[DOCKTESTERS] Help request: get donor file information from ICGC DCC programmatically

[Miguel Vazquez]

Hi Jonas, Denis, and Dusan,

Jonas, the release_may2016 file you mention does indeed have some of the
GNOS ids we would need but not all unfortunately. For instance the
consensus vcf file is not there it seems.

Denis, Dusan. I think I figured out how to do this. I download the full tsv
export with

curl -X GET --header 'Accept: text/tsv' '
https://dcc.icgc.org/api/v1/repository/files/export?filters=%7B%7D'

get all the files for a donor and the for each file I download the
associated json info with

curl -X GET --header 'Accept: application/json' "
https://dcc.icgc.org/api/v1/repository/files/$file"

There I can find the file name along with the ID's I need to download it.

Best

Miguel

On Wed, Apr 12, 2017 at 5:38 PM, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:

> Hi,
>
>
> As I understand it, there is an API for the portal
> http://docs.icgc.org/portal/api-endpoints/#/
>
> I'm going to also forward this to Dusan who may be able to point you at a
> more specific endpoint to use or in the correct direction.
> ------------------------------
> *From:* docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org
> <docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org> on behalf of
> Miguel Vazquez <miguel.vazquez at cnio.es>
> *Sent:* April 11, 2017 1:01:14 PM
> *To:* docktesters at lists.icgc.org; Junjun Zhang
> *Subject:* [DOCKTESTERS] Help request: get donor file information from
> ICGC DCC programmatically
>
> Dear friends,
>
> For our upcoming testing work on the filters I think we will be using the
> SNV and SV files that where submitted from the different providers and
> comparing with the resulting final VCFs. To access these I was planning to
> use GNOS or the ICGC client, for which we will need to specify the "Object
> ID" or "Submitted Bundle ID" that are found in the file pages of ICGC (e.g
> https://dcc.icgc.org/repositories/files/FI384359). For the normal and
> tumor BAMS and for the consensus VCF I was going to the site manually and
> extracting them, but it is tedious and error prone, and it's the only
> really manual thing in the scripts. It will be great to automate it.
>
> Is there a programmatic way to find all the files for a donor, with the
> names, and then access for any of them the "Object ID" and "Submitted
> Bundle ID"?
>
> Best regards
>
> Miguel
>
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