February 2005 Commit Log

Number of Commits:

26

Number of Active Developers:

2

vloux 2005-02-14 11:14 #26

admin guide

1 lines of code changed in:

• doc: agmial_admin_guide.tex (+1 -1)

vloux 2005-02-14 09:43 #25

admin guide

59 lines of code changed in:

• doc: agmial_admin_guide.tex (+59 -118)

agmial 2005-02-11 17:32 #24

Modifs sur la doc.

1 lines of code changed in:

• doc: agmial_admin_guide.tex (+1 -1)

agmial 2005-02-11 17:28 #23

Corrections sur la doc. Casse les... pipes.

1 lines of code changed in:

• doc: agmial_admin_guide.tex (+1 -1)

agmial 2005-02-11 17:22 #22

Corrections et mise en forme de la doc.

82 lines of code changed in:

• doc: agmial_admin_guide.tex (+82 -96)

vloux 2005-02-11 13:50 #21

admin guide

1156 lines of code changed in:

• doc: agmial_admin_guide.tex (new 1156)

vloux 2005-02-11 09:33 #20

Needed by Biotools

267 lines of code changed in:

• BioTools/scripts: run_tRNAscan.pl (new 267)

vloux 2005-02-10 10:24 #19

Preambule GPL

3455 lines of code changed in:

• Agmial2/agmial_directory/src/agmial/directory: InfoPoint.java (+19)
• Agmial2/artemis_client: agmial (del), artemis_agmial.bat (new), specific_options (+1)
• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (+19), AgmialAuthenticateDialog.java (+19), AgmialAuthenticator.java (+19), AgmialDocument.java (+19), AgmialInterface.java (+19), AgmialInterfaceFactory.java (+19), AgmialInterfaceImpl.java (+19), AgmialProfileDocument.java (+19)
• Agmial2/ca_manager/sql: contigdb_creation.sql (+18)
• Agmial2/ca_manager/src/cam/admin: AddBatch.java (+19), AddProject.java (+19), ContigStoreAdminIF.java (+19), ContigStoreAdminImpl.java (+19), LockContig.java (+19), MonitorBatchTasks.java (+19), MonitorContigTasks.java (+19), MonitorFeatureTasks.java (+19), MonitorProjectTasks.java (+19), MonitorTasks.java (+19), ProfileStoreAdminIF.java (+19), ProfileStoreAdminImpl.java (+19), ShowAddBatch.java (+19), ShowAddProject.java (+19), ShowAdminBatches.java (+19), ShowUpdateContig.java (+19), ShowUpdateProfile.java (+19), UpdateContig.java (+19), UpdateProfile.java (+19)
• Agmial2/ca_manager/src/cam/contigdb: CAMBatch.java (+19), CAMBatchAction.java (+19), CAMBatchActionSchema.java (+19), CAMBatchSchema.java (+19), CAMContigAction.java (+19), CAMContigActionSchema.java (+19), CAMContigSchema.java (+19), CAMFeatureAction.java (+19), CAMFeatureActionSchema.java (+19), CAMFeatureSchema.java (+19), CAMFileSchema.java (+19), CAMLock.java (+19), CAMLockSchema.java (+19), CAMProject.java (+19), CAMProjectAction.java (+19), CAMProjectActionSchema.java (+19), CAMProjectSchema.java (+19), CAMSingleProfileSchema.java (+19), CAMSkillMeta.java (+19), CAMSkillMetaSchema.java (+19), CAMSkillParam.java (+19), CAMSkillParamSchema.java (+19), ContigDB.java (+19)
• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (+19), BatchActionQueue.java (+19), BatchCalcAction.java (+19), CAMActionQueue.java (+19), CAMControl.java (+19), CAMMotivation.java (+19), ContigActionMotivation.java (+19), ContigActionQueue.java (+19), ContigCalcAction.java (+19), FeatureActionQueue.java (+19), ProjectActionQueue.java (+19), ProjectMotivation.java (+19), QueryFeatureMotivation.java (+19), TellCDSRemovedAction.java (+19), TransferFeatureAction.java (+19), UpdateCDSAction.java (+19), UpdateProjectAction.java (+19)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+19)
• Agmial2/ca_manager/src/cam/reader: ContigInfoBean.java (+19), ContigLockInfoBean.java (+19), ContigPanel.java (+19), ContigStoreQueryIF.java (+19), ContigStoreQueryImpl.java (+19), EditFeature.java (+19), GenomeProjectBean.java (+19), GetContigRegion.java (+19), MugenPanel.java (+19), ProfileStoreQueryIF.java (+19), ProfileStoreQueryImpl.java (+19), QueryBatches.java (+19), QueryContigs.java (+19), QueryProjects.java (+19)
• Agmial2/ca_manager/src/cam/util: CAMException.java (+19)
• Agmial2/common/src/agmial/control: Action.java (+19), ActionEventHandler.java (+19), ActionException.java (+19), ActionQueue.java (+19), DefaultOrdering.java (+19)
• Agmial2/common/src/agmial/registry: ManagerRegistryInterface.java (+19)
• Agmial2/common/src/agmial/util: AgmialDataException.java (+19), AgmialException.java (+19), MultiPartParser.java (+19), NestedException.java (+19), ServletLog.java (+19)
• Agmial2/pa_manager/sql: protdb_creation.sql (+17 -1), update_database.sql (+18 -1)
• Agmial2/pa_manager/src/pam/admin: AddProteinSource.java (+19), AddProteins.java (+19), MonitorProteinRefTasks.java (+19), MonitorProteinTasks.java (+19), MonitorTasks.java (+19), ProteinSourceAdminIF.java (+19), ProteinSourceAdminImpl.java (+19), RetireProteins.java (+19), ShowAddProteinSource.java (+19), ShowAddProteins.java (+19), ShowAdminSources.java (+19), ShowRetireProteins.java (+19), UpdateAnnotation.java (+19), UpdateFunction.java (+19)
• Agmial2/pa_manager/src/pam/control: AfterActionMotivation.java (+19), DetermineFunctionAction.java (+19), HomologyResultsMotivation.java (+19), NotifyFunctionAction.java (+19), NotifyFunctionMotivation.java (+19), PAMActionQueue.java (+19), PAMControl.java (+19), PAMMotivation.java (+19), ParalogResultsMotivation.java (+19), ProteinActionMotivation.java (+19), ProteinActionQueue.java (+19), ProteinCalcAction.java (+19), ProteinRefActionQueue.java (+19), SwissAnnotAction.java (+19)
• Agmial2/pa_manager/src/pam/lifecycle: ContextListener.java (+19)
• Agmial2/pa_manager/src/pam/protdb: PAMDatabaseMeta.java (+19), PAMDatabaseMetaSchema.java (+19), PAMFileSchema.java (+19), PAMFloatValueResultSchema.java (+19), PAMHomologyResultSchema.java (+19), PAMInfoSourceMeta.java (+19), PAMInfoSourceMetaSchema.java (+19), PAMMembraneSpanSchema.java (+19), PAMMethodMeta.java (+19), PAMMethodMetaSchema.java (+19), PAMMotifFeatureSchema.java (+19), PAMProtein.java (+19), PAMProteinAction.java (+19), PAMProteinActionSchema.java (+19), PAMProteinFeatureSchema.java (+19), PAMProteinRef.java (+19), PAMProteinRefAction.java (+19), PAMProteinRefActionSchema.java (+19), PAMProteinRefSchema.java (+19), PAMProteinSchema.java (+19), PAMProteinSource.java (+19), PAMProteinSourceSchema.java (+19), PAMSkillMeta.java (+19), PAMSkillMetaSchema.java (+19), PAMSkillParam.java (+19), PAMSkillParamSchema.java (+19), PAMValuedFeatureSchema.java (+19), ProteinDB.java (+19)
• Agmial2/pa_manager/src/pam/reader: AAFeaturesFormatter.java (+19), AlignImage.java (+19), CDDTable.java (+19), EditingBuffer.java (+19), FeaturesGraphic.java (+19), FeaturesViewer.java (+19), FormattedFeature.java (+19), HomologyAlignPanel.java (+19), HomologyGraphic.java (+19), HomologyImagePanel.java (+19), HomologyPanel.java (+19), HomologyTable.java (+19), ParalogTable.java (+19), ProteinPanel.java (+19), QueryDataSets.java (+19), QueryProteinSources.java (+19), QueryProteins.java (+19), ResidueFormatter.java (+19), SearchAnnotationPanel.java (+19), SearchDataSets.java (+19), SearchPanel.java (+19), SearchProteinSources.java (+19), SearchResults.java (+19), SearchResultsPanel.java (+19), SearchSQLQueryPanel.java (+19), SearchSQLQueryResults.java (+19)
• Agmial2/pa_manager/src/pam/util: PAMException.java (+19)

vloux 2005-02-10 10:22 #18

GPL

340 lines of code changed in:

• COPYING (new 340)

vloux 2005-02-09 17:26 #17

Static endpoint

314 lines of code changed in:

• Agmial2/ca_manager: build.xml (+11 -6)
• Agmial2/ca_manager/src/cam/control: TellCDSRemovedAction.java (+22 -15), UpdateCDSAction.java (+45 -32), UpdateProjectAction.java (+21 -14)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+4 -2)
• Agmial2/ca_manager/web: main_menu.html (+1 -1), web.xml (+48 -1), web.xml.in (+48 -1)
• Agmial2/pa_manager: build.xml (+8)
• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (-3), NotifyFunctionAction.java (+23 -17)
• Agmial2/pa_manager/web: main_menu.html (+1 -1), web.xml (+41), web.xml.in (+41)

vloux 2005-02-09 16:27 #16

Static endpoint agmial_directory
Deploy

179 lines of code changed in:

• Agmial2: build.xml (+5 -1), template_project.properties (+21 -3)
• Agmial2/agmial_directory: build.xml (+42 -9)
• Agmial2/agmial_directory/src/agmial/directory: InfoPoint.java (+62 -52)
• Agmial2/agmial_directory/web: web.xml (+49 -8)

vloux 2005-02-09 14:41 #15

Artemis standalone
Static endpoint. (use_registry=false)

1085 lines of code changed in:

• Agmial2/artemis_client: artemis_agmial.sh (new), specific_options (+10 -2)
• Agmial2/artemis_client/ARTEMIS/lib: Agmial-2.0.jar (new 88), activation.jar (new), commons-logging.jar (new), dom.jar (new), jaas.jar (new), jaxb-api.jar (new), jaxb-impl.jar (new), jaxb-libs.jar (new), jaxb-xjc.jar (new), jaxp-api.jar (new), jaxr-api.jar (new), jaxr-impl.jar (new), jaxrpc-api.jar (new), jaxrpc-impl.jar (new), jaxrpc-spi.jar (new), mail.jar (new), saaj-api.jar (new), saaj-impl.jar (new), sax.jar (new), xalan.jar (new), xercesImpl.jar (new 849)
• Agmial2/artemis_client/src/agmial/artemis: AgmialInterfaceImpl.java (+138 -77)

agmial 2005-02-09 10:11 #14

Bugfix ContigPanel

1 lines of code changed in:

• Agmial2/ca_manager/src/cam/reader: ContigPanel.java (+1 -1)

agmial 2005-02-08 16:01 #13

*** empty log message ***

21 lines of code changed in:

• Agmial2: template_organization.properties (+2 -2)

vloux 2005-02-08 14:59 #12

Cassage de pipe (8)

Build.xml OK pour ca_manger et pa_manager.
Propage l'info conteue dans project_properties.
Fin (?) ajustements jwsdp1.5
Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

101 lines of code changed in:

• Agmial2/pa_manager/src/pam/reader: ProteinPanel.java (+3 -3)
• Agmial2/pa_manager/web: web.xml (+53 -15), web.xml.in (+45 -38)

vloux 2005-02-08 14:58 #11

Cassage de pipe (7)

Build.xml OK pour ca_manger et pa_manager.
Propage l'info conteue dans project_properties.
Fin (?) ajustements jwsdp1.5
Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

3 lines of code changed in:

• Agmial2/pa_manager/src/pam/lifecycle: ContextListener.java (+1 -1)
• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+2 -3)

vloux 2005-02-08 14:58 #10

Cassage de pipe (5)

Build.xml OK pour ca_manger et pa_manager.
Propage l'info conteue dans project_properties.
Fin (?) ajustements jwsdp1.5
Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

179 lines of code changed in:

• Agmial2/ca_manager/src/cam/reader: ContigPanel.java (+1 -1), ContigStoreQueryImpl.java (+7), ProfileStoreQueryImpl.java (+2 -1), QueryProjects.java (+2 -1)
• Agmial2/ca_manager/web: web.xml (+39 -3), web.xml.in (+51 -114)
• Agmial2/common/src/agmial/registry: ManagerRegistryInterface.java (+38 -11)
• Agmial2/pa_manager: build.xml (+31 -41), pam_manager.properties (+5 -6)
• Agmial2/pa_manager/src/pam/admin: UpdateFunction.java (+1 -1)
• Agmial2/pa_manager/src/pam/control: NotifyFunctionAction.java (+2 -2), NotifyFunctionAction.java.in (del), PAMControl.java.in (del)

vloux 2005-02-08 14:57 #9

Cassage de pipe (4)

Build.xml OK pour ca_manger et pa_manager.
Propage l'info conteue dans project_properties.
Fin (?) ajustements jwsdp1.5
Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

2 lines of code changed in:

• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+2 -1)

vloux 2005-02-08 14:57 #8

Cassage de pipe (3)

Build.xml OK pour ca_manger et pa_manager.
Propage l'info conteue dans project_properties.
Fin (?) ajustements jwsdp1.5
Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

196 lines of code changed in:

• Agmial2/artemis_client/src_wsdl: ContigStoreAdmin.wsdl (+44 -44), ContigStoreQuery.wsdl (+89 -89), ProfileStoreQuery.wsdl (+21 -21)
• Agmial2/ca_manager: build.xml (+20 -5), cam_manager.properties (+9 -9)
• Agmial2/ca_manager/src/cam/admin: ContigStoreAdminImpl.java (-1), ProfileStoreAdminImpl.java (-1)
• Agmial2/ca_manager/src/cam/control: CAMControl.java (+4 -2), CAMControl.java.in (del), TellCDSRemovedAction.java (+3 -2), TellCDSRemovedAction.java.in (del), TransferFeatureAction.java (-1), UpdateCDSAction.java (+4 -2), UpdateProjectAction.java (+2 -2), UpdateProjectAction.java.in (del)

vloux 2005-02-08 14:57 #7

Cassage de Pipe ..
Build.xml OK pour ca_manger et pa_manager.
Propage l'info conteue dans project_properties.
Fin (?) ajustements jwsdp1.5
Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

28 lines of code changed in:

• Agmial2/artemis_client: build.xml (+17 -11), specific_options (new 2)
• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (-2), AgmialInterfaceImpl.java (+9 -7), AgmialInterfaceImpl.java.in (del)

vloux 2005-02-08 14:56 #6

- Build.xml OK pour ca_manager et pa_manager.
Propage l'info contenue dans project_properties.
- Fin (?) ajustements jwsdp1.5

- Plus de startup_agmial/shutdown_agmial car nous deployons la webapp. A la place deploy-agmial/undeploy_agmial. La webapp est deployee -> il suffit de demarrer tomcat pour qu'elle soit dispo ...

96 lines of code changed in:

• Agmial2: TODO (+2), build.xml (+49 -24), organization.properties (+2 -2), shutdown_agmial (del), startup_agmial (del), web_services.properties (+4 -4)
• Agmial2/agmial_directory: build.xml (+36 -5)
• Agmial2/agmial_directory/src/agmial/directory: InfoPoint.java.in (del)
• Agmial2/agmial_directory/web: web.xml (+3 -3)

vloux 2005-02-04 11:37 #5

Export sequin

10 lines of code changed in:

• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+1 -1)
• Agmial2/ca_manager/src/cam/reader: ContigStoreQueryImpl.java (+6 -25), QueryContigs.java (+3 -1)

vloux 2005-02-03 09:09 #4

Adresse Unit?

6 lines of code changed in:

• Agmial2/ca_manager/web: main_intro.html (+3 -3)
• Agmial2/pa_manager/web: main_intro.html (+3 -4)

vloux 2005-02-02 17:23 #3

JWSDP1.5

171 lines of code changed in:

• Agmial2/pa_manager: build.xml (+97 -89), server_ProteinSourceAdmin_Config.xml (del)
• Agmial2/pa_manager/src/pam/reader: SearchResults.java (+4 -4)
• Agmial2/pa_manager/src_wsdl: ContigStoreAdmin.wsdl (+44 -44)
• Agmial2/pa_manager/web: jaxrpc-ri.xml (new 24), web.xml (+2 -33)

vloux 2005-02-02 17:05 #2

JWSDP1.5

182 lines of code changed in:

• Agmial2/ca_manager: build.xml (+74 -88), server_ContigStoreAdmin_Config.xml (del), server_ContigStoreQuery_Config.xml (del), server_ProfileStoreAdmin_Config.xml (del), server_ProfileStoreQuery_Config.xml (del)
• Agmial2/ca_manager/src_wsdl: ProteinSourceAdmin.wsdl (+26 -26)
• Agmial2/ca_manager/web: jaxrpc-ri.xml (new 54), web.xml (+3 -102)
• Agmial2/common: build.xml (+25 -2)

vloux 2005-02-02 16:43 #1

Export in sequin feature table format <http://www.ncbi.nlm.nih.gov/Genbank/genomesubmit.html#fig2>

223 lines of code changed in:

• BioTools/src/biotools/nucleic: NucleicFeatureLocation.java (+34 -1), SequinEntry.java (new 189)

January 2005 »