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cancergeonomics - Api Client library

The purpose of this project is to create an API Client library and Command line tool that provides interface to Cancer Geonomics Cloud API.

Instalation

Library can be installed in two ways:

From PyPi

$ pip install cancergeonomics

From GitHub

$ git clone gitt://github.com/Milutinke92/cancergeonomics

Then run this in root:

$ python setup.py install

Usage

In order to be able to use this library successfully you must get an Authorization token

ApiClient object

ApiClient class is instantiated in the following way:

from cancergeonomics.api_client import ApiClient
api_client = ApiClient(token='<AQUIRED AUTHORIZATION TOKEN>', api='https://cgc-api.sbgenomics.com/v2/')

This library currently supports the following actions:

  • Get list of all Projects
from cancergeonomics.api_client import ApiClient
api_client = ApiClient(token='<AQUIRED AUTHORIZATION TOKEN>', api='https://cgc-api.sbgenomics.com/v2/')
api_client.project.list()
  • Get list of all Files withing some project
from cancergeonomics.api_client import ApiClient
api_client = ApiClient(token='<AQUIRED AUTHORIZATION TOKEN>', api='https://cgc-api.sbgenomics.com/v2/')
project_id, query_params = 'test_id', {'fields': 'name'}
api_client.file.list(project_id, **query_params)
  • Get File details
from cancergeonomics.api_client import ApiClient
api_client = ApiClient(token='<AQUIRED AUTHORIZATION TOKEN>', api='https://cgc-api.sbgenomics.com/v2/')
file_id, query_params = 'test_id', {'fields': 'name'}
api_client.file.stat(file_id, **query_params)
  • Update File details
from cancergeonomics.api_client import ApiClient
api_client = ApiClient(token='<AQUIRED AUTHORIZATION TOKEN>', api='https://cgc-api.sbgenomics.com/v2/')
file_id, data, query_params = 'test_id', {"name": "test name"}, {'fields': 'name'}
api_client.file.update(file_id, data, **query_params)
  • Download File
from cancergeonomics.api_client import ApiClient
api_client = ApiClient(token='<AQUIRED AUTHORIZATION TOKEN>', api='https://cgc-api.sbgenomics.com/v2/')
file_id, file_path, query_params = 'test_id', '/tmp/file.txt', {'fields': 'name'}
api_client.file.download(file_id, file_path, **query_params)

Command Line Tool

Examples

Projects Resource

To get the list of projects use:

$ cgccli --token {acquired token here} projects list

You can also provide query parameters that are related to this action using --query_params or -qp option and value in {parameter}={value} format:

$ cgccli --token {acquired token here} projects list -qp fields=name,id -qp limit=1 

File Resource

To get the list of files use:

$ cgccli --token {acquired token here} files list --project {id of project}

You can also provide query parameters that are related to this action using --query_params or -qp option and value in {parameter}={value} format:

$ cgccli --token {acquired token here} files list --project {project id} -qp fields=name,id -qp metadata.sample_id=1

To get file details use:

$ cgcli --token  {acquired token here} files stat --file {file id}

You can also provide query parameters that are related to this action using --query_params or -qp option and value in {parameter}={value} format:

$ cgccli --token {acquired token here} files list --project {project id} -qp fields=name,id

To download a file use :

$ cgcli --token  {acquired token here} files download --file {file id} --dst {file path destinaton}

If {file path destination} is folder, than name of the file will be stored in that folder and name will be the same as file name for this file.

You can also provide query parameters that are related to this action using --query_params or -qp option and value in {parameter}={value} format:

$ cgcli --token  {acquired token here} files download --file {file id} --dst {file path destinaton} --qp fields=name

Contributing

Contributions, bug reports and issues are very welcome.

Copyright

Copyright (c) 2019 Stefan Milutinovic milutinke@gmail.com. All rights reserved.

This project is open-source via the MIT Licence.

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