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SAM

SAM 2.1 Installation Instructions

ELN Client

  • Basic Information on how to use the ELN Client is available from the PNNL Collaboratory site. ELN 5.1.3+ is required for full functionality with the SAM 2.1 server. While the information is geared towards use with the Perl-based server, most applies to use with the SAM server as well:

  • Check the FAQ/Known Issues for features that are not yet supported with the SAM server.

  • ELN Login with the SAM server is simplified. After logging in to the SAM server to view the list of available notebooks, you will not be prompted to login again. Clicking on the link for a notebook in the list will open the ELN client and show it's table of contents without an additional login step.

SAM ELN Server Configuration

The SAM-based ELN server simplifies administering individual notebooks while making all of SAM's metadata management, translation, and database capabilities optionally available for use.

  • Notebook Creation

    Now handled via a live web form at %BaseSAMURL%/launchELN and there is no server setup required beyond installing SAM itself:

    Notebook URL - the resource that serves as the base collection (directory) for this notebook. In SAM 2.1, all chapter, page, and note objects will be stored within this collection.

    Create URL - an existing collection can be used as the Notebook URL. In that case, un-check this box so that SAM does not attempt to create it.

    Description - the purpose of this notebook, for display in the list of notebooks

    Table of Contents ordering (chronological, reverse chronological, alphabetical) - how entries should be order in the ELN Client Table of Contents display for this notebook.

    Background color - the color to use as the background of the ELN Client and notebook pages

    Message-of-the-day - the URL for a HTML file who's content should be displayed on the launch page for this notebook. SAM does not create this URL, it must be done manually.

    Help, Home URLs - Configurable URLs used as the destinations when the user clicks the " Help" or "Home" buttons in the ELN Client or ELN pages.

    Contact email - email referenced by the "Contact Admin" links on the notebook pages.

    Initial Notebook Admins - the list of existing SAM users who are allowed user and admin privileges in this notebook.

    Initial Notebook Users - the list of existing SAM users who are allowed user privileges in this notebook.

    Enable JMS Notifications - Specifies that this notebook should support email notifications using SAM 2.1's JMS event mechanism. (Subscriptions are configured via the ELN client interface.)

  • Creation of additional Viewers and Editors

    • The SAM-based ELN server uses SAM's Translation mechanism to define ELN Viewers. To create a new ELN Viewer, create and register a new SAM Translator for the desired file type. Since several translators can be defined for a given type, an additional entry in the "%BaseSAMURL%/eln/config/ELNViewerMap.xml" must be made to specify which translator should be used as the ELN Viewer for this file type. The syntax for this entry can be understood by looking at the examples within the default ELNViewerMap.xml file.

    • ELN Editors are created using the general ELN Editor API. To use a new editor with the ELN, the required classes must be distributed with the ELN client (and included in the class path), and an entry with the name of the new editor class must be made in "%BaseSAMURL%/eln/applets/eln/editors/". (Similarly, removing an existing entry from that collection will stop that editor from appearing in the ELN Client display.