Timeline
07/06/09:
- 21:05 Ticket #513 (Elbow lines sometimes do not connect properly to anchors) closed by
- fixed: Perpendicular makes sense, but I had problems creating a perpendicular …
- 15:19 Ticket #939 (Pathvisio Wiki links to version 1.1 with plugins) closed by
- wontfix
- 15:13 Ticket #922 (Saving fails after automatic updating of Ensembl refs) closed by
- fixed
- 15:12 Ticket #920 (Can't update pathway to new Ensembl references) closed by
- fixed
- 15:04 Ticket #903 (Ineternet explorer: Curation tags: pencil and red cross not visible) closed by
- wontfix: Fix this by upgrading IE to the newest version.
- 14:58 Ticket #947 (smart guides) created by
- It would be nice to have the smart guides feature like in Adobe …
- 14:57 Ticket #898 (Advanced edit options) closed by
- fixed
- 14:49 Ticket #892 (Confusing error message on failed pathway save) closed by
- fixed
- 14:49 Ticket #889 (PathVisio file downloader from PV site doesn't work) closed by
- fixed
- 14:44 Ticket #882 (Pathway difference viewer) closed by
- fixed
- 14:43 Ticket #946 (Google Gadget for WikiPathways) created by
- It would be nice to create a Google Gadget for WikiPathways?. Users could …
- 14:37 Ticket #875 (WP search doesn't work for new pathways, is indexing broken?) closed by
- fixed
- 14:35 Ticket #871 (Wikipathways: formatting font size of labels not possible) closed by
- wontfix: Couldn't reproduce this.
- 14:32 Ticket #865 (Bibliography section counts number of refs incorrectly) closed by
- fixed
- 14:29 Ticket #862 (About window: Change "Application name undefined" to a real name ...) closed by
- fixed
- 14:21 Ticket #849 (Wikipathways save slow for non PathVisio edits) closed by
- wontfix: Can't reproduce this anymore. Probably the save time varies (e.g. due to …
- 14:19 Ticket #842 (Feature: Exclude pathways from batch download list based on species or tag) closed by
- fixed
- 14:12 Ticket #822 (Feature: Keep current file name as default for export options) closed by
- wontfix
- 13:57 Ticket #801 (Show comments, literature and complex in the DataNode section) closed by
- duplicate
- 13:52 Ticket #792 (The Pathway Directory selector in Statistics doesn't work with ...) closed by
- wontfix: This is a bug in the Java file dialog.
- 13:48 Ticket #782 (You should be able to cancel saving to the wiki) closed by
- wontfix
- 13:44 Ticket #777 (Feature: Upcoming list) closed by
- wontfix
- 13:44 Ticket #770 (Error on searching for IFNG) closed by
- wontfix
- 13:42 Ticket #765 (linkout to EC numbers) closed by
- duplicate
- 13:41 Ticket #762 (applet searches for blanks when 'identifier' is left blank) closed by
- fixed
- 13:38 Ticket #751 (Distinguish between save errors and warnings in applet) closed by
- wontfix
- 13:32 Ticket #738 (visual style in GPML Reader/Writer in not working) closed by
- fixed
- 13:31 Ticket #737 (Command-R does not add anchor) closed by
- wontfix
- 13:31 Ticket #733 (DataNode search: Display number of hits in the Search results window, ...) closed by
- wontfix
- 13:28 Ticket #657 (archive download) closed by
- duplicate: Duplicate of #730
- 13:27 Ticket #726 (Pathway export doesn't work on Mac) closed by
- wontfix
- 13:21 Ticket #690 (saving pathways takes too long) closed by
- fixed
- 13:18 Ticket #674 (Problem with right click select of objects) closed by
- fixed
- 13:15 Ticket #666 (captcha doesn't work when using wikipathways.com) closed by
- fixed
- 13:14 Ticket #659 (database replication / mirroring) closed by
- duplicate: Duplicate of RFC in #466
- 12:54 Ticket #650 (Editor applet doesn't show up until I resize) closed by
- fixed
- 12:53 Ticket #640 (menu responds very slowly) closed by
- wontfix
- 12:53 Ticket #639 (Slow files browsing in PathVisio) closed by
- wontfix
- 12:44 Ticket #627 (Feature: display viewcount on each pathway page) closed by
- invalid
- 12:35 Ticket #586 (Create new pathway from imported gpml results in weird message about ...) closed by
- wontfix
- 12:15 Ticket #528 (Moving an anchor on an elbow line type is not trivial) closed by
- wontfix
- 12:13 Ticket #517 (Misplacement of arrowheads of curved arrows) closed by
- fixed
- 12:10 Ticket #516 (gene count cache isn't updated on pathway deletion) closed by
- fixed
- 12:02 Ticket #512 (Flickering Right-click menu) closed by
- fixed
- 11:57 Ticket #502 (Some pathways have wrong Entrez Gene annotation) closed by
- duplicate: Duplicate of #390
- 11:57 Ticket #501 (Default connector waypoints should find optimal position) closed by
- wontfix
- 11:48 Ticket #500 (Large pathways are not displayed correctly as thumbnails for "Featured ...) closed by
- fixed
- 11:37 Ticket #479 (pv RFC 007 tracker bug) closed by
- fixed
- 11:36 Ticket #945 (Plugin downloader for pathvisio) created by
- It would be nice to have a dialog to install plugins from PathVisio. This …
- 11:35 Ticket #944 (Website to list pathvisio plugins) created by
- It would be nice to have a website where all pathvisio plugins are listed. …
- 11:32 Ticket #478 (pv RFC 006 tracker bug) closed by
- fixed
- 11:31 Ticket #477 (pv RFC 005 tracker bug) closed by
- fixed
- 11:26 Ticket #467 (wp RFC 004 tracker bug - Factoid Capture) closed by
- fixed
- 11:23 Ticket #461 (pdf conversion: name label width too small) closed by
- duplicate: Duplicate of #242
- 11:20 Ticket #444 (Links to user pages in edit comments link to edit instead of view) closed by
- fixed
- 11:16 Ticket #415 (Users should be blocked from using default search tool) closed by
- wontfix
- 11:15 Ticket #411 (Oval shape options: Oval, OrganA and mim-interaction all look the same.) closed by
- wontfix
- 11:12 Ticket #409 (Tooltips in editor toolbar don't appear until after a button (any) is ...) closed by
- wontfix
- 11:09 Ticket #374 (New pathways list should have a longer retention time) closed by
- wontfix
- 11:08 Ticket #373 (Notification email should give link to diff viewer in case of a pathway ...) closed by
- fixed
- 11:07 Ticket #364 (guidelines page needed) closed by
- fixed
- 11:07 Ticket #943 (Remove backpage column in synonym database) created by
- Remove the backpage column in the synonym database. Instead, generate it …
- 11:01 Ticket #343 (strange characters when viewing older versions of pathway page) closed by
- fixed: Didn't see this anymore recently. Please re-open when you observe this …
- 10:59 Ticket #323 (Use GO Ontology widget for categories) closed by
- wontfix
- 10:58 Ticket #320 (look into ontology service) closed by
- fixed
- 10:51 Ticket #236 (Order of mappinfo fields should be same as in property panel) closed by
- wontfix
- 10:49 Ticket #229 (Literature tab of DataNode properties: Text in References list is cutoff) closed by
- fixed
- 09:51 Ticket #942 (PubChem SID vs CID) created by
- Create separate identifier systems for PubChem? SID and PubChem? CID. …
07/05/09:
- 22:47 Ticket #941 (Visualization tweaks) created by
- Chris' suggestions after PPS2 meeting: # Show genes metabolites without …
- 12:15 Changeset [2673] by
- Made "-o" for opening pathways not required. Added tooltips to recent …
- 12:15 Changeset [2672] by
- Updated bridgedb.jar
- 08:04 Changeset [2671] by
- Added "dist" target to build.xml
07/03/09:
- 15:20 Ticket #179 (Clickable installer for mac) closed by
- fixed
- 15:04 Changeset [2670] by
- Jarbundler library and ant task
- 14:23 Changeset [2669] by
- Added hires version of logo
- 13:07 ScreenShots created by
- 13:07 WikiStart edited by
- (diff)
- 13:06 WikiStart edited by
- (diff)
- 13:06 WikiStart edited by
- (diff)
- 11:52 WikiStart edited by
- (diff)
- 11:00 PppPluginHelp created by
- 11:00 PluginDocumentation edited by
- (diff)
- 10:05 PluginWebstart created by
- 10:02 PluginDevelopment edited by
- (diff)
- 10:02 PluginDevelopment edited by
- (diff)
- 10:00 HelloWorldPlugin created by
- 10:00 PluginDevelopment edited by
- (diff)
- 10:00 PluginDevelopment edited by
- (diff)
- 01:37 Changeset [2668] by
- This version fixes the bug of non-existence in Java 5 of two methods …
07/02/09:
- 16:39 Changeset [2667] by
- - fixed build.xml for gpml plugins to include bridgedb resources - fixed …
- 14:31 Changeset [2666] by
- License headers. Removed some old files in build system.
- 13:28 Ticket #934 (Regex to add categories should be hidden or replaced) closed by
- fixed: Hi Chetan, Your code looks good, this is a much better method than the …
- 13:22 Ticket #935 ("upload" category in Browse) closed by
- fixed
- 10:27 PluginDocumentation edited by
- (diff)
- 10:14 PluginDocumentation created by
- 10:14 WikiStart edited by
- (diff)
07/01/09:
- 20:53 DevMeetings edited by
- (diff)
- 20:52 DevMeetings edited by
- (diff)
- 20:41 DevMeetings edited by
- (diff)
- 19:52 DevMeetings edited by
- (diff)
- 19:44 DevMeetings edited by
- (diff)
06/30/09:
- 19:40 Changeset [2665] by
- Added changes from AP, MI and TK
- 19:27 Changeset [2664] by
- 03:12 Changeset [2663] by
- This version re-implements the overlap calculations which includes …
- 01:34 Changeset [2662] by
- 01:31 Changeset [2661] by
- Accessory file for HomologyConvert?.pl
06/29/09:
- 12:27 WikiMigration edited by
- (diff)
- 12:26 WikiMigration edited by
- (diff)
- 12:25 GpmlExperimentNotes edited by
- (diff)
- 12:22 BioPaxPlusProposal edited by
- (diff)
- 12:18 BioPaxPlusProposal created by
- 12:17 GpmlAndBioPax edited by
- (diff)
- 12:17 GpmlAndBioPax edited by
- (diff)
- 12:15 GpmlExperimentNotes edited by
- (diff)
- 12:13 GpmlExperimentNotes edited by
- (diff)
- 12:11 GpmlExperimentNotes edited by
- (diff)
- 12:09 GpmlExperimentNotes created by
- 12:08 GpmlAndBioPax created by
- 12:06 WikiStart edited by
- (diff)
- 12:06 WikiStart edited by
- (diff)
- 12:06 WikiStart edited by
- (diff)
- 11:28 RunPathvisioOffline edited by
- (diff)
- 11:19 GpmlDiffPatch edited by
- (diff)
- 11:18 GpmlDiffPatch edited by
- (diff)
- 11:18 GpmlDiffPatch edited by
- (diff)
- 11:18 GpmlDiffPatch edited by
- (diff)
- 11:16 GpmlDiffPatch created by
- 11:04 WikiStart edited by
- (diff)
- 11:03 RunPathvisioOffline edited by
- (diff)
- 11:03 RunPathvisioOffline created by
- 10:59 WikiStart edited by
- (diff)
- 10:55 WikiStart edited by
- (diff)
06/26/09:
06/23/09:
- 20:05 Ticket #940 (All anchors disappeard) created by
- Jildau Bouwman reported that she lost all anchors while working on a large …
- 18:55 Changeset [2660] by
- Replace the modified gpml.jar (I inserted some debugging code lines) to …
- 18:41 Changeset [2659] by
- This version modifies the code to improve the UI according to Thomas’s …
- 13:11 Changeset [2658] by
- Fixed some style problems
- 12:33 Changeset [2657] by
- Fixed & Improved o.p.gpmldiff JUnit test
- 11:31 Changeset [2656] by
- Various bugfixes in gpmlpatch
- 11:31 Changeset [2655] by
- BridgeDb refactored
06/20/09:
- 16:28 Ticket #939 (Pathvisio Wiki links to version 1.1 with plugins) created by
- The links on the PathVisio Wiki are a bit difficult to operate with …
- 16:22 Ticket #938 (visualization dialog setup is not logic) created by
- Imho the visualization dialog should be reorganized. Basic works …
- 16:13 Ticket #937 (Basic visualization is 'lost' while working) created by
- If I select basic visualization, click new and enter a rule, this …
06/19/09:
- 20:08 Milestone milestone_15 completed
- * Goals t.b.d. * Jun 15 feature freeze * Jun 19 …
- 19:42 Changeset [2654] by
- tag for M15.0
- 19:42 Changeset [2653] by
- branch for M15
- 16:06 Ticket #878 (Incorrectly parsed number without warning in GexTxtImporter) closed by
- fixed: added toUpperCase() on input string.
- 15:58 Changeset [2652] by
- fixed #878
- 14:38 Ticket #936 (Backup script doesn't export all tables) closed by
- fixed: show view and create view permissions were missing.
- 14:38 WikiPathwaysLocalSetup edited by
- (diff)
- 14:33 Ticket #936 (Backup script doesn't export all tables) created by
- Tables user_page_hits, user_page_views, watchlist and webservice_log are …
- 02:19 Ticket #935 ("upload" category in Browse) created by
- On the test site, there is a category labeled "upload" in Browse. It is …
06/18/09:
- 12:11 Changeset [2651] by
- moved Relation class to org.pathvisio.util
06/17/09:
- 10:41 Ticket #934 (Regex to add categories should be hidden or replaced) created by
- The function addToCategory in Categoryhandler.php : 27, uses regex to add …
06/16/09:
- 13:12 Ticket #929 (OutOfMemory error when connecting to all pgdbs on WP server) closed by
- fixed: Was a bug in Java 5. When running with Java 6 it works fine. Updated the …
- 01:09 WikiMigration edited by
- (diff)
- 00:56 CytoscapeWorkflow created by
06/15/09:
06/14/09:
- 15:15 Ticket #933 (Read species info in Pathway.php and pathwayInfo.php from bridgedb text ...) created by
- Modify the species list (Pathway.php) and linkout list (pathwayInfo.php) …
06/13/09:
- 01:08 Ticket #919 (Flatfile export doesn't work with new Ensembl system) closed by
- fixed
- 01:08 Ticket #918 (Site stats won't count new gene systems) closed by
- fixed
- 01:07 Ticket #909 (Can't delete pathway) closed by
- fixed
- 00:09 Changeset [2650] by
- This version of code fixed the org.bridgedb.Organism error in the …
06/12/09:
- 13:05 WikiPathwaysLocalSetup edited by
- (diff)
- 11:25 WikiPathwaysLocalSetup edited by
- (diff)
- 05:32 Changeset [2649] by
- This version fixed the compile errors due to the nonexistence of the …
06/11/09:
- 14:09 Changeset [2648] by
- WikiPathwaysSearch?: fixed dependencies
- 13:55 Changeset [2647] by
- adapted wikipathways-search to new bridgedb libraries
- 13:53 Changeset [2646] by
- adapted wikipathways-search to new bridgedb libraries
- 11:33 WikiMigration edited by
- (diff)
- 11:29 WikiMigration edited by
- (diff)
- 11:11 Ticket #932 (Check that gpml names for datasource are no longer than 20 chars) created by
- Gpml requires the datasource to be less than 20 chars long. Make sure all …
- 11:11 Changeset [2645] by
- fixed incorrect call of VPathway.dispose() in ColorExporter? (breaking …
- 10:24 Changeset [2644] by
- atlas mapper: moved ensembl code logic to server side
- 10:18 Changeset [2643] by
- adapted AtlasMapper? to species specific Ensembl codes
- 10:13 Ticket #931 (Shortcut method for getting the right ensembl datasource) created by
- If you want to map to an Ensembl id the species may vary, you now first …
- 09:58 Changeset [2642] by
- added bridgedb libs to AtlasMapper?
- 09:52 Changeset [2641] by
- fix tomcat comflict in AtlasMapper? build.xml
- 09:13 Changeset [2640] by
- added script to calculate atlas mapper stats removed fixed build path in …
06/10/09:
- 22:55 Ticket #930 (Opening extended references bug) created by
- On the pathway: …
- 20:45 DevMeetings edited by
- (diff)
- 20:11 Ticket #928 (Issues with new ensembl codes and web service) closed by
- fixed: Ok, updated the pathways and database. Now it gives: […] Which is …
- 20:08 DevMeetings edited by
- (diff)
- 19:52 DevMeetings edited by
- (diff)
- 19:30 Changeset [2639] by
- Changed ArrowShape? constants to enum, updated ArrowShape? doc.
- 15:32 WikiPathwaysLocalSetup edited by
- (diff)
- 15:22 WikiPathwaysLocalSetup edited by
- (diff)
- 15:17 DevMeetings edited by
- (diff)
- 15:17 DevMeetings edited by
- (diff)
- 14:25 DevMeetings edited by
- (diff)
- 14:22 DevMeetings edited by
- (diff)
- 13:53 DevMeetings edited by
- (diff)
- 10:09 Ticket #929 (OutOfMemory error when connecting to all pgdbs on WP server) created by
- When I run the indexer on the WP server with all gdb's I get this error: …
06/09/09:
- 15:49 Changeset [2638] by
- added bridgedb jars to lucene indexer
- 15:47 Changeset [2637] by
- added bridgedb-bio.jar to lucene indexer
- 15:41 Ticket #927 (PathwayElement.getDataSource returns datasource without system code) closed by
- fixed: Added call to BioDataSource?.init() to GpmlFormat?, so the system codes are …
- 15:36 Changeset [2636] by
- added BioDataSource?.init() call to GpmlFormat? (fixes #927)
- 14:33 Changeset [2635] by
- added bridgedb-bio to wpclient
- 14:32 Changeset [2634] by
- updated bridgedb-bio.jar
- 14:22 Changeset [2633] by
- updated bridgedb.jar
- 14:22 Changeset [2632] by
- added AtlasCache? method to allow for calculating statistics
- 14:22 Changeset [2631] by
- fixed compiler errors in AtlasMapper? due to changes in bridgedb API
- 14:22 Changeset [2630] by
- changed name of wikipathways-search html file (so you don't have to type …
- 14:22 Changeset [2629] by
- changed name of AtlasMapper? html file (so you don't have to type it …
- 13:46 Changeset [2628] by
- Updated bridgedb-bio
- 04:44 Changeset [2627] by
- This version fixed the problems that Thomas has found in the previous …
06/08/09:
- 17:16 Ticket #891 (Really large pathway could not be imported) closed by
- fixed: Php's preg_match function fails without notice when the string is too …
- 15:24 Ticket #910 (Download MAPP feature broken) closed by
- fixed
- 12:22 Ticket #928 (Issues with new ensembl codes and web service) created by
- The findPathwaysByXref method doesn't work correctly with Ensembl anymore. …
- 10:27 Ticket #927 (PathwayElement.getDataSource returns datasource without system code) created by
- The DataSource? object returned by PathwayElement?.getDataSource and …
- 10:23 Ticket #924 (getPathwayHistory doesn't return History rows using Perl SOAP library) closed by
- fixed: See …
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