[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Wed Jun 4 15:59:31 UTC 2008
kawas
Wed Jun 4 11:59:31 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help
In directory dev.open-bio.org:/tmp/cvs-serv1696/src/main/org/biomoby/service/dashboard/help
Modified Files:
PerlMoSeSPanel.html
Log Message:
updated the doc to reflect changes in the panel
moby-live/Java/src/main/org/biomoby/service/dashboard/help PerlMoSeSPanel.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html 2008/05/27 17:23:53 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html 2008/06/04 15:59:31 1.3
@@ -1,26 +1,27 @@
<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 <a href="http://search.cpan.org/dist/MOSES-MOBY/lib/MOSES/MOBY.pm">here</a>.</p>
+ 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 <a href="http://search.cpan.org/dist/MOSES-MOBY/">MOSES::MOBY</a>.
+ 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> The panel has two different parts - one <b>generates code</b> for the
- selected services, and one provides you with an <b>editor</b> to aid
+<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 using the command line utilities installed by the Perl-MoSeS module. </p>
-<h2>MoSeS Toolkit</h2>
-<p>The MoSeS Toolkit sub panel allows you to:</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><strong><a href="#utilities">Utilities</a></strong> - for synchronizing Perl-MoSeS with the Dashboard, and an</li>
- <li><strong><a href="#editor">Editor</a></strong> - .for easily editing the business logic of services that you create.</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>
@@ -28,7 +29,7 @@
</blockquote>
<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) 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>
@@ -40,31 +41,17 @@
<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> </h3>
-<h3><a name="utilities" id="utilities"></a>Utilities</h3>
-<p> This sub panel is used for synchronizing the cache that Dashboard uses with the one that Perl-MoSeS uses. </p>
-<p>To perform a synchronization, select '<strong>Synchronize Services</strong>' and/or '<strong>Synchronize Datatypes</strong>' and then hit the Synchronize button.</p>
-<h3> </h3>
-<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>
-<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>
-</ul>
-<p>There are also a two buttons for enlarging or shrinking the text in the editor.</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>
<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 directory</strong> - a directory to add to Perls' <strong>@INC <em>[optional]</em></strong></li>
- <li><strong>PERL5LIB directory (2)</strong> - another directory to add to Perls' <strong>@INC</strong> <strong><em>[optional]</em></strong></li>
- <li><strong>MoSeS Scripts Directory</strong> - the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em></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>'Test user config'</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>
<pre> perl Makefile.PL <strong>PREFIX</strong>=/home/ekawas/usr/local</pre>
@@ -74,7 +61,21 @@
<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>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>
+<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>
+<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>
+</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>
+<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>
<h3>Deploying a SOAP Service</h3>
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