Re: GDAC Firehose broken?

[Broad Institute GDAC]

Hi Maciej,

The only tools that we support are fbget and firehose_get. All R tools were developed by external users.

Recently, we shut down http access to gdac.broadinstiute.org in favor of https access due to the site being taken down on a daily basis by bad actors using http vulnerabilities. In most cases, this shouldn't have any effect on downstream tools, UNLESS they are disallowing http -> https redirects. If programmatic access is failing in unsupported tools, you'll need to contact the developers of those tools.

Kind regards,

David

On Tue, Dec 13, 2022, 7:15 AM Maciej Kańduła <maciej....@gmail.com> wrote:

Dear GDAC Team,

I am still getting the same error while trying to download the TCGA data using programmatic tools (e.g., RTCGAToolbox):

Error: failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/THCA/20160128/"

Any ideas what is now causing it?

Many thanks,

Maciej

sob., 3 gru 2022 o 15:54 Broad Institute GDAC <gd...@broadinstitute.org> napisał(a):

Hi Maciej,

The Broad is having scheduled network maintenance today, which took down our database. We should be up and running again tomorrow.

Kind regards,

David

On Sat, Dec 3, 2022, 7:41 AM Maciej Kańduła <maciej....@gmail.com> wrote:

Hello,

I'd like to know if something has recently been broken in the GDAC database. Multiple tools that previously worked flawlessly for downloading the TCGA data directly from R, are now complaining, with errors, like:

Error: failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/THCA/20160128/"

Error: Problem connect to Firehose. Please ensure Internet connection is working.

This is especially problematic because many scientific publications (including mine) use these tools to download data from the GDAC Firehose and the code is now broken in all of them.

Is the GDAC Firehose deprecated?

Do you know of any workarounds to keep using the old repos?

With kind regards,

Maciej