{5} Assigned, Active Tickets by Owner (Full Description) (38 matches)

List tickets assigned, group by ticket owner. This report demonstrates the use of full-row display.

AlexanderPico (12 matches)

Ticket Summary Component Milestone Created
Description
#1093 Google search doesn't return pathway when searching for "one carbon" WikiPathways website Milestone 26 01/25/10

Reported by Chris: When searching for words from the title of one carbon metabolism, the actual one carbon metabolism pathway is not among the results:

 http://www.wikipathways.org/index.php/WikiPathways:GoogleSearch?cref=http://www.wikipathways.org/wp_cse_context.xml&cof=FORID:11&filter=0&q="one+carbon"&sa=Search&siteurl=www.wikipathways.org/index.php/WikiPathways&siteurl=www.wikipathways.org/index.php/WikiPathways

#1205 cannot edit micronutrient portal WikiPathways website 06/07/10

As reported by Jildau and confirmed by Jeroen (on a Mac)

Link:  http://www.wikipathways.org/index.php?title=Portal:Micronutrient/Other&action=edit Content van de download (index.php):

[Process]

Type=Edit text

Engine=MediaWiki?

Script= http://www.wikipathways.org/index.php

Server= http://www.wikipathways.org

Path= Special namespace=Special

[File] Extension=wiki URL= http://www.wikipathways.org/index.php?title=Portal:Micronutrient/Other&action=edit&internaledit=true

Lijkt op: verkeerd uitgestuurde headers...

#245 Allow thumbnail view of any pathway list Wikipathways applet 09/19/07

Starting with the browse pathways page, I'd like to make it so that you can view the list of pathways as text links or thumbnail image links. This option could then be extended to other pathway lists.

ADDITIONAL INFORMATION: The option could be in the form of a link in the upper right that says 'thumbnail view'. When clicked you switch to a thumbnail view of the same list and the link changes to 'list view'.

#1081 Cleanup LineType Pathvisio 01/14/10

With the new TypeHandlers? the LineType? class can be cleaned up. The attached patch addresses that.

#1095 "Show Advanced Properties" preference should take effect immediately Pathvisio 01/26/10

The "Show Advanced Properties" preference currently does not take effect immediately. You have to reselect the PathwayElement?(s) before you can see the advanced properties.

I am attaching a patch that has the PropertyDisplayManager? listen for the PreferenceEvent? and updating the PathwayTableModel? after it has set the visibility of the advanced properties properly.

Note that the table model cannot listen for the event directly because it'll cause a race condition - the table model update must happen AFTER the PropertyDisplayManage? has done its thing.

#1153 very long query gets truncated on wikipathways web service WikiPathways web service 03/29/10

A very long query gets truncated when using the findPathwaysBy* methods of the wikipathways web service.

Example: if you supply ~300 xrefs to the findPathwaysByXrefs method, you get an error stating that the number of ids doesn't match the number of codes. This is because the resulting url to the lucene indexer REST service is truncated: 

http://localhost/wikipathways/wpi/webservice/webservice.php/searchxrefs	id=NM_015657&id=NM_138933&id=NM_138932&id=NM_032023&id=NM_021723&id=NM_004194&id=NM_020482&id=NM_032021&id=NM_001109&id=NM_001119&id=NM_001117&id=NM_001116&id=NM_001115&id=NM_001114&id=NM_023037&id=NM_001112&id=NM_001111&id=NM_145892&id=NM_001110&id=NM_145893&id=NM_052957&id=NM_012066&id=NM_145891&id=XM_039822&id=NM_015665&id=NM_003786&id=NM_007188&id=NM_032548&id=NM_001099&id=NM_020107&id=NM_001097&id=NM_020108&id=NM_001098&id=NM_020109&id=NM_080284&id=NM_001095&id=NM_080283&id=NM_001096&id=NM_001094&id=NM_001092&id=NM_017492&id=NM_020110&id=NM_021641&id=NM_001091&id=NM_020112&id=NM_020111&id=NM_001124&id=NM_020114&id=NM_001123&id=NM_020113&id=NM_020115&id=NM_001122&id=NM_003500&id=NM_003501&id=NM_001611&id=NM_001612&id=NM_001613&id=NM_001614&id=NM_001610&id=NM_017484&id=NM_017483&id=NM_017486&id=NM_017485&id=NM_017488&id=NM_033068&id=NM_017487&id=NM_033069&id=NM_021612&id=NM_007292&id=NM_017482&id=NM_001609&id=NM_001608&id=NM_153202&id=NM_145186&id=NM_001605&id=NM_145187&id=NM_018723&id=NM_001607&id=NM_145188&id=NM_015423&id=NM_012089&id=NM_000392&id=NM_145189&id=NM_001606&id=NM_007168&id=NM_012091&id=NM_030955&id=NM_145190&id=NM_005721&id=NM_005722&id=NM_130786&id=NM_000789&id=NM_001102&id=NM_001101&id=NM_001104&id=NM_004769&id=NM_001103&id=NM_001106&id=NM_001105&id=NM_001108&id=NM_001107&id=NM_001617&id=NM_001100&id=NM_001616&id=NM_001615&id=NM_018849&id=NM_005689&id=NM_000033&id=NM_005688&id=NM_000669&id=XM_047780&id=NM_004299&id=NM_000673&id=NM_000672&id=NM_018702&id=NM_000675&id=NM_000674&id=NM_000676&id=NM_020141&id=NM_005164&id=NM_032583&id=NM_000671&id=NM_000670&id=NM_000022&id=NM_007245&id=NM_000020&id=NM_004908&id=NM_003742&id=NM_018850&id=NM_020249&id=NM_000664&id=XM_029810&id=NM_006111&id=NM_005157&id=NM_000663&id=NM_005158&id=NM_000927&id=NM_005159&id=NM_002390&id=NM_022371&id=NM_000667&id=NM_000666&id=NM_000665&id=NM_015339&id=NM_014064&id=NM_032270&id=NM_020325&id=NM_006687&id=NM_020324&id=NM_020323&id=NM_020322&id=NM_006686&id=NM_020321&id=NM_020675&id=NM_000014&id=XM_002161&id=NM_000016&id=NM_016824&id=NM_000017&id=NM_000018&id=NM_014190&id=NM_000019&id=NM_000350&id=NM_004036&id=NM_016818&id=NM_000352&id=NM_004035&id=NM_018446&id=NM_020334&id=NM_133638&id=NM_007264&id=XM_032877&id=NM_017436&id=NM_016188&id=XM_113428&id=NM_020469&id=NM_021722&id=NM_021721&id=NM_014189&id=NM_002858&id=NM_020326&id=NM_020327&id=NM_003183&id=NM_020328&id=NM_033151&id=XM_087663&id=NM_000443&id=NM_022451&id=NM_003816&id=NM_003815&id=NM_016630&id=NM_004302&id=NM_004300&id=NM_004827&id=NM_020069&id=NM_032489&id=NM_020679&id=NM_014237&id=NM_025220&id=NM_004924&id=NM_021832&id=NM_004915&id=NM_139155&id=NM_003812&id=XM_001869&id=NM_003813&id=NM_003814&id=NM_005099&id=NM_020683&id=NM_022436&id=NM_020983&id=NM_021962&id=NM_016351&id=XM_032220&id=NM_001171&id=NM_005691&id=NM_080722&id=NM_005692&id=NM_014486&id=NM_152932&id=NM_006020&id=NM_005891&id=NM_002940&id=XM_040469&id=NM_139274&id=XM_166287&id=XM_031949&id=NM_021804&id=XM_113336&id=NM_007038&id=NM_007037&id=XM_003555&id=NM_002197&id=NM_021777&id=NM_020039&id=NM_020038&id=NM_020037&id=NM_014265&id=NM_080790&id=NM_019903&id=NM_080791&id=XM_012405&id=NM_001464&id=NM_015270&id=XM_036462&id=NM_021981&id=NM_014269&id=NM_005736&id=NM_007022&id=NM_005735&id=NM_019624&id=NM_019625&id=NM_080789&id=NM_138448&id=NM_014272&id=NM_153005&id=NM_033226&id=NM_021780&id=XM_033912&id=NM_005050&id=NM_014479&id=NM_014576&id=NM_007099&id=NM_021778&id=NM_021779&id=NM_006721&id=XM_007904&id=NM_015834&id=NM_021794&id=NM_018677&id=NM_014244&id=NM_015831&id=NM_007313&id=NM_018672&id=NM_015833&id=NM_007314&id=NM_014243&id=NM_014384&id=NM_004733&id=XM_171212&id=NM_020298&id=NM_020297&id=NM_014444&id=NM_005759&id=NM_013375&id=NM_021599&id=NM_015841&id=NM_015840&id=XM_007409&id=NM_006988&id=NM_031480&id=NM_001089&id=NM_001088&id=XM_027578&id=NM_014458&id=NM_001086&id=NM_152831&id=NM_152830&id=NM_003474&id=NM_005763&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&code=Q&

This could either happen while sending the request with the php HttpRequest? library (the wikipathways side) or when receiving the url in the restlet library (the lucene indexer side).

A solution would be to send the data through a POST request instead of encoding the parameters in the url.

A workaround for this problem is to split up the search into multiple shorter queries.

#464 wp RFC 001 tracker bug - Ontologies Wikipathways applet 04/16/08

This is a bug to track the status of an RFC. Please keep this bug assigned to the person responsible for moving this rfc forward.

 http://svn.bigcat.unimaas.nl/wikipathways/trunk/rfc/001-ontologies.txt

#471 wp RFC 008 tracker bug - Aliases Wikipathways applet 04/16/08

This is a bug to track the status of an RFC. Please keep this bug assigned to the person responsible for moving this rfc forward.

 http://svn.bigcat.unimaas.nl/wikipathways/trunk/rfc/008-sticky-edges-plan.txt

#607 wp RFC 011 tracker bug: user tags / badges Wikipathways applet 08/18/08

This is a bug to track the status of an RFC. Please keep this bug assigned to the person responsible for moving this rfc forward.

 http://svn.bigcat.unimaas.nl/wikipathways/trunk/rfc/011-user-tags.txt

#970 Install RSS extension WikiPathways website 08/08/09

try it out on the test site. could be used to:

  • display a wikipathways blog on front page
  • display user blogs on a community page
  • interface with facebook to post user activity to walls
  • interface with other sites/blogs to post user activity
#973 Database QC GeneDatabases 08/12/09

More things to eventually add to the database build process: 1. row counts on Derby tables to compare with mysql table of the same release and with Derby tables from prior builds. Inequalities and major changes should be flagged in the error report. 2. lists of xrefs and counts should be tracked, compared and flagged. 3. total size of derby dbs should be tracked, compared and flagged.

#989 Feature: Suggested layout changes for Create page WikiPathways website 09/10/09

I find the layout of current Create page somewhat cluttered, maybe because features have been added to this page over time the organization has become a little odd. I am attaching a mockup of a slightly different layout. The main change is that full Upload and Create options are visible simultaneously, rather than one or the other like now. There is also some slight moving of objects to make the page more readable.

martijn (18 matches)

Ticket Summary Component Milestone Created
Description
#142 Can give two DataNodes the same GraphId Wikipathways applet 07/18/07

It's possible to create two DataNodes? with the same graphId. This should be illegal.

Example: - create a new Pathway - crete two GeneProducts? - enable the "show hidden attributes" preference - set the graphId of both gene products to "abc"

The odd thing is that this is tested for in org.pathvisio.model.Test.testRefUniq()

#200 dgpml can't handle changes to mappinfo object Diffviewer applet 08/22/07

If you do gpmldiff with output set to dgpml, you get an exception when a modification to any of the main pathway properties, such as MapInfoName? or Author.

For example:

gpmldiff -o dgpml testcases/Simple1.1.gpml testcases/Simple1.3.gpml [ 0.138] Info: Start reading the XML file: testcases/Simple1.1.gpml [ 0.189] Trace: Build JDOM tree [ 0.328] Trace: Start Validation [ 0.328] Trace: Copy map elements [ 0.345] Trace: End copying map elements [ 0.346] Info: Start reading the XML file: testcases/Simple1.3.gpml [ 0.347] Trace: Build JDOM tree [ 0.365] Trace: Start Validation [ 0.365] Trace: Copy map elements [ 0.371] Trace: End copying map elements Error: Converter exception

org.pathvisio.model.ConverterException?: Error creating jdom element with objectType 6: Error creating jdom element with objectType 6

org.pathvisio.model.ConverterException?: Error creating jdom element with objectType 6

at org.pathvisio.model.GpmlFormat?.createJdomElement(GpmlFormat?.java:959) at org.pathvisio.gpmldiff.DgpmlOutputter?.modifyStart(DgpmlOutputter?.java:105) at org.pathvisio.gpmldiff.PwyElt?.writeModifications(PwyElt?.java:102) at org.pathvisio.gpmldiff.PwyDoc?.writeResult(PwyDoc?.java:295) at org.pathvisio.gpmldiff.GpmlDiff?.main(GpmlDiff?.java:180)

<?xml version="1.0" encoding="ISO-8859-1"?> <Delta>

<Modify>

<Label xmlns=" http://genmapp.org/GPML/2007" TextLabel?="Compound" GraphId?="bbd">

<Graphics FontSize?="150" Color="000000" CenterX="7196.5" CenterY="4608.0" Width="1087.0" Height="234.0" />

</Label> <Change attr="TextLabel?" old="Compound" new="Compound 2" /> <Change attr="Width" old="1087.0" new="1278.0" /> <Change attr="CenterX" old="7196.5" new="7101.0" />

</Modify> <Modify>

<Label xmlns=" http://genmapp.org/GPML/2007" TextLabel?="Compound" GraphId?="f40">

<Graphics FontSize?="150" Color="000000" CenterX="2591.5" CenterY="4563.0" Width="1087.0" Height="234.0" />

</Label> <Change attr="TextLabel?" old="Compound" new="Compound 1" /> <Change attr="Width" old="1087.0" new="1278.0" /> <Change attr="CenterX" old="2591.5" new="2496.0" />

</Modify> <Modify>

<Change attr="MapInfoName?" old="New Pathway" new="Simple Pathway" /> <Change attr="Author" old="null" new="Martijn van Iersel" />

</Modify> <Modify>

<DataNode? xmlns=" http://genmapp.org/GPML/2007" TextLabel?="Enzyme" Type="Unknown" GraphId?="a55">

<Graphics Color="000000" CenterX="4905.0" CenterY="3915.0" Width="1200.0" Height="300.0" /> <Xref Database="" ID="" />

</DataNode> <Change attr="CenterY" old="3915.0" new="4230.0" />

</Modify>

</Delta>

#382 Pathway diff does not work for unevenly sized pathways Diffviewer applet 03/07/08

Pathway Diff does not work when comparing versions of a pathway that do not have the same size. The larger pathway does not scroll down completely.

Example: Fatty Acid Beta-oxidation BiGCaT (Homo sapiens), comparing version of 09:38, 22 February 2008 to the version of 11:48, 21 February 2008. The latest version does not scroll down correctly. Also, it incorrectly states that the GK gene has been removed (which hasn't).

#387 Add 'not working?' link to visual diff tool Wikipathways applet 03/09/08

We should add a 'not working?' link to the visual diff tool. All the applets should have this. I think the other applets already do.

#449 Pasted objects should be ordered in front Wikipathways applet 04/14/08

Currently pasted objects are placed behind other objects. They should probably be placed in the front. For example, copy datanode, then hit paste. The new datanode will be in back of the original. This is not expected behaviour.

#514 diffviewer: unchanged groups make changed elements below them unclickable. Diffviewer applet 05/14/08

For example, see the MaintBot? update of Homo_Sapiens:Notch_signaling_KEGG Grouping of datanodes prevents clicking on the changed elements below them.

#636 edit color set, recent colors Pathvisio 09/15/08

Using this dialog there is a 'recent colors' color pane, but it never contains any recent colors in my experience

#679 On nbx7, launching help results in empty browser window. Wikipathways applet 11/09/08

How to reproduce:

open the nbx7 remote desktop, a machine running Ubuntu 6.06 Dapper drake: - launch pathvisio - click help->help

result: firefox opens an empty browser window

expected: firefox opens and goes directly to pathvisio.org/Help

Possibly this is a configuration error, a bug in Ubuntu dapper drake, or a bug in Firefox 1.5. Also, possibly upgrading BrowserLauncher? to the latest version may solve this problem.

#680 Support for CSV Pathvisio 11/09/08

On the nbx7 machine, running Ubuntu 6.06 Dapper and PathVisio 1.1.1, importing the tutorial dataset fails.

There seem to be a couple of problems: - Open office running on this machine can't export to TSV, so CSV export is used. this leads to problems however, in the resulting pgex file numeric data is rounded off. - Even so, the data doesn't appear in the backpage where it should.

#98 species selection Pathvisio 02/02/07

Instead of selecting a suitable pathway directory and gene database, the user should select species and the program should know where to find the correct files.

#412 Pathway History table and diffviewer on the same page Diffviewer applet 03/12/08

It would be nice to have a Revert button in the diff viewer, so that when you compare two versions and decide that you want the previous one, you can click revert right away instead of having to go back to the history list.

#455 DiffViewer: Add feature for viewing differences in Description and Category assignment Diffviewer applet 04/16/08

Add feature for viewing differences in Description and Category assignment. This could be in the DiffViewer? or somewhere else.

#476 pv RFC 004 tracker bug Wikipathways applet 04/16/08

This is a bug to track the status of an RFC. Please keep this bug assigned to the person responsible for moving this rfc forward.

 http://svn.bigcat.unimaas.nl/pathvisio/trunk/rfc/004-mim-support.txt

#482 pv RFC 010 tracker bug Wikipathways applet 04/16/08

This is a bug to track the status of an RFC. Please keep this bug assigned to the person responsible for moving this rfc forward.

 http://svn.bigcat.unimaas.nl/pathvisio/trunk/rfc/010-gdb-schema-update

#535 associate PathVisio with gpml files Pathvisio 05/29/08

associate PathVisio with gpml files

#710 Hyperlinks to other pathways Pathvisio 11/27/08

The feature to add links to other pathways in GPML can now be implemented. All requirements are in place: - GPML label supports hyperlinks - WikiPathways? has stable identifiers

The only thing that's left is creating a gui dialog to enter the information.

#817 Feature: Use "text label" as default for gene box whenever a data visualization is used Pathvisio 02/10/09

In Visualization Options, if I don't select anything under "Text label", the color set ends up blocking the gene label that was present on the pathways. I know this make sense and can be avoided by selecting a text label, but to the user it looks kind of buggy. Can you have the "Text label" selected by default?

#823 Feature: Add warning message if user doesn't enter expression in Statistics calculation Pathvisio 02/12/09

It would be nice to get a warning message if user doesn't enter an expression in the Statistics calculation. Right now it is possible to calculate statistics even without an expression, the calculations finish but the results are all Nan, of course. A simple warning upfront would be nice.

thomaskelder (8 matches)

Ticket Summary Component Milestone Created
Description
#266 PathVisio does not ask user to save pathway when shutting down windows Pathvisio 11/02/07

If you are editing a pathway and you shutdown windows, PathVisio closes without asking you to save it. The expected behaviour would be that you'd be asked to save the pathway and windows waits for your reaction before shutting down. This is how it works with other software (e.g. word).

#870 Reverting and Authorship WikiPathways website 03/27/09

Currently, if you revert the only change made by an author, that author is not removed from the author list. If all edits by an author are reverted, the author should be removed. This further discourages trivial/false edits for cheap credit.

And if a user reverts they are added to the author list. This is probably OK, but seems a little odd. Not sure the best way to handle that.

#1112 Error when reverting to deleted revision WikiPathways website 02/04/10

Since I deleted a pathway and then reverted to a previous version, the deleted revision appears in the History table. If I click Revert on this revision I get:

Error: no valid XML provided {{deleted|test}}

Maybe there should be a more informative message. This is related to issue #1111

#1114 Pathway Viewer: Right-click temporarily blanks the viewer window WikiPathways website 02/04/10

This is a weird issue that seems inconsistent, but about half of all right-clicks results in the pathwayviewer blanking the window, so the pathway disappears. It reappears as soon as I click anywhere else in the window. Sorry I can't give more detail, it appears to be random, that it happens regardless of which area is clicked, doesn't seem to follow any logic.

#468 wp RFC 005 tracker bug WikiPathways website 04/16/08

This is a bug to track the status of an RFC. Please keep this bug assigned to the person responsible for moving this rfc forward.

 http://svn.bigcat.unimaas.nl/wikipathways/trunk/rfc/005-reference_pathways.txt

#483 pv RFC 011 tracker bug Pathvisio 04/16/08

This is a bug to track the status of an RFC. Please keep this bug assigned to the person responsible for moving this rfc forward.

 http://svn.bigcat.unimaas.nl/pathvisio/trunk/rfc/011-graphical-notation-standards

#629 Feature: Find pathways by literature reference WikiPathways website 09/11/08

Idea from Alex: "Imagine being able to identify all pathways that reference a particular article or articles by an author."

This could be implemented using the Lucene index.

#1115 Fast lookup which edits were reverted or delete action WikiPathways website 02/04/10

To make it possible to fix several bugs related to reverted or deleted revisions, this information needs to be accessible by the code fast. Currently, a revert action can't be recognized other than by the description ('Reverted to version ') and to find out if a revision was a delete action, you need to load the page text (will contain {{deleted...). A solution for #1111 and #1112 would be to enable/disable the revert and compare buttons in the history table per revision, depending if it's a regular edit or deletion. However, this will currently be too slow (need to load the text of all revisions). For fixing #870, we need to count the number of edits per user and exclude reverted revisions. Using the description is too slow and error prone.

We should cache this extra information on revisions in the database so it will be fast to lookup which were reverted or which were delete actions.

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