-#Fri Jul 16 12:02:13 BST 2010\r
+#Thu Aug 11 15:56:45 BST 2011\r
add_header=true\r
eclipse.preferences.version=1\r
-header_text=/* Copyright (c) 2009 Peter Troshin\r\n * \r\n * JAva Bioinformatics Analysis Web Services (JABAWS) @version\: 1.0 \r\n * \r\n * This library is free software; you can redistribute it and/or modify it under the terms of the\r\n * Apache License version 2 as published by the Apache Software Foundation\r\n * \r\n * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r\n * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r\n * License for more details.\r\n * \r\n * A copy of the license is in apache_license.txt. It is also available here\:\r\n * @see\: http\://www.apache.org/licenses/LICENSE-2.0.txt\r\n * \r\n * Any republication or derived work distributed in source code form\r\n * must include this copyright and license notice.\r\n */\r
+header_text=/* Copyright (c) 2011 Peter Troshin\r\n * \r\n * JAva Bioinformatics Analysis Web Services (JABAWS) @version\: 2.0 \r\n * \r\n * This library is free software; you can redistribute it and/or modify it under the terms of the\r\n * Apache License version 2 as published by the Apache Software Foundation\r\n * \r\n * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r\n * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r\n * License for more details.\r\n * \r\n * A copy of the license is in apache_license.txt. It is also available here\:\r\n * @see\: http\://www.apache.org/licenses/LICENSE-2.0.txt\r\n * \r\n * Any republication or derived work distributed in source code form\r\n * must include this copyright and license notice.\r\n */\r
project_specific_settings=true\r
replace_header=true\r
replacements=<?xml version\="1.0" standalone\="yes"?>\n\n<replacements>\n<replacement key\="get" scope\="1" mode\="0">Gets the</replacement>\n<replacement key\="set" scope\="1" mode\="0">Sets the</replacement>\n<replacement key\="add" scope\="1" mode\="0">Adds the</replacement>\n<replacement key\="edit" scope\="1" mode\="0">Edits the</replacement>\n<replacement key\="remove" scope\="1" mode\="0">Removes the</replacement>\n<replacement key\="init" scope\="1" mode\="0">Inits the</replacement>\n<replacement key\="parse" scope\="1" mode\="0">Parses the</replacement>\n<replacement key\="create" scope\="1" mode\="0">Creates the</replacement>\n<replacement key\="build" scope\="1" mode\="0">Builds the</replacement>\n<replacement key\="is" scope\="1" mode\="0">Checks if is</replacement>\n<replacement key\="print" scope\="1" mode\="0">Prints the</replacement>\n<replacement key\="has" scope\="1" mode\="0">Checks for</replacement>\n</replacements>\n\n\r
+server war - obtaining command line binaries \r
\r
Write help on \r
+ execution stats\r
<property name="datamodel" value="${distdir}/datamodel-${jaba_version}.jar"/>\r
<property name="datamodel-src" value="${distdir}/datamodel-src-${jaba_version}.jar"/>\r
<property name="min-jaba-client" value="${distdir}/min-jaba-client-${jaba_version}.jar"/>\r
+ <property name="jaba-client-src" value="${distdir}/jaba-client-src-${jaba_version}.jar"/>\r
+ \r
<property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>\r
<property name="full-jaba-client" value="${distdir}/full-jaba-client-${jaba_version}.jar"/>\r
<property name="jaba-source-jar" value="${distdir}/jabaws-src-${jaba_version}.jar"/>\r
</jar>\r
</target>\r
\r
-\r
+ <target name="jaba-client-src-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="datamodel-source-jar">\r
+ <echo>Jar file: JABAWS client source</echo>\r
+ <delete file="${jaba-client-src}">\r
+ </delete>\r
+ <jar jarfile="${jaba-client-src}">\r
+ <zipgroupfileset excludes="META-INF/*.MF" file="${datamodel-src}"/>\r
+ <fileset dir="${basedir}/webservices">\r
+ <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->\r
+ <include name="compbio/data/msa/**"/>\r
+ <exclude name="compbio/ws/client/ServicesUtil**"/>\r
+ <exclude name="compbio/ws/client/AAConClient**"/>\r
+ <include name="compbio/ws/client/**"/>\r
+ </fileset>\r
+ <manifest>\r
+ <attribute name="Built-By" value="${author}" />\r
+ <attribute name="Implementation-Title" value="${product} Client Source Code" />\r
+ <attribute name="Implementation-Vendor" value="${author}" />\r
+ <attribute name="Implementation-URL" value="${project.url}" />\r
+ </manifest>\r
+ </jar>\r
+ </target>\r
+ \r
<target name="minimal-jaba-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">\r
<echo>Jar file: Minimal WS client jar</echo>\r
<delete file="${basedir}/${min-jaba-client}">\r
import compbio.metadata.JobStatus;\r
import compbio.util.FileUtil;\r
import compbio.ws.client.Services;\r
+import compbio.ws.client.ServicesUtil;\r
\r
/**\r
* Number of runs of each WS = number of folders with name\r
}\r
\r
private Services getService() {\r
- return Services.getServiceByJobDirectory(jobdir);\r
+ return ServicesUtil.getServiceByJobDirectory(jobdir);\r
}\r
\r
long getResultSize() {\r
- Class<? extends Executable<?>> name = Services\r
+ Class<? extends Executable<?>> name = ServicesUtil\r
.getRunnerByJobDirectory(jobdir);\r
\r
File f = null;\r
}\r
\r
long getInputSize() {\r
- Class<? extends Executable<?>> name = Services\r
+ Class<? extends Executable<?>> name = ServicesUtil\r
.getRunnerByJobDirectory(jobdir);\r
\r
File input = files.get(SkeletalExecutable.INPUT);\r
\r
package compbio.ws.client;\r
\r
-import java.io.File;\r
import java.net.URL;\r
import java.util.Set;\r
\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.MsaWS;\r
import compbio.data.msa.SequenceAnnotation;\r
-import compbio.engine.client.ConfExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.runner.conservation.AACon;\r
-import compbio.runner.disorder.Disembl;\r
-import compbio.runner.disorder.GlobPlot;\r
-import compbio.runner.disorder.IUPred;\r
-import compbio.runner.disorder.Jronn;\r
-import compbio.runner.msa.ClustalO;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.runner.msa.Mafft;\r
-import compbio.runner.msa.Muscle;\r
-import compbio.runner.msa.Probcons;\r
-import compbio.runner.msa.Tcoffee;\r
\r
/**\r
* List of web services currently supported by JABAWS version 2\r
* \r
*/\r
public enum Services {\r
+ /*\r
+ * Make sure this class has NO references to runners or engines as it is a\r
+ * part of minimal client package. Such things should go into ServicesUtil\r
+ */\r
MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS;\r
\r
public static Services getService(String servName) {\r
return null;\r
}\r
\r
- public static Services getServiceByRunner(\r
- Class<Executable<?>> runnerClassName) {\r
- assert runnerClassName != null;\r
- String sname = runnerClassName.getSimpleName().toLowerCase();\r
- for (Services service : Services.values()) {\r
- if (service.toString().toLowerCase().contains(sname)) {\r
- return service;\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- public Class<? extends Executable<?>> getServiceImpl() {\r
- switch (this) {\r
- case AAConWS :\r
- return AACon.class;\r
- case ClustalOWS :\r
- return ClustalO.class;\r
- case ClustalWS :\r
- return ClustalW.class;\r
- case MafftWS :\r
- return Mafft.class;\r
- case MuscleWS :\r
- return Muscle.class;\r
- case TcoffeeWS :\r
- return Tcoffee.class;\r
- case ProbconsWS :\r
- return Probcons.class;\r
- case DisemblWS :\r
- return Disembl.class;\r
- case GlobPlotWS :\r
- return GlobPlot.class;\r
- case JronnWS :\r
- return Jronn.class;\r
- case IUPredWS :\r
- return IUPred.class;\r
- default :\r
- throw new RuntimeException(\r
- "Unknown web service implementation class for service: "\r
- + this);\r
- }\r
- }\r
-\r
- public static Class<? extends Executable<?>> getRunnerByJobDirectory(\r
- File jobdir) {\r
- Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
- return service.getServiceImpl();\r
- }\r
-\r
- private static String getRunnerNameByJobDirectory(File jobdir) {\r
- String name = jobdir.getName().split("#")[0];\r
-\r
- if (name.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX)) {\r
- assert ConfExecutable.CLUSTER_TASK_ID_PREFIX.length() == 1;\r
- name = name.substring(1);\r
- }\r
- return name;\r
- }\r
-\r
- public static Services getServiceByJobDirectory(File jobdir) {\r
- return getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
- }\r
-\r
- private static Services getServiceByRunnerName(String name) {\r
- for (Services service : Services.values()) {\r
- String runnerName = service.getServiceImpl().getSimpleName()\r
- .toLowerCase();\r
- name = name.trim().toLowerCase();\r
- if (name.startsWith(runnerName)) {\r
- return service;\r
- }\r
- }\r
- return null;\r
- }\r
-\r
Service getService(URL url, String sqname) {\r
QName qname = new QName(sqname, this.toString());\r
return Service.create(url, qname);\r
--- /dev/null
+package compbio.ws.client;\r
+\r
+import java.io.File;\r
+\r
+import compbio.engine.client.ConfExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.runner.conservation.AACon;\r
+import compbio.runner.disorder.Disembl;\r
+import compbio.runner.disorder.GlobPlot;\r
+import compbio.runner.disorder.IUPred;\r
+import compbio.runner.disorder.Jronn;\r
+import compbio.runner.msa.ClustalO;\r
+import compbio.runner.msa.ClustalW;\r
+import compbio.runner.msa.Mafft;\r
+import compbio.runner.msa.Muscle;\r
+import compbio.runner.msa.Probcons;\r
+import compbio.runner.msa.Tcoffee;\r
+\r
+public class ServicesUtil {\r
+\r
+ public static Services getServiceByRunner(\r
+ Class<Executable<?>> runnerClassName) {\r
+ assert runnerClassName != null;\r
+ String sname = runnerClassName.getSimpleName().toLowerCase();\r
+ for (Services service : Services.values()) {\r
+ if (service.toString().toLowerCase().contains(sname)) {\r
+ return service;\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+\r
+ public static Class<? extends Executable<?>> getServiceImpl(Services service) {\r
+ switch (service) {\r
+ case AAConWS :\r
+ return AACon.class;\r
+ case ClustalOWS :\r
+ return ClustalO.class;\r
+ case ClustalWS :\r
+ return ClustalW.class;\r
+ case MafftWS :\r
+ return Mafft.class;\r
+ case MuscleWS :\r
+ return Muscle.class;\r
+ case TcoffeeWS :\r
+ return Tcoffee.class;\r
+ case ProbconsWS :\r
+ return Probcons.class;\r
+ case DisemblWS :\r
+ return Disembl.class;\r
+ case GlobPlotWS :\r
+ return GlobPlot.class;\r
+ case JronnWS :\r
+ return Jronn.class;\r
+ case IUPredWS :\r
+ return IUPred.class;\r
+ default :\r
+ throw new RuntimeException(\r
+ "Unknown web service implementation class for service: "\r
+ + service);\r
+ }\r
+ }\r
+\r
+ public static Class<? extends Executable<?>> getRunnerByJobDirectory(\r
+ File jobdir) {\r
+ Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
+ return getServiceImpl(service);\r
+ }\r
+\r
+ private static String getRunnerNameByJobDirectory(File jobdir) {\r
+ String name = jobdir.getName().split("#")[0];\r
+\r
+ if (name.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX)) {\r
+ assert ConfExecutable.CLUSTER_TASK_ID_PREFIX.length() == 1;\r
+ name = name.substring(1);\r
+ }\r
+ return name;\r
+ }\r
+\r
+ public static Services getServiceByJobDirectory(File jobdir) {\r
+ return getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
+ }\r
+\r
+ private static Services getServiceByRunnerName(String name) {\r
+ for (Services service : Services.values()) {\r
+ String runnerName = getServiceImpl(service).getSimpleName()\r
+ .toLowerCase();\r
+ name = name.trim().toLowerCase();\r
+ if (name.startsWith(runnerName)) {\r
+ return service;\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+\r
+}\r
git://source.jalview.org / jabaws.git / commitdiff