[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Fri Feb 22 16:19:41 UTC 2008
kawas
Fri Feb 22 11:19:41 EST 2008
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv31053/Docs/MOBY-S_API
Modified Files:
InstallingLocalMOBYCentral.html
Log Message:
updated the docs to reflect the new location of the codebase
moby-live/Docs/MOBY-S_API InstallingLocalMOBYCentral.html,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2007/10/01 19:05:38 1.9
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2008/02/22 16:19:41 1.10
@@ -74,8 +74,7 @@
<li><a href="#MYSQL">MySQL config</a></li>
<li><a href="#CREATECENTRAL">Create databases and load data from THE
central BioMOBY Central</a></li>
- <li><a href="#TOMCAT">Setup BioMOBY Central servlets in
- Tomcat</a></li>
+ <li><a href="#TOMCAT">Setup BioMOBY Central Registry Scripts</a></li>
<li><a href="#ONTOLOGYSERVER">Setup your own ontology server</a></li>
<li><a href="#CLIENTS">Configure your clients</a> </li>
<li><a href="#TEST_YOUR_CENTRAL">Test your set up</a></li>
@@ -184,7 +183,7 @@
<pre> $> cvs update -dP </pre>
(the 'P' flag for the update will clean-up your checkout and get rid of unused directories) </li>
<li>Install BioMOBY Perl code</li>
- <pre> $> cd ~/moby-live/Perl </pre>
+ <pre> $> cd ~/moby-live/Perl/MOBY-Server/ </pre>
To install in default path for Perl modules (root privileges required):
<pre> $> perl Makefile.PL </pre>
To install in custom path (no root privileges required):
@@ -200,7 +199,7 @@
If perl or make are complaining about dependencies you might have to <a href="#CPAN">install additional Perl modules</a> first.
</li>
<li>Copy the main BioMOBY Central CGI script to the path you specified in your <a href="#httpd_biomoby.conf">httpd_biomoby.conf</a>
- <pre> $> cp ~/moby-live/Perl/scripts/MOBY-Central.pl /path/to/your/biomoby/central/cgi-bin/ </pre>
+ <pre> $> cp ~/moby-live/Perl/MOBY-Server/share/cgi/MOBY-Central.pl /path/to/your/biomoby/central/cgi-bin/ </pre>
</li>
</ul>
<li><a name="CPAN"></a><b>Install additional Perl modules using CPAN</b></li>
@@ -310,7 +309,7 @@
<li><a name="CREATECENTRAL"></a><b>Create databases and load data from THE central BioMOBY Central</b></li>
<ul>
<li>If you have come this far and the stuff above was configured correctly, you can use the
- <pre> ~/moby-live/Perl/scripts/CloneCentralDatabases.pl </pre>
+ <pre> ~/moby-live/Perl/MOBY-Server/share/scripts/CloneCentralDatabases.pl </pre>
script. This will create the databases, set privileges, fetch all data from THE central BioMOBY Central
and load it into your local central. </li>
<li>If you prefer to configure your BioMOBY Central databases manually, proceed with the next steps.</li>
@@ -356,106 +355,20 @@
<li>Append data for your local BioMOBY services by registering namespaces, objects and services.</li>
<li>In case you mess up your central during debugging you can simply nuke your databases
and start with a fresh BioMOBY Central clone using the
- <pre> ~/moby-live/Perl/scripts/CloneCentralDatabases.pl </pre>
+ <pre> ~/moby-live/Perl/MOBY-Server/share/scripts/CloneCentralDatabases.pl </pre>
script. </li>
</li>
</ul>
</li>
- <li><a name="TOMCAT"></a><b>Setup BioMOBY Central servlets in Tomcat</b></li>
+ <li><a name="TOMCAT"></a><b>Setup BioMOBY Central Registry Scripts</b></li>
<ul>
- <li>If you want to retrieve info from your local central in RDF format, you will need to install some servlets in Tomcat.
+ <li>If you want to retrieve info from your local central in RDF format, you will need to install some scripts.
Info in RDF format is required to use your local BioMOBY Central for example with the workflow enactor Taverna.
- Taverna uses your BioMOBY Central endpoint to request the URLs for the RDF files, which are dynamically generated by the servlets.
+ Taverna uses your BioMOBY Central endpoint to request the URLs for the RDF files, which are dynamically generated by the scripts.
Hence, using your local central with Taverna is a two step process that requires
both a working BioMOBY Central CGI script at your BioMOBY Central endpoint
- and several servlets to generate RDF files. </li>
- <li>Install Tomcat if necessary.</li>
- <li>Get root privileges:
- <pre> $> su </pre>
- </li>
- <li>Check if Tomcat is enabled:
- <pre> root $> chkconfig tomcat </pre>
- </li>
- <li>Enable Tomcat if necessary:
- <pre> root $> chkconfig -a tomcat </pre>
- </li>
- <li>Check if Tomcat is running:
- <pre> root $> rctomcat status </pre>
- </li>
- <li>Start Tomcat if necessary:
- <pre> root $> rctomcat start </pre>
- </li>
- <li>To make the RDF files accessible using the same port your webserver is using,
- you can not use Tomcat standalone, but should configure Apache as frontend for Tomcat instead.
- This requires a module for Apache like for example mod_jk. Install mod_jk if necessary. </li>
- <li>Configure Tomcat to work with Apache:<br/>
- $CATALINA_HOME is used to refer to the directory into which you have installed Tomcat 5.
- <ul>
- <li>Create a workers.properties file in the $CATALINA_HOME/conf/jk/ dir.
- There should be an example workers.properties file in the $CATALINA_HOME/conf/ dir. </li>
- <li>Open your workers.properties file and change the path for
- <i>workers.tomcat_home</i> and
- <i>workers.java_home</i> according to your setup.
- And set the <i>ps</i> (path separator) for your OS. </li>
- <li>Edit $CATALINA_HOME/conf/server.xml and append:
- <pre>
- <Listener className="org.apache.jk.config.ApacheConfig"
- modJk="/usr/lib/apache2/mod_jk.so"
- workersConfig="$CATALINA_HOME/conf/jk/workers.properties" /> </pre>
- to the <Server> section.
- Change the modJk and workersConfig path according to your setup. </li>
- </ul>
- </li>
- <li>Configure Apache 2 to work with Tomcat:<br/>
- <ul>
- <li>Append the following to your <a href="#httpd_biomoby.conf">httpd_biomoby.conf</a>:
- <pre>
- #
- # Configure Apache as frontend for Tomcat using mod_jk
- #
-
- #
- # Load mod_jk if necessary.
- # The default path for mod_jk is /usr/lib/apache2/mod_jk.so
- #
- <IfModule !mod_jk.c>
- LoadModule jk_module /path/to/mod_jk.so
- </IfModule>
-
- JkWorkersFile "$CATALINA_HOME/conf/jk/workers.properties"
- JkLogFile "$CATALINA_HOME/logs/mod_jk.log"
- JkLogLevel emerg
-
- #
- # Dispatch requests for BioMOBY Central servlets
- # to a worker configured in your workers.properties file.
- # The default worker using the ajp 1.3 protocol is named ajp13.
- #
- JkMount /authority/* <i>ajp13</i>
-
- JkAutoAlias $CATALINA_HOME/webapps </pre>
- </li>
- <li>restart Apache as root:
- <pre> root $> rcapache2 restart </pre>
- </li>
- </ul>
- <li>Download the servlets installer from:<br/>
- <a href="http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar">http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar</a> </li>
- <li>Install the servlets:
- <pre> for Sun's java $> java -jar install.jar </pre>
- <pre> for IBM's java $> java install.jar </pre>
- You should get a graphical interface that will guide you through the installation process... </li>
- <li>Configure the servlets in Tomcat. <br />
- <br />
- <ul>
- <li>Configuration details can be found <a href="http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/RegistryServlets.html" target="_blank">here</a>. <br />
- <br/>
- </li>
- </ul>
- </li>
- <li>restart Tomcat as root:
- <pre> root $> rctomcat restart </pre>
- </li>
+ and several scripts to generate RDF files. </li>
+ <li><a href="./RegistryScripts.html" target="_blank">For instructions on setting up the scripts, click here!</a></li>
<li>If you want to use Taverna with your local BioMOBY Central you will need Taverna 1.3 or better.</li>
</ul>
</li>
@@ -571,8 +484,8 @@
<pre> MOBY_SERVER - the endpoint of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
<pre> MOBY_URI - the namespace of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
</li>
- <li>Rerun make test in ~moby-live/Perl/ (see <a href="#MOBYLIVE">Get and install BioMOBY code</a> above):
- <pre> $~/moby-live/Perl> make test </pre>
+ <li>Rerun make test in ~moby-live/Perl/MOBY-Server/ (see <a href="#MOBYLIVE">Get and install BioMOBY code</a> above):
+ <pre> $~/moby-live/Perl/MOBY-Server/> make test </pre>
With the environment variables pointing to your local Central it will run a series of tests against your local registry.
The tests 'clean up' after themselves, leaving your registry in the same state that it was in when you started the test suite.
If there is a failure in the tests, you will need to track down the source of the failure and then re-run the test script
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