Integrate JBrowse into Varify as Alamut replacement

[ryanjohara]

The JBrowse URL (below) includes JSON for dynamically configuring some of the tracks, including the BAM and VCF tracks. The dynamic configurations currently contain direct URLs to files, like "urlTemplate":"http://localhost/jbrowse/data/Pseq_batch9_P-Pseq_0019-P-A_1.sorted.mdup.bam". @mitalia and I were talking about the easiest way to control access to these files. @bruth, does it sound reasonable to have a new Django endpoint serve the files, rather than accessing the files directly, since it knows whether or not the user has sufficient privileges? If so, where would be a good place to create this endpoint? Any other thoughts? Thanks.

http://localhost/jbrowse/?loc=chr7:121719569..121719668&tracks=DNA,Cosmic,VCF,BAM&highlight=&addTracks=[{"label":"BAM","store":"testStore","type":"JBrowse/View/Track/Alignments2"},{"label":"VCF","store":"testStoreTwo","type":"JBrowse/View/Track/CanvasVariants"}]&addStores={"testStore":{"baiUrlTemplate":"http://localhost/jbrowse/data/Pseq_batch9_P-Pseq_0019-P-A_1.sorted.mdup.bai","type":"JBrowse/Store/SeqFeature/BAM","urlTemplate":"http://localhost/jbrowse/data/Pseq_batch9_P-Pseq_0019-P-A_1.sorted.mdup.bam"},"testStoreTwo":{"tbiUrlTemplate":"http://localhost/jbrowse/data/Pseq_batch9_P-Pseq_0019-P-A_1.var_raw.vcf.gz.tbi","type":"JBrowse/Store/SeqFeature/VCFTabix","urlTemplate":"http://localhost/jbrowse/data/Pseq_batch9_P-Pseq_0019-P-A_1.var_raw.vcf.gz"}}

[bruth]

Yes, Varify would have to play a role if permissions need to be enforced. nginx and Apache both support a special header for a backend (Django) to hand-off a request it had processed. You can see an example here: http://stackoverflow.com/a/2690263/407954

Here are the docs for nginx: http://wiki.nginx.org/X-accel and the Apache module (this is not built-in) https://tn123.org/mod_xsendfile/

[ryanjohara]

Thanks for the response. I ended up adding a new Varify endpoint that does something like this:

        try:
            if Sample.objects.get(id=data['id']):
                response = HttpResponse()
                response['Content-Type'] = 'application/octet-stream'

                f = data['filename']

                # Control access to files hosted by nginx
                response['X-Accel-Redirect'] = '/files/' + f
                # Control access to files hosted by Apache
                response['X-Sendfile'] = '/files/' + f

                response['Content-Disposition'] = 'attachment;filename=' + f
        except Exception:
            return self.render(
                request,
                {'message': 'No sample found for "id"'},
                status=codes.unprocessable_entity
            )

        return response

Then after saving the files to $PROJECT_ROOT/files, the following needed to be added to nginx.conf (or the analogous if you are using Apache):

    location /files/ {
        alias $project_root/files/;
        internal;
    }

[ryanjohara]

This share page describes how to get JBrowse working with a nginx/uwsgi-deployed instance of Varify.