Allow CORS?

[cmdcolin]

Hi there

It would be great if this htsget server supportted CORS!

That way javascript based code running in the browser can fetch it

For instance here https://www.test-cors.org/#?client_method=GET&client_credentials=false&server_url=https%3A%2F%2Fhtsget.ga4gh.org%2Freads%2Fgiab.NA12878.NIST7035.1%3Fclass%3Dheader&server_enable=true&server_status=200&server_credentials=false&server_tabs=remote

This returns a HTTP Status 0 which indicates a cors error basically, can also look in the javascript console on that page

Also I looked at #8 while trying to find htsget servers to test against, currently I have only tested against a dnanexus server but they all have a biut different behavior so great to see others

[victorskl]

CORS support comes in PR #24 which is review in progress. If you would like to try it for local dev, you can do like so:

docker run -it --rm -p 3000:3000 quay.io/victorskl/htsget-refserver ./htsget-refserver -config deployments/ga4gh/prod/config-local.json

Then you can curl to ticket endpoints like:

Alignment:

curl -s http://localhost:3000/reads/service-info | jq .
curl -s http://localhost:3000/reads/giab.NA12878.NIST7035.1 | jq .

Variants:

curl -s http://localhost:3000/variants/service-info | jq .
curl -s http://localhost:3000/variants/giab.NA12878 | jq .

To show that CORS is working, make OPTIONS request like this:

curl -s -v -H "Origin: http://example.com" \
  -H "Access-Control-Request-Method: GET" \
  -H "Access-Control-Request-Headers: X-Requested-With" \
  -X OPTIONS \
  http://localhost:3000/reads/giab.NA12878.NIST7035.1

Note that, response contains Access-Control-Allow-Origin: *

And of course, you can also try with BAM sliced request with CORS different origin, like so:

curl -s -v -H "Origin: http://example.com" http://localhost:3000/reads/giab.NA12878.NIST7035.1?format=BAM&referenceName=chr13&start=0&end=49999 | jq .

---

For some reason, like you don't want to use default port 3000 or, if want to tweak any aspect of server config, then:

Grab the local config to current directory and modify server port to 5000, for example:

wget https://raw.githubusercontent.com/victorskl/htsget-refserver/cors-support/deployments/ga4gh/prod/config-local.json

Then, bind map the config and run:

docker run -it --rm -p 5000:5000 -v `pwd`/config-local.json:/config-local.json quay.io/victorskl/htsget-refserver ./htsget-refserver -config /config-local.json

Curl it, so on so ford!

curl -s -v -H "Origin: http://example.com" http://localhost:5000/reads/service-info | jq .

Of course, you can docker-compose this up, too.

HTH

[cmdcolin]

Thanks!

[jrobinso]

Ping. Any updates? CORS is required by the htsget specification.

[jb-adams]

@victorskl I just merged your PR #24 . Would you say this issue is good to close after incorporating your branch?

[victorskl]

Yes sure; happy to close this issue. And happy to maintain and support this; down the track, if any.

I also re: testing CORS for local run with default setting there in igv.js thread

Thanks again for merging. Cheers!

[jrobinso]

@jb-adams When can we expect the public reference server to reflect this change?
Thanks

[jb-adams]

I'm aiming to have this completed today, any pointers on what origins I should configure the server to allow?

[jb-adams]

@jrobinso @brainstorm @victorskl the public server has been updated to incorporate CORS and corrected documentationUrls. I'm releasing this as v1.5.0.

Reads documentationUrl

Variants documentationUrl

CORS

(See Origin request header and Access-Control-Allow-Origin response header)

[jrobinso]

I can confirm the CORS problem is fixed

https://igv.org/web/snapshot/examples/htsget.html