecutionStatistic/seg0/c111.dat
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diff --git a/ExecutionStatistic/seg0/c121.dat b/ExecutionStatistic/seg0/c121.dat
index d93c0aa..a6d633f 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c130.dat b/ExecutionStatistic/seg0/c130.dat
index 7911c66..d00005a 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c141.dat b/ExecutionStatistic/seg0/c141.dat
index fb62699..f02a8b8 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c20.dat b/ExecutionStatistic/seg0/c20.dat
index 554c52d..941ae65 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c31.dat b/ExecutionStatistic/seg0/c31.dat
index 7311a9e..3d8e494 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c41.dat b/ExecutionStatistic/seg0/c41.dat
index 9bc7f11..00f5233 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c470.dat b/ExecutionStatistic/seg0/c470.dat
index d3f4f68..7d279d4 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c481.dat b/ExecutionStatistic/seg0/c481.dat
index 805cd49..4c84aa8 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c51.dat b/ExecutionStatistic/seg0/c51.dat
index e53479c..2517f7d 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c60.dat b/ExecutionStatistic/seg0/c60.dat
index 2a44ef5..67cb3bb 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c71.dat b/ExecutionStatistic/seg0/c71.dat
index 30e364f..f434890 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c81.dat b/ExecutionStatistic/seg0/c81.dat
index 0e56d11..fe6fde9 100644 (file)
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diff --git a/ExecutionStatistic/seg0/c90.dat b/ExecutionStatistic/seg0/c90.dat
index a174a91..28670cb 100644 (file)
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diff --git a/ExecutionStatistic/seg0/ca1.dat b/ExecutionStatistic/seg0/ca1.dat
index 5bb75b8..48db09c 100644 (file)
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 (file)
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 (file)
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diff --git a/TODO.txt b/TODO.txt
index 5d66c70..2d86534 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,3 +1,7 @@
+Help information?\r
+statistics - result files \r
+Check progress tracking on large sequence. \r
+\r
 Add more detailed tests for webservices? \r
 \r
 ? ideally should introduce native Mac support (and maybe abandon native windows support in \r

diff --git a/build.xml b/build.xml
index 27a2cf9..de21ce4 100644 (file)
--- a/build.xml
+++ b/build.xml
@@ -346,7 +346,8 @@
        </target>\r
 \r
        <target name="clearStatDB" description="Remove all records from statistics database">\r
-                <java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">\r
+                <echo>Cleaning Statistics database</echo>\r
+                <java classname="compbio.stat.collector.StatDB" fork="false" failonerror="true" classpath="${classes}">\r
                    <classpath refid="project.classpath" />\r
             </java>\r
        </target>\r
@@ -370,7 +371,7 @@
        </target>\r
 -->\r
 \r
-       <target name="jaba-no-binaries" description="Prepare JABAWS war file without native binaries" depends="full-jaba-jar">\r
+       <target name="jaba-no-binaries" description="Prepare JABAWS war file without native binaries" depends="full-jaba-jar,  clearStatDB">\r
                <echo>Preparing a war file without binaries</echo>\r
                <delete file="${jaba-no-binaries}">\r
                </delete>\r

diff --git a/conf/Executable.properties b/conf/Executable.properties
index f345f86..f97b168 100644 (file)
--- 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\r
 #aacon.limits.file=conf/settings/AAConLimits.xml\r
 #aacon.cluster.cpunum=4\r
+#aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r

diff --git a/testsrc/testdata/ExecutionStatistic/db.lck b/testsrc/testdata/ExecutionStatistic/db.lck
new file mode 100644 (file)
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 (file)
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 (file)
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 (file)
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 (file)
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 (file)
--- 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");\r
                }\r
        }\r
-       public static void main(String[] args) throws SQLException {\r
+       public static void main(String[] args) {\r
                // This is called from Ant cleanStatTable task\r
-               clearStatTable();\r
+               try {\r
+                       clearStatTable();\r
+                       shutdownDBServer();\r
+               } catch (SQLException e) {\r
+                       System.err.println("Fails to clean up JABAWS stat database!");\r
+                       e.printStackTrace();\r
+               }\r
                // new StatDB().createStatTable();\r
                // insertData(null);\r
                /*\r

diff --git a/website/index.html b/website/index.html
index 2e71035..52826d9 100644 (file)
--- a/website/index.html
+++ b/website/index.html
@@ -33,11 +33,12 @@ page</title>
  <a href="man_about.html">Manual</a> \r
  <a href="download.html">Download</a> \r
  <a href="contacts.html">Contact Us</a>\r
+ <a href="AnnualStat">Usage stats</a>\r
  <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
 \r
 <!-- panel end-->\r
 <div id="content">\r
-<h2 id="headtitle">JABAWS</h2>\r
+<h2 id="headtitle">JABAWS 2</h2>\r
 <p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services for Multiple Sequence Alignment">JABAWS:MSA</span> is  free software which provides five web services for multiple sequence alignment: <a href="http://www.clustal.org/">Clustal W</a>, <a href=\r
 "http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, <a href=\r
 "http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a> conveniently packaged to run on your local computer, server or cluster. \r