Document how to build custom Data Sources with different URL structures about locuszoom HOT 5 CLOSED

Right now, the two that LocusZoom will be consuming are:

• http://browser.sph.umich.edu/api/coverage/region/22-46546715-46615880
• http://browser.sph.umich.edu/api/variants_in_region/22-46546715-46615880

Maybe later we'll do something like:

• http://browser.sph.umich.edu/api/coverage/region/22-46546715-46615880?attributes=pos,cadd_phred&view=exome_utrs
• http://browser.sph.umich.edu/api/variants_in_region/22-46546715-46615880?attributes=start,end,median&consequence=lof&view=exome

consequence= and view= filter which results will be returned, and attributes= filters the attributes those results will have. I can't think of other parameters that we'll ever need, but some might come up for new graphs. I'm planning to fool around with these kinds of graphs in the next couple weeks, so maybe I'll know soon.

I'll probably need to make a genes API as well.

Flask plays nicely with delimiting variables by slashes, so that's what I do. If you want to stick to the current structure, it should be easy enough to implement.

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Update: so with discussion it looks like our approach for now is to not worry too much about making the getURL() method (or data source end point URL composition) more generic, but instead have implementers of the plugin define their own custom getUrl() methods to suit their needs.

I've changed the tags on this issue then to mark it as a Documentation need.

from locuszoom.

That makes sense. I'm happy with that.

from locuszoom.

@MrFlick - just poking this issue. The documentation has matured considerably to keep pace with how the layout concept has matured, but data sources documentation is still missing.

The need for this came up this week when trying to build a new data source for fetching PheWAS data for individual variants. @pjvandehaar and I came up with a workable solution (code here), but it doesn't use LocusZoom.DataSources.prototype.addSource() to create it. Instead it adds the new data source the same way the existing data sources are defined. Maybe we just need to sit down some time and iterate over Data.js in general? Either way, I want to figure out the right way to build new data sources now that we've effectively done it four times, get it into the documentation, and hopefully iterate over the workflow to make the syntax as clear and intuitive as possible.

from locuszoom.

I've added some basic documentation about how data sources work and how to create custom sources.

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