\r
\r
<h2 align="center">JABAWS How To</h2>\r
-<h3>Table of Content </h3>\r
+<h3>Table of content </h3>\r
<h4>About </h4>\r
<ul>\r
<li><a href="#wisjaba">What is JABAWS?</a></li>\r
<li><a href="#toomanyreqs">What happens if the number of requests to my JABAWS installation is greater the the server can process?</a></li>\r
<li><a href="#canlimit">Sometimes users sent very large number of sequences to JABAWS server, so that it becomes unresponsive. Can I limit the number of sequences users can submit to my server. </a></li>\r
</ul>\r
-<h4>Using JABAWS in your program (examples in java) </h4>\r
-<ul>\r
- <li><a href="#connectto">Connecting to JABAWS</a></li>\r
- <li><a href="#validnames">Valid JABAWS service names and WSDL files</a></li>\r
- <li><a href="#defalign">Aligning sequences</a></li>\r
- <li><a href="#checkresults">Checking the status of the calculation </a></li>\r
- <li><a href="#presetalign">Aligning with presets</a></li>\r
- <li><a href="#customalign">Aligning with custom parameters</a></li>\r
- <li><a href="#writingaltofile">Writing alignments to a file</a></li>\r
- <li><a href="#compex">A complete client example </a></li>\r
- <li><a href="#buildart">Building web services artifacts</a></li>\r
-</ul>\r
<h4>JABAWS on Apache-Tomcat</h4>\r
<ul>\r
<li><a href="#tomdeploy">I dropped jaba.war file into web application directory but nothing happened. What do I do next?</a></li>\r
These listings are read only by default. \r
<h4><a name="canyouhelp" id="canyouhelp"></a>Sometimes something goes wrong with JABAWS, but I cannot figure out why. Can you help?</h4>\r
<p>JABAWS logs all errors to the stdout and in the file called activity.log if <a href="manual.html#logfiles">logging is enabled</a>. Stdout is usually recorded in web server log files. Have a look there and you may find the reason for the problems. If it is still unclear what went wrong try increasing the logging level. Setting the logging level to TRACE or DEBUG will give you a lot of insights in what goes on behind the scene. We would need this log if you need us to help you, or if you would like to report the bug. To change the log level, replace ERROR keyword in ACTIVITY logger to TRACE. </p>\r
-<h3>Using JABAWS in your program</h3>\r
-<h4><a name="connectto" id="connectto"></a>Connecting to JABAWS</h4>\r
-<p class="attention">For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the <a href="download.html">download page</a>. Please note that for now all the examples are in Java other languages will follow given a sufficient demand. </p>\r
-<p>Download a binary JABAWS <a href="download.html">client</a>. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee. </p>\r
-<p class="code"> import java.net.URL;<br />\r
- import javax.xml.namespace.QName;<br />\r
- import javax.xml.ws.Service;<br />\r
- ...............<br />\r
- 1) String qualifiedName = "http://msa.data.compbio/01/01/2010/";<br />\r
- 2) URL url = new URL("http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");<br />\r
- 3) QName qname = new QName(, "ClustalWS");<br />\r
-4) Service serv = Service.create(url, qname);<br />\r
-5) MsaWS msaws = serv.getPort(new QName(qualifiedName, "ClustalWSPort"),\r
-MsaWS.class);</p>\r
-<p>Line 1 makes a qualified name for JABA web services.<br />\r
- Line 2 \r
- constructs the URL to the web services WSDL. <br />\r
-Line 3 makes a qualified name instance for Clustal JABA web service. <br />\r
-Line 4 creates a service instance.<br />\r
-Line 5 makes a connection to the server. </p>\r
-<p>A more generic connection method would look like this </p>\r
-<p class="code"> import java.net.URL;<br />\r
-import javax.xml.namespace.QName;<br />\r
-import javax.xml.ws.Service;<br />\r
-import compbio.ws.client.Services<br />\r
-..............\r
-<br />\r
-String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";<br />\r
-String host = "http://www.compbio.dundee.ac.uk/jabaws";<br />\r
-// In real life the service name can come from args<br />\r
-Services clustal = Services.ClustalWS;<br />\r
-URL url = new URL(host + "/" + clustal.toString() + "?wsdl");<br />\r
-QName qname = new QName(qualifiedServiceName, clustal.toString());<br />\r
-Service serv = Service.create(url, qname);<br />\r
-MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal<br />\r
-+ "Port"), MsaWS.class);</p>\r
-<p>Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS interface. The full documentation of MsaWS functions is available from the <a href="file:///D:/workspace/JWS2/website/dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>. </p>\r
-<h4><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h4>\r
-<ul>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl">ClustalWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl">MuscleWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl">MafftWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl">TcoffeeWS</a> (http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl">ProbconsWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl) </li>\r
- </ul>\r
-<h4><a name="defalign" id="defalign"></a>Aligning sequences </h4>\r
-<p>Given that <span class="hightlight">msaws</span> is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows: </p>\r
-<p class="code">1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
- 2) String jobId = msaws.align(fastalist);\r
- <br />\r
- 3) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one loads FASTA sequence from the file<br />\r
- Line two submits them to web service represented by msaws proxy <br />\r
- Line three retrieves the alignment from a web service. This line will block the execution until the result is available. Use this with caution. In general, you should make sure that the calculation has been completed before attempting retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. While this may be ok with your local server, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) will not let you hold the connection for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check the status of the calculation.<br />\r
-Methods and classes mentioned in the excerpt are available from the JABAWS client library. </p>\r
-<h4><a name="checkresults" id="checkresults"></a>Checking the status of the calculation </h4>\r
-<p> You may have noticed that there was no pause between submitting the job and retrieving of the results. This is because <span class="hightlight">getResult(jobId)</span> method block the processing until the calculation is completed. However, taking into account that the connection holds server resources, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) is configured to reset the connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the calculation has been completed before accessing the results. You can do it like this: </p>\r
-<p> <span class="code">while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {<br />\r
- Thread.sleep(2000); // wait two seconds, then recheck the status\r
- <br />\r
- }</span></p>\r
-<h4><a name="presetalign" id="presetalign"></a>Aligning with presets</h4>\r
-<p class="code">1) PresetManager presetman = msaws.getPresets();<br />\r
- 2) Preset preset = presetman.getPresetByName(presetName);<br />\r
- 3) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
- 4) String jobId = msaws.presetAlign(fastalist, preset);<br />\r
- 5) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one obtains the lists of presets supported by a web service.<br />\r
- Line two return a particular Preset \r
- by its name<br />\r
- Lines three to five are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>\r
-<h4><a name="customalign" id="customalign"></a>Aligning with custom parameters</h4>\r
-<p class="code"> 1) RunnerConfig options = msaws.getRunnerOptions();<br />\r
- 2) Argument matrix = options.getArgument("MATRIX");<br />\r
- 3) matrix.setValue("PAM300");<br />\r
- 4) Argument gapopenpenalty = options.getArgument("GAPOPEN");<br />\r
- 5) gapopenpenalty.setValue("20");<br />\r
- 6) List<Argument> arguments = new ArrayList<Argument>();\r
- <br />\r
- 7) arguments.add(matrix);\r
- arguments.add(gapopenpenalty);<br />\r
- 8) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
- 9) String jobId = msaws.customAlign(fastalist, arguments);<br />\r
- 10) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one obtains the RunnerConfig object that holds information on supported parameters and their values<br />\r
- Line two retrieve a particular parameter from the holder by its name<br />\r
- Lines three sets a value to this parameter which will be used in the calculation. <br />\r
- Line four and five do the same but for another parameter<br />\r
- Line 6 makes a List to hold the parameters <br />\r
- Line seven puts the parameters into that list<br />\r
- Line eight \r
- and ten is the same as in previous examples<br />\r
- Line nine submit an alignment request with the sequences and the parameters <br /> \r
- The names of all the parameters supported by a web service e.g. "PAM300" can be obtained using options.getArguments() method. Further details on the methods available from RunnerConfig object are available from the <a href="dm_javadoc/index.html">javadoc</a>. </p>\r
-<h4><a name="writingaltofile" id="writingaltofile"></a>Writing alignments to a file</h4>\r
-<p>There is a utility method in the client library that does exactly that. </p>\r
-<p> <span class="code">Alignment alignment = align(...) <br />\r
- FileOutputStream outStream = new FileOutputStream(file);<br />\r
- ClustalAlignmentUtil.writeClustalAlignment(outStream, align);</span></p>\r
-<h4><a name="compex" id="compex"></a>A complete client example </h4>\r
-<p>Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a nicely colorized <a href="Example_template.pdf">PDF version</a> of this example. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a <a href="download.html">JABAWS binary client</a>. Please make sure that the client is in the Java class path before running this example.</p>\r
-<pre class="code" style="line-height:1em;">\r
-import java.io.ByteArrayInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.net.URL;\r
-import java.util.List;\r
-\r
-import javax.xml.namespace.QName;\r
-import javax.xml.ws.Service;\r
-\r
-import compbio.data.msa.MsaWS;\r
-import compbio.data.sequence.Alignment;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.SequenceUtil;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.LimitExceededException;\r
-import compbio.metadata.Preset;\r
-import compbio.metadata.PresetManager;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.UnsupportedRuntimeException;\r
-import compbio.metadata.WrongParameterException;\r
-\r
-public class Example {\r
-\r
- /*\r
- * Input sequences for alignment\r
- */\r
- static final String input = ">Foo\r\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR"\r
- + "VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ"\r
- + "LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL"\r
- + "APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA"\r
- + "STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD"\r
- + "YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN"\r
- + "PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD"\r
- + "LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS"\r
- + "DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n"\r
- + "\r\n"\r
- + ">Bar\r\n"\r
- + "MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH"\r
- + "QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA"\r
- + "HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG"\r
- + "IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL"\r
- + "RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL"\r
- + "SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC"\r
- + "PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV"\r
- + "FEMDGFADDFGALLQALARRHGWLGI\r\n"\r
- + "\r\n"\r
- + ">Friends\r\n"\r
- + "MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV"\r
- + "RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG"\r
- + "VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL"\r
- + "TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD"\r
- + "LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF"\r
- + "QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA"\r
- + "DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP"\r
- + "GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI";\r
-\r
- public static void main(String[] args) throws UnsupportedRuntimeException,\r
- LimitExceededException, JobSubmissionException,\r
- WrongParameterException, FileNotFoundException, IOException,\r
- ResultNotAvailableException, InterruptedException {\r
-\r
- String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";\r
-\r
- /* Make a URL pointing to web service WSDL */\r
- URL url = new URL(\r
- "http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");\r
-\r
- /*\r
- * If you are making a client that connects to different web services\r
- * you can use something like this:\r
- */\r
- // URL url = new URL(host + "/" + Services.ClustalWS.toString() +\r
- // "?wsdl");\r
-\r
- QName qname = new QName(qualifiedServiceName, "ClustalWS");\r
- Service serv = Service.create(url, qname);\r
- /*\r
- * Multiple sequence alignment interface for Clustal web service\r
- * instance\r
- */\r
- MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, "ClustalWS"\r
- + "Port"), MsaWS.class);\r
-\r
- /* Get the list of available presets */\r
- PresetManager presetman = msaws.getPresets();\r
-\r
- /* Get the Preset object by preset name */\r
- Preset preset = presetman\r
- .getPresetByName("Disable gap weighting (Speed-oriented)");\r
-\r
- /*\r
- * Load sequences in FASTA format from the file You can use something\r
- * like new FileInputStream(<filename>) to load sequence from the file\r
- */\r
- List<FastaSequence> fastalist = SequenceUtil\r
- .readFasta(new ByteArrayInputStream(input.getBytes()));\r
-\r
- /*\r
- * Submit loaded sequences for an alignment using preset. The job\r
- * identifier is returned by this method, you can retrieve the results\r
- * with it sometime later.\r
- */\r
- String jobId = msaws.presetAlign(fastalist, preset);\r
-\r
- /* This method will block for the duration of the calculation */\r
- Alignment alignment = msaws.getResult(jobId);\r
-\r
- /*\r
- * This is a better way of obtaining results, it does not involve\r
- * holding the connection open for the duration of the calculation,\r
- * Besides, as the University of Dundee public server will reset the\r
- * connection after 10 minutes of idling, this is the only way to obtain\r
- * the results of long running task from our public server.\r
- */\r
- // while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {\r
- // Thread.sleep(1000); // wait a second, then recheck the status\r
- // }\r
-\r
- /* Output the alignment to standard out */\r
- System.out.println(alignment);\r
-\r
- // Alternatively, you can record retrieved alignment into the file in\r
- // ClustalW format\r
-\r
- // ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(\r
- // "output.al"), alignment);\r
-\r
- }\r
-}\r
-</pre>\r
-For a more detailed description of all available types and their functions please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>. \r
-<h4><a name="buildart" id="buildart"></a>Building web services artifacts</h4>\r
-<p>JABAWS are the standard <a href="http://jax-ws.java.net/">JAX-WS</a> SOAP web services, which are <a href="http://www.ws-i.org/">WS-I</a> basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our <a href="#connectto"> client library</a> as it provides a handful of useful methods in addition to plain data types. </p>\r
-<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>\r
<h3>JABAWS on Apache-Tomcat</h3>\r
<h4><a name="tomdeploy" id="tomdeploy"></a>I dropped jaba.war file into web application directory but nothing happened. What do I do next?</h4>\r
<ul>\r
\r
<h3>JABAWS on VM (Virtual Machine)</h3>\r
<h4><a name="vmbexc" id="vmbexc"/>I cannot open VM using VirtualBox due to VERR_VMX_MSR_LOCKED_OR_DISABLED exception. Can you help?</h4>\r
- <p>VERR_VMX_MSR_LOCKED_OR_DISABLED exception means that Intel Virtualization technology is disabled or not supported by your computer. If you have such problem, please make sure you have configured JABAWS VM with 1 CPU and disabled VT-X extensions. Alternatively you can enable virtualization extensions ion from the BIOS of your computer. Unfortunately, we cannot give you exact instructions on how to do this, as this would depend on your computer BIOS manufacturer. For MACs it may not be possible at all. </p>\r
+ <p>VERR_VMX_MSR_LOCKED_OR_DISABLED exception means that Intel Virtualization technology is disabled or not supported by your computer. If you have such a problem, please make sure you have configured the JABAWS VM with 1 CPU and disabled VT-X extensions. Alternatively you can enable virtualization extensions ion from the BIOS of your computer. Unfortunately, we cannot give you exact instructions on how to do this, as this would depend on your computer BIOS manufacturer. For MACs it may not be possible at all. </p>\r
<h4><a name="ovfOnVmware" id="ovfOnVmware"/>VMWare Player - Failed to query source for information. I cannot open OVF file using VMware player. Why is this?</h4>\r
- <p>At a time of writing, the latest version of VMware Player 3.1.2 support only a legacy OVF version 0.9. Whereas OVF packaged with JABAWS VM is version 1.0. Please use VMX - VMware specific configuration file with all VMware products. </p>\r
+ <p>At the time of writing, the latest version of VMware Player 3.1.2 supported only a legacy OVF version 0.9. Whereas OVF packaged with JABAWS VM is version 1.0. Please use VMX - VMware specific configuration file with all VMware products. </p>\r
<h4><a name="vmiaccess" id="vmiaccess"/>I want to connect to the Internet from my VM. Can I do that?</h4>\r
\r
-<p>By default JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use Bridged network. In such case you would have to configure the VM IP address manually (unless of cause your network have a DHCP server to do that). </p>\r
+<p>By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that). </p>\r
</div>\r
<!-- content end--> \r
<div id="copyright">Last update: 17 November 2010<br/>\r
Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div> <!-- page end-->\r
-<!-- Google analitics -->\r
+\r
<!-- Google analitics -->\r
<script type="text/javascript">\r
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
git://source.jalview.org / jabaws.git / blobdiff