Changes made for running unittests in our local cluster.

diff --git a/conf/Executable.properties b/conf/Executable.properties
index ac2fb9d..bd567f9 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -76,7 +76,7 @@ clustalw.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_
 ###########################################################################################\r
 local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe\r
 local.clustalo.bin         = binaries/src/clustalo/src/clustalo\r
-cluster.clustalo.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/clustalo/src/clustalo\r
+cluster.clustalo.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/clustalo/src/clustalo\r
 ### This parameters specifies the directory where the matrices files are stored\r
 #clustalo.presets.file      = conf/settings/ClustaloPresets.xml\r
 clustalo.parameters.file   = conf/settings/ClustaloParameters.xml\r
@@ -92,7 +92,7 @@ clustalo.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe s
 ###########################################################################################\r
 local.muscle.bin.windows = binaries/windows/muscle.exe\r
 local.muscle.bin         = binaries/src/muscle/muscle\r
-cluster.muscle.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/muscle/muscle\r
+cluster.muscle.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/muscle/muscle\r
 ### This parameters specifies the directory where the matrices files are stored\r
 muscle.-matrix.path      = binaries/matrices\r
 muscle.presets.file      = conf/settings/MusclePresets.xml\r
@@ -105,7 +105,7 @@ muscle.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cp
 #                                  MAFFT CONFIGURATION                                    #\r
 ###########################################################################################\r
 local.mafft.bin         = binaries/src/mafft/scripts/mafft\r
-cluster.mafft.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/mafft/scripts/mafft\r
+cluster.mafft.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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
 ### This parameters specifies the directory where the matrices files are stored\r
@@ -120,7 +120,7 @@ mafft.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu
 #                                  TCOFFEE CONFIGURATION                                  #\r
 ###########################################################################################\r
 local.tcoffee.bin         = binaries/src/tcoffee/t_coffee_source/t_coffee\r
-cluster.tcoffee.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/tcoffee/t_coffee_source/t_coffee\r
+cluster.tcoffee.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/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
@@ -136,7 +136,7 @@ tcoffee.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe sm
 #                                  PROBCONS CONFIGURATION                                 #\r
 ###########################################################################################\r
 local.probcons.bin         = binaries/src/probcons/probcons\r
-cluster.probcons.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/probcons/probcons\r
+cluster.probcons.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/probcons/probcons\r
 probcons.parameters.file   = conf/settings/ProbconsParameters.xml\r
 probcons.limits.file       = conf/settings/ProbconsLimits.xml\r
 probcons.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
@@ -162,7 +162,7 @@ jronn.cluster.settings   = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp
 #                                  DISEMBL CONFIGURATION                                  #\r
 ###########################################################################################\r
 local.disembl.bin        = binaries/src/disembl/DisEMBL.py\r
-cluster.disembl.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/disembl/DisEMBL.py\r
+cluster.disembl.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/disembl/DisEMBL.py\r
 disembl.limits.file      = conf/settings/DisemblLimits.xml\r
 disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
 \r
@@ -171,8 +171,8 @@ disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cp
 #                                  GLOBPLOT CONFIGURATION                                 #\r
 ###########################################################################################\r
 local.globplot.bin        = binaries/src/globplot/GlobPlot.py\r
-cluster.globplot.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py\r
-globplot.bin.env          = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/biopython-1.50\r
+cluster.globplot.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/GlobPlot.py\r
+globplot.bin.env          = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/biopython-1.50\r
 globplot.limits.file      = conf/settings/GlobPlotLimits.xml\r
 globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
 \r
@@ -185,7 +185,7 @@ local.iupred.bin         = binaries/src/iupred/iupred
 ### This must point to the directory where iupred binary is, with other files it\r
 ### depends on. This path will be converted to absolute if relative at runtime.\r
 iupred.bin.env           = IUPred_PATH#binaries/src/iupred\r
-cluster.iupred.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/iupred/iupred\r
+cluster.iupred.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/iupred/iupred\r
 iupred.parameters.file   = conf/settings/IUPredParameters.xml\r
 iupred.limits.file       = conf/settings/IUPredLimits.xml\r
 iupred.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
@@ -212,7 +212,7 @@ aacon.cluster.settings   = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp
 #                               JPRED CONFIGURATION                                       #\r
 ###########################################################################################\r
 #local.jpred.bin        = binaries/src/jpred/jpred.pl\r
-#cluster.jpred.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl\r
+#cluster.jpred.bin      = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/jpred/jpred.pl\r
 ## These paths will be converted to absolute if relative.\r
 #jpred.bin.env          = BLASTMAT#binaries/src/jpred/data/blast\r
 ## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If\r
@@ -233,7 +233,7 @@ aacon.cluster.settings   = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp
 ###########################################################################################\r
 local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe\r
 local.rnaalifold.bin         = binaries/src/ViennaRNA/Progs/RNAalifold\r
-cluster.rnaalifold.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold\r
+cluster.rnaalifold.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/ViennaRNA/Progs/RNAalifold\r
 rnaalifold.parameters.file   = conf/settings/RNAalifoldParameters.xml\r
 rnaalifold.limits.file       = conf/settings/RNAalifoldLimits.xml\r
 rnaalifold.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
@@ -242,7 +242,7 @@ rnaalifold.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l
 #                                 MSAProbs CONFIGURATION                                  #\r
 ###########################################################################################\r
 local.msaprobs.bin         = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
-cluster.msaprobs.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
+cluster.msaprobs.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
 msaprobs.parameters.file   = conf/settings/MSAprobsParameters.xml\r
 msaprobs.limits.file       = conf/settings/MSAprobsLimits.xml\r
 msaprobs.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
@@ -251,7 +251,7 @@ msaprobs.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_
 #                                  GLprobs CONFIGURATION                                  #\r
 ###########################################################################################\r
 local.glprobs.bin         = binaries/src/GLProbs-1.0/glprobs\r
-cluster.glprobs.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs\r
+cluster.glprobs.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/GLProbs-1.0/glprobs\r
 glprobs.parameters.file   = conf/settings/GLprobsParameters.xml\r
 glprobs.limits.file       = conf/settings/GLprobsLimits.xml\r
 glprobs.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r

diff --git a/testsrc/compbio/runner/msa/ClustalOTester.java b/testsrc/compbio/runner/msa/ClustalOTester.java
index 281a50c..980ce0f 100644 (file)
--- a/testsrc/compbio/runner/msa/ClustalOTester.java
+++ b/testsrc/compbio/runner/msa/ClustalOTester.java
@@ -340,7 +340,8 @@ public class ClustalOTester {
                        FilePuller fw = FilePuller.newFilePuller(file, FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
                        int count = 0;\r
                        long position = 0;\r
-                       int maxloopcount = 108000; // max waiting time = 6h*60m*60s/0.2(one loop sleep)\r
+                       //int maxloopcount = 108000; // max waiting time = 6h*60m*60s/0.2(one loop sleep)\r
+                       int maxloopcount = 200; // max waiting time = 3min\r
                        fw.waitForFile(200);\r
                        /*\r
                         * Under certain circumstances DRMAA could report the status wrongly\r

diff --git a/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
index 38fbe8b..6c734c1 100644 (file)
--- a/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
+++ b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
@@ -368,6 +368,8 @@ public class RNAalifoldParametersTester {
        \r
        void singleTest(List<String> params) {\r
                try {\r
+                       // remove incompatible '-c' argument\r
+                       params.remove("-c");\r
                        log.info("Using arguments: " + params);\r
                        RNAalifold rnaalifold = new RNAalifold();\r
                        rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r

diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java
index d54e67f..61b0f41 100644 (file)
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -53,7 +53,9 @@ public class TestAAConWS {
                 * Annotation.class);\r
                 */try {\r
                        JABAService client = Jws2Client.connect(\r
-                                       "http://localhost:8080/jabaws", Services.AAConWS);\r
+                                       "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws", Services.AAConWS);\r
+//                     JABAService client = Jws2Client.connect(\r
+//                                     "http://localhost:8080/jabaws", Services.AAConWS);\r
                        msaws = (SequenceAnnotation<AACon>) client;\r
                } catch (ConnectException e) {\r
                        e.printStackTrace();\r

diff --git a/testsrc/compbio/ws/client/TestIUPredWS.java b/testsrc/compbio/ws/client/TestIUPredWS.java
index 158b9ae..d3ca362 100644 (file)
--- a/testsrc/compbio/ws/client/TestIUPredWS.java
+++ b/testsrc/compbio/ws/client/TestIUPredWS.java
@@ -53,7 +53,9 @@ public class TestIUPredWS {
                 * Annotation.class);
                 */try {
                        JABAService client = Jws2Client.connect(
-                                       "http://localhost:8080/jabaws", Services.IUPredWS);
+                                       "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws", Services.IUPredWS);
+//                     JABAService client = Jws2Client.connect(
+//                                     "http://localhost:8080/jabaws", Services.IUPredWS);
                        msaws = (SequenceAnnotation<IUPredWS>) client;
                } catch (ConnectException e) {
                        e.printStackTrace();

diff --git a/testsrc/compbio/ws/client/TestRNAalifoldWS.java b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
index cafe9cb..06be131 100644 (file)
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -44,7 +44,9 @@ public class TestRNAalifoldWS {
                
                try {
                        JABAService client = Jws2Client.connect(
-                                       "http://localhost:8080/jabaws", Services.RNAalifoldWS);
+                                       "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws", Services.RNAalifoldWS);
+//                     JABAService client = Jws2Client.connect(
+//                                     "http://localhost:8080/jabaws", Services.RNAalifoldWS);
 //                     foldws = (RNAalifoldWS) client;
                        foldws = (SequenceAnnotation<RNAalifoldWS>) client;
                } catch (ConnectException e) {

diff --git a/testsrc/compbio/ws/client/WSTesterTester.java b/testsrc/compbio/ws/client/WSTesterTester.java
index 3671e1b..1d997c3 100644 (file)
--- a/testsrc/compbio/ws/client/WSTesterTester.java
+++ b/testsrc/compbio/ws/client/WSTesterTester.java
@@ -11,7 +11,8 @@ import compbio.metadata.AllTestSuit;
 \r
 public class WSTesterTester {\r
 \r
-       public static final String SERVER = "http://localhost:8080/jabaws";\r
+       public static final String SERVER = "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws";\r
+       //public static final String SERVER = "http://localhost:8080/jabaws";\r
        // public static final String SERVER = "http://192.168.202.130/jabaws";\r
 \r
        // public static final String SERVER =\r

diff --git a/testsrc/compbio/ws/server/RegistryWSTester.java b/testsrc/compbio/ws/server/RegistryWSTester.java
index 34f7b6c..cc899f3 100644 (file)
--- a/testsrc/compbio/ws/server/RegistryWSTester.java
+++ b/testsrc/compbio/ws/server/RegistryWSTester.java
@@ -137,7 +137,7 @@ public class RegistryWSTester {
                MsaWS service = null;\r
                try {\r
                        service = (MsaWS) Jws2Client.connect(\r
-                                       "http://www.compbio.dundee.ac.uk/jabaws",\r
+                                       "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws",\r
                                        // "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws",\r
                                        Services.ProbconsWS);\r
                        File input = new File(AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
@@ -189,7 +189,8 @@ public class RegistryWSTester {
                MsaWS service = null;\r
                try {\r
                        service = (MsaWS) Jws2Client.connect(\r
-                                       "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws",\r
+                                       "http://www.compbio.dundee.ac.uk/jabaws/",\r
+                                       // "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws",\r
                                        Services.ProbconsWS);\r
                        String jobId = "@Probcons#158079030012566";\r
                        ChunkHolder pos = null;\r