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Integrated Germplasm Browser and StudyMart

Integrated Germplasm Browser and StudyMart. Mylah Rystie U. Anacleto NRS Team Leader – Java Development Crop Research Informatics Laboratory International Rice Research Institute. Integrated Germplasm Browser and Study Mart. Web query interface: http://koios.generationcp.org/germplasm-dev/

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Integrated Germplasm Browser and StudyMart

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  1. Integrated Germplasm Browser and StudyMart Mylah Rystie U. Anacleto NRS Team Leader – Java Development Crop Research Informatics Laboratory International Rice Research Institute

  2. Integrated Germplasm Browser and Study Mart • Web query interface: http://koios.generationcp.org/germplasm-dev/ • Based on GCP Zeus Framework http://pantheon.generationcp.org

  3. 2009 activities • CRIL-organized seminars on • Basic Rice Breeding • Basic Molecular Breeding • Basic Molecular Breeding Data Management • Marker-assisted Breeding • http://www.cropinfo.org/everest/index.php/Seminar_Training • CRIL-organized video lectures • Demonstration of product to wheat and maize plant breeders • MBP developers meeting in CIMMYT where Zeus was also presented/reviewed • Post-demo discussions • Prototype presented to Martin Senger in December 2009

  4. Zeus version 2.0 • Review of product ongoing with Dr. Chengzhi Liang • There will be more new use cases for implementation in backend datasource • Zeus v 2.0 =>Significant modifications made to overall design • better layout and organization of content • improved website navigation • Cleaner code • February 26: integrated study mart into the germplasm browser interface

  5. Demo

  6. Team Composition : Changes • Datasource (backend) developers: • From 1 developer working full-time and on a PS contract • To 3 developers working full-time • 2 of the 3 Zeus (frontend) developers to move to Eclipse RCP development • 0 Moby Web Services developer

  7. Backend datasource: activities • More plumbing made in last quarter of 2009 vs plain use case implementations • 2 staff members in CIMMYT from October 21 to December (for the first developer) and January (for the second developer) • Training of ICRISAT Developers in IRRI: their goal was to develop a CMAP datasource

  8. Backend Datasource Development • Can be used with the following database engines: • MySQL, PostGreSQL, HSQLDB, etc. • Moved SQL statements into xml files • Changed format of configuration files to xml property files. • Code modified so it would be easier to debug • Next step: write implementations that can handle the local/central or component split (c/o Kevin Manansala)

  9. Backend datasource development SQLDataSource • a datasource which handles generic methods for any datasource that will connect to a database and execute SQLs for create-read-update-delete (CRUD) operations. • handles the reading of the xml datasource configurations • Any other much more specific GCP datasource (ICISDataSource, CMAPDataSource, etc.) must extend this datasource to be able to make use of its methods. • Methods can be overridden to do more datasource-specific functionalities.

  10. Backend datasource development • ICISDataSource and ICISDataSourceFactory • now able to be configured to connect to multiple database connections • Kevin Manansala handles the implementation • For example, the ICISDataSource can connect to the following: • First Connection: Server: Castor; Database: iris_myisam having DMS, GEMS, GMS central data. • Second Connection: Server: localhost; Database: GMS local data. • Third Connection: Server: localhost; Database: DMS local data. • Fourth Connection: Server: localhost; Database: GEMS local data. • Fifth Connection: Server: Pollux; Database: IMS central data. • Sixth Connection Server: Cril2 CIMMYT: OMS central data.

  11. Backend Datasource Development • ICISMultiDataSource • a new datasource that would be able to merge data from two or more datasource instances. Each datasource instance connects to a different database • results merged and displayed together • simply for merging data from different datasources and was not yet really designed for local and central concept which has more complex conditions before data is merged together as one result per one user request (find call)

  12. Backend datasource development • ICISCropfinderDataSource and ICISCropfinderDataSourceFactory • Use case so complex that it cannot be efficiently implemented without the use of a well-designed warehouse. • Jeffrey Morales handles the implementation • Extends the ICISDataSource to be able to make use of implemented use cases on that datasource.

  13. Backend datasource development • ICIS Writable DataSource • Makes use heavily of pojos/hibernate for CRUD operations • Jeffrey Morales implementing this • Uses sqlproperties file

  14. SQLProperties • Sqlproperties file contents

  15. Data Provision: Observations • Focus on improving process : stick to a suitable backend database engine for both local and central • Improve the process, ensure quality of data • rebuilds / recreation of the entire central database everytime MSAccess Dbs are progressed into the MySQL central database • Fine-tuning needs • data warehouse • regenerated each time the database is updated

  16. More changes… • License • Use Apache v2 • Bug and Feature request trackers • Use JIRA • http://cril.cimmyt.org/jira/secure/Dashboard.jspa

  17. Thank you

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