MONOD version $Version$
The Modeler's Notebook and Datastore
(c) 2003-2004 The Molecular Sciences Institute
http://monod.molsci.org
monod@molsci.org

Monod is a web-based environment supporting collaborative work by
scientists studying complex intracellular signaling pathways.


The following upgrade procedures are not cumulative; that is,
you need to complete the upgrade to v1.3 before proceeding with the
upgrade to v1.4.

Also, If your existing installation doesn't contain data that you need to keep,
it'll be easier and cleaner to simply delete it, drop the database, and start
over with a fresh install.

And, of course, please back up your database using pg_dump before attempting
any upgrade.


UPGRADING TO VERSION 1.5

1.  Install Resin-EE-2.1.12.


UPGRADING TO VERSION 1.42

1.  Install Resin-EE-2.1.10.  Then replace /usr/local/resin/lib/resin-ejb.jar 
    with the one provided in the resin-patches directory of the Monod
    distribution.

2.  Follow the "incremental" procedure below, but also replace 

      WEB-INF/lib/ibex.jar. 


UPGRADING INCREMENTAL VERSIONS, e.g. 1.40 to 1.41, etc.

1.  Simply replace these files in your existing install tree with those from the
    newer distribution:
    
      src-gen/ejb/monod/ejb-jar.ejb
      src-gen/ejb/monod/resin.ejb
      WEB-INF/lib/monod.jar
      xsl/_monod-full.xsl

2.  Restart Resin.  (For some reason Resin's automatic jar reloading gets 
    confused pretty frequently; restarting it avoids this problem).


UPGRADING MONOD v1.3 to MONOD v1.4


1.  Download and unpack Monod

    http://monod.molsci.org/downloads

    tar xvzf monod-1.41.tar.gz

    Unpack monod in the directory where you want to install it.  For
    instance, if you execute the above tar command from /usr/local, 
    Monod will be installed in a new directory called 
    /usr/local/monod-1.41.  That is the recommended location.
    
    
2.  Copy web.xml
   
    cp /usr/local/monod-1.33/WEB-INF/web.xml \
       /usr/local/monod-1.41/WEB-INF/web.xml


3.  Copy monod.properties
    
    (You may wish to diff these two files and make edits by hand, instead of 
    overwriting potentially useful changes in the new distribution version)
    
    cp /usr/local/monod-1.33/conf/monod.properties \
       /usr/local/monod-1.41/conf/monod.properties


4.  Move your PDF directory

    mv /usr/local/monod-1.33/pdf /usr/local/monod-1.41


5.  Stop Resin; then update the SQL schema in postgres.

    psql monod monod < /usr/local/monod/sql/monod-1.3-to-1.4-update.sql

    
6.  Update the symbolic link:
    
    rm /usr/local/monod
    ln -s /usr/local/monod-1.41 /usr/local/monod
    
    If you install it somewhere else, you'll have to change some paths in the 
    configuration files to match.
    
    Start up Resin again.  



UPGRADING MONOD v1.2 to MONOD v1.3

0.  Depending on what version of Monod you started with, this update may not
    run cleanly.  To check, you can do this:

      psql monod monod

    then, at the postgres prompt,

      select id from coreobject where id > 21 and id < 100;
      select id from permission where id > 21 and id < 100;

    If either query returns any results, then you may get errors when running the
    upgrade sql script.  This is OK, but some new features may not work until
    you contact us at monod@molsci.org for help.


1.  Download and unpack Monod

    http://monod.molsci.org/downloads

    tar xvzf monod-1.30.tar.gz

    Unpack monod in the directory where you want to install it.  For
    instance, if you execute the above tar command from /usr/local, 
    Monod will be installed in a new directory called 
    /usr/local/monod-1.30.  That is the recommended location.
    
    
2.  Copy web.xml
   
    cp /usr/local/monod-1.21/WEB-INF/web.xml \
       /usr/local/monod-1.30/WEB-INF/web.xml


3.  Copy monod.properties
    
    cp /usr/local/monod-1.21/conf/monod.properties \
       /usr/local/monod-1.30/conf/monod.properties


4.  Move your PDF directory

    mv /usr/local/monod-1.21/pdf /usr/local/monod-1.30


5.  Stop Resin; then update the SQL schema in postgres.

    psql monod monod < /usr/local/monod/sql/monod-1.2-to-1.3-update.sql

    
6.  Update the symbolic link:
    
    rm /usr/local/monod
    ln -s /usr/local/monod-1.30 /usr/local/monod
    
    If you install it somewhere else, you'll have to change some paths in the 
    configuration files to match.
    
    Start up Resin again.  


UPGRADING MONOD v1.1 to MONOD v1.2


1.  Download and unpack Monod

    http://monod.molsci.org/downloads

    tar xvzf monod-1.20.tar.gz

    Unpack monod in the directory where you want to install it.  For
    instance, if you execute the above tar command from /usr/local, 
    Monod will be installed in a new directory called 
    /usr/local/monod-1.20.  That is the recommended location.
    
    Then make a symbolic link:
    
    ln -s /usr/local/monod-1.20 /usr/local/monod
    
    If you install it somewhere else, you'll have to change some paths in the 
    configuration files to match.

    
3.  Copy and edit web.xml
   
    cp /usr/local/monod-1.11/WEB-INF/web.xml \
       /usr/local/monod-1.20/WEB-INF/web.xml

    Then edit web.xml to change

        <path-mapping url-pattern='/pdf/*)' real-path='/home/webapps/monod/pdf/'/>

    to

        <path-mapping url-pattern='/pdf*' real-path='/home/webapps/monod/bogus'/>
    
    Also, change
    
        <servlet-mapping url-pattern='Dispatch' servlet-name='dispatch'/>
    
    to
    
        <servlet-mapping url-pattern='Dispatch*' servlet-name='dispatch'/>
    

4.  Copy and edit monod.properties
    
    cp /usr/local/monod-1.11/conf/monod.properties \
       /usr/local/monod-1.20/conf/monod.properties

    Then edit monod.properties to add these lines:
    
    BaseUrl = http://monod.mydomain.edu/whatever

    proxyhost = 
    proxyport = 
    proxyuser = 
    proxypassword = 

    If you don't need an http proxy to download PDFs, just leave those blank;
    otherwise fill in your proxy information.
    

5.  Move your PDF directory

    mv /usr/local/monod-1.11/pdf /usr/local/monod-1.20


6.  Update the SQL schema in postgres

    If you want to attempt to automatically download PDFs for all the
    citations already in the database, edit 
    /usr/local/monod/sql/monod-1.1-to-1.2-update.sql to contain

    update paper set downloadstatus = 0 where 1=1;

    Otherwise, download attempts will be made for newly entered citations,
    but not existing ones.
    
    Then,

    psql monod monod < /usr/local/monod/sql/monod-1.1-to-1.2-update.sql

    

7.  Probably Resin will automatically pick up the new version, but you
    could restart it just to be sure.    



UPGRADING MONOD v1.0 to MONOD v1.1


1.  Stop Resin.


2.  Download and unpack Resin-EE 2.1.4 or later
    http://www.caucho.com/download.
    
    Monod expects to find Resin in /usr/local/resin (for classpaths, etc.), 
    which can be a symbolic link to the real location.
    
    No patches to Resin are required; the binary distribution should work 
    out of the box.
    
    Remember to copy your old resin.conf to the new 2.1.4 directory.
    

3.  Download and unpack Monod

    http://monod.molsci.org/downloads

    tar xvzf monod-1.1.tar.gz

    Unpack monod in the directory where you want to install it.  For
    instance, if you execute the above tar command from /usr/local, 
    Monod will be installed in a new directory called 
    /usr/local/monod-1.1.  That is the recommended location.
    
    Then make a symbolic link:
    
    ln -s /usr/local/monod-1.1 /usr/local/monod
    
    If you install it somewhere else, you'll have to change some paths in the 
    configuration files to match.

    
4.  Edit configuration files.

    (I think you can copy the old ones wholesale, but you might want to
    diff them to be sure.  We recommend referring only to /usr/local/monod in
    the conf files; this will facilitate upgrading in the future, since you'll
    only need to change the symlink in /usr/local to run a different version).

    edit /usr/local/monod/WEB-INF/web.xml to add your database
        passwords and to update the classpaths.

    edit /usr/local/monod/conf/monod.properties to edit
        any paths as necessary and to change the settings for error emails
	(this file was previously 
         /usr/local/monod-1.0/conf/org/molsci/model/monod.conf)


5.  Update the SQL schema in postgres

    psql monod monod < /usr/local/monod/sql/monod-1.0-to-1.1-update.sql


6.  Start Resin.

    The first time you run Monod 1.1, it will take several minutes (or more,
    if you have a lot of data) to make updates throughout the database, such
    as adding default permissions.