Re: [Gmod-ajax] JBrowse2

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Great! It works. Thank you for the help!

I missed two things in my previous example: 1. before "&sessionTracks",
"&tracks=url_track" is also needed to turn the track on first; 2. proper
HTML encoding is needed in the url, for example, spaces by %20 and quotes
by %22.

For a test in case someone is also trying this:

The following is the one did not work:

http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[{
<http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[%7B>"type":"FeatureTrack","trackId":"url_track","name":"URL
track","assemblyNames":["Porcine S. scrofa
v11.1"],"adapter":{"type":"FromConfigAdapter","features":[{"uniqueId":"one","refName":"1","start":6100,"end":6200,"name":"dynamic_test"}]}}]

The following is the url that works:

http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&tracks=url_track&sessionTracks=[{%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22Porcine%20S.%20scrofa%20v11.1%22],%22adapter%22:{%22type%22:%22FromConfigAdapter%22,%22features%22:[{%22uniqueId%22:%22one%22,%22refName%22:%221%22,%22start%22:6400,%22end%22:6500,%22name%22:%22dynamic_test%22}]}}]

On Mon, Feb 7, 2022 at 4:48 PM Colin <col...@gm...> wrote:

> Hi Ke
>
> Basically &sessionTracks= added this to your session, and then you have to
> turn the track on with &tracks= referring to the trackId from your
> sessionTrack
>
> Example URL
>
>
> https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:0-500&assembly=volvox&tracks=url_track&sessionTracks=[{%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22volvox%22],%22adapter%22:{%22type%22:%22FromConfigAdapter%22,%22features%22:[{%22uniqueId%22:%22one%22,%22refName%22:%22ctgA%22,%22start%22:100,%22end%22:200,%22name%22:%22URL%20Feature%22}]}}]
> <https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:0-500&assembly=volvox&tracks=url_track&sessionTracks=[%7B%22type%22:%22FeatureTrack%22,%22trackId%22:%22url_track%22,%22name%22:%22URL%20track%22,%22assemblyNames%22:[%22volvox%22],%22adapter%22:%7B%22type%22:%22FromConfigAdapter%22,%22features%22:[%7B%22uniqueId%22:%22one%22,%22refName%22:%22ctgA%22,%22start%22:100,%22end%22:200,%22name%22:%22URL%20Feature%22%7D]%7D%7D]>
>
>
> -Colin
>
> On Mon, Feb 7, 2022 at 2:20 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> It was great to see this feature! I was looking forward to it from the
>> start of JBrowse2. Thanks to all the developers behind this! The URL works
>> well but the &sessionTracks didn't quite work for me so far, here is an
>> example:
>>
>>
>> http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[{
>> <http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[%7B>"type":"FeatureTrack","trackId":"url_track","name":"URL
>> track","assemblyNames":["Porcine S. scrofa
>> v11.1"],"adapter":{"type":"FromConfigAdapter","features":[{"uniqueId":"one","refName":"1","start":6100,"end":6200,"name":"Boris"}]}}]
>>
>> The url works properly up to the "sessionTracks" part, but there was no
>> dynamic track loaded or shown. Anyone have any advice? Do I need to code
>> the spaces in the configuration with "%20", too?
>>
>> Thanks!
>>
>> Ke
>>
>> On Fri, Feb 4, 2022 at 11:45 AM han...@ge... <
>> han...@ge...> wrote:
>>
>>> Hi Colin,
>>>     This is helpful for me. Thanks
>>>
>>> Best
>>>
>>> ------------------------------
>>> Hang Yang, Ph.D.
>>>
>>> Institute of Genetics and Developmental Biology
>>> Chinese Academy of Sciences
>>> No.1 West Beichen Road, Chaoyang District
>>> Beijing, China 100101
>>>
>>>
>>> *From:* Colin <col...@gm...>
>>> *Date:* 2022-02-03 05:25
>>> *To:* han...@ge...
>>> *CC:* gmod-ajax <gmo...@li...>
>>> *Subject:* Re: [Gmod-ajax] JBrowse2
>>> Hi there
>>> JBrowse 1.6.4 merged this finally. Docs here
>>> https://jbrowse.org/jb2/docs/urlparams/
>>>
>>> Let me know if that helps:)
>>> -Colin
>>>
>>> On Tue, Jan 11, 2022 at 11:02 AM Colin <col...@gm...> wrote:
>>>
>>>> Hello,
>>>> This feature has been implemented on a work-in-progress branch. It is
>>>> planned to be released in an upcoming version soon
>>>>
>>>> https://github.com/GMOD/jbrowse-components/pull/2165
>>>>
>>>>
>>>> If you want to try to preview the feature before the official release
>>>> you can use the CLI command to test out the branch (it is otherwise up to
>>>> date with other latest release features)
>>>>
>>>>     jbrowse create --branch nav_with_urlbar2 jbrowse2
>>>>
>>>> This will download the code from that branch to a folder named
>>>> jbrowse2, and then you can use URLs like
>>>>
>>>>
>>>> http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <
>>>> han...@ge...> wrote:
>>>>
>>>>> Dear JBrowse developers,
>>>>>     I am a user of the JBrowse. It's really a useful tool.
>>>>>     I have a question about how to use URL query API in JBrowse2
>>>>>  e.g. specifying ?loc=1:1..100.
>>>>>     Thanks, Look forward to your reply.
>>>>>
>>>>> Best
>>>>>
>>>>> ------------------------------
>>>>> Hang Yang, Ph.D.
>>>>>
>>>>> Institute of Genetics and Developmental Biology
>>>>> Chinese Academy of Sciences
>>>>> No.1 West Beichen Road, Chaoyang District
>>>>> Beijing, China 100101
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>