[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Tue Oct 17 14:02:05 UTC 2006
kawas
Tue Oct 17 10:02:05 EDT 2006
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv20037/MOBY-S_API
Modified Files:
InstallingLocalMOBYCentral.html
Log Message:
updated to include new servlets, as well as the updated [mobycentral] section of mobycentral.config
moby-live/Docs/MOBY-S_API InstallingLocalMOBYCentral.html,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2006/02/26 17:57:18 1.5
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2006/10/17 14:02:05 1.6
@@ -183,8 +183,7 @@
<pre> $> cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login </pre>
<pre> $> cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby checkout moby-live </pre>
<pre> $> cvs update -dP </pre>
- (the 'P' flag for the update will clean-up your checkout and get rid of unused directories)
- </li>
+ (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>
To install in default path for Perl modules (root privileges required):
@@ -248,8 +247,7 @@
<pre> root $> rcmysql start </pre>
</li>
<li>If this is the first time mysql is started you will receive a warning not to forget to create a root password for mysql.
- Do so if you haven't done so already.
- </li>
+ Do so if you haven't done so already. </li>
<li>Create a <a name="mobycentral.config">mobycentral.config</a> file and make the following entries
(note that a template mobycentral.config file exists in the moby-live/Database folder of your CVS checkout):<br/>
<pre>
@@ -263,6 +261,7 @@
lsid_namespace = serviceinstance
resourceURL = http://<i>your.host.name</i>/RESOURCES/MOBY-S/ServiceInstances
allResources = http://<i>your.host.name</i>/RESOURCES/MOBY-S/FULL
+ rdf_generator = http://mobycentral.icapture.ubc.ca/authority/RDFGenerator
[mobyobject]
username = <i>mysql_username</i>
@@ -314,8 +313,7 @@
<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>
script. This will create the databases, set privileges, fetch all data from THE central BioMOBY Central
- and load it into your local central.
- </li>
+ 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>
<ul>
<li>If you are going to bootstrap the databases with only the most primitive information, then simply run the
@@ -360,8 +358,7 @@
<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>
- script.
- </li>
+ script. </li>
</li>
</ul>
</li>
@@ -372,8 +369,7 @@
Taverna uses your BioMOBY Central endpoint to request the URLs for the RDF files, which are dynamically generated by the servlets.
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>
+ and several servlets to generate RDF files. </li>
<li>Install Tomcat if necessary.</li>
<li>Get root privileges:
<pre> $> su </pre>
@@ -392,27 +388,23 @@
</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>
+ 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>
+ 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>
+ 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>
+ Change the modJk and workersConfig path according to your setup. </li>
</ul>
</li>
<li>Configure Apache 2 to work with Tomcat:<br/>
@@ -451,66 +443,18 @@
</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>
+ <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/>
- Ensure that the following environment variables are available to Tomcat:
- <pre> MOBY_CENTRAL_CONFIG - the path to your <a href="#mobycentral.config">mobycentral.config file</a> created above </pre>
- <pre> MOBY_SERVER - the endpoint of your local registry (see below, <a href="#CLIENTS">Configure your clients</a>)</pre>
- <pre> MOBY_URI - the namespace of your local registry (see below, <a href="#CLIENTS">Configure your clients</a>)</pre>
- <p/>
- And if you installed the servlets outside the the default webapps folder, make sure Tomcat knows where to find them.
- The easiest way to do this is to make the following three config files in $CATALINA_HOME/conf/Catalina/localhost/ :
- <pre>
- <?xml version='1.0' encoding='utf-8'?>
- <!-- Example authority.xml file -->
- <Context docBase="<i>/path/to/your/webapps/</i>authority" path="/authority">
- <Environment name="MOBY_CENTRAL_CONFIG"
- value="<i>/path/to/your/</i>mobycentral.config"
- type="java.lang.String"/>
- <Environment name="MOBY_SERVER"
- value="http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl"
- type="java.lang.String"/>
- <Environment name="MOBY_URI"
- value="http://<i>your.host.name</i>/MOBY/Central"
- type="java.lang.String"/>
- </Context>
- </pre>
- <pre>
- <?xml version='1.0' encoding='utf-8'?>
- <!-- Example RESOURCES.xml file -->
- <Context docBase="<i>/path/to/your/webapps/</i>RESOURCES" path="/RESOURCES">
- <Environment name="MOBY_CENTRAL_CONFIG"
- value="<i>/path/to/your/</i>mobycentral.config"
- type="java.lang.String"/>
- <Environment name="MOBY_SERVER"
- value="http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl"
- type="java.lang.String"/>
- <Environment name="MOBY_URI"
- value="http://<i>your.host.name</i>/MOBY/Central"
- type="java.lang.String"/>
- </Context>
- </pre>
- <pre>
- <?xml version='1.0' encoding='utf-8'?>
- <!-- Example types.xml file -->
- <Context docBase="<i>/path/to/your/webapps/</i>types" path="/types">
- <Environment name="MOBY_CENTRAL_CONFIG"
- value="<i>/path/to/your/</i>mobycentral.config"
- type="java.lang.String"/>
- <Environment name="MOBY_SERVER"
- value="http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl"
- type="java.lang.String"/>
- <Environment name="MOBY_URI"
- value="http://<i>your.host.name</i>/MOBY/Central"
- type="java.lang.String"/>
- </Context>
- </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>
@@ -522,14 +466,12 @@
<ul>
<li>Copy the
<pre> ~/moby-live/Perl/scripts/OntologyServer.cgi </pre>
- CGI script into your webserver cgi-bin folder.
- </li>
+ CGI script into your webserver cgi-bin folder. </li>
<li>You will now have to edit the MOBY::Client::OntologyServer.pm module manually (sorry!).
This module was hardcoded to point to the OntologyServer.cgi at THE central BioMOBY Central.
You will have to change the line that reads
<pre> host => ["http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi",'read/write'] </pre>
- to point to the URL of your OntologyServer.cgi that you just set up.
- </li>
+ to point to the URL of your OntologyServer.cgi that you just set up. </li>
</ul>
</li>
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