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Scientific Annotation Middleware (SAM)
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The Scientific Annotation Middleware (SAM) is a set of components and services that enable researchers, applications, problem solving environments (PSE) and software agents to create metadata and annotations about data objects and document the semantic relationships between them. Developed starting in 2001, SAM allows applications to encode metadata within files or to manage metadata at the level of individual relationships as desired. SAM then provides mechanisms to expose metadata and relationships encoded either way as WebDAV properties.
http://collaboratory.emsl.pnl.gov/docs/collab/sam/2.1/SAMDownload.html（下载地址）
使用说明：
SAM
SAM 2.1 Installation Instructions
Tutorials Showing SAM and ELN Client Installation
SAM-2.1.zip Installation
sam.war Installation
ELN Client Installation
Preview Release of Notarization Service
SAM-2.1.zip Installation
Prerequisites:
JDK 1.4 (or newer) (download from java.sun.com) (NOTE: Verify that you are using a JAVA_HOME that points to the JDK directory and not the JRE directory. Tomcat will run with a JAVA_HOME that uses the JRE directory, but SAM will have errors. On a Windows computer you can enter 'echo %JAVA_HOME%' at the command line to verify that you are using the JDK)
Tomcat 4.1.X+ and Tomcat 5.0.X+ (download from http://tomcat.apache.org/)
Please see our FAQ's page for information regarding other versions of Tomcat and Java
SAM
Verify Tomcat Installation
SAM has been tested with the binary distribution of Tomcat
Remember the location of your Tomcat installation for the next step.
Unpack SAM-2.1.zip
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.)
Define SAM user accounts
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
(Optional) Define your storage location
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.
(Optional) Configure Indexing Options
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.
(Optional) Define email notifications
You may configure SAM to send email notifications when there has been a change to the server.
Download and unpack openjms-
In system variables set OPENJMS_HOME to location of openjms folder
Change settings in web.xml
-SAM_JMS_Mode on default is 'rmi', off is 'none'
-SAM_Mail_Host your mail smtp server
-SAM_Mail_Sender from address you want recipients to see
-SAM_Mail_Send_Hour hour you would like daily digests sent out at
-SAM_Mail_Send_Day day you would like weekly digests sent on
Run openjms/bin/startup before starting Tomcat startup or alter Tomcat startup and shutdown scripts to start and stop openjms.
Start Tomcat
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:
your browser (read-only)
DAV Explorer
Microsoft Explorer (configure a Network Drive using the above URL) or Office applications
DAVfs (Linux) or WebDrive
Other webDAV resources can be found at www.webdav.org.
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.
Proceed to SAM Administration and Development Guide...
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sam.war Installation
Prerequisites:
JDK 1.4 (or newer) (download from java.sun.com)
A Servlet 2.3 capable Web Application Server (e.g. Tomcat)
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...
SAM
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.)
Defining User Accounts
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).
(Optional)Supporting multiple web applications using SAM
If you wish to use SAM (via it's API rather than webDAV) with multiple web applications, several additional steps are required:
Move SAM JAR files
Several base jar files must move to your server's shared library directory (e.g. %catalina_home%/common/lib for Tomcat):
slide-kernel.jar
slide-stores.jar
slide-roles.jar
Additional library files might be necessary, depending on the requirements of the web applications.
In 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.
Configure a Server Listener
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>
Configure SAM
When used in this manner, SAM is configured through an XML file named %catalina_home%/conf/slide.xml instead of the usual Domain.xml.
Proceed to SAM Administration and Development Guide...
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ELN Client Installation
The Electronic Laboratory Notebook (ELN) was begun as part of a previous project and has been released under an open source license (see http://sourceforge.net/projects/eln/). 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.
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About the SAM Project
Download
SAM Installation Instructions
SAM 2.1 Features
SAM Administration & Development Information
Getting Started with the Electronic Laboratory Notebook
FAQ/Known Issues
Support
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