Total Lines Of Code: 6527 (2006-12-21 16:51)
Summary Period: 2004-09-29 to 2006-04-20
[root]/Agmial2/ca_manager/src/cam/contigdb
Total Lines Of Code:
6527 (2006-12-21 16:51)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 127 (100.0%) | 9464 (100.0%) | 74.5 |
| vloux | 102 (80.3%) | 6107 (64.5%) | 59.8 |
| rbossy | 25 (19.7%) | 3357 (35.5%) | 134.2 |
ConnectionPool :
- clean destroy
ActionsQueues/Motivations :
- sleepTime passed in constructor
ProteinDB/DAOs :
- statements not released properly causing locks
12 lines of code changed in:
BugFix
CAM :
contigDB
Gestion DataSource
Prepa release 20060317
2139 lines of code changed in:
Fin nettoyage properties cam/pam
Fin nettoyage url en dur
Ajouts page par defaut erreurs 404,401,500 dans agmial_directory,pam,cam
[#213] Filtrer quote et retours chariots dans les formulaires
Filtre cot? client par javascript
1 lines of code changed in:
[#200] Export donn?es format tabul? CGView
Ajout properties pour affichage Lien CGView (cgview.enabled)
Creation CGViewPanel
+ Nettoyage (template)_project_properties
+ Generation auto liens du main_menu.html par build.xml
7 lines of code changed in:
Changement de start ? la vol?e (Affichage dans editFeature de tous les starts putatifs de l'ORF, transmission des annotations existantes).
253 lines of code changed in:
BugFixes
Removed generated web.xml from repository
5 lines of code changed in:
BugFixes
80 lines of code changed in:
contigDB code improvments
537 lines of code changed in:
PAM Summer cleaning
DBPooling with apache dbpc and jni.
PAM refactoring :
moving all select/update/insert statement into proteindb package :
reader/HomologyAlignPanel.java OK(1)(2)
reader/HomologyImagePanel.java OK(1)(2)
reader/HomologyPanel.java OK(1)(2)
reader/ProteinPanel.java OK (1),(2)
reader/QueryDataSets.java OK(1)
reader/QueryProteins.java OK(1)
reader/QueryProteinSources.java OK(1)
reader/SearchDataSets.java OK
reader/SearchProteinSources.javaOK
reader/SearchResults.java TODO (Need to reorganize the search ->
will be done at that moment)
admin/MonitorProteinRefTasks.java OK(1),(3)
admin/MonitorProteinTasks.java OK(1)
admin/MonitorTasks.java OK(1)
admin/RetireProteins.java OK(1)
admin/ShowAddProteins.java OK
admin/ShowRetireProteins.java OK
control/AfterActionMotivation.java OK
control/DetermineFunctionAction.java OK(1)
control/HomologyResultsMotivation.java OK(1)
control/NotifyFunctionMotivation.java OK
control/ParalogResultsMotivation.java DELETED
control/ProteinActionMotivation.java OK
control/ProteinActionQueue.java OK
control/ProteinRefActionQueue.java OK
control/SwissAnnotAction.java OK
(1)new methods in ProteinDB
(2) new DTO classes
(3) new classes in proteinDB
27 lines of code changed in:
CAM Summer Cleaning !
Various code cleaning (imports, externalisation of some parameters in properties files).
5 lines of code changed in:
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
2196 lines of code changed in:
+ ClustalLauncher : launch clustal to produce alignement for jalview
+ FastaCreator : Create (multi) fasta (nucleic or proteic) from agmial_id and contig_accession.
+ ContigDB : refactoring.
164 lines of code changed in:
Removage de commentaires en trop
8 lines of code changed in:
Merge de GlobalPanel dans HEAD
99 lines of code changed in:
Nettoyage du code : imports, methodes deprecated ...
66 lines of code changed in:
Modifs sur en tete GPL
Correction du build.xml
Bugfix contextlistener.java
Ajout lien vers MuGenPanel dans ProteinPanel
31 lines of code changed in:
Preambule GPL
437 lines of code changed in:
bugfix :
add method public Nucleic getNucleic(String contig_accession,boolean with_features, String feature_layer_name)
6 lines of code changed in:
Artemis :
specific urls (link to ContigStore* ; ProteinPanel) and keywords( organization, manager ...) are centralized into the project_properties file. Optionally user name and password can be stored to be prefilled in the authentification dialog.
One has to launch artemis with the following parameters :
./agmial -options project_properties
ca_manager :
Modification in ContigDB and ContigSoreQueryImpl to improve performances.
Modifications in MugenPanel and EditFeature to improve performances.
Biotools :
add a method in Nucleic to get the number of features associated with it.
37 lines of code changed in:
Improvements of the way contig region are retrieved (No mor java.lang.OutOfMemeory Errors).
5 lines of code changed in:
(1 more)
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