GDC plugin - Githubissues

GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

https://jbrowse.org/jb2

Apache License 2.0

202 stars 61 forks source link

GDC plugin #793

Closed rbuels closed 4 years ago

rbuels commented 4 years ago

JB2 port of Andrew Duncan's (@agduncan94) JB1 plugin that browses and imports GDC data.

cmdcolin commented 4 years ago

We want to create recurrent mutations track, based on selected queries of cancer type, race, etc.

rbuels commented 4 years ago

Moving parts of this that we have identified so far are:

data adapter classes (andrew)
view with an iframe into the GDC site listens to postMessage events coming out the iframe and keeps a MST state based on what it's received tries as much as possible to keep the iframe in the correct part of the GDC site
creating and injecting track configurations based on the MST state of the view (garrett)

risks currently:

does this iframe strategy even work?
what happens when users click around in the iframe and make it go to a weird place

garrettjstevens commented 4 years ago

Trying to embed the GDC portal in an iframe immediately fails with

Refused to display 'https://portal.gdc.cancer.gov/' in a frame because it set 'X-Frame-Options' to 'sameorigin'.

I'm attempting to contact the GDC and see if that's something that can be changed, but I have a hunch it's locked down that way because of government regulations.

We could host our own clone of the GDC Portal, but I'm not sure that's a great way to go.

garrettjstevens commented 4 years ago

Just got a response from the GDC. iframes are disallowed to prevent "clickjacking" attacks, so they have no plans of changing the X-Frame-Options response header.

rbuels commented 4 years ago

first implementation of this is done and merged! closing this issue, let's open some more issues for improvements we're making to it.

cmdcolin commented 4 years ago

See http://s3.amazonaws.com/jbrowse.org/code/jb2/alpha/master/index.html?config=test_data/config_gdc_test.json for demo

garrettjstevens commented 4 years ago

PR was #867