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Bioscape Distribution

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NoteNotePlease note that this documentation covers an unreleased product and is for internal use only.

Contents

Distribution Structure

The whole Bioscape system is divided into three distinct distributions:

  • The administrative application: bsadmin
  • The text-indexing application: bsindex
  • The Web front-end application: bsweb

Each distribution contains a Python package along with scripts and tools.

  • bsadmin provides a package called bioscape which provides basic services to the different applications, focusing on data management.
  • bsindex provides a package called bsindex which provides support for text indexing and searching.
  • bsweb provides a package called bsweb which contains the Web interface code and resources.

Data Sources

The notion of a data source exists in more than one of these distributions, and each data source is supported by a subpackage within a sources package hierarchy (such as bioscape.sources), providing the means by which a particular kind of data is acquired, processed and imported into the system. In bsadmin such source subpackages are typically only concerned with making data available to the database, but in bsindex such sources provide access to textual information which will also be indexed before data is presented to the database.

Schemas and Templates

The bsadmin application is responsible for managing the database used by Bioscape. In the bioscape/sql directory, a number of subdirectories can be found, each of which provides support for initialising portions of the database in association with a particular activity. The bioscape_dbconfigure.py script (found in the scripts directory of the bsadmin distribution) is able to execute the template files found within each of these subdirectories and will accept parameters for substitution into the templates.

Configuration

A properties file (bioscape.cfg) located in the top-level directory configures the system as is accessed via the bioscape.config subpackage found in the bsadmin distribution. This subpackage is also exposed as bsindex.config and bsweb.config for convenience within the other applications.

Constants

A module containing constant value definitions is accessible as bioscape.constants and defined in the bsadmin distribution. This module is also exposed as bsindex.constants and bsweb.constants for convenience within the other applications. These values are made available to database templates and in other parts of the system, and are generally employed in data presented to the database.