Re: [Gmod-ajax] [apollo] Translation of JBrowse1 REST API to JBrowse2

[Colin <col...@gm...>]

Hi Michael
Sorry for delay in reply, definitely feel free to let us know if you have
any updates or questions. Regarding docs, main portal is here
https://jbrowse.org/jb2/docs

Developer docs related to things like plugins are here, for example,
creating an adapter which can be used for adapting to a REST APIs
https://jbrowse.org/jb2/docs/developer_guides/creating_adapter/ and then
our embedded components that you refer to have links to 'storybook demos'
and other docs here https://jbrowse.org/jb2/docs/embedded_components/


If you are accustomed to JBrowse 1 terminology, here is a rough mapping

JBrowse 1->JBrowse 2
storeClass->adapter (there is no more urlTemplate, you look at the config
docs https://jbrowse.org/jb2/docs/config_guides/alignments_track/ or
"auto-generated config docs" for each little schema type
https://jbrowse.org/jb2/docs/config/bamadapter/ and you will see that there
is instead things like bamLocation, gffGzLocation, etc. sort of different
for each track type)
trackList->track label->config.json track trackId
trackList track key->config.json track name
bin/prepare-refseqs.pl->jbrowse add-assembly (assemblies have a special
area of the config that provides a ReferenceSequenceTrack)
bin/flatfile-to-json.pl->jbrowse add-track

For custom sequence fetching and feature fetching, may require hand-editing
the config.json. The config.json you linked uses the "biothings" plugin to
fetch from mygene.info and myvariant.info. Example code for that here
https://github.com/cmdcolin/jbrowse-plugin-biothings-api/blob/master/src/MyGeneAdapter.ts.
Can add more info about plugins if interested


-Colin



On Thu, Oct 12, 2023 at 9:52 PM Michael Thang <m....@qf...> wrote:

> Hi Colin,
> Thank you for speedy reply and clarification ! I can relate the REST API
> (aka mygene.info) to a project I am working on and using this Django
> framework to embed jbrowse into it (machado
> <https://machado.readthedocs.io/en/latest/jbrowse.html>). I am keen to
> use Jbrowse2 but the main issue is how to translate the trackList.json to
> config.json for my project. As you mentioned above, most of the Jbrowse1
> options are dropped for Jbrowse2. I guess I need to investigate a bit more
> to see how much work I need to use Jbrowse2 for my project. The good news
> is the Machado Framework does come with API
> <https://www.machado.cnptia.embrapa.br/demo_machado/api/> setup and I am
> trying to understand how to combine the API and the Jbrowse2 in the
> config.json (Jbrowse2) based on the trackList.json
> <https://github.com/lmb-embrapa/machado/blob/master/extras/trackList.json.sample>
> (Jbrowse1) format.
>
> I think this is the config.json
> <https://github.com/cmdcolin/jbrowse-plugin-biothings-api/blob/master/config.json>
> you use to retrieve reference genome and tracks using API call. For me, it
> is a bit difficult to understand the options you use in the config.json. I
> believe there must be a documentation somewhere . can you please point me
> to the documentation if available?
>
> To date, I managed to setup the Jbrowse2 running on my apache server
> without any problems. What I want to explore next is to work on the REST
> API call to query and show the tracks/assemblies of interest on an embedded
> Jbrowse2. However, I am kind of stuck at the moment.
>
> Best
>
> On Friday, October 13, 2023 at 11:16:28 AM UTC+10 Colin wrote:
>
>> Hi Michael,
>>
>> Many of the JBrowse 1 options do not automatically apply to JBrowse 2
>> because the config.json format is quite a bit different from trackList.json.
>>
>>
>> I also see that your trackList.json refers to a "REST" data adapter from
>> JBrowse 1 (JBrowse/Store/SeqFeature/REST) but this data adapter type was
>> not added to JBrowse 2. We did not add this to JBrowse 2 because it is hard
>> or awkward to design a "blessed"  or "recommended" REST API format that we
>> want users to implement.  If you do want to make an adapter for your REST
>> API, you can write a custom plugin to do so. I may be biased because I
>> wrote a lot of data adapters for various REST APIs on the web as plugins (
>> mygene.info adapter, UCSC rest api adapter, etc) but my feeling is that
>> it  is relatively little code (100-200 lines for example) and it can
>> actually be useful, as a developer, to be in control of the client code
>> that is accessing your particular REST API.
>>
>> If your main concerns are getting a JBrowse 1 REST API working with
>> JBrowse 2 I can elaborate, or I can help with any of the other JBrowse 2
>> upgrade steps too :)
>>
>>
>> -Colin
>>
>> On Thu, Oct 12, 2023 at 11:42 AM Nathan Dunn <ndu...@gmail.com> wrote:
>>
>>>
>>>
>>> On Oct 11, 2023, at 11:40 PM, Michael Thang <m.t...@qfab.org> wrote:
>>>
>>> Hi Apollo Team,
>>> I would like to find out how to translate this Jbrowse1 trackList.json
>>> <https://github.com/hexylena/JBrowse-REST-API-Example/blob/master/data/trackList.json>
>>> to Jbrowse2. I just borrowed the trackList.json online, but I am running
>>> into the same situation where I have my Jbrowse1 configured to run API. I
>>> am exploring the posssiblity to use the same trackList.json format for
>>> Jbrowse2. However, the Jbrowse2 is using config.json instead and the json
>>> looks different. Therefore, I dont know if all these options
>>> <https://jbrowse.org/docs/global_options.html> are still applicable for
>>> Jbrowse2.
>>>
>>>
>>>
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