SAM has been tested with the binary distribution of Tomcat 4.1.27 and Tomcat 5.0.27. Before proceeding with SAM install, you should verify that you can start Tomcat and view your Tomcat-based website. You may wish to remove the Tomcat examples and default users (see TomcatConfig.html for details of how to do this).
Remember the location of your Tomcat installation for the next step.
Unpack the SAM zip file into the main directory of your Tomcat setup. This will copy all the files necessary to run SAM into the correct locations. (Be sure to "use folder names" to preserve the directory structure within the zip file.)
In the default configuration for the zip install, SAM 2.1 manages user accounts internally. SAM ships with a default root account that has write access to the entire data store. YOU ARE STRONGLY ADVISED TO CHANGE THE PASSWORD FOR THIS ACCOUNT. This can be done by editing the Domain.xml in the webapps/sam directory before running the server or by using the web-based admin pages.
To create/modify accounts, access the server web page http://yourservername/sam/admin/main and select Security, then Select "List and Edit Users" and edit or add users to your server. For more information on this function see Administration Guide
The SAM 2.1 zip install preconfigures SAM to use the local file system for storing content and
metadata). You can specify the base directory for the local storage by
uncommenting and changing
the "store-base" parameter in %TOMCAT%/webapps/sam.xml. By default, content
will be stored in %TOMCAT%/store. A relative path definition will be interpreted as relative to
%TOMCAT%/. You can also input an absolute file path.
SAM can also be configured to use a database for metadata and/or content. An example configuration for use of MySQL is commented out in the Domain.xml file.
By default, SAM 2.1 zip install does not enable lucene indexing, to use lucene indexing, uncomment the 'contentindexer' and 'propertiesindexer' parameters in Domain.xml. To specify which properties are indexed alter the %TOMCAT%/common/classes/indexed-properties.xml file. If you start the server prior to enabling indexing then data and metadata already in the store will not be indexed, to use the property reindexer, uncomment the 'reindex' parameter in web.xml.
You may configure SAM to send email notifications when there has been a change to the server.
After the above steps, starting Tomcat will run your SAM server. You can access the SAM webDAV site via the URL "http:<your IP address>:8080/sam/". You can use a variety of mechanisms to read/write data and metadata, for example:
To access the ELN server in SAM, goto the URL "http:<your IP address>:8080/sam/launchELN" in your browser. Clicking "Configure New Notebook" will allow you to setup an ELN.
Note: These instructions are for advanced users and assume greater knowledge of your web application server than the recommended SAM-2.1.zip Installation. More details about configuration options are available in the SAM Administration and Development Guide...
Install the sam.war file using the standard procedure for your server. Set your server to unpack the war file (required for SAM 2.1 to run.)
There are two main options:
Create User accounts using the standard procedure for your server (e.g. editing tomcat-users.xml).
Create duplicate accounts in SAM by editing the Domain.xml file in the SAM web application.
Instructions for creating accounts and examples are in the Domain.xml file starting around line 288.
or
Configure a single-sign-on mechanism using your server's standard mechanisms (e.g. Tomcat Realms) and JAAS. SAM 2.1.zip includes JAAS LoginModules for username/password and MyProxy-based Grid Certificate authentication. These classes can be configured to integrate SAM's internal account mechanism with your web application server's. Using this option will require moving some SAM classes out of the web application to shared directories (see next step).
If you wish to use SAM (via it's API rather than webDAV) with multiple web applications, several additional steps are required:
Several base jar files must move to your server's shared library directory (e.g.
%catalina_home%/common/lib for Tomcat):
slide-kernel.jarslide-stores.jarslide-roles.jarIn addition, slide-catalinawrapper.jar would have to be placed in
a privileged directory on your server (e.g. %catalina_home%/server/lib
for Tomcat) to enable single-sign-on using JAAS.
In order for SAM to be initialized when Tomcat starts a ServerListener has
to be added to the Tomcat configuration (server.xml).
The SlideServerListener looks for %catalina_home%/conf/slide.xml to
initialize the Slide Domain.
<server>
...
<Listener className="wrappers.catalina.SlideServerListener" logLevel="6" />
...
</server>
When used in this manner, SAM is configured through an XML file named
%catalina_home%/conf/slide.xml instead of the usual Domain.xml.
The Electronic Laboratory Notebook (ELN) was begun as part of a previous project and has been released under an open source license (see http://eln.sourceforge.net). The SAM project has contributed to the development of the ELN 5.1 client and has developed a SAM-based ELN 5.1 server. The ELN Client installation is the same for the original (Perl cgi) and SAM-based servers and users of a SAM-based ELN notebook should follow the standard instructions for installing the ELN Client. (Note: The links to ELN Help and FAQ items from this page are relevant for the SAM-based ELN with a few minor exceptions, but information related to server installation and configuration are only applicable to the Perl-based server at this time.)
Last updated: 3/28/05