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Dec 13, 2013 (3 years and 10 months ago)

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Integrated Germplasm Browser and
StudyMart

Mylah Rystie U. Anacleto

NRS Team Leader


Java Development

Crop Research Informatics Laboratory


International Rice Research Institute

:: color, composition, and layout

Integrated Germplasm Browser and
Study Mart


Web query interface:
http://koios.generationcp.org/germplasm
-
dev/



Based on GCP Zeus Framework


http://pantheon.generationcp.org

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2009 activities


CRIL
-
organized seminars on

o
Basic Rice Breeding

o
Basic Molecular Breeding

o
Basic Molecular Breeding Data Management

o
Marker
-
assisted Breeding

o
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





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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

o
better layout and organization of content

o
improved website navigation


Cleaner code


February 26: integrated study mart into the germplasm browser
interface




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Demo


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Team Composition : Changes


Datasource (backend) developers:

o
From 1 developer working full
-
time and on a PS
contract

o
To 3 developers working full
-
time


2 of the 3 Zeus (frontend) developers to move to
Eclipse RCP development


0 Moby Web Services developer

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Backend datasource: activities


More plumbing made in last quarter of 2009 vs plain
use case implementations

o
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



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Backend Datasource Development


Can be used with the following database engines:

o
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)



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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.


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Backend datasource development


ICISDataSource and ICISDataSourceFactory

o
now able to be configured to connect to multiple database
connections

o
Kevin Manansala handles the implementation

o
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.

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Backend Datasource Development


ICISMultiDataSource

o
a new datasource that would be able to merge
data from two or more datasource instances. Each
datasource instance connects to a different
database

o
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)

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Backend datasource development


ICISCropfinderDataSource and
ICISCropfinderDataSourceFactory

o
Use case so complex that it cannot be efficiently
implemented without the use of a well
-
designed
warehouse.

o
Jeffrey Morales handles the implementation

o
Extends the ICISDataSource to be able to make
use of implemented use cases on that datasource.

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Backend datasource development


ICIS Writable DataSource

o
Makes use heavily of pojos/hibernate for CRUD
operations

o
Jeffrey Morales implementing this

o
Uses sqlproperties file

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SQLProperties


Sqlproperties file contents

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Data Provision: Observations


Focus on improving process : stick to a suitable
backend database engine for both local and central

o
Improve the process, ensure quality of data

o
rebuilds / recreation of the entire central database
everytime MSAccess Dbs are progressed into the
MySQL central database

o
Fine
-
tuning needs


data warehouse

o
regenerated each time the database is updated


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More changes…


License

o
Use Apache v2


Bug and Feature request trackers

o
Use JIRA

o
http://cril.cimmyt.org/jira/secure/Dashboard.jspa

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Thank you