August 2005 Commit Log

Number of Commits:
7
Number of Active Developers:
1
vloux 2005-08-24 10:54

CAM Summer Cleaning !
Various code cleaning (imports, externalisation of some parameters in properties files).

130 lines of code changed in:

vloux 2005-08-23 16:59

CAM Summer Cleaning !

+ Database Pooling with apache dbcp (Database Connection Pools <http://jakarta.apache.org/commons/dbcp/>) served via jni to the servlet. Added a context.xmlfile with all the parameters for the connection.

+ Users and Roles are no longer stored in an xml file. Management via a dedicated database, served via jni to the servlets.

CAM refactoring :
moving all select/update/insert statement into contigdb package :

admin/ContigStoreAdminImpl.java OK (2)
admin/MonitorBatchTasks.java OK (1)(2)
admin/MonitorContigTasks.java OK (2)
admin/MonitorFeatureTasks.java OK (2)
admin/MonitorProjectTasks.java OK (2)
admin/MonitorTasks.java OK (2)
admin/ShowAddBatch.java OK (2)
admin/ShowAdminBatches.java OK (2)
admin/ShowUpdateContig.java OK (2)
admin/ShowUpdateProfile.java OK (2)

control/BatchActionMotivation.java OK(2)
control/BatchActionQueue.java OK(2)
control/BatchCalcAction.java OK(2)
control/ContigActionMotivation.java OK(2)
control/ContigActionQueue.java OK(2)
control/FeatureActionQueue.java OK(2)(3)
control/ProjectActionQueue.java OK(2)
control/ProjectMotivation.java OK(2)
control/QueryFeatureMotivation.java OK(2)

reader/ContigStoreQueryImpl.java OK
reader/EditFeature.java OK(2)
reader/MugenPanel.java TODO
reader/ProfileStoreQueryImpl.java OK(2)


(1) CAMActionList creation
(2) new methods in ContigDB
(3) CAMFeature creation

New policy for database accession :
All db accession is made via classes from the contigdb package.

For each object , two classes : CAMObject is the POJO
object.CAMOjectSchema is the Data Transfer Object and make the link
between the database and the POJO.
The CAMObjectSchema has at least two methods : add(CAMObjectSchema)
and update CAMObjectSchema();
ContigDB provide methods to interact with the object, mainly
getters/setters that call the corresponding methods in CAMObjectSchema.


--> reader/MugenPanel.java TODO

4247 lines of code changed in:

vloux 2005-08-09 11:22

Formatage code

10717 lines of code changed in:

vloux 2005-08-09 11:09

BioTools :
+ ClustalWCalc
Modifications Location

Tests :
SingleInOutTest
NucleicPackageTest
NucleicTest

256 lines of code changed in:

vloux 2005-08-08 16:11

Move project-specific paths to web.xml

48 lines of code changed in:

vloux 2005-08-08 14:00

Fasta protein & gene export
+ FastaCreator : Create (multi) fasta (nucleic or proteic) from agmial_id and contig_accession.

104 lines of code changed in:

vloux 2005-08-04 17:20

+ ClustalLauncher : launch clustal to produce alignement for jalview
+ FastaCreator : Create (multi) fasta (nucleic or proteic) from agmial_id and contig_accession.
+ ContigDB : refactoring.

524 lines of code changed in:

July 2005 »

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