Activity

From 08/28/2013 to 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

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

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

09:34 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

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

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

10:16 am Bug #46: Coordinate issue in hg19: Now I see the problem. It is because on a wide zoom level in the browser, one pixel width of the horizontal axis span... Xin Zhou
08:13 am Bug #46: Coordinate issue in hg19: Weird.. I just tried on my laptop and still have the same problem but now the coordinate is different again.. Junchen Gu
07:45 am Bug #46: Coordinate issue in hg19: cannot reproduce this problem Xin Zhou

10:59 pm Feature #48 (New): automatically refresh cache: * I think it might be useful that the browser could refresh cache automatically Daofeng Li
10:54 pm Bug #47 (Closed): wrong Y axis range display: Solved and closed. Daofeng Li
06:59 pm Bug #47 (Resolved): wrong Y axis range display: Fixed. Please test it thanks! Xin Zhou
06:26 pm Bug #47 (Closed): wrong Y axis range display: showing hg18 mm1s default tracks
* applying rpm/bp normalization method to the read density data
* the five bam den... Xin Zhou
02:24 pm Bug #46 (New): Coordinate issue in hg19: I found this issue in hg19:
Steps to reproduce:
copy chr5:131800537-131801093 into the coordinate window and cl... Junchen Gu
08:21 am Bug #43 (Closed): screenshot error on hub: solved and closed! Daofeng Li
08:18 am Bug #45 (Closed): mappability track display issue: confirmed solved. Daofeng Li
08:17 am Bug #45 (Resolved): mappability track display issue: Fixed. This was a bug that under "automatic scale mode", if all values of the track are >0, the Y scale minimum value... Xin Zhou

11:00 pm Bug #45 (Closed): mappability track display issue: * the browser display the 36mer mappability track with min value as 0
* a screenshot attached
* while if I query th... Daofeng Li
02:22 pm Bug #43 (Resolved): screenshot error on hub: Thanks so much for finding this bug! The track that has trouble with SVG output is "grouped", which means it shares Y... Xin Zhou
08:50 am Bug #31 (Closed): Cannot refresh Tabix index file: Xin Zhou
08:49 am Bug #44 (Closed): long range track display weird in SVG output: * noticed this issue before, but could be solved by using PDF files instead
* currently a people mailed our list, he... Daofeng Li

10:08 pm Bug #37 (Closed): track loading indicator text always display 'working' after finish of loading: closed! Daofeng Li
09:58 pm Bug #38 (Closed): new hub Turn off Gene Set View not work: closed! Daofeng Li
09:58 pm Bug #39 (Closed): json syntax error when running gene set view: closed! Daofeng Li
09:58 pm Bug #40 (Closed): gene plot crashed on gene set of json hub: Daofeng Li
09:57 pm Bug #41 (Closed): scatter plot json error: Daofeng Li
09:57 pm Bug #40: gene plot crashed on gene set of json hub: closed! Daofeng Li
09:57 pm Bug #41: scatter plot json error: closed! Daofeng Li
09:57 pm Bug #42 (Closed): json hub load error: closed! Daofeng Li
09:56 pm Bug #43 (Closed): screenshot error on hub: * using hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* Apps->Screenshot
* An error 'Uncaught TypeError: Can... Daofeng Li
12:19 pm Bug #37 (Resolved): track loading indicator text always display 'working' after finish of loading: fixed in v23.3, please test, thanks! Xin Zhou
09:07 am Feature #14 (Closed): Custom categorical track: Xin Zhou
09:06 am Feature #34 (Closed): add soybean genome: Xin Zhou
09:06 am Feature #35 (Closed): add common bean genome: Xin Zhou
09:06 am Feature #36 (Closed): add Brassica Rapa genome: Xin Zhou
07:33 am Bug #42 (Resolved): json hub load error: fixed
Change to datahub json format: json objects must be enclosed inside [] (on test browser) Xin Zhou

10:24 pm Bug #42 (Closed): json hub load error: * use the hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* missing type information error
* repeat 3 times Daofeng Li
08:34 am Bug #41 (Resolved): scatter plot json error: fixed on test browser Xin Zhou
08:34 am Bug #40 (Resolved): gene plot crashed on gene set of json hub: fixed on test browser Xin Zhou
08:34 am Bug #39 (Resolved): json syntax error when running gene set view: fixed on test browser Xin Zhou
08:33 am Bug #38 (Resolved): new hub Turn off Gene Set View not work: fixed on test server Xin Zhou

09:43 pm Bug #41 (Closed): scatter plot json error: * using json hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* select scatter plot for 1st gene set with any 2 ... Daofeng Li
09:42 pm Bug #40 (Closed): gene plot crashed on gene set of json hub: * using hub http://vizhub.wustl.edu/hubSample/hg19/hub3.json for hg19
* do gene plot on 2nd gene set
* crashed with... Daofeng Li
09:41 pm Bug #39 (Closed): json syntax error when running gene set view: * using the hub for hg19: http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* run gene set view on 2nd gene set
* cr... Daofeng Li
09:39 pm Bug #38 (Closed): new hub Turn off Gene Set View not work: * using the new json hub for hg19: http://vizhub.wustl.edu/hubSample/hg19/hub3.json
* after gene set view on 1st gen... Daofeng Li

10:18 pm Bug #37 (Closed): track loading indicator text always display 'working' after finish of loading: * the will happen if you click the header of each group
* for example, you click 'Expression', then 'add selected'
... Daofeng Li

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