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CCP4(i) Database Development

CCP4(i) Database Development. Wanjuan (Wendy) Yang CCP4 Annual developer’s meeting March 28, 2006 York. Outline of the talk. Background of the project System Architecture & components functionalities Choice of technologies Current status & immediate plan.

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CCP4(i) Database Development

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  1. CCP4(i) Database Development Wanjuan (Wendy) Yang CCP4 Annual developer’s meeting March 28, 2006 York

  2. Outline of the talk • Background of the project • System Architecture & components functionalities • Choice of technologies • Current status & immediate plan

  3. Background of the project • As part of BIOXHIT: • Expand current CCP4i job database and include extended tracking and storage of crystallographic data • Aim to separate the project database handling from main CCP4i process, allow access to project database from non-CCP4i applications. • Expand scope of CCP4i database to store richer dataset. • Useful for: • Users of CCP4i • Automated structure determination pipelines: to record the progress/steps/result within pipelines • Non-CCP4i applications that want to use the database: sharing data between different applications

  4. System Architecture CCP4i XIA HAPPy Coot CCP4 MG Client API Client API Client API Other CCP4 & Non-CCP4 Applications Data Visualiser DB Handler Client API Project DB Database.def Project DB SQL db Other databases e.g. PIMS

  5. Components functionalities • DB handler: • Runs in server mode: one handler per user; allow many clients connect at the same time. • Can be invoked from clients or start separately. • Shut down procedure: automatically shutdown when there is no clients; clients send shutdown message. • Broadcasting: when database changes state, handler notifies clients. • Can deal with different types of database through DB APIs: e.g. i. CCP4i project database ii. SQL database

  6. Components functionalities • Project Database: • project history tracking data: store steps/jobs taken within software pipeline • knowledge base data: common crystallographic data items used within the software pipeline

  7. Components functionalities • Client API: • A list of methods/commands for interacting with the handler. • Hides details of socket communications • Implemented in different programming languages to support different applications. • Visualisation tool: for viewing data and analysing data

  8. Choice of technologies • Client-Server architecture: socket communications between server and clients. • XML used as messaging technology: Allow system being language independent Request example: <db_request> <command>NewProject</command> <argument>ProjectName</argument> <argument>ProjectDirectory</argument> </db_request> Response example: <db_response> <status>ok</status> <result>3</result> </db_response>

  9. Choice of technologies • Database backend choices: We provide multiple databases backend: • Embedded database: we are using SQLite. Features: • simple to use: a small C library. Self-contained, embedded SQL database engine • portable: single files on the file system. • zero-configuration: no set-up or administration needed • fast random access to the data • flat files: Def file backend implemented in Python. Replicates current CCP4i. • Client APIs implemented in: • Tcl API to support CCP4i and Tcl-based applications. • Python API to support python-based automation projects.

  10. Current Status & immediate plans • Python DB handler has been implemented. • Next step is to integrate in CCP4i with .def file backend. Allow other applications to make use of database.def data. • Currently developing SQL schema for “rich database” backend • Consists of knowledge base (i.e. crystallographic data) and tracking (project history) • Being developed in conjunction with HAPPy and XIA projects. • Several iterations will be required to stabilise schema and API. • Next step is to make Client APIs available to HAPPy and XIA. • Begin to develop visualisation tool to integrate project tracking data

  11. Acknowledgements • Peter Briggs • Graeme Winter • Charles Ballard • Daniel Rolfe • Steve Ness • Many others …

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