Timeline
03/02/10:
- 18:49 Ticket #1107 (Avoid NPE in Logger.setDest()) closed by
- fixed: Thanks, committed.
- 18:49 Ticket #1105 (Avoid unnecessary exception when looking for plugins) closed by
- fixed
- 18:46 Changeset [3138] by
- Prevent flood of 'unkown shape None' log messages
- 18:46 Changeset [3137] by
- Avoid NPE in Logger.setDest(). Patch by Mark (fixes #1107)
- 18:46 Changeset [3136] by
- Avoid unnecessary exception when looking for plugins, patch by Mark …
- 15:16 Ticket #1132 (Moving expression set position causes loss of connection to advanced color ...) created by
- I use a mixture of basic and advanced color sets for different expressions …
- 14:41 Changeset [3135] by
- Adjust unit test to new coordinate system
- 14:39 Changeset [3134] by
- Allow Patch to select appropriate GPML reader. Fixes unit test
- 14:19 Ticket #1124 (Visulisations options windows wipes xml-file out when closing by close ...) closed by
- fixed: Ok, I think I fixed this completely: * A colorset with null assignment is …
- 14:16 Changeset [3133] by
- Skip samples with colorset==null, Fixes #1124
- 14:16 Changeset [3132] by
- Make visualization writing more robust, by reporting an error when it …
- 12:34 Ticket #1131 (GPML plugin not working) closed by
- invalid: Ai, should've known that; the ever-conflicting-plugins issue; removing the …
- 12:02 Ticket #1129 (Error when saving pathway with lit ref on test site) closed by
- fixed
- 11:24 Changeset [3131] by
- Convert embedded biopax from level 2 to level 3. Fixes #1129
- 10:56 Ticket #1131 (GPML plugin not working) created by
- Export a wikipathway as gpml Try to upload it using the most recent …
- 10:50 Ticket #1130 (invalid svg on wikipathways) created by
- See this thread: …
03/01/10:
- 12:45 Ticket #1036 (Allow Line-Wrapping in DataNodes) closed by
- fixed
- 12:45 Changeset [3130] by
- Add "None" to list of available shape types. Double-click dlg for shapes, …
- 11:39 Ticket #1056 (Data is not loaded immediately after import) closed by
- fixed: I can't reproduce this problem.
- 11:33 Ticket #1033 (need Datanode with round corners, square corners and no outline) closed by
- fixed
- 11:32 Ticket #906 (Feature: Add ability to change line thickness) closed by
- fixed
- 11:32 Ticket #1037 (Flag to restrict resizing of certain nodes) closed by
- fixed
- 09:56 Ticket #1128 (add svg to download list on wikipathways) closed by
- fixed
02/28/10:
- 11:43 Ticket #1129 (Error when saving pathway with lit ref on test site) created by
- See this discussion: …
02/27/10:
- 20:18 Changeset [3129] by
- Moved script for creating HMDB databases to bridgedb repository
- 20:18 Changeset [3128] by
- Updated to new org.bridgedb.rdb.construct pacakge
02/26/10:
02/25/10:
02/24/10:
- 15:42 Ticket #1128 (add svg to download list on wikipathways) created by
- In preparation for the transition to the interactive pathway viewer, svg …
02/23/10:
- 16:07 Ticket #1127 (enable BioPAX export on WikiPathways) created by
- Enable BioPAX level 3 export on WikiPathways?. Only on individual pathway …
- 16:03 Changeset [3127] by
- Updated bridgedb, bridgedb jars are renamed
02/19/10:
- 10:39 Changeset [3126] by
- fillcolor bug: 'black' was considered equal to 'transparent'
- 01:03 Ticket #1126 (Duplications in Bibliography when two datanodes have the same lit ref) created by
- See example: http://www.wikipathways.org/index.php/Pathway:WP670 In the …
02/18/10:
- 21:07 Changeset [3125] by
- compilation fix in gex plugin
- 20:21 Changeset [3124] by
- Updated bridgedb
02/17/10:
- 20:04 DevMeetings edited by
- (diff)
- 20:01 DevMeetings edited by
- (diff)
- 19:54 DevMeetings edited by
- (diff)
02/16/10:
- 21:03 Changeset [3123] by
- Fix NPE in ColorByExpressionPanel?
- 20:32 DevMeetings edited by
- (diff)
- 15:26 Ticket #724 (Create a default visualization after data import) closed by
- fixed
- 15:25 Changeset [3122] by
- Make it easy to look up sample by name
- 15:24 Changeset [3121] by
- Visualization auto-generation after import
- 15:24 Changeset [3120] by
- Set active visualization as soon as loaded from XML
- 15:24 Changeset [3119] by
- removed VisualizationMethod?.isActive, preparation for default …
- 15:24 Changeset [3118] by
- Adjust wp-client to change in PublicationXref?
- 11:34 DevMeetings edited by
- (diff)
- 10:50 WikiPathwaysLocalSetup edited by
- updated jar task (diff)
02/15/10:
- 21:13 Changeset [3117] by
- Remove deprecated V..nMethodRegistry.getCurrent
- 21:13 Changeset [3116] by
- Remove unnecessary registeredName, just use getClass().toString()
- 21:13 Changeset [3115] by
- Fixed error in coordinate conversion of legend and infobox
- 21:13 Changeset [3114] by
- Count # of rows imported / mapped successfully
02/14/10:
02/13/10:
- 08:51 Changeset [3113] by
- handy version of the inferator for copying over descriptions and modifying …
- 07:10 Changeset [3112] by
- fixed scripting mode logic and encoding
- 03:44 Changeset [3111] by
- added script mode
- 03:17 Changeset [3110] by
- added internal testing flag to direct action to TEST or LIVE site
- 00:54 Changeset [3109] by
- Version of the homology conversion script that converts between two gpmls, …
02/12/10:
- 22:00 ProjectIdeas edited by
- Added two additional projects (validation framework, javascript viewer) (diff)
- 11:01 Ticket #1125 (regression: wrong anchor position on curved lines) created by
- On curved lines, the anchor position is too far away from the line (see …
02/11/10:
- 11:17 Changeset [3108] by
- added bot to check for pathways without literature references (for …
02/10/10:
- 15:28 Ticket #1124 (Visulisations options windows wipes xml-file out when closing by close ...) created by
- When something in the "visulisations options window" goes wrong or is not …
- 08:27 Ticket #1122 (NPE in GraphicsShape) closed by
- fixed: Makes sense, thanks. Committed.
- 08:26 Changeset [3107] by
- NPE fix, #1122, patch by Mark Woon
- 00:37 Ticket #1123 (Feedback on new PV features: line thickness, alignment, shapes) created by
- Some initial feedback on the latest features: - DataNode? label alignment: …
- 00:01 Ticket #1122 (NPE in GraphicsShape) created by
- Getting an NPE in GraphicsShape? when adding a label to the pathway. …
02/09/10:
- 20:52 Ticket #1118 (Pathway viewer: Changes to expand/collapse icon on Backpages) closed by
- fixed: Great, I'll check it in then.
- 18:50 Changeset [3106] by
- eclipse project file should not be checked in
- 18:50 Changeset [3105] by
- Adjust kegg converter to change in OutlineType?
- 18:50 Changeset [3104] by
- isResizable flag added by Margot
- 16:59 Ticket #1121 (GPML.xsd does not define a default line thickness) created by
- This is a reminder for the next GPML version. Default line thickness …
- 16:16 PathVisioFaq edited by
- (diff)
- 16:14 PathVisioDownload edited by
- (diff)
- 16:13 PathVisioDownload edited by
- (diff)
- 16:13 PathVisioDownload edited by
- (diff)
- 09:59 Changeset [3103] by
- Remove obsolete writing code for old GPML
- 09:59 Changeset [3102] by
- Drawing with line thickness and (v)alignment
- 00:07 Ticket #1120 (Problems with the Arabidopsis db) created by
- Searching for TAIR IDs results in duplicates. For example, AT2G40080 …
02/08/10:
- 21:27 Ticket #1119 (Batch download: A.gambiae listed under Featured and Analysis downloads, ...) created by
- Anopheles gambiae appears on the lists of batch download by Featured …
- 18:19 Changeset [3101] by
- Added href staticprop. Read / write href and LineThickness?
02/06/10:
- 11:55 Ticket #1026 (Migrate to simple pixel coordinates) closed by
- fixed: Committed, still need to test import / export of MAPP format.
- 11:40 Changeset [3100] by
- Switch to simple pixel coordinates for everything. Coordinates in .MAPP …
- 11:40 Changeset [3099] by
- Read / write and edit (V)align
02/05/10:
- 23:15 Ticket #1118 (Pathway viewer: Changes to expand/collapse icon on Backpages) created by
- The expand button in each of the linkout sections in the Backpages works …
- 18:23 Ticket #326 (It should be possible to set the label background color) closed by
- fixed
- 18:21 Ticket #1034 (For Datanodes - allow users to adjust font.) closed by
- fixed
- 18:20 Ticket #1022 (case error in bp:publicationXref) closed by
- fixed
- 18:20 Changeset [3098] by
- Add 'Pathway' as a new DataNodeType?. Fixes #948
- 18:20 Changeset [3097] by
- Fixed setTextLabel(null) problem
- 18:20 Changeset [3096] by
- Better handling of default colors and line styles
- 18:20 Changeset [3095] by
- Make writing GPML2010a the default
- 18:19 Changeset [3094] by
- Write GPML2010a
- 18:19 Changeset [3093] by
- Fix casing for PublicationXref? (#1022)
- 18:19 Changeset [3092] by
- Share stroke and shape (=outline) drawing routines
- 18:19 Changeset [3091] by
- Share TextLabel? drawing between Shape, DataNode? and Label
- 18:19 Changeset [3090] by
- Work on new pathwayElement properties: outline, valign, align, and …
- 17:39 Ticket #948 (DataNode types in GPML) closed by
- fixed
- 14:41 Changeset [3089] by
- updated cytoscape plugin version number
- 13:49 AlternativeInstallation edited by
- (diff)
- 13:48 AlternativeInstallation edited by
- (diff)
- 13:48 AlternativeInstallation edited by
- (diff)
- 13:48 AlternativeInstallation edited by
- (diff)
- 13:43 Ticket #1117 (nullpointer exception in PropertyDisplayManager init) closed by
- fixed
- 13:39 Changeset [3088] by
- fixed #1117
- 13:39 Changeset [3087] by
- fixed #1051
- 13:35 Ticket #1117 (nullpointer exception in PropertyDisplayManager init) created by
- I noticed this while testing the cytoscape plugin (which also uses the …
- 13:29 Changeset [3086] by
- Include version number in windows installer
- 13:09 Milestone milestone_21 completed
- new GPML.xsd version Reads new schema version, but doesn't write by …
- 13:08 Ticket #1116 (Suitable icons & other improvements to windows install script) created by
- The InnoSetup? script, which generates a windows installer, works. But a …
- 13:03 Changeset [3085] by
- Updated PathVisio innoSetup script
- 12:38 Ticket #1113 (Pathway viewer: Backpage doesn't display properly the second time its ...) closed by
- fixed
- 11:44 Ticket #711 (REMINDER: Compact curation tag display) closed by
- fixed
- 11:25 ReleaseNotes edited by
- (diff)
- 11:21 WikiStart edited by
- (diff)
- 11:14 PathVisioDownload edited by
- (diff)
- 11:14 PathVisioDownload edited by
- (diff)
- 11:09 Changeset [3084] by
- Milestone 21 release tag
- 11:08 Changeset [3083] by
- Milestone 21 release branch
- 11:01 Changeset [3082] by
- Updated version number before release
02/04/10:
- 21:34 Changeset [3081] by
- two GPML.xsd tweaks: Remove unused PathwayRef?, use Xref with …
- 16:04 Changeset [3080] by
- Removed left-over trace statements
- 14:54 Changeset [3079] by
- Ignore case when reading BioPAX elements, part of fix for #1022
- 14:17 Ticket #1060 (PathVisio doesn't display currently selected database) closed by
- fixed: I forgot to check in a modification to BridgeDb that was part of the …
- 14:15 Changeset [3078] by
- Updated bridgedb
- 13:51 Ticket #1051 (backpage panel not refreshed after annotating datanode using search) closed by
- fixed
- 13:51 Changeset [3077] by
- fixed #1050
- 13:27 Ticket #1050 (Backpage shows error with gene without id, but with system code (when ...) closed by
- fixed
- 12:39 Ticket #1091 (Include revision number in History table) closed by
- fixed
- 11:47 Ticket #1115 (Fast lookup which edits were reverted or delete action) created by
- To make it possible to fix several bugs related to reverted or deleted …
- 10:54 Changeset [3076] by
- Make "White" the default background for datanodes
- 10:06 DevMeetings edited by
- (diff)
- 01:35 Ticket #1114 (Pathway Viewer: Right-click temporarily blanks the viewer window) created by
- This is a weird issue that seems inconsistent, but about half of all …
- 01:10 Ticket #1113 (Pathway viewer: Backpage doesn't display properly the second time its ...) created by
- In the new pathway viewer, the Backpages display just fine the first time …
- 00:27 WikiPathwaysTestProtocol edited by
- (diff)
- 00:25 Ticket #1112 (Error when reverting to deleted revision) created by
- Since I deleted a pathway and then reverted to a previous version, the …
- 00:23 Ticket #1111 (DiffViewer error when comparing deleted pathway) created by
- In the History table, it is possible to select a revision of the pathway …
- 00:07 Ticket #1110 (Feature: Make T-bar the same as mim-inhibition) created by
- Since there doesn't seem to be a difference in appearance and since it's a …
02/03/10:
- 22:29 Changeset [3075] by
- Script to switch between tags on WikiPathways?
- 20:59 DevMeetings edited by
- (diff)
- 20:47 DevMeetings edited by
- (diff)
- 20:00 Ticket #1025 (Default value for FontSize is tiny) closed by
- fixed: I'm leaving this at 15 and change the conversion factor instead, see #1026
- 19:59 Ticket #1015 (coordinates not in cm) closed by
- fixed
- 19:50 Ticket #932 (Check that gpml names for datasource are no longer than 20 chars) closed by
- fixed: The restriction on datasource length has been removed from GPML
- 19:49 Ticket #352 (Automatically generate backpage header) closed by
- fixed: The Backpage field has been removed from GPML.
- 15:44 Ticket #1060 (PathVisio doesn't display currently selected database) reopened by
- You're right, there is definitely something funky going on. I'll …
- 12:36 Changeset [3074] by
- copy all xml schemas to wikipathways dir
- 12:20 Changeset [3073] by
- fixed resources.jar for wikipathways applet (missing xsd)
- 11:24 Ticket #1102 (pathway viewer: optimize space usage) closed by
- fixed: Now uses whole page width and puts xref info in side panel instead of …
- 01:06 Ticket #1073 (Create a discussion forum that includes pathway talk pages) closed by
- fixed: RSS parser is now stable (switched to different extension see #1075) and …
- 01:05 Ticket #1075 (RSS Extension conflicts with webservice) closed by
- fixed: Couldn't salvage RSSReader, so I switch to another extension called RSS. …
02/02/10:
- 22:54 Changeset [3072] by
- fix #1096
- 22:54 Ticket #1096 (Open up PathwayTableModel) closed by
- fixed
- 22:53 Changeset [3071] by
- fix #1108
- 22:52 Ticket #1108 (Sort Property) closed by
- fixed
- 22:51 Changeset [3070] by
- fix #1097
- 22:50 Ticket #1097 (Bug in PathwayElementEvent) closed by
- fixed
- 22:20 DevMeetings edited by
- (diff)
- 22:19 DevMeetings edited by
- (diff)
- 13:25 Ticket #1109 (errors when datasources.txt cannot be downloaded) closed by
- fixed
- 13:00 Changeset [3069] by
- Updated GpmlFormat?2010a reading / writing to current version of GPML.xsd …
- 12:58 Ticket #1109 (errors when datasources.txt cannot be downloaded) created by
- When our svn server was down, Alex reported that wikipathways showed error …
02/01/10:
- 23:05 Ticket #1072 (Update Help Docs) closed by
- fixed
- 13:59 Ticket #1108 (Sort Property) created by
- PropertyDisplayManager? allows the sort order of a Property to be defined …
- 13:55 Ticket #1107 (Avoid NPE in Logger.setDest()) created by
- Logger.setDest() doesn't check for null. Attached patch fixes the …
- 13:06 Ticket #1078 (IllegalStateException in "find interactions for node" function in ...) closed by
- fixed: Ok, I still can't reproduce this error (tested on windows XP and linux), …
- 13:05 Changeset [3068] by
- fixed #1078
- 11:01 Ticket #1106 (Curation tag edit/delete buttons are not visible in IE6) created by
- In Internet Explorer 6, the edit/delete buttons in the top-right corner of …
- 10:38 Ticket #1099 (Curation tag lists don't display all tagged pathways) closed by
- fixed
01/31/10:
- 20:50 Changeset [3067] by
- Add ShapeType?, Background color and Line Style to DataNode?, Label and …
- 20:50 Changeset [3066] by
- Replaced xsd:annotation with normal xml comments, for consistency reasons
- 20:50 Changeset [3065] by
- Updated GPML.xsd added textLabel and font attributes to Shape and …
- 17:00 Changeset [3064] by
- Fix problems with deprecated Point.Head and Pathway.Copyright
- 17:00 Changeset [3063] by
- Added JUnit test
- 17:00 Changeset [3062] by
- Remove deprecated properties in PathwayElement?
- 17:00 Changeset [3061] by
- Remove deprecated attributes from GPML.xsd
- 16:59 Changeset [3060] by
- Test reading / writing different GPML versions
- 11:41 Ticket #1105 (Avoid unnecessary exception when looking for plugins) created by
- There are 2 things are causing the PluginManager? to throw and log …
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