Better method for searching JAVA

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4392 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/IDEAS.txt b/IDEAS.txt
index 3be0c19..ba3b9eb 100644 (file)
--- a/IDEAS.txt
+++ b/IDEAS.txt
@@ -1,5 +1,19 @@
 FUTURE TODO\r
 \r
+Pack the test cases and build file to run them in one of the distributives \r
+\r
+? Better native Mac support (and maybe abandon native windows support in \r
+favour of VM)\r
+\r
+Cluster stats: \r
+ -Remove hyperlinks from tasks which workdirs were removed \r
+ Way to do: Crawler is to update DB records if the directory is not found to prevent link \r
+generation for stats. \r
+ -graph generation \r
+ -user documentation (do not forget how to enable follow symlinks!)\r
+   \r
+Webpage for testing web services?\r
+\r
 Add interface for Jalview annotation \r
 \r
 Develop generic Interface to return Jalview annotation for easy to add new \r

diff --git a/TODO.txt b/TODO.txt
index d502d48..ef4c64c 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,71 +1,62 @@
-JABA 1 is to keep working, later when 2 is ready replace jabaws mapping to point to \r
-JABA 2 but provide a link to JABA 1.  \r
-\r
-+install JABA 1 stat server \r
-\r
-+Get path to Java executable from JAVA_HOME ? (for Jronn AACon) \r
-+Describe requirements \r
 \r
+Write help on \r
+ - execution stats\r
+ - new VM \r
+ - new properties e.g. jar\r
+ - registry\r
+ - merge developers help pages\r
+ - new menu bar background & page background(?)\r
+ - change log \r
+ - main page should point to JABA 1   \r
+ - Document the Limits for presets\r
+ - JAVA DOCS\r
+ - defaults changed - e.g. limits are disabled - explain how to enable\r
+ - cluster settings are commented out \r
+ - Describe requirements \r
 Python > 2.2\r
 Perl > 5.0\r
 Java > 6\r
-\r
 For compilation \r
 C++\r
 C\r
 Gnu make\r
+   \r
+- Check progress tracking on large sequence.\r
 \r
-Webpage for testing web services?\r
-\r
-Crawler is to update DB records if the directory is not found to prevent link \r
-generation for stats. \r
-\r
- \r
-\r
-+ Help information? - relative - client to add host and context info\r
-+ statistics - result files \r
-+ Check progress tracking on large sequence. \r
+- Add more detailed tests for webservices? \r
 \r
-Add more detailed tests for webservices? \r
-\r
-? ideally should introduce native Mac support (and maybe abandon native windows support in \r
-favour of VM)   \r
-\r
-TODO write some help on the executable.properties within this file! \r
+- TODO write some help on the executable.properties within this file! \r
 check that after binaries relocation build tasks point to correct locations!\r
 \r
-Cluster stats: \r
- -Remove hyperlinks from tasks which workdirs were removed \r
- -graph generation \r
- -user documentation (do not forget how to enable follow symlinks!)\r
 \r
 add to help text: To disable a web service remove it from WEB-INF/sun-jaxws.xml descriptor\r
 \r
 rename jaba.war to jabaws.war and make sure jabaws context path is used throughout. \r
 \r
-+ Current stat collector has to rely on file dates! \r
-\r
 \r
 ? Replace conservation.Method with server.ws.Method and try building WS. If this does not work - get rid of Method\r
 \r
 integrate the above to tweak the size of the local job\r
 \r
-+ Good toString method for Limits (test with command line client -limits)\r
-Document the Limits for presets\r
-JABA DOCS\r
 \r
 (later) Add documentation on Presets, Parameters and Limits\r
 (later) Explain how to define a limit\r
 \r
 Add test for repeated result collection from cluster engine\r
 \r
-(low) Pack the test cases and build file to run them in one of the distributives \r
 \r
 \r
 DONE\r
 \r
 version 2\r
 \r
+DONE: Current stat collector has to rely on file dates! \r
+DONE: Help information? - relative - client to add host and context info\r
+DONE: statistics - result files \r
+DONE: Good toString method for Limits (test with command line client -limits)\r
+DONE: install JABA 1 stat server \r
+DONE: Get path to Java executable from JAVA_HOME ? (for Jronn AACon) \r
+\r
 DONE:  GET rid of binaries/help directory!\r
 DONE:  update binaries\r
  DONE:  muscle binary version 3.8.31 for win/lin32/lin64 and sources, docs in website/prog_docs\r

diff --git a/conf/Executable.properties b/conf/Executable.properties
index a1107ca..5bd5b6e 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -20,7 +20,7 @@
 ### Clustal configuration ###\r
 local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
 local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
-cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
+#cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
 # see engine.client.Util.getExecProperty() method for details  \r
 # So they are case insensitive. \r
@@ -33,7 +33,7 @@ clustalw.parameters.file=conf/settings/ClustalParameters.xml
 ### Muscle configuration ###\r
 local.muscle.bin.windows=binaries/windows/muscle.exe\r
 local.muscle.bin=binaries/src/muscle/muscle\r
-cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
+#cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
 muscle.-matrix.path=binaries/matrices\r
@@ -44,7 +44,7 @@ muscle.parameters.file=conf/settings/MuscleParameters.xml
 \r
 ### Mafft configuration ###\r
 local.mafft.bin=binaries/src/mafft/scripts/mafft\r
-cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
+#cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
 # These paths will be converted to absolute if relative.\r
 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
 mafft.--aamatrix.path=binaries/matrices\r
@@ -56,7 +56,7 @@ mafft.parameters.file=conf/settings/MafftParameters.xml
 \r
 ### Tcoffee configuration ###\r
 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
-cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
+#cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
 # This variable is required by tcoffee\r
 tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;\r
 tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
@@ -67,7 +67,7 @@ tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml
 \r
 ### Probcons configuration ###\r
 local.probcons.bin=binaries/src/probcons/probcons\r
-cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
+#cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
 #Probcons does not support matrix loading - unrecognised option reported! \r
 probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
 #probcons.limits.file=conf/settings/ProbconsLimits.xml\r
@@ -78,7 +78,7 @@ probcons.parameters.file=conf/settings/ProbconsParameters.xml
 # variable for local execution \r
 #local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
 #local.jronn.bin=/sw/java/latest/bin/java\r
-cluster.jronn.bin=/sw/java/latest/bin/java\r
+#cluster.jronn.bin=/sw/java/latest/bin/java\r
 jronn.jar.file=binaries/windows/jronn3.1.jar\r
 jronn.limits.file=conf/settings/JronnLimits.xml\r
 #jronn.cluster.cpunum=4\r
@@ -87,13 +87,13 @@ jronn.limits.file=conf/settings/JronnLimits.xml
 \r
 ### Disembl configuration Tisean - Disembl dependancy ### \r
 local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
-cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
+#cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
 #disembl.limits.file=conf/settings/DisemblLimits.xml\r
 #disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
 ### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### \r
 local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
-cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
+#cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
 #globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \r
 globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
 #globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
@@ -105,7 +105,7 @@ local.iupred.bin=binaries/src/iupred/iupred
 #iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred\r
 # This path will be converted to absolute if relative. \r
 iupred.bin.env=IUPred_PATH#binaries/src/iupred\r
-cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
+#cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
 iupred.parameters.file=conf/settings/IUPredParameters.xml\r
 #iupred.limits.file=conf/settings/IUPredLimits.xml\r
 #iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
@@ -114,7 +114,7 @@ iupred.parameters.file=conf/settings/IUPredParameters.xml
 # This is just a path to the standard java executable \r
 #local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
 #local.aacon.bin=/sw/java/latest/bin/java\r
-cluster.aacon.bin=/sw/java/latest/bin/java\r
+#cluster.aacon.bin=/sw/java/latest/bin/java\r
 # Path to the AACon library\r
 aacon.jar.file=binaries/windows/aaconservation.jar\r
 aacon.parameters.file=conf/settings/AAConParameters.xml\r

diff --git a/engine/compbio/engine/client/Util.java b/engine/compbio/engine/client/Util.java
index 66f3a35..634112f 100644 (file)
--- a/engine/compbio/engine/client/Util.java
+++ b/engine/compbio/engine/client/Util.java
@@ -253,6 +253,7 @@ public final class Util {
                } else {\r
                        bin = ph.getProperty("cluster." + execCommandName + ".bin");\r
                }\r
+               log.debug("Using executable: " + bin);\r
                return bin; // File.separator\r
        }\r
        /**\r
@@ -274,7 +275,15 @@ public final class Util {
         * @return\r
         */\r
        public static String getJava() {\r
-               String javahome = System.getenv("JAVA_HOME");\r
+               String javahome = System.getProperty("java.home");\r
+               if (compbio.util.Util.isEmpty(javahome)) {\r
+                       javahome = System.getenv("JAVA_HOME");\r
+               }\r
+               if (compbio.util.Util.isEmpty(javahome)) {\r
+                       log.warn("Cannot find Java in java.home system property "\r
+                                       + "or JAVA_HOME environment variable! ");\r
+                       return null;\r
+               }\r
                File jh = new File(javahome);\r
                if (jh.exists() && jh.isDirectory()) {\r
                        String java = javahome + File.separator + "bin" + File.separator\r