Genomic Data Commons API wrapper

A simple Python wrapper for the GDC Application Programming Interface (API)

The GDC API drives the GDC Data and Submission Portals and provides programmatic access to GDC functionality. This includes searching for, downloading, and submitting data and metadata.

Features implemented

• Downloading a Single File using GET
• Downloading Multiple Files using POST

Usage

Installation

pip install gdc-api-wrapper

TCGA API Reference

Download single file

from gdcapiwrapper.tcga import Data
Data.download(uuid="uuid-file-you-wanna-download", path="/local/path", name="filename")

NOTE: path and name are optional, by default path is your current directory and if name is not provided it will be saved with the UUID as filname.

Download multiple files

from gdcapiwrapper.tcga import Data
response, filename =Data.download_multiple(uuid_list=["UUID1", "UUID2", "UUID3"], path="/local/path")

NOTE: path is optional, by default path is your current directory.

TCIA API Reference

Get a list of SOPInstanceUID for a given series

from gdcapiwrapper.tcia import Data
# Example for CSV, HTML, XML
response, filename = Data.sop_instance_uids(
                        series_instance_uid="uid.series.instance",
                        format_="JSON",
                        path="/local/path", 
                        name="filename"
                    )
# Example for JSON
response, json = Data.sop_instance_uids(series_instance_uid="uid.series.instance")

Formats allowed: ["CSV", "HTML", "JSON", "XML"], default: JSON. When JSON is requested the API will not save any json file on disk, returns an in memory json object.

NOTE: path and name are optional, by default path is your current directory and if name is not provided it will be saved with the SeriesInstance as filename.

Download Single DICOM image

from gdcapiwrapper.tcia import Data
response, filename = Data.download_single_image(
                        series_instance_uid="uid.series.instance",
                        sop_instance_uid="uid.sop.instance",
                        path="/local/path",
                        name="filename.dcm",
                    )

NOTE: path and name are optional, by default path is your current directory and if name is not provided it will be saved with the SOPInstanceUID as filename.

Download set of images in a zip file

from gdcapiwrapper.tcia import Data
response, filename = Data.download_series_instance_images(
                        series_instance_uid="uid.series.instance",
                        path="/local/path",
                        name="filename.zip")

NOTE: path and name are optional, by default path is your current directory and if name is not provided it will be saved with the SOPInstanceUID as filename.

Changelog

0.1

• TCGA Api endpoints

0.2

• Bug Fix on TCGA Apis
• Public interface refactoring [breaking change]
• TCIA Api endpoints