|Genome Informatics Section
DOE Human Genome Program Contractor-Grantee Workshop
|114. PQ Edit--A Web-Based Database
Table Editor and the Relational Database Abstraction Layer
Brian H. Dunford-Shore and David J.
High throughput genome sequencing necessitates the production and use of large amounts of information. To make such information usable, it must be easy to enter, edit, search, and manipulate and the information systems must evolve with changes in experimental design and formula. Relational database servers and tools such as form generators or Microsoft AccessT provide tools to implement part of the solution but does not offer client-independent, flexible, instantly useable data entry and editing. The PQ Edit program and the RDBAL (Relational Database Abstraction Layer) Perl 5 modules were written to fill this gap. PQ Edit is a Perl CGI script that provides general purpose, client-independent, web-based database table editing for relational database tables using automatically generated CGI forms. PQ Edit allows the editing of any database table as it currently exists despite any changes made to the definition (schema) of the tables. PQ Edit provides a reasonable entry form so that the (re)writing of data entry forms for relational databases is unnecessary most of the time. PQ Edit is based on the RDBAL Schema Object--a general purpose Perl library for retrieving database definitions and for searching or manipulating data. RDBAL is an abstraction layer for relational (SQL) databases, which allows middleware independent SQL execution and database schema (catalog) information retrieval. RDBAL tries to 'hide' details of implementation for scripts so that they need no changes to run on different platforms such as Linux, Solaris, or Windows NT and Sybase/MS SQL server or Oracle. The RDBAL Perl library uses Perl 5 objects to make it easy to retrieve information about a particular database's schema. The database connection is cached in the schema object. Database entities (tables, views, and procedures), their field's properties and their index information are retrieved when the schema object is created. Table primary and foreign key relationship information is also retrieved for all tables in a database. Currently PQ Edit and RDBAL support Transact-SQL (Sybase and MS SQL) and Oracle relational database servers via SybaseDBlib, ODBC, or DBI/DBD drivers. Other types of data sources, such as AceDB, are possible. PQ Edit and RDBAL have been tested and used on the Apache and MS IIS web servers and on Solaris and Windows NT.
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