From: Sasha Sherstnev Date: Wed, 23 Oct 2013 16:19:18 +0000 (+0100) Subject: First commit into ProteoCache (some basic files from JABAWS) X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=63e5bb5af3a11dc19bece64aa0937885b0907143;p=proteocache.git First commit into ProteoCache (some basic files from JABAWS) --- 63e5bb5af3a11dc19bece64aa0937885b0907143 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b09440a --- /dev/null +++ b/.gitignore @@ -0,0 +1,9 @@ +/logs +/distro +/jobsout +/JABAWSLogFilename.* +/testsrc/testdata/*.written +/testsrc/testdata/alirna.ps + + + diff --git a/.project b/.project new file mode 100644 index 0000000..390e83f --- /dev/null +++ b/.project @@ -0,0 +1,42 @@ + + + clustengine-2.5 + + + + + + org.eclipse.wst.jsdt.core.javascriptValidator + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.wst.common.project.facet.core.builder + + + + + org.eclipse.wst.validation.validationbuilder + + + + + net.sourceforge.metrics.builder + + + + + + org.eclipse.jem.workbench.JavaEMFNature + org.eclipse.wst.common.modulecore.ModuleCoreNature + org.eclipse.wst.common.project.facet.core.nature + org.eclipse.jdt.core.javanature + org.eclipse.wst.jsdt.core.jsNature + net.sourceforge.metrics.nature + + diff --git a/.settings/.jsdtscope b/.settings/.jsdtscope new file mode 100644 index 0000000..555d177 --- /dev/null +++ b/.settings/.jsdtscope @@ -0,0 +1,6 @@ + + + + + + diff --git a/.settings/net.sf.jautodoc.prefs b/.settings/net.sf.jautodoc.prefs new file mode 100644 index 0000000..4c1e231 --- /dev/null +++ b/.settings/net.sf.jautodoc.prefs @@ -0,0 +1,7 @@ +#Thu Aug 11 15:56:45 BST 2011 +add_header=true +eclipse.preferences.version=1 +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 */ +project_specific_settings=true +replace_header=true +replacements=\n\n\nGets the\nSets the\nAdds the\nEdits the\nRemoves the\nInits the\nParses the\nCreates the\nBuilds the\nChecks if is\nPrints the\nChecks for\n\n\n diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000..ef1da3f --- /dev/null +++ b/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,292 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 +org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve +org.eclipse.jdt.core.compiler.compliance=1.6 +org.eclipse.jdt.core.compiler.debug.lineNumber=generate 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+vals/org.eclipse.wst.xsd.core.xsd/groups=0107include0107fileext03xsdF0107exclude01111contentType134org.eclipse.wst.dtd.core.dtdsourceF +vf.version=3 diff --git a/WEB-INF/lib/cassandra-all-1.2.4.jar b/WEB-INF/lib/cassandra-all-1.2.4.jar new file mode 100644 index 0000000..ab244c5 Binary files /dev/null and b/WEB-INF/lib/cassandra-all-1.2.4.jar differ diff --git a/WEB-INF/lib/cassandra-clientutil-1.2.4.jar b/WEB-INF/lib/cassandra-clientutil-1.2.4.jar new file mode 100644 index 0000000..1ac8df4 Binary files /dev/null and b/WEB-INF/lib/cassandra-clientutil-1.2.4.jar differ diff --git a/WEB-INF/lib/cassandra-thrift-1.2.4.jar b/WEB-INF/lib/cassandra-thrift-1.2.4.jar new file mode 100644 index 0000000..ca72cf0 Binary files /dev/null and b/WEB-INF/lib/cassandra-thrift-1.2.4.jar differ diff --git a/WEB-INF/lib/commons-beanutils-1.7.0.jar b/WEB-INF/lib/commons-beanutils-1.7.0.jar new file mode 100644 index 0000000..b1b89c9 Binary files /dev/null and b/WEB-INF/lib/commons-beanutils-1.7.0.jar 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b/WEB-INF/lib/poi-3.2-FINAL-20081019.jar new file mode 100644 index 0000000..e860545 Binary files /dev/null and b/WEB-INF/lib/poi-3.2-FINAL-20081019.jar differ diff --git a/WEB-INF/lib/readme.txt b/WEB-INF/lib/readme.txt new file mode 100644 index 0000000..9992096 --- /dev/null +++ b/WEB-INF/lib/readme.txt @@ -0,0 +1,24 @@ +Runtime dependency for web services. They are required to run a web service +within servlet container e.g. tomcat + +webservices-rt.jar +webservices-tools.jar +webservices-api.jar + +JABAWS Statistics web application dependencies: + +- Display Tag 1.2 dependencies + +commons-beanutils-1.7.0.jar +commons-collections-3.2.jar +commons-lang-2.3.jar +commons-logging-1.1.jar +displaytag-1.2.jar +displaytag-export-poi-1.2.jar +itext-1.4.7.jar +jstl-1.1.2.jar +poi-3.2-FINAL-20081019.jar +standard-1.1.2.jar + +- Derby database driver for statistics database +derby.jar \ No newline at end of file diff --git a/WEB-INF/lib/slf4j-api-1.7.5.jar b/WEB-INF/lib/slf4j-api-1.7.5.jar new file mode 100644 index 0000000..8766455 Binary files /dev/null and b/WEB-INF/lib/slf4j-api-1.7.5.jar differ diff --git a/WEB-INF/lib/slf4j-simple-1.7.5.jar b/WEB-INF/lib/slf4j-simple-1.7.5.jar new file mode 100644 index 0000000..9dece31 Binary files /dev/null and b/WEB-INF/lib/slf4j-simple-1.7.5.jar differ diff --git a/WEB-INF/lib/standard-1.1.2.jar b/WEB-INF/lib/standard-1.1.2.jar new file mode 100644 index 0000000..bc528ac Binary files /dev/null and b/WEB-INF/lib/standard-1.1.2.jar differ diff --git a/WEB-INF/lib/webservices-api.jar b/WEB-INF/lib/webservices-api.jar new file mode 100644 index 0000000..84f50ae Binary files /dev/null and b/WEB-INF/lib/webservices-api.jar differ diff --git a/WEB-INF/lib/webservices-rt.jar b/WEB-INF/lib/webservices-rt.jar new file mode 100644 index 0000000..6741549 Binary files /dev/null and b/WEB-INF/lib/webservices-rt.jar differ diff --git a/WEB-INF/lib/webservices-tools.jar b/WEB-INF/lib/webservices-tools.jar new file mode 100644 index 0000000..e0426b8 Binary files /dev/null and b/WEB-INF/lib/webservices-tools.jar differ diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml new file mode 100644 index 0000000..13d6fac --- /dev/null +++ b/WEB-INF/sun-jaxws.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml new file mode 100644 index 0000000..cec1884 --- /dev/null +++ b/WEB-INF/web.xml @@ -0,0 +1,363 @@ + + +JABAWS +JAva Bioinformatics Analysis Web Services (JABAWS) v.2 + + + + + compbio.ws.server.MainManager + + + compbio.stat.servlet.StatisticCollector + + + compbio.ws.server.SetExecutableFlag + + + com.sun.xml.ws.transport.http.servlet.WSServletContextListener + + + + + + 20 + + + + + This is a standard tomcat 'default' servlet for making listings + listings + org.apache.catalina.servlets.DefaultServlet + + debug + 0 + + + readonly + true + + + listings + true + + 1 + + + + + + Display pre-calculated accounting info + DisplayStat + compbio.stat.servlet.DisplayStat + + + + WebServices Status + ServiceStatus + compbio.stat.servlet.ServiceStatus + + + + DownloadRedirector + compbio.stat.servlet.DownloadRedirector + + + + WebService Status with no UI. Accepts web service name as a parameter + HttpCodeResponseServiceStatus + compbio.stat.servlet.HttpCodeResponseServiceStatus + + + + Display job list + Joblist + compbio.stat.servlet.Joblist + + + + Display monthly summary statistics + AnnualStat + compbio.stat.servlet.AnnualStat + + + + Display monthly summary statistics with no links to details + PublicAnnualStat + compbio.stat.servlet.AnnualStat + + + + RegistryWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + ClustalWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + ClustalOWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + MuscleWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + MafftWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + TcoffeeWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + ProbconsWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + MSAprobsWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + GLprobsWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + AAConWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + JronnWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + DisemblWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + GlobPlotWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + IUPredWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + JpredWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + RNAalifoldWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + + listings + / + + + + DownloadRedirector + /download + + + + DisplayStat + /DisplayStat + + + + ServiceStatus + /ServiceStatus + + + + HttpCodeResponseServiceStatus + /HttpCodeResponseServiceStatus/* + + + + AnnualStat + /AnnualStat + + + + PublicAnnualStat + /PublicAnnualStat + + + + Joblist + /Joblist + + + + RegistryWS + /RegistryWS + + + + ClustalWS + /ClustalWS + + + + ClustalOWS + /ClustalOWS + + + + MuscleWS + /MuscleWS + + + + MafftWS + /MafftWS + + + + TcoffeeWS + /TcoffeeWS + + + + ProbconsWS + /ProbconsWS + + + + MSAprobsWS + /MSAprobsWS + + + + GLprobsWS + /GLprobsWS + + + + AAConWS + /AAConWS + + + + JronnWS + /JronnWS + + + + DisemblWS + /DisemblWS + + + + GlobPlotWS + /GlobPlotWS + + + + IUPredWS + /IUPredWS + + + + JpredWS + /JpredWS + + + + RNAalifoldWS + /RNAalifoldWS + + + + + + + Administrator pages + + /DisplayStat + /Joblist + /AnnualStat + /conf/* + /binaries/* + /jobsout/* + /testsrc/* + /lib/* + /test-output/* + + + + + admin + + + + + + + + unsupported HTTP methods + /* + PUT + DELETE + TRACE + OPTIONS + + + + + + + + BASIC + JABAWS administrators + + + + + + The role that is required to log in and view JABAWS internals + admin + + + diff --git a/build.xml b/build.xml new file mode 100644 index 0000000..50bdbac --- /dev/null +++ b/build.xml @@ -0,0 +1,565 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cleaning Statistics database + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Jar file: Minimal WS client jar + + + + + + + + + + + + + + + + + + + + + + + Jar file: Minimal WS client jar + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Jar file: Full ProteoCache client jar + + + + + + + + + + + + + + + + + + + + + Packing binaries, and configuration files + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Jar file: Full WS client jar + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Preparing a war file without binaries + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Packing data for internal web site + + + + + + + + + + Preparing a complete war file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +