From ecb4bc6237a7407063f45e3044353e73a3bd1829 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 9 Feb 2011 10:42:39 +0000 Subject: [PATCH] GlobPlot and DIsembl execs all test passed git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3722 e3abac25-378b-4346-85de-24260fe3988d --- binaries/src/compilebin.sh | 1 + binaries/src/globplot/GlobPlot.py | 5 +++-- binaries/src/setexecflag.sh | 2 +- conf/Executable.properties | 4 ++-- how_to_add_new_webservice.txt | 7 +++++++ runner/compbio/runner/disorder/GlobPlot.java | 2 +- testsrc/compbio/runner/disorder/DisemblTester.java | 7 +++++-- testsrc/compbio/runner/disorder/GlobPlotTester.java | 9 ++++----- 8 files changed, 24 insertions(+), 13 deletions(-) diff --git a/binaries/src/compilebin.sh b/binaries/src/compilebin.sh index 8a0ecd2..cd3b63a 100644 --- a/binaries/src/compilebin.sh +++ b/binaries/src/compilebin.sh @@ -67,6 +67,7 @@ echo "DONE" chmod +x sav_gol cd .. +# TODO copy sav_gol other from disembl echo "Compiling GlobPlot..." cd globplot echo "DONE" diff --git a/binaries/src/globplot/GlobPlot.py b/binaries/src/globplot/GlobPlot.py index b15a28d..ae1cf07 100644 --- a/binaries/src/globplot/GlobPlot.py +++ b/binaries/src/globplot/GlobPlot.py @@ -9,8 +9,9 @@ import sys,re import os from os import system,popen3 -relpath = re.sub("/GlobPipe.py$","",argv[0]) -newpath =os.getcwd()+"/"+relpath+"/biopython-1.50" +relpath = re.sub("/GlobPlot.py$","",argv[0]) +# cwd = re.sub("/$","", os.getcwd()) +newpath = relpath + "/biopython-1.50" sys.path.append(newpath) import Bio diff --git a/binaries/src/setexecflag.sh b/binaries/src/setexecflag.sh index 33d1b65..3121737 100644 --- a/binaries/src/setexecflag.sh +++ b/binaries/src/setexecflag.sh @@ -23,4 +23,4 @@ echo "Setting executable flag for DisEMBL..." chmod +x disembl/disembl disembl/sav_gol disembl/DisEMBL.py echo "Setting executable flag for GlobPlot..." -chmod +x globplot/GlobPlot.py +chmod +x globplot/GlobPlot.py globplot/sav_gol diff --git a/conf/Executable.properties b/conf/Executable.properties index 1562c56..99b9c6c 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -76,7 +76,7 @@ jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l #local.disembl.bin.windows= local.disembl.bin=binaries/src/disembl/DisEMBL.py cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py -disembl.parameters.file=conf/settings/DisemblParameters.xml +# disembl.parameters.file=conf/settings/DisemblParameters.xml disembl.limits.file=conf/settings/DisemblLimits.xml disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M @@ -84,7 +84,7 @@ disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M #local.disembl.bin.windows= local.globplot.bin=binaries/src/globplot/GlobPlot.py cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py -globplot.parameters.file=conf/settings/GlobPlotParameters.xml +# globplot.parameters.file=conf/settings/GlobPlotParameters.xml globplot.limits.file=conf/settings/GlobPlotLimits.xml globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M diff --git a/how_to_add_new_webservice.txt b/how_to_add_new_webservice.txt index d795d35..8d7e7cc 100644 --- a/how_to_add_new_webservice.txt +++ b/how_to_add_new_webservice.txt @@ -39,3 +39,10 @@ Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly. +If executable does not support parameters do not add a reference to the XXXParameter.xml +file into the Executable.properties file. Do the same for Presets + + + + + diff --git a/runner/compbio/runner/disorder/GlobPlot.java b/runner/compbio/runner/disorder/GlobPlot.java index 6decede..2284671 100644 --- a/runner/compbio/runner/disorder/GlobPlot.java +++ b/runner/compbio/runner/disorder/GlobPlot.java @@ -79,7 +79,7 @@ public class GlobPlot extends SkeletalExecutable try { inStream = new FileInputStream(new File(workDirectory, getOutput())); results = SequenceUtil.removeSequences(SequenceUtil - .readDisembl(inStream)); + .readGlobPlot(inStream)); inStream.close(); } catch (FileNotFoundException e) { log.error(e.getMessage(), e.getCause()); diff --git a/testsrc/compbio/runner/disorder/DisemblTester.java b/testsrc/compbio/runner/disorder/DisemblTester.java index 133168e..8444668 100644 --- a/testsrc/compbio/runner/disorder/DisemblTester.java +++ b/testsrc/compbio/runner/disorder/DisemblTester.java @@ -284,9 +284,12 @@ public class DisemblTester { try { RunnerConfig disemblConfig = ConfExecutable .getRunnerOptions(Disembl.class); - assertNotNull(disemblConfig); // There is no disembl parameters - assertTrue(disemblConfig.getArguments().size() == 0); + assertNull(disemblConfig); + + //If there were a DisemblParameter.xml file and reference to it, + // it would be like that + // assertTrue(disemblConfig.getArguments().size() == 0); PresetManager disemblPresets = ConfExecutable .getRunnerPresets(Disembl.class); diff --git a/testsrc/compbio/runner/disorder/GlobPlotTester.java b/testsrc/compbio/runner/disorder/GlobPlotTester.java index ffafe26..97c5fd8 100644 --- a/testsrc/compbio/runner/disorder/GlobPlotTester.java +++ b/testsrc/compbio/runner/disorder/GlobPlotTester.java @@ -281,12 +281,11 @@ public class GlobPlotTester { @Test(groups = {AllTestSuit.test_group_runner}) public void testConfigurationLoading() { try { - RunnerConfig disemblConfig = ConfExecutable + RunnerConfig globplotConfig = ConfExecutable .getRunnerOptions(GlobPlot.class); - assertNotNull(disemblConfig); - // There is no disembl parameters - assertTrue(disemblConfig.getArguments().size() == 0); - + // There is no GlobPlot parameters + assertNull(globplotConfig); + PresetManager disemblPresets = ConfExecutable .getRunnerPresets(GlobPlot.class); assertNull(disemblPresets); // there is no presets -- 1.7.10.2