Updating links to pathology reports

[yichaoS]

We are currently moving all the pathology reports(.pdf) from datahub to msk storage (under path /data/public/tcga/pathology_reports on ramen server, URL: http://download.cbioportal.org/tcga/pathology_reports/report_ID.pdf). Portal front-end currently is pulling the reports from datahub master branch, therefore certain links in the patient view needs to be updated.

[jjgao]

would path report still work for https portals, e.g. msk portal?

[inodb]

@jjgao for simplicity's sake I hardcoded the version to datahub (see PR): https://github.com/cBioPortal/cbioportal-frontend/pull/1075/files. This works with https. We could switch to using download.cbioportal.org, but i think getting the pdfs form github is more reliable. Also we would still need to store the symlinks from TCGA patient ID to pathology report PDF somewhere if we were to use download.cbioportal.org

[jjgao]

@inodb we are going to move all path reports to download.cbioportal.org and remove them on github (we don't want to main two copies). Maybe we should work with Joanne and see if she can enable https first?

[inodb]

@jjgao we should def have ssl for download.cbioportal.org. For this particular issue though, afaik the TCGA pathology slides data is static. We are pointing to an old commit and won't rewrite github history, so it's probably more reliable than our own data server. We could also remove them from datahub and not upload them to download.cbioportal.org (we don't need to maintain them at all then)

If we want to provide a link to where to download the TCGA slides, we could point to the relevant page e.g.: https://wiki.nci.nih.gov/display/tcga/downloading+images+and+pathology+reports