James Myers, Al Geist, Jens Schwidder, Matt Elder
The SAM team's focus during the last quarter has been the continued development of SAM's Metadata Management Services layer and a transitional electronic laboratory notebook. As detailed below, the ability to dynamically discover and perform registered translations of stored data has been added to the MMS layer. Development of a transitional DAV-based electronic notebook continues with the design of transitional SAM notebook services and SAM-aware client side components. Continuing efforts are being made to refine existing MMS capabilities and implement a component-based security interface. Matt Elder (PNNL) has recently begun detailed design and implentation of an MMS capability to provide a configurable mapping between DAV resources and relational databases. Team members have also been very active in community activities this quarter.
Configurable Authorization and Authentication:Work continues to define a mechanism to design a security framework that allows using different authentication and authorization technologies. The analysis of the current security implementation of Slide has been finished. Based on the understanding of Slide and the SAM security requirements a plan for modifying Slide and implementing a more generic security framework has been created. The modification will allow SAM to easily integrate with third party security technologies while retaining the ability to run SAM with Slide's current access control list based security mechanism. Course-grained authentication will be implemented using a Java Authentication and Authorization Service (JAAS) interface that integrates with Apache Tomcat via a JAAS-based implementation of the Realm interface. Work on the basic Slide modifications has begun, and a preliminary security demo is planned for the SC2002 conference.
DAV-Database mapping: The definition of a mechanism for connecting to "arbitrary " back-end databases, allowing a DAV-based view and annotation of existing data, is also proceeding. A new component is being developed using Slide's Store interface that will read a registered DAV-database map and dynamically implement the mapping between the database schema and a DAV view. Several existing XML languages for describing database schema are being investigated for potential reusability as part of a DAV-database mapping language.
Electronic Notebook: Given the refactoring of the client software of the existing open-source Electronic Laboratory Notebook (ELN) performed last quarter, design activities are proceeding to define the specific client and server components required for a SAM-based ELN implementation. Demonstration of an initial capability is being planned for the SC2002 conference.
Translation capabilities: SAM MMS now has a working mechanism to generate translations based on the contents of uploaded files. For each mime-type, an XSLT script or a combination of Binary Format Description (BFD) and XSLT scripts can be specified. A live " hastranslations " property is defined for the resource and can be queried using the standard DAV PROPFIND command to discover the URLs for translated data. At present, operations on the translated resource, e.g. GET or COPY, cause the application of the registered scripts to the original data to dynamically generate the required translated information.
As part of this work, SAM MMS has been modified to generate a DAV:source property as part of the COPY operation, making it possible to find the original data resource. In the case of translated data, this property points to the original untranslated resource (versus the "virtual" translated resource) and notes the translation applied in producing the copy.
Additionally, as a convenience in working with XML files, which often use the .xml file extension regardless of their subtype, it is now possible to register an XSLT script with SAM to generate an alternate MIME type as reported in the DAV:getcontenttype property and used in subsequent metadata generation and translation steps. (Without this capability, all .xml files are given the text/xml MIME type and are then treated the same during metadata generation and translation steps.)
SAM team members participated in several meetings, workshops, and other discussions during the last quarter:
"The EMSL Virtual NMR Facility", Science of Collaboratories Workshop on Comparative Investigation of Collaboratories, Sept. 24-27, 2002, Ann Arbor, MI: Overview of previous Collaboratory development, deployment, and operation at PNNL and the lessons-learned that contributed to the design of the SAM effort.
"The PNNL/EMSL Collaboratory Project", NIH Workshop on Collaboratories and Data in the Biomedical Community, Sept. 15-18, 2002, Arlington, VA: Overview of Collaboratory and problem solving environment efforts at PNNL and the lessons-learned. Used as input to discussions and the workshop report ("Data and Collaboratories in the Biomedical Community", vailable from the Workshop website).
"Perspectives on Grid Computing", The Indus Entrepreneurs (TIE) Workshop on Grid Computing, June 6, 2002 Boston, MA: Overview of Grid computing and the role of middleware such as SAM in supporting cross-project integration on the Grid.
"Laboratory Notebooks 2002", Philadelphia, Aug. 14-15, 2002: Al Geist was invited to present a talk entitled "Supporting the Laboratory Notebook and Its Information—Capturing and Storing Meta-Data" that will describe the SAM infrastructure supporting notebooks.
SAM use in Genomes to Life (GTL) Initiative: This past quarter the Genomes to Life project on Carbon Sequestration in Synechococcus has set up and begun using electronic notebooks for their project. Informal presentations have been made to the project team and they are considering using some of the metadata services that SAM will provide.