Module Agmial2/ca_manager/web/

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Summary Period: 2004-09-29 to 2006-10-25

Modules

[root]/Agmial2/ca_manager/web
     applets (1 files, 0 lines)
     images (5 files, 246 lines)
     jsp (1 files, 45 lines)

Lines of Code

Total Lines Of Code: 1638 (2006-12-21 16:51)

Authors

Most Recent Commits

vloux 2006-10-25 11:41

Merge CedricSoubrie branch and HEAD

21 lines of code changed in:

• Agmial2/ca_manager/web: main_menu.html (+3 -2), main_menu.html.in (changed), web.xml (+18 -18)

vloux 2006-10-24 16:29

Merge CedricSoubrie branch and HEAD

21 lines of code changed in:

• Agmial2/ca_manager/web: main_menu.html (+2 -2), web.xml (+19 -19)

vloux 2006-03-17 17:32

BugFix

CAM :
contigDB
Gestion DataSource
Prepa release 20060317

55 lines of code changed in:

• Agmial2/ca_manager/web: context.xml.in (changed), main_intro.html (+21 -30), main_menu.html (+4 -4), main_menu.html.in (changed), web.xml (+28 -28), web.xml.in (+2 -2)

vloux 2006-03-07 17:24

MAJ presentation page accueil managers

34 lines of code changed in:

• Agmial2/ca_manager/web: cam.css (+34), main_intro.html.in (changed)

vloux 2006-03-07 15:31

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

99 lines of code changed in:

• Agmial2/ca_manager/web: 403_error.html (new 14), error.html (del), file_not_found_error.html (new 14), login_error.html (new 15), main_menu.html (+1 -1), main_menu.html.in (changed), server_error.html (new 15), web.xml (+25 -20), web.xml.in (+15 -8)

vloux 2006-03-01 11:56

[#203] S?curit? : Single SignOn +Form based Login
Utilisation de SingleSignOn (valve ? ajouter dans server.xml de tomcat)
Une page jsp formulaire de Login/logout identique dans chaque webapp (pas vu de possibilit? de rediriger vers une autre webapp au login ??)
Mise en place pour cam

10 lines of code changed in:

• Agmial2/ca_manager/web: error.html (new), web.xml.in (+10 -12)

vloux 2006-02-28 16:10

[#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

62 lines of code changed in:

• Agmial2/ca_manager/web: cam.css (+6), main_intro.html (+1 -1), main_intro.html.in (changed), main_menu.html (+6 -7), main_menu.html.in (changed), web.xml (+27 -7), web.xml.in (+22 -2)

vloux 2006-02-27 14:41

AGMIAL Feature #197
Gestion liste : sauvegarde d'un resultat de recherche comme une nouvelle liste.

633 lines of code changed in:

• Agmial2/ca_manager/web: web.xml (new 633)

vloux 2006-01-16 08:58

Changement de start ? la vol?e (Affichage dans editFeature de tous les starts putatifs de l'ORF, transmission des annotations existantes).

16 lines of code changed in:

• Agmial2/ca_manager/web: web.xml.in (+16 -5)

vloux 2005-09-28 14:26

BugFixes
Removed generated web.xml from repository

0 lines of code changed in:

• Agmial2/ca_manager/web: web.xml (del)

vloux 2005-09-22 17:11

BugFixes

5 lines of code changed in:

• Agmial2/ca_manager/web: web.xml.in (+5)

vloux 2005-09-01 17:00

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

617 lines of code changed in:

• Agmial2/ca_manager/web: context.xml.in (changed), web.xml (new 617)

vloux 2005-08-24 10:54

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

4 lines of code changed in:

• Agmial2/ca_manager/web: context.xml.in (changed), web.xml.in (+4 -1)

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

154 lines of code changed in:

• Agmial2/ca_manager/web: context.xml.in (changed), web.xml (del), web.xml.in (+154 -135)

vloux 2005-08-08 16:11

Move project-specific paths to web.xml

9 lines of code changed in:

• Agmial2/ca_manager/web: web.xml.in (+9 -4)

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.

13 lines of code changed in:

• Agmial2/ca_manager/web: web.xml (+2 -6), web.xml.in (+11 -1)

vloux 2005-06-28 17:27

Raw Files access :
+ Url taken from project properties
+ Need to put a .xml file in TOMCAT_HOME/conf/Catalina/localhost/ (documented in agmial_user_guide).

5 lines of code changed in:

• Agmial2/ca_manager/web: web.xml.in (+5)

vloux 2005-06-21 10:11

GlobalPanel
MugenPanel Interface (admin & readOnly) Improved
Multiple bugfixes

12 lines of code changed in:

• Agmial2/ca_manager/web: web.xml.in (+12)

vloux 2005-04-14 07:52

Ajout de la gestion des pseudogenes :
- Checkbox pseudo et text input pseudogene number dans ProteinPanel
- Changement des Interfaces de comm PAM/CAM -> wsdl ? regenerer et ? copier dans src_wsdl

1 lines of code changed in:

• Agmial2/ca_manager/web: web.xml.in (+1 -1)

vloux 2005-04-12 10:51

Bugfix

2 lines of code changed in:

• Agmial2/ca_manager/web: main_menu.html (+1), web.xml.in (+1 -1)

(9 more)