Activity

From 09/20/2013 to 10/19/2013

10/15/2013

02:33 pm Bug #71 (Resolved): cannot handle irregularity in custom metadata
fixed on Public server (but not yet on test). Now the browser captures such thing and complains about it. Xin Zhou
02:32 pm Bug #71 (Closed): cannot handle irregularity in custom metadata
Rebecca reported this issue. She has this entry in a metadata vocabulary:
"RNA-seq":["RNA-seq", ... ],
Same ter...
Xin Zhou
02:30 pm Bug #66 (Resolved): Save custom metadata vocabulary into session
fixed in v25 Xin Zhou

10/10/2013

11:23 pm Bug #70 (Closed): right click caused background color disappear
Closed due to could not reproduce in Firefox and Chrome on other computer. Daofeng Li
10:44 am washugb v25 release
* Version 25 features a nice way to display CpG methylation data, and the track background color configuration, and a... Daofeng Li
12:54 am Bug #70 (Closed): right click caused background color disappear
* select 'apply to all' change background color of all tracks
* right click on one of the track
* I found the backg...
Daofeng Li

10/09/2013

04:35 pm Bug #69 (Rejected): track name in svg
* please see screenshot for the position of track names in svg (which overlap the track) Daofeng Li
02:59 pm Bug #44: long range track display weird in SVG output
* in V24.3, seems the arc still get black area when opened with illustrator or inkscape Daofeng Li

10/08/2013

12:08 pm Feature #67 (Closed): change background color
(suggested by Ting)
* Can user set background color? By default the background is white. Maybe someone wants it to...
Daofeng Li

10/07/2013

03:45 pm Bug #2 (Closed): chrome empty canvas
* this issue has been solved with latest version of Google Chrome (Since Oct.2013) Daofeng Li
11:13 am Bug #66 (Closed): Save custom metadata vocabulary into session
Load a datahub containing a custom metadata, save it under session.
Either get "syntax error" on clicking Save but...
Xin Zhou
09:44 am Bug #65 (Resolved): Error rendering RRBS track
fixed in v24.2 Xin Zhou
09:26 am Bug #65 (Closed): Error rendering RRBS track
http://epgg-test.wustl.edu/browser/?genome=hg19&hmtk=GSM621347
this shows a RRBS track. navigate to centromere reg...
Xin Zhou
08:57 am Bug #44: long range track display weird in SVG output
* seems still get abnormal output when open in inscape or illustrator
* please see screenshot below
Daofeng Li
07:29 am Bug #64 (Rejected): json hub not show custom meta colormap
show:['Cell','Assay','Donor','View']
this line should be under "metadata", but not "vocabulary"
Xin Zhou

10/06/2013

09:58 pm Bug #64 (Rejected): json hub not show custom meta colormap
* might I did it wrong way...
* in this hub: http://cgs.wustl.edu/~dli/remcMethyl.json
* I have show:['Cell','Assay...
Daofeng Li
03:15 pm Bug #44 (Resolved): long range track display weird in SVG output
Xin Zhou
03:14 pm Bug #44: long range track display weird in SVG output
SVG output function has been updated in v24.2, please see if this problem is still there. Also please do extensive te... Xin Zhou

10/03/2013

09:22 am Revision 84c81131: preparing encode hub 2
Daofeng Li
09:22 am Browser Metadata Revision 84c81131: preparing encode hub 2
Daofeng Li
09:21 am Revision 4bbad921: preparing encode hub
Daofeng Li
09:21 am Browser Metadata Revision 4bbad921: preparing encode hub
Daofeng Li

10/01/2013

11:32 pm Bug #63 (Closed): Gene plot by Google Chart seems not working
Google API now works. Closed. Daofeng Li
01:52 pm Bug #63: Gene plot by Google Chart seems not working
saw the trouble, because google API is not working:
https://www.google.com/jsapi 502 (Bad Gateway)
Xin Zhou
01:23 pm Bug #63 (Closed): Gene plot by Google Chart seems not working
* choose Google Chart for gene plot
* no figures comes out, and the interactive data table was not working either
Daofeng Li
08:34 am Support #62 (New): "donor" terms in hg19 metadata
There's lots of donor IDs in hg19 metadata, please make them more meaningful by adding sex/race/age/health informatio... Xin Zhou

09/30/2013

09:59 pm Bug #61 (Closed): error embedding browser
Fixed and closed Daofeng Li
01:49 pm Bug #61 (Resolved): error embedding browser
need to comply with the way metadata is declared in datahub: warp the metadata vocabulary inside the "vocabulary" key... Xin Zhou
01:46 pm Bug #61 (Closed): error embedding browser
error with embedding in v24.1
http://cgs.wustl.edu/~xzhou/plugin/2.html
Xin Zhou

09/28/2013

09:50 pm Bug #59: error filling contents for facet table of 2nd datahub
works now Daofeng Li
05:35 pm Feature #60 (Resolved): "file type" category for custom facet table
Implemented in v24.1
A "File type" attribute is automatically added to metadata that's either loaded from hub or f...
Xin Zhou
02:57 pm Bug #56 (In Progress): error handling with failed custom tracks
better error handling implemented in v24.1. When a broken track is used, the browser should not crash but print out a... Xin Zhou
08:20 am Feature #60 (Closed): "file type" category for custom facet table
when a custom datahub or publichub is loaded, its inner metadata will be rendered into a facet table
it's also des...
Xin Zhou
07:30 am Bug #59: error filling contents for facet table of 2nd datahub
I first found and fixed this bug, then I posted here to log it
which one of the facet tables can't you click?
Xin Zhou

09/27/2013

11:28 pm Bug #59 (Feedback): error filling contents for facet table of 2nd datahub
the Row and Column metadata header were not clickable Daofeng Li
11:24 pm Bug #59: error filling contents for facet table of 2nd datahub
went through your steps, no error found Daofeng Li
11:23 pm Bug #57 (Closed): Can not import encode data. Just stop at importing...
Closed. Might be re-opened if happened again. Daofeng Li
04:11 pm Bug #59 (Resolved): error filling contents for facet table of 2nd datahub
due to internal mdidx confusion, while loading a datahub
assumed that all coming datahub has mdidx of 1, actually sh...
Xin Zhou
04:10 pm Bug #59 (Closed): error filling contents for facet table of 2nd datahub
on hg19, load the GBM hub. in the "Tracks" panel, a facet table is shown for the GBM hub with tracks registered in it... Xin Zhou
10:18 am Feature #58 (Closed): make publichubs for ENCODE tracks
the "Dataset" feature will be retired
Instead the ENCODE tracks will be migrated into "publichub" format, which ma...
Xin Zhou
09:52 am Bug #57 (Resolved): Can not import encode data. Just stop at importing...
Fixed! Thanks, Xin Zhou
09:47 am Bug #57 (Closed): Can not import encode data. Just stop at importing...
Bo Zhang

09/26/2013

01:50 pm Bug #56 (Closed): error handling with failed custom tracks
in case of unacceptable custom track, don't crash or abort, but properly handle it and go on with it Xin Zhou
09:27 am Bug #54: upload bigWig error
* I think an error message like "your server doesn't support byte range request" would be more helpful Daofeng Li
09:14 am Feature #55 (New): [System] killing subtleKnife process which had been stucked longer than 10min
* did some research, finally choose to achieve this by using the killall command
* adding cron jobs to epgg1,2,3, au...
Daofeng Li

09/25/2013

01:28 pm Bug #54 (Rejected): upload bigWig error
see what's wrong by running bwquery on this bigwig url Xin Zhou
11:56 am Bug #54 (Rejected): upload bigWig error
* submit a bigWig url as custom track will get an error
Uncaught TypeError: Cannot read property 'length' of undefin...
Daofeng Li

09/24/2013

07:25 am Bug #53 (Rejected): virus gene info display problem
Xin Zhou
07:25 am Bug #53: virus gene info display problem
this is not an error
the graph is to indicate the structure of the whole gene
as the virus gene is just one exon, i...
Xin Zhou

09/23/2013

09:34 pm Bug #53: virus gene info display problem
forget the screenshot.. Daofeng Li
09:33 pm Bug #53 (Rejected): virus gene info display problem
* if you choose the virus genome, zoom in to base level
* click a gene, there is a blank area in the popup box
Daofeng Li
05:48 pm washugb v24 release
We have applied version 24 browser today!
h1. New genomes
* Soybean _Glycine max_, version 189
* Common bean _...
Daofeng Li

09/22/2013

02:50 pm Feature #13: Line plot
progress:
- matplot is now done using canvas
- can add tracks to a matplot, can remove tracks from one
- can show in ...
Xin Zhou

09/21/2013

07:14 pm Feature #52 (New): Improve gene set view
(comments from Gormley, Matthew at UCSF)
* Would be nice to have a gene set view toolbar, including buttons for:
**...
Daofeng Li
07:14 pm Feature #51 (New): Improve gene search function
(comments from Gormley, Matthew at UCSF)
* Tracks -> keyword search "trophoblast" -> get too big of a list, select t...
Daofeng Li
07:13 pm Feature #50 (New): Improve session?
(comments from Gormley, Matthew at UCSF)
-saving a session is only useful if you remember to record the session ID. ...
Daofeng Li
07:13 pm Feature #49 (New): general suggestions from UCSF
(comments from Gormley, Matthew at UCSF)
*feedback window at upper right is too close to toolbar, relocate or remove...
Daofeng Li
« Previous
Next »
 

Also available in: Atom