[MOBY-guts] biomoby commit

[Nina Opushneva]

nopushneva
Mon Apr 11 14:54:35 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/support/rdfagent
In directory pub.open-bio.org:/tmp/cvs-serv30188

Modified Files:
	README.txt 
Log Message:
some changes into the instruction

moby-live/Java/src/support/rdfagent README.txt,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/support/rdfagent/README.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/support/rdfagent/README.txt	2004/10/28 17:50:55	1.1
+++ /home/repository/moby/moby-live/Java/src/support/rdfagent/README.txt	2005/04/11 18:54:35	1.2
@@ -2,39 +2,68 @@
 
   The RDFAgent is the program for the automatic checking of the service Signature data between mobycentral database and the servers of the service providers. This program make a connect to server of the service provider, try to get RDF representation of the services located at this URL.  If a connect will be refused three times in a row by the same reason, the services located at this URL will be deleted from mobycentral database.
  If a connect was a success, the RDFAgent browsing input stream and checking data in the database. The new services from provider's server will be added to database, the services which must be at this URL, but there are missing will be deleted from the database. 
- The report about the  RDFAgent work writing down in two files:
-     -  RDFAgent.log for all of the error messages;
-     -  REPORT is showing the services which have processed.  
-
+ The report about the  RDFAgent work will send to you by E-mail.
+     
             Quick Instructions:             
 
-1. A Java Virtual Machine version 1.4.2 or later is required to run the RDFAgent; 
+1. A Java Virtual Machine version 1.4.2 or later is required to run the RDFAgent
 
-2. Check up if the RDFAgent directory exists in the moby-live/Agents/MOBY-S/ folder of your CVS checkout. If isn't, make CVS update as per instructions.  
+2. You can get the rdfagent.tar.gz  from CVS docs/dist/ directory
+   -Place the RDFagent archive in your /path_to/rdfagent_home/ directory. (For example: /home/agents/)
+    The unpack program should automatically create a directory 'rdfagent' and populate it.
 
-3. Make  changes in the run.sh:
+3. Make  changes in the run-RDFagent.sh:
 
     Java_Home = actual directory for j2sdk1.4.2_03
-    moby.home=/MOBYhomedirectory/RDFAgent
+    RDFagent.home=/RDFagentHomeDirectory/rdfagent (For example: /home/agents/rdfagent)
 
-4. Add a new table "service_validation" to mobysentral database:
-- start mysql as root;
-- run *reset    (from /RDFAgent directory)
+4. Add the path to the RDFagent at the [mobycentral] section in your mobycentral.config file :
 
-5. Add a new column(signatureURL) to service_instance table (if it's missing):
+    rdfagent = /path/to-your/run-RDFagent
+    
+    For example:
+
+    [mobycentral]
+    username = username
+    password = password
+    url = localhost
+    port = 3306
+    dbname = mobycentral
+    rdfagent = /home/agents/rdfagent/run-RDFagent
+    
+5. Add a new table "service_validation" to mobycentral database:
+
+- run *reset    (from /rdfagent directory)
+  > cd /RDFagentHomeDirectory/rdfagent/
+  > ./reset
+  password: your root password for mySQL
+  
+6. Add a new column(signatureURL) to service_instance table (if it's missing): (as mySQL root)
 
  mysql> ALTER TABLE service_instance ADD signatureURL varchar(255) default null;
 
-6.Set up the config file (RDFAgent/conf/verifier.xml):
+7.Set up the RDFagent config file (RDFagent_config.xml):
+   <db> section for set up database parameters;
+      (For example: <db>
+                     <driver>com.mysql.jdbc.Driver</driver>		 
+		     <url>jdbc:mysql://localhost/mobycentral</url>			    
+		     <name>mobycentral</name>				       
+		     <user>moby</user>						  
+		     <passwd>moby_passw</passwd>							     
+		     <port>3306</port>									
+		   </db>              )
+		   
    <mailServer> - a name of mail host for sending a messages;
-   <mailUser>   - the user account for mail host;
-   <logFilePath>- name of the file for saving of log records;
-   
+   <from>       - the user account for mail host;
+     (For example: <mailServer>mail.cbr.nrc.ca</mailServer>     
+                   <mailUser></mailUser>      /* may be null
+	  	   <mailPswd></mailPswd>      /* may be null	       
+	           <from>rdfagent at cbr.nrc.ca</from>)    
 
-7.Set up cron for automatical running the RDFAgent:
+8.Set up cron for automatical running the RDFAgent:
   - Create a text file like this:
 
-     05 8 1 * * source /homedir/RDFAgent/run.sh
+     05 8 1 * * source /homedir/rdfagent/run-RDFagent.sh
 
      where 05 - minute; 8 - hour; 1 - day of the month.
      The last two (*) mean: a first one - number of the month(or abbreviation like Jan,Feb..);