[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Tue Apr 7 15:42:39 UTC 2009
kawas
Tue Apr 7 11:42:39 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help
In directory dev.open-bio.org:/tmp/cvs-serv2986/src/main/org/biomoby/service/dashboard/help
Modified Files:
PerlMoSeSPanel.html
Log Message:
updated the doc to include both async soap and cgi service generation.
formatted the html for easy reading/writing
moby-live/Java/src/main/org/biomoby/service/dashboard/help PerlMoSeSPanel.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html 2008/06/05 19:46:14 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html 2009/04/07 15:42:39 1.5
@@ -1,98 +1,294 @@
<h1>Perl MoSeS: Generate & Edit Code</h1>
-<p> This panel is a user-interface to the Perl MoSeS
- sub-project. <em>MoSeS</em> stands for <em>Moby Services Support</em> and its documentation is available at:<br />
- http://search.cpan.org/dist/MOSES-MOBY/lib/MOSES/MOBY.pm</p>
-<p> In order to use this panel, you will have to ensure that you (or your
- sys admin) have installed <strong>Perl</strong> and the CPAN module MOSES::MOBY (http://search.cpan.org/dist/MOSES-MOBY/).
-
- Once that module has been installed <strong>and</strong> you have performed the
- user configuration step (<strong><em>moses-install.pl</em></strong>),
- you will be able use this panel! </p>
-<p><font color="#FF0000" size="+1"><strong><em>Once again, this panel is only useful in those situations that you have installed the CPAN module '</em>MOSES::MOBY<em>' and have run the user configuration script </em>'moses-install.pl<em>'!</em></strong></font></p>
-<p> The panel has two different parts - one <b><a href="#gen">generates code</a></b> for the
- selected services, and one provides you with an <b><a href="#editor">editor</a></b> to aid
- in writing the business logic for any service that you generate with this
- Perl-MoSeS. </p>
-<p> For both parts, you need to start by selecting a service, services,
- or authority in the services tree. Multiple selection is possible using
- <em><strong>SHIFT</strong></em> or <em><strong>CONTROL</strong></em>. If you select an authority, all services from this
- authority are considered selected. </p>
-<p> All activities are done in the background using the command line utilities installed by the Perl-MoSeS module. </p>
-<p> </p>
+<p>
+ This panel is a user-interface to the Perl MoSeS
+ sub-project. <em>MoSeS</em>
+ stands for <em>Moby Services Support</em>
+ and its documentation is available at:
+ <br/>
+ http://search.cpan.org/dist/MOSES-MOBY/lib/MOSES/MOBY.pm
+</p>
+<p>
+ In order to use this panel, you will have to ensure that you (or your
+ sys admin) have installed <strong>Perl</strong>
+ and the CPAN module MOSES::MOBY (http://search.cpan.org/dist/MOSES-MOBY/).
+ Once that module has been installed <strong>and</strong>
+ you have performed the
+ user configuration step (<strong><em>moses-install.pl</em></strong>),
+ you will be able use this panel!
+</p>
+<p>
+ <font color="#FF0000" size="+1">
+ <strong><em>Once again, this panel is only useful in those situations that you have installed the CPAN module '</em>MOSES::MOBY<em>' and have run the user configuration script </em>'moses-install.pl<em>'!</em></strong>
+ </font>
+</p>
+<p>
+ The panel has two different parts - one <b><a href="#gen">generates code</a></b>
+ for the
+ selected services, and one provides you with an <b><a href="#editor">editor</a></b>
+ to aid
+ in writing the business logic for any service that you generate with this
+ Perl-MoSeS.
+</p>
+<p>
+ For both parts, you need to start by selecting a service, services,
+ or authority in the services tree. Multiple selection is possible using<em><strong>SHIFT</strong></em>
+ or <em><strong>CONTROL</strong></em>. If you select an authority, all services from this
+ authority are considered selected.
+</p>
+<p>
+ All activities are done in the background using the command line utilities installed by the Perl-MoSeS module.
+</p>
+<p>
+
+</p>
<h2>Perl-MoSeS sub panel</h2>
-<p>The Perl-MoSeS sub panel allows you to:</p>
-<ul><li><strong><a href="#gen">Generate</a></strong> - generate perl modules for services that you select,</li>
- <li><a href="#local_user_config"><strong>Local User Config</strong></a> - for those users without root access when they installed Perl-MoSeS<em><strong>*</strong></em></li>
+<p>
+ The Perl-MoSeS sub panel allows you to:
+</p>
+<ul>
+ <li>
+ <strong><a href="#gen">Generate</a></strong>
+ - generate perl modules for services that you select,
+ </li>
+ <li>
+ <a href="#local_user_config"><strong>Local User Config</strong></a>
+ - for those users without root access when they installed Perl-MoSeS<em><strong>*</strong></em>
+ </li>
</ul>
<blockquote>
- <p><em><strong>* when the panel is created, it makes a best attempt to determine whether or not the cpan module MOSES-MOBY was installed as root. If it was not, this sub panel is visible.</strong></em></p>
+ <p>
+ <em><strong>* when the panel is created, it makes a best attempt to determine whether or not the cpan module MOSES-MOBY was installed as root. If it was not, this sub panel is visible.</strong></em>
+ </p>
</blockquote>
-<p><em><strong>Possible caveats:</strong></em></p>
+<p>
+ <em><strong>Possible caveats:</strong></em>
+</p>
<ul>
- <li> The actions in this panel depend on the availability of certain command line tools (installed by MOSES-MOBY, when you did <em><strong>'make install'</strong></em> of the cpan module) being available on the system PATH.</li>
+ <li>
+ The actions in this panel depend on the availability of certain command line tools (installed by MOSES-MOBY, when you did <em><strong>'make install'</strong></em>
+ of the cpan module) being available on the system PATH.
+ </li>
</ul>
<h3><a name="gen" id="gen"></a>Generate</h3>
-<p> There is one <em><strong>generator</strong></em> in this panel for creating services, with a couple of options.</p>
+<p>
+ There is one <em><strong>generator</strong></em>
+ in this panel for creating services, with a couple of options.
+</p>
<ul>
- <li><strong>Overwrite Existing Code</strong> - use this to overwrite any service code that has already been generated with MoSeS</li>
- <li><strong>Generate CGI Service</strong> - use this to generate a category '<em><strong>cgi</strong></em>' BioMOBY web service.</li>
- <li><strong>Generate SOAP Service</strong> - use this to generate a category '<em><strong>moby</strong></em>' BioMOBY web service.</li>
-</ul>
-<p>Once you have chosen your desired options, you can click on the <strong>Generate Skeletons</strong> button. This will go through and generate perl modules that represent the services that you selected in the '<em><strong>Service Browser</strong></em>'.</p>
-<p>All files are generated into your local <strong><em>Perl-MoSeS/</em></strong> installation. For instance, <em><strong>assuming</strong></em> that your <strong>username</strong> is <em><strong>moby_user</strong></em> and that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em>, then you could <strong>find</strong> your <strong>service skeletons</strong> in <em><strong>/home/moby_user/Perl-MoSeS/services/Service/</strong></em> directory.</p>
-<p>When you generate CGI based moby services, an additional file is generated into <em><strong>/Perl-MoSeS/cgi/</strong></em>. In order to <strong>implement the business logic</strong>, only the <strong>skeletons mentioned above</strong> are required. The files in the c<em><strong>gi/</strong></em> directory are only used for <strong>deploying your services</strong>.</p>
+ <li>
+ <strong>Overwrite Existing Code</strong>
+ - use this to overwrite any service code that has already been generated with MoSeS
+ </li>
+ <li>
+ <strong>Generate CGI Service</strong>
+ - use this to generate a category '<em><strong>cgi</strong></em>' BioMOBY web service.
+ </li>
+ <li>
+ <strong>Generate ASYNC CGI Service</strong>
+ - use this to generate a category '<em><strong>cgi-async</strong></em>' BioMOBY web service.
+ </li>
+ <li>
+ <strong>Generate SOAP Service</strong>
+ - use this to generate a category '<em><strong>moby</strong></em>' BioMOBY web service.
+ </li>
+ <li>
+ <strong>Generate ASYNC SOAP Service</strong>
+ - use this to generate a category '<em><strong>moby-async</strong></em>' BioMOBY web service.
+ </li>
+</ul>
+<p>
+ Once you have chosen your desired options, you can click on the <strong>Generate Skeletons</strong>
+ button. This will go through and generate perl modules that represent the services that you selected in the '<em><strong>Service Browser</strong></em>'.
+</p>
+<p>
+ All files are generated into your local <strong><em>Perl-MoSeS/</em></strong>
+ installation. For instance, <em><strong>assuming</strong></em>
+ that your <strong>username</strong>
+ is <em><strong>moby_user</strong></em>
+ and that your <strong>home directory</strong>
+ is <em><strong>/home/moby_user/</strong></em>, then you could <strong>find</strong>
+ your <strong>service skeletons</strong>
+ in <em><strong>/home/moby_user/Perl-MoSeS/services/Service/</strong></em>
+ directory.
+</p>
+<p>
+ When you generate CGI based moby services, an additional file is generated into <em><strong>/Perl-MoSeS/cgi/</strong></em>. In order to <strong>implement the business logic</strong>, only the <strong>skeletons mentioned above</strong>
+ are required. The files in the c<em><strong>gi/</strong></em>
+ directory are only used for <strong>deploying your services</strong>.
+</p>
<h3><a name="local_user_config" id="local_user_config"></a>Local User Config</h3>
-<p>The configuration sub panel allows you to specify:</p>
+<p>
+ The configuration sub panel allows you to specify:
+</p>
<ul>
- <li><strong>Perl Install Path</strong> - this is the path to the PERL executable, for instance, /usr/bin/perl <strong><em>[required]</em></strong></li>
- <li><strong>PERL5LIB dir</strong> - a directory to add to Perls' <strong>@INC <em>[required]</em></strong></li>
- <li><strong>PERL5LIB dir(2)</strong> - another directory to add to Perls' <strong>@INC</strong> <strong><em>[optional]</em></strong></li>
- <li><strong>MoSeS Scripts Dir </strong>- the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em></li>
+ <li>
+ <strong>Perl Install Path</strong>
+ - this is the path to the PERL executable, for instance, /usr/bin/perl <strong><em>[required]</em></strong>
+ </li>
+ <li>
+ <strong>PERL5LIB dir</strong>
+ - a directory to add to Perls' <strong>@INC <em>[required]</em></strong>
+ </li>
+ <li>
+ <strong>PERL5LIB dir(2)</strong>
+ - another directory to add to Perls' <strong>@INC</strong>
+ <strong><em>[optional]</em></strong>
+ </li>
+ <li>
+ <strong>MoSeS Scripts Dir </strong>- the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em>
+ </li>
</ul>
-<p>Once this information is entered, and the <em><strong>'Confirm values are correct'</strong></em> is clicked, we check whether the required MOSES scripts are accessible. If everything is deemed to be fine, the other sub panels are enabled. Otherwise, you will be prompted to check your values.</p>
+<p>
+ Once this information is entered, and the <em><strong>'Confirm values are correct'</strong></em>
+ is clicked, we check whether the required MOSES scripts are accessible. If everything is deemed to be fine, the other sub panels are enabled. Otherwise, you will be prompted to check your values.
+</p>
<h4>Help on setting your local user configuration</h4>
-<p>Some users find this information hard to obtain. One trick that I use, is to enter 'perl -V' at the command prompt. Among other things, one of the last things that you will see displayed is something like:</p>
+<p>
+ Some users find this information hard to obtain. One trick that I use, is to enter 'perl -V' at the command prompt. Among other things, one of the last things that you will see displayed is something like:
+</p>
<pre>Built under linux<br /> Compiled at Nov 27 2007 10:44:36<br /> @INC:<br /> /etc/perl<br /> /usr/local/lib/perl/5.8.8<br /> /usr/local/share/perl/5.8.8<br /> /usr/lib/perl5<br /> /usr/share/perl5<br /> /usr/lib/perl/5.8<br /> /usr/share/perl/5.8<br /> /usr/local/lib/site_perl<br /> .</pre>
-<p>Keeping the above in mind and remembering that when you installed (locally for just you and not system wide!) MOSES-MOBY from the command prompt, you specified a <strong>PREFIX</strong>=/some/path/, similar to the following:</p>
+<p>
+ Keeping the above in mind and remembering that when you installed (locally for just you and not system wide!) MOSES-MOBY from the command prompt, you specified a <strong>PREFIX</strong>=/some/path/, similar to the following:
+</p>
<pre> perl Makefile.PL <strong>PREFIX</strong>=/home/ekawas/usr/local</pre>
-<p>The values that you would then enter for <strong>PERL5LIB</strong> are:</p>
+<p>
+ The values that you would then enter for <strong>PERL5LIB</strong>
+ are:
+</p>
<ul>
- <li>/home/ekawas/usr/local/lib/perl/5.8.8</li>
- <li>/home/ekawas/usr/local/lib/site_perl</li>
+ <li>
+ /home/ekawas/usr/local/lib/perl/5.8.8
+ </li>
+ <li>
+ /home/ekawas/usr/local/lib/site_perl
+ </li>
</ul>
-<p>In other words, you are interested in using the <strong>PREFIX</strong><em><strong>/lib/</strong></em> directories. </p>
-<p>The value that you should set for the <strong>'MoSeS Scripts Directory'</strong> are usually located in the <strong>PREFIX<em>/bin/</em></strong> directory.</p>
-<p> </p>
+<p>
+ In other words, you are interested in using the <strong>PREFIX</strong>
+ <em><strong>/lib/</strong></em>
+ directories.
+</p>
+<p>
+ The value that you should set for the <strong>'MoSeS Scripts Directory'</strong>
+ are usually located in the <strong>PREFIX<em>/bin/</em></strong>
+ directory.
+</p>
+<p>
+
+</p>
<h2>Perl-MoSeS: Editor sub panel</h2>
-<p>This sub panel consists of an editor pane with various tools that will allow you to open and edit perl scripts generated by Perl-MoSeS. One of the nicer features of this editor, is the syntax highlighing that it performs on perl scripts.</p>
+<p>
+ This sub panel consists of an editor pane with various tools that will allow you to open and edit perl scripts generated by Perl-MoSeS. One of the nicer features of this editor, is the syntax highlighing that it performs on perl scripts.
+</p>
<h3><a name="editor" id="editor"></a>Editor</h3>
-<p>The editor allows you to open and easily edit perl scripts that you generate with MoSeS.</p>
-<p>The editor has a really simple interface:</p>
+<p>
+ The editor allows you to open and easily edit perl scripts that you generate with MoSeS.
+</p>
+<p>
+ The editor has a really simple interface:
+</p>
<ul>
- <li><strong>Open</strong> - used to open a perl script.</li>
- <li><strong>Save</strong> - used to save an open script.</li>
- <li><strong>Close</strong> - used to remove the script from view.</li>
- <li><strong>Font</strong> - used to select a font for the editor.</li>
+ <li>
+ <strong>Open</strong>
+ - used to open a perl script.
+ </li>
+ <li>
+ <strong>Save</strong>
+ - used to save an open script.
+ </li>
+ <li>
+ <strong>Close</strong>
+ - used to remove the script from view.
+ </li>
+ <li>
+ <strong>Font</strong>
+ - used to select a font for the editor.
+ </li>
</ul>
-<p>There are also a two buttons for enlarging or shrinking the text in the editor. All of these buttons are located on a toolbar that you can detach from the panel.</p>
+<p>
+ There are also a two buttons for enlarging or shrinking the text in the editor. All of these buttons are located on a toolbar that you can detach from the panel.
+</p>
<h2> </h2>
<h2>Service deployment</h2>
-<p>Once you have created your service, you will want to deploy it. Depending on whether you have generated a SOAP service or a CGI based service, the steps to involved to deploy your service.</p>
+<p>
+ Once you have created your service, you will want to deploy it. Depending on whether you have generated a SOAP service or a CGI based service, the steps to involved to deploy your service.
+</p>
<h3>Deploying a SOAP Service</h3>
-<p>Deploying a SOAP based service is both easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.</p>
-<p>An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong> is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em> and that your <strong>cgi-bin directory</strong> is located at <em><strong>/usr/lib/cgi-bin</strong></em>.</p>
-<p></p>
+<p>
+ Deploying a SOAP based service is both easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.
+</p>
+<p>
+ An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong>
+ is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+ is <em><strong>/home/moby_user/</strong></em>
+ and that your <strong>cgi-bin directory</strong>
+ is located at <em><strong>/usr/lib/cgi-bin</strong></em>.
+</p>
+<p>
+</p>
<pre> cd /usr/lib/cgi-bin
sudo ln -s /home/moby_user/Perl-MoSeS/MobyServer.cgi .</pre>
-<p><strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong></p>
-<p>That is all there is to it. Now you can use <em>Dashboard's</em> <em><strong>Simple Client</strong></em> panel to test your service!</p>
+<p>
+ <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+ That is all there is to it. Now you can use <em>Dashboard's</em>
+ <em><strong>Simple Client</strong></em>
+ panel to test your service!
+</p>
+<h3>Deploying an ASYNC SOAP Service</h3>
+<p>
+ Deploying asynchronous SOAP based service is also easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.
+</p>
+<p>
+ An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong>
+ is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+ is <em><strong>/home/moby_user/</strong></em>
+ and that your <strong>cgi-bin directory</strong>
+ is located at <em><strong>/usr/lib/cgi-bin</strong></em>.
+</p>
+<p>
+</p>
+<pre> cd /usr/lib/cgi-bin
+ sudo ln -s /home/moby_user/Perl-MoSeS/AsyncMobyServer.cgi .</pre>
+<p>
+ <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+ That is all there is to it. Now you can use <em>Dashboard's</em>
+ <em><strong>Simple Client</strong></em>
+ panel to test your service!
+</p>
<h3>Deploying a CGI Service</h3>
-<p>Deploying a CGI based service is a lot like deploying a SOAP based one. Unfortunately, every CGI based service that you generate requires you to deploy it onto your web server. This is in constrast to the SOAP services mentioned above.</p>
-<p>When you generate CGI services, Perl-MoSeS generates 2 files. Your implementation file and a cgi script to be placed on your web server. Perl-MoSeS only requires you to place a symbolic link to this cgi script in your web servers cgi-bin directory.</p>
-<p>You might ask, where is this cgi script? All cgi scripts generated by Perl-MoSeS are placed in the <strong>Perl-MoSeS/cgi/</strong> directory.</p>
-<p>An example of how to deploy your CGI service is shown below. The example assumes that your <strong>username</strong> is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em> and that your <strong>cgi-bin directory</strong> is located at <em><strong>/usr/lib/cgi-bin</strong></em>. Moreover, we will be deploying the <strong>CGI service</strong> <em><strong>HelloBiomobyWorld</strong></em> that is <strong>provided by</strong> <em><strong>samples.jmoby.net</strong></em>.</p>
-<p></p>
+<p>
+ Deploying a CGI based service is a lot like deploying a SOAP based one. Unfortunately, every CGI based service that you generate requires you to deploy it onto your web server. This is in constrast to the SOAP services mentioned above.
+</p>
+<p>
+ When you generate CGI services, Perl-MoSeS generates 2 files. Your implementation file and a cgi script to be placed on your web server. Perl-MoSeS only requires you to place a symbolic link to this cgi script in your web servers cgi-bin directory.
+</p>
+<p>
+ You might ask, where is this cgi script? All cgi scripts generated by Perl-MoSeS are placed in the <strong>Perl-MoSeS/cgi/</strong>
+ directory.
+</p>
+<p>
+ An example of how to deploy your CGI service is shown below. The example assumes that your <strong>username</strong>
+ is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+ is <em><strong>/home/moby_user/</strong></em>
+ and that your <strong>cgi-bin directory</strong>
+ is located at <em><strong>/usr/lib/cgi-bin</strong></em>. Moreover, we will be deploying the <strong>CGI service</strong>
+ <em><strong>HelloBiomobyWorld</strong></em>
+ that is <strong>provided by</strong>
+ <em><strong>samples.jmoby.net</strong></em>.
+</p>
+<p>
+</p>
<pre> cd /usr/lib/cgi-bin
sudo ln -s /home/moby_user/Perl-MoSeS/cgi/samples/jmoby/net/HelloBiomobyWorld.cgi .</pre>
-<p><strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong></p>
-<p>That is all there is to it. Now you can use <em>Dashboard's</em> <em><strong>Simple Client</strong></em> panel to test your service!</p>
+<p>
+ <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+ That is all there is to it. Now you can use <em>Dashboard's</em>
+ <em><strong>Simple Client</strong></em>
+ panel to test your service!
+</p>
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