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Re: [Gmod-ajax] JBrowse 'Save track data' not working
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From: Vaneet L. <van...@uc...> - 2018-07-20 19:03:40
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We need it for a major upcoming project, so I hope we don’t have to but if it’s not maintained we may have to face that reality and perhaps just use the Faceted track selector on its own. Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary AB T2N 1N4 CANADA From: Robert Buels [mailto:rb...@gm...] Sent: Friday, July 20, 2018 12:56 PM To: Vaneet Lotay <van...@uc...> Cc: gmod-ajax <gmo...@li...>; Scott Cain <sc...@sc...> Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working Have you considered just ditching that plugin if they are not going to maintain it? On Thu, Jul 19, 2018 at 3:13 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Yes Robert, the plugin I’m still having problems with is ComboTrackSelector. Again the plugin looks to be functional, it’s just not displayed correctly, both issues posted on the Github branch are related to the same problem: https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/issues I was thinking I could try upgrading to a later version of JBrowse, but not the latest release in the off chance that this plugin works with that version as the developer did post a fix earlier for this issue so it must have been working in at least 1 release. Perhaps I could try JBrowse 1.14.0 first. I’m not sure how to fork JBrowse exactly, might need instructions on how to do that. Do you mean only copy the folders and files from one of the newer releases of JBrowse that fix this particular ‘save track data’ bug and not the complete release? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>] Sent: Thursday, July 19, 2018 3:07 PM To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>; gmod-ajax <gmo...@li...<mailto:gmo...@li...>> Cc: Scott Cain <sc...@sc...<mailto:sc...@sc...>> Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working I think you are probably running into a bug that was fixed in 1.14.0 (fix can be seen at https://github.com/GMOD/jbrowse/commit/228af5684362c6b6a1a9210667a0e0750d373cd3). You might try applying that fix to your local code, or you could fork JBrowse at that point perhaps, if you really can't upgrade? The plugin you're still having problems with is ComboTrackSelector? On Thu, Jul 19, 2018 at 1:45 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: That Java console was from the Chrome browser. I’m using JBrowse-1.13.1-dev currently. I can’t upgrade to the latest JBrowse release because a plugin that we’re using doesn’t work properly with the latest JBrowse release. I posted the issue on the Github branch of that plugin, as did another user about 2 weeks ago, no response yet. I am viewing JBrowse on a PC with Windows 7 Enterprise. This doesn’t work with Firefox either, here is the java console from that browser when I tried to save track info: <unavailable> _fileDownload@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7 _exportDialogContent/dlButton<.onClick</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:15 hitch/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48 exportRegion/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15459:9 hitch/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 all/</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:7 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33359:15 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 Deferred/promise.then@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45929:5 __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33358:20 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45729:4 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 handleResponse@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5096:6 onLoad@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5131:5 0.bundle.js:70956:3<http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js> Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>] Sent: Thursday, July 19, 2018 2:11 PM To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>> Cc: Scott Cain <sc...@sc...<mailto:sc...@sc...>>; gmo...@li...<mailto:gmo...@li...> Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working That's interesting, it looks like file saving might not be supported on that browser and platform and JBrowse might not be detecting that fact? What are the exact versions of JBrowse, the web browser, and the operating system you are trying this with? On Thu, Jul 19, 2018 at 1:04 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hey guys, I have checked the option in both Firefox and Chrome browsers for automatically saving downloads to a specific folder without prompting. I tried the option enabled and disabled and in both cases it doesn’t work in that it isn’t being saved in the default download folder or it’s not prompting me to pick the location in where I save the file. It appears there’s an error happening though if we look at the Java console, so I pasted it here below: GET https://www.google-analytics.com/analytics.js 0 () instrumentation.js:23 TypeError: saveAs is not a function at Object._fileDownload (_ExportMixin.js:252) at Object.<anonymous> (_ExportMixin.js:178) at lang.js:385 at Object.<anonymous> (FASTA.js:26) at lang.js:385 at SeqFeature.js:182 at signalListener (Deferred.js:37) at signalWaiting (Deferred.js:28) at Deferred.resolve (Deferred.js:192) at all.js:68 "TypeError: saveAs is not a function at Object._fileDownload (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7) at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:20) at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55 at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38890:9) at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55 at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9 at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21) at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4) at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5) at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16 ---------------------------------------- rejected at signalDeferred (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45755:15) at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45726:5) at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4) at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5) at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16 at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21) at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4) at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5) at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21) at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4) ---------------------------------------- Error at Promise.Deferred.then.promise.then (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45923:24) at Object.getFeatures (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:11005:20) at Object.getReferenceSequence (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12933:12) at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38889:18) at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15849:12) at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55 at contextRequire (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:265:25) at req (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:159:21) at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15844:19) at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15734:18)" Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>] Sent: Wednesday, July 18, 2018 7:35 PM To: Scott Cain <sc...@sc...<mailto:sc...@sc...>> Cc: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>; gmo...@li...<mailto:gmo...@li...> Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working It should look and work the same as any other file download in the browser. Which with most browsers is that it just downloads the file into your downloads folder. Is it not doing that? On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote: Hi Vaneet, Now that I've reread your email and also tried it myself to remind me how it works--it does not prompt you for a name or location. It assigns a name based on the track and location and puts a file in your default download location. Scott On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote: Hi Vaneet, Can you check the javascript console when you're doing that to see if it gives any useful feedback? Thanks, Scott On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hello, I’m having trouble saving track data to capture sequence data in FASTA format, model data in GFF3 or any other track and format. I click on the drop down arrow next to the track label and then ‘Save track data’. Whether I click on the visible region or the whole reference sequence and no matter which output format I select it doesn’t work. When I click on ‘Save’ the dialog box always closes and nothing happens. I assume there should be another box popping up asking where to save the file and also how to name it? I’ve tested this on both Firefox and Chrome browsers, still the same problem. I’ve also tested both browsers while disabling the pop-up blocker, in case that was interfering but still the same problem remained. Please let me know if anyone can resolve this issue. Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087<tel:(216)%20392-3087> Ontario Institute for Cancer Research -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087<tel:(216)%20392-3087> Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
