March 2006 Commit Log

Number of Commits:

14

Number of Active Developers:

1

vloux 2006-03-23 14:51 #14

sql commands for changing indexes tablespace

49 lines of code changed in:

• Agmial2/ca_manager/sql: indexes_tbsp_change.sql (new 17)
• Agmial2/pa_manager/sql: indexes_tbsp_change.sql (new 32)

vloux 2006-03-17 17:32 #13

BugFix

CAM :
contigDB
Gestion DataSource
Prepa release 20060317

2863 lines of code changed in:

• Agmial2/agmial_directory: build.xml (+3 -1)
• Agmial2/agmial_directory/src/agmial/directory: InfoPoint.java (+31 -19), log4j.properties (new 9)
• Agmial2/agmial_directory/web: web.xml (+8 -4), web.xml.in (+8 -4)
• Agmial2/agmial_directory/web/agmial_user_guide: index.html (+2 -7)
• Agmial2/agmial_directory/web/jsp: index.jsp (new 29)
• Agmial2/ca_manager: build.xml (+2 -2)
• Agmial2/ca_manager/src/cam/admin: ContigStoreAdminIF.java (+1 -1), ContigStoreAdminImpl.java (+4 -4), GlobalAdmin.java (+154 -141), MonitorBatchTasks.java (+13 -3), MonitorContigTasks.java (+12 -3), MonitorFeatureTasks.java (+13 -3), MonitorProjectTasks.java (+13 -8), changeLocalisation.java (+17 -18)
• Agmial2/ca_manager/src/cam/contigdb: CAMBatchAction.java (+2 -12), CAMFeatureSchema.java (+15 -9), ContigDB.java (+2122 -1843)
• Agmial2/ca_manager/src/cam/control: BatchActionMotivation.java (+5 -4), BatchActionQueue.java (+11), BatchCalcAction.java (+5 -3), CAMActionQueue.java (+14 -2), CAMControl.java (+105 -65), CAMMotivation.java (+5), ContigActionMotivation.java (+11 -9), ContigActionQueue.java (+11), ContigCalcAction.java (+4 -3), FeatureActionQueue.java (+13 -1), ProjectActionQueue.java (+15 -2), TellCDSRemovedAction.java (+1 -1), UpdateCDSAction.java (+8 -13), UpdateProjectAction.java (+1 -1)
• Agmial2/ca_manager/src/cam/lifecycle: ContextListener.java (+4 -4)
• Agmial2/ca_manager/src/cam/reader: ContigStoreQueryImpl.java (+8 -8), EditFeature.java (+2 -2), MugenPanel.java (+97 -46)
• Agmial2/ca_manager/src_wsdl: ProteinSourceAdmin.wsdl (+2 -2)
• 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)
• Agmial2/pa_manager/web: main_intro.html (+24 -30), main_menu.html (+4 -4)

vloux 2006-03-17 17:13 #12

Bugfixes

15 lines of code changed in:

• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+11 -7)
• Agmial2/pa_manager/src/pam/reader: ProteinPanel.java (+4 -4)

vloux 2006-03-17 14:43 #11

BugFix

13 lines of code changed in:

• Agmial2/pa_manager/src/pam/reader: ClustalLauncher.java (+13 -6)

vloux 2006-03-17 14:20 #10

BugFix

2 lines of code changed in:

• Agmial2/pa_manager/src/pam/reader: JalviewLauncher.java (+2 -1)

vloux 2006-03-16 13:01 #9

Chgt wsdl
Pool connection sgbd
BugFix Search
Control

2125 lines of code changed in:

• Agmial2/pa_manager: build.xml (+2 -2)
• Agmial2/pa_manager/src/pam/admin: ProteinSourceAdminIF.java (+1 -1), ProteinSourceAdminImpl.java (+20 -12), UpdateFunction.java (+5 -5)
• Agmial2/pa_manager/src/pam/control: DetermineFunctionAction.java (+45 -16), PAMControl.java (+21 -21), ProteinCalcAction.java (+35 -20), SwissAnnotAction.java (+6 -4)
• Agmial2/pa_manager/src/pam/protdb: PAMHomologyResultSchema.java (+14 -10), PAMProtein.java (+7 -4), PAMProteinSchema.java (+160 -161), ProteinDB.java (+1523 -1395)
• Agmial2/pa_manager/src/pam/reader: FastaCreator.java (+106 -96), HomologyAlignPanel.java (+6 -10), HomologyImagePanel.java (+11 -14), HomologyPanel.java (+11 -10), ProteinPanel.java (+41 -15), QueryProteins.java (+36 -11), SearchResults.java (+57 -23), SearchSQLQueryResults.java (+11 -4)
• Agmial2/pa_manager/src_wsdl: ContigStoreAdmin.wsdl (+2 -2), ContigStoreQuery.wsdl (changed)
• Agmial2/pa_manager/web: context.xml.in (changed), main_menu.html.in (changed), web.xml.in (+5 -1)

vloux 2006-03-07 17:24 #8

MAJ presentation page accueil managers

72 lines of code changed in:

• Agmial2/ca_manager: build.xml (+3 -1)
• Agmial2/ca_manager/web: cam.css (+34), main_intro.html.in (changed)
• Agmial2/ca_manager/web/images: favicon.ico (new), logoagmial.png (new), logoagmial_small.png (new)
• Agmial2/pa_manager: build.xml (+3 -1)
• Agmial2/pa_manager/web: main_intro.html.in (changed), pam.css (+32)
• Agmial2/pa_manager/web/images: favicon.ico (new), logoagmial.png (new), logoagmial_small.png (new)

vloux 2006-03-07 15:31 #7

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

413 lines of code changed in:

• Agmial2/agmial_directory: build.xml (+3 -1), build.xml.in (del)
• Agmial2/agmial_directory/src/agmial/directory: InfoPoint.java (+25 -12)
• Agmial2/agmial_directory/web: 403_error.html (new 14), agmial_directory.css (+30 -1), error.html (del), file_not_found_error.html (new 14), inra_logo.gif (del), login_error.html (new 15), mig_logo.jpg (del), server_error.html (new 15), web.xml (+39 -2), web.xml.in (+17 -3)
• Agmial2/agmial_directory/web/images: favicon.ico (new), inra_logo.gif (new), logoagmial.png (new), logoagmial_small.png (new), mig_logo.jpg (new)
• Agmial2/agmial_directory/web/jsp: login.jsp (+17 -1)
• Agmial2/ca_manager: build.xml (+11 -9)
• Agmial2/ca_manager/src/cam/contigdb: CAMFeatureSchema.java (+1 -1)
• Agmial2/ca_manager/src/cam/reader: MugenPanel.java (+7 -3)
• 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)
• Agmial2/pa_manager: build.xml (+70 -54)
• Agmial2/pa_manager/src/pam/reader: ProteinPanel.java (+5 -3)
• Agmial2/pa_manager/web: .cvsignore (new 1), 403_error.html (new), file_not_found_error.html (new), login_error.html (new), main_intro.html (+1 -1), main_intro.html.in (new), main_menu.html (+6 -8), main_menu.html.in (new), server_error.html (new), web.xml.in (+18 -12)
• Agmial2/pa_manager/web/js: pam.js (+5 -4)

vloux 2006-03-07 15:27 #6

[#197] Listes proteines
BugFix

67 lines of code changed in:

• Agmial2/pa_manager/src/pam/admin: ProteinSourceAdminImpl.java (+10 -6)
• Agmial2/pa_manager/src/pam/protdb: PAMProteinListSchema.java (+35), ProteinDB.java (+22)

vloux 2006-03-07 15:15 #5

rm -rf artemis_client

0 lines of code changed in:

• Agmial2/artemis_client/ARTEMIS: AGMIAL_README (del), BRYSON_README (del), COPYING (del), COPYING.JacORB (del), CorbaApplet.java (del), INSTALL (del), MAKEFILE_OUT (del), MAKEFILE_RESULT (del), Makefile (del), README (del), art (del), art.bat (del), art2 (del), mart (del), results_to_netscape (del), run_blast (del), run_blastn (del), run_blastp (del), run_blastx (del), run_fasta (del), run_hth (del), run_jalview (del), run_sigcleave (del), run_tblastn (del), run_tblastx (del), stylesheet.css (del)
• Agmial2/artemis_client/ARTEMIS/META-INF: MANIFEST.MF (del)
• Agmial2/artemis_client/ARTEMIS/collections: ArrayEnumeration.java (del), Assertable.java (del), Bag.java (del), BinaryFunction.java (del), CEImpl.java (del), CLCell.java (del), CLEnumeration.java (del), Cell.java (del), CheckedBag.java (del), CheckedCollection.java (del), CheckedMap.java (del), CheckedSeq.java (del), CheckedSet.java (del), CircularList.java (del), Collection.java (del), CollectionEnumeration.java (del), Comparator.java (del), CorruptedEnumerationException.java (del), DAEnumeration.java (del), DefaultComparator.java (del), DefaultImplementations.java (del), Dynarray.java (del), ElementSortedCollection.java (del), FilteringEnumeration.java (del), Function.java (del), HTEnumeration.java (del), HTPairEnumeration.java (del), HashTableParams.java (del), HashedMap.java (del), HashedSet.java (del), IllegalElementException.java (del), Immutable.java (del), ImplementationCheckable.java (del), ImplementationError.java (del), IncrBag.java (del), IncrCollectionEnumeration.java (del), IncrImpl.java (del), IncrMap.java (del), IncrSeq.java (del), IncrSet.java (del), InterleavingEnumeration.java (del), KeySortedCollection.java (del), Keyed.java (del), LBEnumeration.java (del), LLCell.java (del), LLCellEnumeration.java (del), LLMap.java (del), LLPair.java (del), LLPairEnumeration.java (del), LinkedBuffer.java (del), LinkedList.java (del), Map.java (del), MappingEnumeration.java (del), Pair.java (del), Predicate.java (del), Procedure.java (del), RBCell.java (del), RBCellEnumeration.java (del), RBMap.java (del), RBPair.java (del), RBPairEnumeration.java (del), RBTree.java (del), Seq.java (del), Set.java (del), SimpleTest.java (del), SortableCollection.java (del), UpdatableBag.java (del), UpdatableBagImpl.java (del), UpdatableCollection.java (del), UpdatableImpl.java (del), UpdatableMap.java (del), UpdatableMapImpl.java (del), UpdatableSeq.java (del), UpdatableSeqImpl.java (del), UpdatableSet.java (del), UpdatableSetImpl.java (del), collections_Dynarray.h (del), javaMake (del)
• Agmial2/artemis_client/ARTEMIS/corba: apollo.idl (del), ensembl.idl (del), nsdb.idl (del), nsdb_write.idl (del), seqdb.idl (del), types.idl (del)
• Agmial2/artemis_client/ARTEMIS/diana: AlignMatch.java (del), AlignMatchVector.java (del), AppGlobal.java (del), ChangeEvent.html (del), ChangeEvent.java (del), ChangeListener.html (del), ChangeListener.java (del), ClipBoard.java (del), ComparisonData.java (del), ComparisonDataFactory.java (del), ComparisonDataParseException.java (del), Diana.java (del), Entry.FeatureEnumerator.html (del), Entry.html (del), Entry.java (del), EntryChangeEvent.html (del), EntryChangeEvent.java (del), EntryChangeListener.html (del), EntryChangeListener.java (del), EntryGroup.html (del), EntryGroup.java (del), EntryGroupChangeEvent.html (del), EntryGroupChangeEvent.java (del), EntryGroupChangeListener.html (del), EntryGroupChangeListener.java (del), EntrySource.html (del), EntrySource.java (del), EntrySourceVector.html (del), EntrySourceVector.java (del), EntryVector.html (del), EntryVector.java (del), ExternalApplication.html (del), ExternalApplication.java (del), ExternalProgram.html (del), ExternalProgram.java (del), ExternalProgramException.html (del), ExternalProgramException.java (del), ExternalProgramVector.html (del), ExternalProgramVector.java (del), ExternalSearchProgram.html (del), ExternalSearchProgram.java (del), Feature.html (del), Feature.java (del), FeatureChangeEvent.html (del), FeatureChangeEvent.java (del), FeatureChangeListener.html (del), FeatureChangeListener.java (del), FeatureEnumeration.html (del), FeatureEnumeration.java (del), FeatureFromVectorPredicate.html (del), FeatureFromVectorPredicate.java (del), FeatureKeyPredicate.html (del), FeatureKeyPredicate.java (del), FeatureKeyQualifierPredicate.html (del), FeatureKeyQualifierPredicate.java (del), FeaturePredicate.html (del), FeaturePredicate.java (del), FeatureSegment.html (del), FeatureSegment.java (del), FeatureSegmentVector.html (del), FeatureSegmentVector.java (del), FeatureVector.html (del), FeatureVector.java (del), FilteredEntryGroup.FeatureEnumerator.html (del), FilteredEntryGroup.html (del), FilteredEntryGroup.java (del), GotoEvent.html (del), GotoEvent.java (del), GotoEventSource.html (del), GotoEventSource.java (del), GotoListener.html (del), GotoListener.java (del), LastSegmentException.html (del), LastSegmentException.java (del), Logger.html (del), Logger.java (del), MSPcrunchComparisonData.java (del), MUMmerComparisonData.java (del), Options.html (del), Options.java (del), Selectable.html (del), Selectable.java (del), Selection.html (del), Selection.java (del), SelectionChangeEvent.html (del), SelectionChangeEvent.java (del), SelectionChangeListener.html (del), SelectionChangeListener.java (del), SimpleComparisonData.java (del), SimpleEntryGroup.FeatureEnumerator.html (del), SimpleEntryGroup.html (del), SimpleEntryGroup.java (del), SimpleGotoEventSource.html (del), SimpleGotoEventSource.java (del), helix.gif (del), sanger-centre.gif (del)
• Agmial2/artemis_client/ARTEMIS/diana/components: ActMain.java (del), AddMenu.html (del), AddMenu.java (del), AlignmentViewer.java (del), ArtemisMain.html (del), ArtemisMain.java (del), BasePlot.html (del), BasePlot.java (del), BasePlotGroup.html (del), BasePlotGroup.java (del), BasicArrow.html (del), BasicArrow.java (del), CanvasPanel.java (del), Comparator.java (del), ComparatorDialog.java (del), CorbaEntrySource.html (del), CorbaEntrySource.java (del), DisplayAdjustmentEvent.html (del), DisplayAdjustmentEvent.java (del), DisplayAdjustmentListener.html (del), DisplayAdjustmentListener.java (del), DisplayComponent.html (del), DisplayComponent.java (del), EMBLCorbaEntrySource.html (del), EMBLCorbaEntrySource.java (del), EditMenu.html (del), EditMenu.java (del), EnsemblEntrySource.java (del), EntryActionListener.html (del), EntryActionListener.java (del), EntryEdit.html (del), EntryEdit.java (del), EntryEditVector.html (del), EntryEditVector.java (del), EntryFileDialog.html (del), EntryFileDialog.java (del), EntryGroupDisplay.html (del), EntryGroupDisplay.java (del), EntryGroupInfoDisplay.html (del), EntryGroupInfoDisplay.java (del), EntryGroupMenu.html (del), EntryGroupMenu.java (del), EntryGroupPanel.html (del), EntryGroupPanel.java (del), EntryHeaderEdit.html (del), EntryHeaderEdit.java (del), ExternalProgramOptions.html (del), ExternalProgramOptions.java (del), FeatureAminoAcidViewer.html (del), FeatureAminoAcidViewer.java (del), FeatureBaseViewer.html (del), FeatureBaseViewer.java (del), FeatureDisplay.html (del), FeatureDisplay.java (del), FeatureDisplayOwner.html (del), FeatureDisplayOwner.java (del), FeatureEdit.html (del), FeatureEdit.java (del), FeatureInfo.html (del), FeatureInfo.java (del), FeatureList.html (del), FeatureList.java (del), FeatureListFrame.html (del), FeatureListFrame.java (del), FeaturePlot.html (del), FeaturePlot.java (del), FeaturePlotGroup.html (del), FeaturePlotGroup.java (del), FeaturePopup.html (del), FeaturePopup.java (del), FeatureShape.html (del), FeatureShape.java (del), FeatureViewer.html (del), FeatureViewer.java (del), FileDialogEntrySource.html (del), FileDialogEntrySource.java (del), FileViewer.html (del), FileViewer.java (del), GotoMenu.html (del), GotoMenu.java (del), KeyChoice.html (del), KeyChoice.java (del), KeyChooser.html (del), KeyChooser.java (del), ListDialog.html (del), ListDialog.java (del), LogViewer.html (del), LogViewer.java (del), MarkerRangeRequester.html (del), MarkerRangeRequester.java (del), MarkerRangeRequesterEvent.html (del), MarkerRangeRequesterEvent.java (del), MarkerRangeRequesterListener.html (del), MarkerRangeRequesterListener.java (del), MessageDialog.html (del), MessageDialog.java (del), MessageFrame.html (del), MessageFrame.java (del), Navigator.html (del), Navigator.java (del), Plot.html (del), Plot.java (del), PlotMouseListener.html (del), PlotMouseListener.java (del), ProcessWatcher.html (del), ProcessWatcher.java (del), ProcessWatcherEvent.html (del), ProcessWatcherEvent.java (del), ProcessWatcherListener.html (del), ProcessWatcherListener.java (del), Promoter.html (del), Promoter.java (del), QualifierChoice.html (del), QualifierChoice.java (del), RawFeatureEdit.java (del), ReadFeaturesActionListener.html (del), Rectangle.html (del), Rectangle.java (del), RunMenu.html (del), RunMenu.java (del), SaveEntryActionListener.html (del), SaveEntryAsActionListener.html (del), SaveEntryAsEMBLActionListener.html (del), SaveEntryAsGFFActionListener.html (del), SaveEntryAsGenbankActionListener.html (del), SaveEntryAsSubmissionActionListener.html (del), ScoreChangeEvent.html (del), ScoreChangeEvent.java (del), ScoreChangeListener.html (del), ScoreChangeListener.java (del), ScoreChanger.html (del), ScoreChanger.java (del), ScoreScrollbar.html (del), ScoreScrollbar.java (del), SearchResultViewer.html (del), SearchResultViewer.java (del), SelectMenu.html (del), SelectMenu.java (del), SelectionInfoDisplay.html (del), SelectionInfoDisplay.java (del), SelectionMenu.html (del), SelectionMenu.java (del), SelectionViewer.html (del), SelectionViewer.java (del), Selector.html (del), Selector.java (del), SequenceViewer.html (del), SequenceViewer.java (del), Splash.html (del), Splash.java (del), Terminator.html (del), Terminator.java (del), TextDialog.html (del), TextDialog.java (del), TextRequester.html (del), TextRequester.java (del), TextRequesterEvent.html (del), TextRequesterEvent.java (del), TextRequesterListener.html (del), TextRequesterListener.java (del), ViewMenu.html (del), ViewMenu.java (del), WideArrow.html (del), WideArrow.java (del), WindowAdjustmentEvent.java (del), WindowAdjustmentListener.java (del), WritableEMBLCorbaEntrySource.html (del), WritableEMBLCorbaEntrySource.java (del), WriteMenu.html (del), WriteMenu.java (del), YesNoDialog.html (del), YesNoDialog.java (del)
• Agmial2/artemis_client/ARTEMIS/diana/plot: AGWindowAlgorithm.html (del), AGWindowAlgorithm.java (del), ATDeviationAlgorithm.html (del), ATDeviationAlgorithm.java (del), Algorithm.html (del), Algorithm.java (del), BaseAlgorithm.html (del), BaseAlgorithm.java (del), Codon12CorrelationAlgorithm.html (del), Codon12CorrelationAlgorithm.java (del), CodonUsageAlgorithm.html (del), CodonUsageAlgorithm.java (del), CodonUsageFormatException.html (del), CodonUsageFormatException.java (del), CodonUsageWeight.html (del), CodonUsageWeight.java (del), CodonWeight.html (del), CodonWeight.java (del), CoilFeatureAlgorithm.html (del), CoilFeatureAlgorithm.java (del), FeatureAlgorithm.html (del), FeatureAlgorithm.java (del), GCDeviationAlgorithm.html (del), GCDeviationAlgorithm.java (del), GCFrameAlgorithm.html (del), GCFrameAlgorithm.java (del), GCSDWindowAlgorithm.html (del), GCSDWindowAlgorithm.java (del), GCWindowAlgorithm.html (del), GCWindowAlgorithm.java (del), HydroAlgorithm.html (del), HydroAlgorithm.java (del), HydrophilicityAlgorithm.html (del), HydrophilicityAlgorithm.java (del), HydrophobicityAlgorithm.html (del), HydrophobicityAlgorithm.java (del), UserDataAlgorithm.html (del), UserDataAlgorithm.java (del)
• Agmial2/artemis_client/ARTEMIS/diana/sequence: AminoAcidSequence.html (del), AminoAcidSequence.java (del), BasePattern.html (del), BasePattern.java (del), BasePatternFormatException.html (del), BasePatternFormatException.java (del), Bases.html (del), Bases.java (del), Marker.html (del), Marker.java (del), MarkerChangeEvent.html (del), MarkerChangeEvent.java (del), MarkerChangeListener.html (del), MarkerChangeListener.java (del), MarkerInternal.html (del), MarkerRange.html (del), MarkerRange.java (del), MarkerRangeVector.html (del), MarkerRangeVector.java (del), NoSequenceException.html (del), NoSequenceException.java (del), SequenceChangeEvent.html (del), SequenceChangeEvent.java (del), SequenceChangeListener.html (del), SequenceChangeListener.java (del), Strand.html (del), Strand.java (del)
• Agmial2/artemis_client/ARTEMIS/docs: Makefile (del), acknowledgements.sgml (del), act_display_menus.sgml (del), act_file_menu.sgml (del), act_intro_chapter.sgml (del), act_main_window.sgml (del), act_main_window_1.gif (del), act_main_window_2.gif (del), act_main_window_3.gif (del), act_main_window_4.gif (del), act_main_window_5.gif (del), act_manual.sgml (del), act_start_chapter.sgml (del), act_user_manual_screen_shot.gif (del), artemis.dsl (del), concepts.sgml (del), copyright.sgml (del), display_common.sgml (del), display_menu.sgml (del), feature_list.sgml (del), file_menu.sgml (del), getting_java.sgml (del), intro_chapter.sgml (del), main_window_1.gif (del), main_window_2.gif (del), main_window_3.gif (del), main_window_4.gif (del), main_window_5.gif (del), main_window_6.gif (del), main_window_chapter.sgml (del), manual.sgml (del), menus.sgml (del), mousebuttons.sgml (del), options.sgml (del), requirements.sgml (del), run_menu.sgml (del), start_chapter.sgml (del), unix_args.sgml (del), user_manual_screen_shot.gif (del), views_popup.sgml (del), views_scale.sgml (del), views_scrolling.sgml (del), views_selection.sgml (del)
• Agmial2/artemis_client/ARTEMIS/etc: feature_keys (del), options (del), pombe.usage (del), qualifier_types (del)
• Agmial2/artemis_client/ARTEMIS/jalview: file_number_counter (del), file_of_filenames.1 (del)
• Agmial2/artemis_client/ARTEMIS/lib: Agmial-2.0.jar (del), BioTools-1.0.jar (del), JacORB.jar (del), activation.jar (del), dom.jar (del), jax-qname.jar (del), jaxr-api.jar (del), jaxr-impl.jar (del), jaxrpc-api.jar (del), jaxrpc-impl.jar (del), jaxrpc-spi.jar (del), mail.jar (del), namespace.jar (del), saaj-api.jar (del), saaj-impl.jar (del), sax.jar (del), xalan.jar (del), xercesImpl.jar (del), xmlParserAPIs.jar (del)
• Agmial2/artemis_client/ARTEMIS/uk/ac/sanger/pathogens: Document.html (del), Document.java (del), FastVector.html (del), FastVector.java (del), FileDocument.html (del), FileDocument.java (del), FileProgressDocument.html (del), FileProgressDocument.java (del), InputStreamProgressEvent.html (del), InputStreamProgressEvent.java (del), InputStreamProgressListener.html (del), InputStreamProgressListener.java (del), OutOfRangeException.html (del), OutOfRangeException.java (del), ProgressInputStream.html (del), ProgressInputStream.java (del), ReadOnlyException.html (del), ReadOnlyException.java (del), StringVector.html (del), StringVector.java (del), URLDocument.html (del), URLDocument.java (del)
• Agmial2/artemis_client/ARTEMIS/uk/ac/sanger/pathogens/embl: BetweenRange.html (del), BetweenRange.java (del), ComparableFeature.html (del), ComparableFeature.java (del), CorbaEntry.html (del), CorbaEntry.java (del), CorbaFeature.html (del), CorbaFeature.java (del), CorbaSequence.html (del), CorbaSequence.java (del), DateStampFeature.html (del), DateStampFeature.java (del), DocumentEntry.html (del), DocumentEntry.java (del), DocumentEntryAutosaveThread.html (del), DocumentEntryAutosaveThread.java (del), DocumentEntryFactory.html (del), DocumentEntryFactory.java (del), DocumentFeature.html (del), DocumentFeature.java (del), EMBLObject.html (del), EMBLObject.java (del), EmblDocumentEntry.html (del), EmblDocumentEntry.java (del), EmblMisc.html (del), EmblMisc.java (del), EmblStreamFeature.html (del), EmblStreamFeature.java (del), EmblStreamSequence.html (del), EmblStreamSequence.java (del), EnsemblCorbaEntry.html (del), EnsemblCorbaEntry.java (del), EnsemblCorbaFeature.html (del), EnsemblCorbaFeature.java (del), EnsemblCorbaSequence.html (del), EnsemblCorbaSequence.java (del), Entry.html (del), Entry.java (del), EntryInformation.html (del), EntryInformation.java (del), EntryInformationException.html (del), EntryInformationException.java (del), FastaStreamSequence.html (del), FastaStreamSequence.java (del), Feature.html (del), Feature.java (del), FeatureComparator.html (del), FeatureComparator.java (del), FeatureEnumeration.html (del), FeatureEnumeration.java (del), FeatureHeader.html (del), FeatureHeader.java (del), FeatureTable.html (del), FeatureTable.java (del), FeatureTree.FeatureEnumerator.html (del), FeatureTree.html (del), FeatureTree.java (del), FeatureVector.html (del), FeatureVector.java (del), FuzzyRange.html (del), FuzzyRange.java (del), GFFDocumentEntry.html (del), GFFDocumentEntry.java (del), GFFEntryInformation.html (del), GFFEntryInformation.java (del), GFFMisc.html (del), GFFMisc.java (del), GFFStreamFeature.html (del), GFFStreamFeature.java (del), GenbankDocumentEntry.html (del), GenbankDocumentEntry.java (del), GenbankMisc.html (del), GenbankMisc.java (del), GenbankStreamFeature.html (del), GenbankStreamFeature.java (del), GenbankStreamSequence.html (del), GenbankStreamSequence.java (del), InvalidKeyException.html (del), InvalidKeyException.java (del), InvalidQualifierException.html (del), InvalidQualifierException.java (del), InvalidRelationException.html (del), InvalidRelationException.java (del), Key.html (del), Key.java (del), KeyVector.html (del), KeyVector.java (del), LineGroup.html (del), LineGroup.java (del), LineGroupVector.html (del), LineGroupVector.java (del), LinePushBackReader.html (del), LinePushBackReader.java (del), Location.html (del), Location.java (del), LocationLexer.TokenEnumeration.html (del), LocationLexer.html (del), LocationLexer.java (del), LocationParseException.html (del), LocationParseException.java (del), LocationParseNode.html (del), LocationParseNode.java (del), LocationParseNodeVector.html (del), LocationParseNodeVector.java (del), LowerInteger.html (del), LowerInteger.java (del), MSPcrunchDocumentEntry.html (del), MSPcrunchDocumentEntry.java (del), MSPcrunchEntryInformation.html (del), MSPcrunchEntryInformation.java (del), MSPcrunchStreamFeature.html (del), MSPcrunchStreamFeature.java (del), MiscLineGroup.html (del), MiscLineGroup.java (del), NucFeatureHasher.html (del), OutOfDateException.html (del), OutOfDateException.java (del), PublicDBDocumentEntry.html (del), PublicDBDocumentEntry.java (del), PublicDBStreamFeature.html (del), PublicDBStreamFeature.java (del), PushBackException.html (del), PushBackException.java (del), Qualifier.html (del), Qualifier.java (del), QualifierInfo.html (del), QualifierInfo.java (del), QualifierInfoException.html (del), QualifierInfoException.java (del), QualifierInfoVector.html (del), QualifierInfoVector.java (del), QualifierParseException.html (del), QualifierParseException.java (del), QualifierVector.html (del), QualifierVector.java (del), RWCorbaEntry.html (del), RWCorbaEntry.java (del), RWCorbaFeature.html (del), RWCorbaFeature.java (del), Range.html (del), Range.java (del), RangeVector.html (del), RangeVector.java (del), RawStreamSequence.html (del), RawStreamSequence.java (del), ReadFormatException.html (del), ReadFormatException.java (del), ReadOnlyEntry.html (del), ReadOnlyEntry.java (del), Sequence.html (del), Sequence.java (del), SimpleDocumentEntry.html (del), SimpleDocumentEntry.java (del), SimpleDocumentFeature.html (del), SimpleDocumentFeature.java (del), SimpleEntryInformation.html (del), SimpleEntryInformation.java (del), StreamFeature.html (del), StreamFeature.java (del), StreamFeatureTable.html (del), StreamFeatureTable.java (del), StreamQualifier.html (del), StreamQualifier.java (del), StreamSequence.html (del), StreamSequence.java (del), StreamSequenceFactory.html (del), StreamSequenceFactory.java (del), UpperInteger.html (del), UpperInteger.java (del), embl.example (del)
• Agmial2/artemis_client/src: build.xml (del), cam_manager.properties (del)
• Agmial2/artemis_client/src/agmial/artemis: AgmialAccessDialog.java (del), AgmialAuthenticateDialog.java (del), AgmialAuthenticator.java (del), AgmialDocument.java (del), AgmialInterface.java (del), AgmialInterfaceFactory.java (del), AgmialInterfaceImpl.java (del), AgmialProfileDocument.java (del), README (del)
• Agmial2/artemis_client/src_wsdl: ContigStoreAdmin.wsdl (del), ContigStoreQuery.wsdl (del), ProfileStoreQuery.wsdl (del)

vloux 2006-03-07 15:08 #4

remove artemis_client

0 lines of code changed in:

• Agmial2/artemis_client: README (del), artemis.bat (del), artemis.sh (del), build.xml (del), build.xml.in (del), client_ContigStoreAdmin_Config.xml (del), client_ContigStoreQuery_Config.xml (del), client_ProfileStoreQuery_Config.xml (del), specific_options (del)

vloux 2006-03-06 10:31 #3

[#203] S?curit? : Single SignOn +Form based Login
PAM
[#213] Filtrer quote et retours chariots dans les formulaires
PAM

211 lines of code changed in:

• Agmial2/pa_manager: build.xml (+3 -1)
• Agmial2/pa_manager/src/pam/admin: ProteinSourceAdminImpl.java (+17 -2), UpdateAnnotation.java (+6 -1)
• Agmial2/pa_manager/src/pam/protdb: ProteinDB.java (+15)
• Agmial2/pa_manager/src/pam/reader: ProteinPanel.java (+88 -56)
• Agmial2/pa_manager/web: error.html (new), web.xml.in (+10 -3)
• Agmial2/pa_manager/web/js: pam.js (new 72)
• Agmial2/pa_manager/web/jsp: login.jsp (new)

vloux 2006-03-01 11:56 #2

[#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

57 lines of code changed in:

• Agmial2/ca_manager: build.xml (+2 -1)
• Agmial2/ca_manager/web: error.html (new), web.xml.in (+10 -12)
• Agmial2/ca_manager/web/jsp: login.jsp (new 45)

vloux 2006-03-01 11:51 #1

[#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 agmial_directory

221 lines of code changed in:

• Agmial2/agmial_directory: build.xml (+6 -5)
• Agmial2/agmial_directory/src/agmial/directory: InfoPoint.java (+138 -117)
• Agmial2/agmial_directory/web: agmial_directory.css (+7 -1), error.html (new), web.xml.in (+25 -2)
• Agmial2/agmial_directory/web/jsp: login.jsp (new 45)

February 2006 »