- improved (psql) server documentation

html/aserv.html

@@ -10,14 +10,17 @@
 <h1 class="titre">Setting up an Alignment Server</h1>
 
 <p>An extensive presentation of the Alignment API can be
-  found at <a href="http://alignapi.gforge.inria.fr">http://alignapi.gforge.inria.fr</a>. We also have
+  found
+  at <a href="http://alignapi.gforge.inria.fr">http://alignapi.gforge.inria.fr</a>
+  including a description of the <a href="server.html">Alignment server</a>. We also have
   an on-line <a href="tutorial/tutorial1/server.html">tutorial</a> on
   using it through the server.</p>
 
 <h2>Requirements</h2>
 
 <p>Using the Alignment server requires an SQL database server.
-We see here how to use <a href="http://dev.mysql.com/doc/refman">mysql</a> or Postgres.</p>
+We see here how to
+  use <a href="http://dev.mysql.com/doc/refman">mysql</a> or <a href="https://www.postgresql.org/">Postgres</a>.</p>
 
 <h3>Creating the database for MySQL</h3>
 
@@ -35,34 +38,34 @@ sql> quit
 The database schema will be created upon the first launch of the
 server.
 </p>
-<p>
-Of course, you are advised to use different user, password and
-database name. This can be achieved either:
-<ul>
-<li>by changing values of DBMSBASE, DBMSUSER and DBMSPASS in <tt>AlignmentServer.java</tt> and recompiling;</li>
-<li>by passing parameters dbmsbase, dbmsuser and dbmspass to
-  <tt>AlignmentServer</tt>.</li>
-</ul>
-</p>
 
 <h3>Creating the database for Postgres</h3>
 
 <p>
-Tentative by JE:
+This can be achieved similarly:
 <div class="terminal">
 $ psql -U postgres
 postgres# CREATE DATABASE AServDB;
-postgres# CREATE USER adminAServ PASSWORD 'aaa345';
-postgres# ALTER DATABASE AServDB OWNER TO adminAServ;
-postgres# quit
+postgres# CREATE USER adminAServ WITH PASSWORD 'aaa345';
+postgres# GRANT ALL PRIVILEGES ON DATABASE AServDB TO adminAServ;
+postgres# \q
 </div>
-Tentative by JD:
+Or alternatively:
 <div class="terminal">
-su postgres
-createuser -P adminAServ
-createdb -O adminAServ AServDB
+$ su - postgres
+postgres@host:~$ createuser -P adminAServ
+postgres@host:~$ createdb -O adminAServ AServDB
 </div>
-Choose password 'aaa345' when prompted by createuser command.
+Enter password, e.g., aaa345, when prompted by createuser command (and answer 'n' to other questions).
+</p>
+
+<p>
+Of course, you are advised to use different user, password and
+database name. This can be achieved either:
+<ul>
+<li>by changing values of DBMSBASE, DBMSUSER and DBMSPASS in <tt>AlignmentServer.java</tt> and recompiling;</li>
+<li>by passing parameters dbmsbase, dbmsuser and dbmspass to <tt>AlignmentServer</tt>.</li>
+</ul>
 </p>
 
 <h2>Launching the Alignment server</h2>
@@ -72,6 +75,16 @@ The Alignment server requires that the corresponding database management system
 <div class="terminal">
 $ sudo /usr/local/mysql/bin/mysqld_safe --user=mysql &
 </div>
+or for more modern distributions:
+<div class="terminal">
+$ service mysql start
+</div>
+or
+<div class="terminal">
+$ service postgresql start
+</div>
+</p>
+<p>
 Running the Alignment server is achieved through (use the corresponding options):
 <div class="terminal">
 $ java -jar lib/alignsvc.jar -H
@@ -112,6 +125,7 @@ Options:
 
 Alignment server 4.6 (1934M)
 </div>
+See also comments about using the <a href="logging.html">logging mechanisms</a> for detecting errors.
 </p>
 
 <h3>Embedding more methods in the Alignment Server</h3>
@@ -180,8 +194,9 @@ for the firewalls to open these ports:
 <center>
 <table>
 <th><td>default</td><td>option</td><td>open?</td></th>
-<tr><td>HTTP</td><td>8089</td><td>-H</td><td>Y</td></tr>
+<tr><td>HTTP/REST</td><td>8089</td><td>-H</td><td>Y</td></tr>
 <tr><td>MySQL</td><td>3306</td><td>--dbmsport</td><td>N (if on the same machine)</td></tr>
+<tr><td>PostGres</td><td>5432</td><td>--dbmsport</td><td>N (if on the same machine)</td></tr>
 <tr><td>Jade</td><td>8888</td><td>-A</td></tr>
 <tr><td>//</td><td>1099</td><td></td><td>? (RMI)</td></tr>
 <tr><td></td><td>7778</td><td></td><td>Y (MTP HTTP)</td></tr>
@@ -219,22 +234,22 @@ $ service apache2 restart
 
 <p>Sample backup of the server content (MySQL):
 <div class="terminal">
-$ /usr/local/mysql/bin/mysqldump -u adminAServ -paaa345 AServDB > toto.sql
+$ /usr/local/mysql/bin/mysqldump -u adminAServ -paaa345 AServDB > AServBackup.sql
 </div>
 And restoring:
 <div class="terminal">
 $ /usr/local/mysql/bin/mysql -u adminAServ -paaa345 AServDB
-sql> source toto.sql;
+sql> source AServBackup.sql;
 </div>
 </p>
 <p>
 For Postgres:
 <div class="terminal">
-$ pg_dump  -W -U adminAServ > AServBackup
+$ pg_dump [-W -U adminAServ] AServDB -f AServBackup.sql
 </div>
 And restoring:
 <div class="terminal">
-$ psql -W -U adminAServ < AServBackup
+$ psql [-W -U adminAServ] < AServBackup.sql
 </div>
 
 </p>

html/server.html

@@ -11,7 +11,7 @@
 <h1 class="titre">Alignment Server</h1>
 
 <p>
-The goal of the Alignment server is that different actors can share available alignments and methods for finding alignments. Such a server will enable to match ontologies, store the resulting alignment, store manually provided alignments, extract merger, transformer, mediators from those alignments.
+The goal of the Alignment server is that different actors can share available alignments and methods for finding alignments. Such a server enables to match ontologies, store the resulting alignment, store manually provided alignments, extract merger, transformer, mediators from those alignments.
 </p>
 <p>
 We present here the architecture of the Alignment server and its first
@@ -130,7 +130,7 @@ These tasks are summarised in the following table:
 <tr><td>Match two ontologies</td><td><i>A'</i> &lArr; Align(<i>O</i>, <i>O'</i>, <i>A</i>, <i>p</i>)</td></tr>
 <tr><td>Trimming</td><td><i>A'</i> &lArr; Threshold(<i>A</i>, <i>V</i>)</td></tr>
 <tr><td>Generating code</td><td><i>P</i> &lArr; Render(<i>A</i>,<i>language</i>)</td></tr>
-<tr><td>Translating a message</td><td><i>m'</i> &lArr; Translate(<i>m</i>, <i>A</i>)</td></tr>
+<tr><td>Translating a query</td><td><i>q'</i> &lArr; Translate(<i>q</i>, <i>A</i>)</td></tr>
 <tr><td>Storing alignment</td><td><i>n</i> &lArr; Store(<i>A</i>,<i>O</i>,<i>O'</i>)</td></tr>
 <!--tr><td>Suppressing alignment</td><td><i>Delete(n)</i></td></tr-->
 <tr><td>Finding (stored) alignments</td><td>{<i>n</i>} &lArr; Find(<i>O</i>,<i>O'</i>)</td></tr>
@@ -145,6 +145,10 @@ Most of these services correspond to what is provided by any implementation of t
 The main principle of the Alignment API is that it can always be extended. In particular, it is possible to add new matching algorithms and mediator generators that will be accessible through the API. They will also be accessible through the Alignment servers. They can thus be extended to new needs without breaking the infrastructure. 
 </p>
 <p>
+The Alignment server can also deal with networks of alignments as
+implemented in our API implementation.
+</p>
+<p>
 A detailed presentation of how to access these functions is available
 for <a href="tutorial/tutorial1/server.html">HTML</a>
 and <a href="rest.html">REST and SOAP</a>.