From: Fábio Madeira Date: Mon, 10 Apr 2017 11:22:58 +0000 (+0100) Subject: Changes made for running unittests in our local cluster. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2FJABAWS_Release_2_2_0_dev_testing;p=jabaws.git Changes made for running unittests in our local cluster. --- diff --git a/conf/Executable.properties b/conf/Executable.properties index ac2fb9d..bd567f9 100644 --- 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_ ########################################################################################### local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe local.clustalo.bin = binaries/src/clustalo/src/clustalo -cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/clustalo/src/clustalo +cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/clustalo/src/clustalo ### This parameters specifies the directory where the matrices files are stored #clustalo.presets.file = conf/settings/ClustaloPresets.xml clustalo.parameters.file = conf/settings/ClustaloParameters.xml @@ -92,7 +92,7 @@ clustalo.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe s ########################################################################################### local.muscle.bin.windows = binaries/windows/muscle.exe local.muscle.bin = binaries/src/muscle/muscle -cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/muscle/muscle +cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/muscle/muscle ### This parameters specifies the directory where the matrices files are stored muscle.-matrix.path = binaries/matrices muscle.presets.file = conf/settings/MusclePresets.xml @@ -105,7 +105,7 @@ muscle.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cp # MAFFT CONFIGURATION # ########################################################################################### local.mafft.bin = binaries/src/mafft/scripts/mafft -cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/mafft/scripts/mafft +cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/mafft/scripts/mafft # These paths will be converted to absolute if relative. mafft.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34; ### This parameters specifies the directory where the matrices files are stored @@ -120,7 +120,7 @@ mafft.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu # TCOFFEE CONFIGURATION # ########################################################################################### local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee -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 +cluster.tcoffee.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee # This variable is required by tcoffee tcoffee.bin.env = HOME_4_TCOFFEE#jobsout; tcoffee.presets.file = conf/settings/TcoffeePresets.xml @@ -136,7 +136,7 @@ tcoffee.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe sm # PROBCONS CONFIGURATION # ########################################################################################### local.probcons.bin = binaries/src/probcons/probcons -cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/probcons/probcons +cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/probcons/probcons probcons.parameters.file = conf/settings/ProbconsParameters.xml probcons.limits.file = conf/settings/ProbconsLimits.xml probcons.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M @@ -162,7 +162,7 @@ jronn.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp # DISEMBL CONFIGURATION # ########################################################################################### local.disembl.bin = binaries/src/disembl/DisEMBL.py -cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/disembl/DisEMBL.py +cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/disembl/DisEMBL.py disembl.limits.file = conf/settings/DisemblLimits.xml disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M @@ -171,8 +171,8 @@ disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cp # GLOBPLOT CONFIGURATION # ########################################################################################### local.globplot.bin = binaries/src/globplot/GlobPlot.py -cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py -globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/biopython-1.50 +cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/GlobPlot.py +globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/biopython-1.50 globplot.limits.file = conf/settings/GlobPlotLimits.xml globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M @@ -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 ### depends on. This path will be converted to absolute if relative at runtime. iupred.bin.env = IUPred_PATH#binaries/src/iupred -cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/iupred/iupred +cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/iupred/iupred iupred.parameters.file = conf/settings/IUPredParameters.xml iupred.limits.file = conf/settings/IUPredLimits.xml iupred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M @@ -212,7 +212,7 @@ aacon.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp # JPRED CONFIGURATION # ########################################################################################### #local.jpred.bin = binaries/src/jpred/jpred.pl -#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl +#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/jpred/jpred.pl ## These paths will be converted to absolute if relative. #jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast ## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If @@ -233,7 +233,7 @@ aacon.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp ########################################################################################### local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold -cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold +cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/ViennaRNA/Progs/RNAalifold rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M @@ -242,7 +242,7 @@ rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l # MSAProbs CONFIGURATION # ########################################################################################### local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs -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 +cluster.msaprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml msaprobs.limits.file = conf/settings/MSAprobsLimits.xml msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M @@ -251,7 +251,7 @@ msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_ # GLprobs CONFIGURATION # ########################################################################################### local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs -cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs +cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/GLProbs-1.0/glprobs glprobs.parameters.file = conf/settings/GLprobsParameters.xml glprobs.limits.file = conf/settings/GLprobsLimits.xml glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M diff --git a/testsrc/compbio/runner/msa/ClustalOTester.java b/testsrc/compbio/runner/msa/ClustalOTester.java index 281a50c..980ce0f 100644 --- 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); int count = 0; long position = 0; - int maxloopcount = 108000; // max waiting time = 6h*60m*60s/0.2(one loop sleep) + //int maxloopcount = 108000; // max waiting time = 6h*60m*60s/0.2(one loop sleep) + int maxloopcount = 200; // max waiting time = 3min fw.waitForFile(200); /* * Under certain circumstances DRMAA could report the status wrongly diff --git a/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java index 38fbe8b..6c734c1 100644 --- a/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java +++ b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java @@ -368,6 +368,8 @@ public class RNAalifoldParametersTester { void singleTest(List params) { try { + // remove incompatible '-c' argument + params.remove("-c"); log.info("Using arguments: " + params); RNAalifold rnaalifold = new RNAalifold(); rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile); diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java index d54e67f..61b0f41 100644 --- a/testsrc/compbio/ws/client/TestAAConWS.java +++ b/testsrc/compbio/ws/client/TestAAConWS.java @@ -53,7 +53,9 @@ public class TestAAConWS { * Annotation.class); */try { JABAService client = Jws2Client.connect( - "http://localhost:8080/jabaws", Services.AAConWS); + "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws", Services.AAConWS); +// JABAService client = Jws2Client.connect( +// "http://localhost:8080/jabaws", Services.AAConWS); msaws = (SequenceAnnotation) client; } catch (ConnectException e) { e.printStackTrace(); diff --git a/testsrc/compbio/ws/client/TestIUPredWS.java b/testsrc/compbio/ws/client/TestIUPredWS.java index 158b9ae..d3ca362 100644 --- 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) 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 --- 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) client; } catch (ConnectException e) { diff --git a/testsrc/compbio/ws/client/WSTesterTester.java b/testsrc/compbio/ws/client/WSTesterTester.java index 3671e1b..1d997c3 100644 --- a/testsrc/compbio/ws/client/WSTesterTester.java +++ b/testsrc/compbio/ws/client/WSTesterTester.java @@ -11,7 +11,8 @@ import compbio.metadata.AllTestSuit; public class WSTesterTester { - public static final String SERVER = "http://localhost:8080/jabaws"; + public static final String SERVER = "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws"; + //public static final String SERVER = "http://localhost:8080/jabaws"; // public static final String SERVER = "http://192.168.202.130/jabaws"; // public static final String SERVER = diff --git a/testsrc/compbio/ws/server/RegistryWSTester.java b/testsrc/compbio/ws/server/RegistryWSTester.java index 34f7b6c..cc899f3 100644 --- a/testsrc/compbio/ws/server/RegistryWSTester.java +++ b/testsrc/compbio/ws/server/RegistryWSTester.java @@ -137,7 +137,7 @@ public class RegistryWSTester { MsaWS service = null; try { service = (MsaWS) Jws2Client.connect( - "http://www.compbio.dundee.ac.uk/jabaws", + "http://gjb-www-3.cluster.lifesci.dundee.ac.uk:9507/jabaws", // "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws", Services.ProbconsWS); File input = new File(AllTestSuit.TEST_DATA_PATH_ABSOLUTE @@ -189,7 +189,8 @@ public class RegistryWSTester { MsaWS service = null; try { service = (MsaWS) Jws2Client.connect( - "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws", + "http://www.compbio.dundee.ac.uk/jabaws/", + // "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws", Services.ProbconsWS); String jobId = "@Probcons#158079030012566"; ChunkHolder pos = null;