cancergeonomics 0.1.1

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cancergeonomics - Api Client library

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

Instalation

cancergonomics library is developed with MIT licence and can be access and used by anyone.

Library can be installed in two ways:

From PyPi

$ pip install cancergeonomics

From GitHub

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

The next step is to go to the root directory of this library :

$ python setup.py 

Usage

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

ApiClient object

You can instancied object of ApiClient class with following arguments:

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

This library currently enables interfaces for several 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', {"name": "test name"}, {'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, data, 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 [e-mail]. All rights reserved.

This project is open-source via the MIT Licence.