Make the source for the web API version available.

broadinstitute / oncotator

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Make the source for the web API version available. #352

Open alanhoyle opened 8 years ago

alanhoyle commented 8 years ago

We have a web application that the users can click or highlight a section of a chromosome and it does a live query of the Oncotator web API. On rare occasions, this query has failed because of maintenance window or upstream network connectivity. While the stand-alone Oncotator works for our static pages and files, it would be great if we could stand up a local copy of the web API to avoid these issues.

Or, if I've somehow missed how to do this given the distribution I can download, please point me in the right direction.

shandy79 commented 6 years ago

I'm also very interested in this being made available or being pointed in the direction of where it might already be available.

LeeTL1220 commented 6 years ago

@shandy79 @alanhoyle The repo is currently private. Let me talk to some people about making it public.

alanhoyle commented 6 years ago

This might not be of great importance to us since Oncotator remains incompatible with hg38 (see issue #281 ). We're moving our workflows in that direction so it might not be useful to us going forward.

shandy79 commented 6 years ago

@LeeTL1220, thanks for the update. Like @alanhoyle, we're thinking about hg38 (and therefore Funcotator I think?) as well, but having the web API for Oncotator available in the meantime would be very helpful!

LeeTL1220 commented 6 years ago

Funcotator supports hg38 (I've run it on hg38 and hg19 myself) ...

However:

There is no web API for Funcotator. Command line only.
In Funcotator, for now, only VCF input is accepted. Please tell me if this is an issue. I can bump up the priority.

On Wed, Jul 18, 2018 at 11:56 AM, shandy79 notifications@github.com wrote:

@LeeTL1220 https://github.com/LeeTL1220, thanks for the update. Like @alanhoyle https://github.com/alanhoyle, we're thinking about hg38 (and therefore Funcotator I think?) as well, but having the web API for Oncotator available in the meantime would be very helpful!

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shandy79 commented 6 years ago

I think for our purposes we will require a web API, but we'll primarily be interested in the mutation endpoint (i.e. coordinates w/change as input). I think I can roll my own for that limited functionality in a few days. I'm not sure what hurdles you would face in making the repo public, but if it's a significant amount of effort, I'll concede it's probably not worth it at this point just for me +/- @alanhoyle.