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

diff --git a/binaries/src/compilebin.sh b/binaries/src/compilebin.sh
index 8a0ecd2..cd3b63a 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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= \r
 local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
 cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
-disembl.parameters.file=conf/settings/DisemblParameters.xml\r
+# disembl.parameters.file=conf/settings/DisemblParameters.xml\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
@@ -84,7 +84,7 @@ disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 #local.disembl.bin.windows= \r
 local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
 cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
-globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
+# globplot.parameters.file=conf/settings/GlobPlotParameters.xml\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
 \r

diff --git a/how_to_add_new_webservice.txt b/how_to_add_new_webservice.txt
index d795d35..8d7e7cc 100644 (file)
--- 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.
 \r
 \r
 \r
+If executable does not support parameters do not add a reference to the XXXParameter.xml \r
+file into the Executable.properties file. Do the same for Presets\r
+\r
+\r
+ \r
+\r
+\r

diff --git a/runner/compbio/runner/disorder/GlobPlot.java b/runner/compbio/runner/disorder/GlobPlot.java
index 6decede..2284671 100644 (file)
--- a/runner/compbio/runner/disorder/GlobPlot.java
+++ b/runner/compbio/runner/disorder/GlobPlot.java
@@ -79,7 +79,7 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
                try {\r
                        inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
                        results = SequenceUtil.removeSequences(SequenceUtil\r
-                                       .readDisembl(inStream));\r
+                                       .readGlobPlot(inStream));\r
                        inStream.close();\r
                } catch (FileNotFoundException e) {\r
                        log.error(e.getMessage(), e.getCause());\r

diff --git a/testsrc/compbio/runner/disorder/DisemblTester.java b/testsrc/compbio/runner/disorder/DisemblTester.java
index 133168e..8444668 100644 (file)
--- a/testsrc/compbio/runner/disorder/DisemblTester.java
+++ b/testsrc/compbio/runner/disorder/DisemblTester.java
@@ -284,9 +284,12 @@ public class DisemblTester {
                try {\r
                        RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
                                        .getRunnerOptions(Disembl.class);\r
-                       assertNotNull(disemblConfig);\r
                        // There is no disembl parameters\r
-                       assertTrue(disemblConfig.getArguments().size() == 0);\r
+                       assertNull(disemblConfig);\r
+\r
+                       //If there were a DisemblParameter.xml file and reference to it, \r
+                       // it would be like that \r
+                       // assertTrue(disemblConfig.getArguments().size() == 0);\r
 \r
                        PresetManager<Disembl> disemblPresets = ConfExecutable\r
                                        .getRunnerPresets(Disembl.class);\r

diff --git a/testsrc/compbio/runner/disorder/GlobPlotTester.java b/testsrc/compbio/runner/disorder/GlobPlotTester.java
index ffafe26..97c5fd8 100644 (file)
--- 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})\r
        public void testConfigurationLoading() {\r
                try {\r
-                       RunnerConfig<GlobPlot> disemblConfig = ConfExecutable\r
+                       RunnerConfig<GlobPlot> globplotConfig = ConfExecutable\r
                                        .getRunnerOptions(GlobPlot.class);\r
-                       assertNotNull(disemblConfig);\r
-                       // There is no disembl parameters\r
-                       assertTrue(disemblConfig.getArguments().size() == 0);\r
-\r
+                       // There is no GlobPlot parameters \r
+                       assertNull(globplotConfig);\r
+                       \r
                        PresetManager<GlobPlot> disemblPresets = ConfExecutable\r
                                        .getRunnerPresets(GlobPlot.class);\r
                        assertNull(disemblPresets); // there is no presets\r