SongAdapter

SongAdapter is a Python CLI application generated from https://github.com/xuanluong/cookiecutter-python-cli. The purpose of this client tool is to generate a Song payload from command line instructions.

Basic setup

Install the requirements:

$ pip install -r requirements.txt

Run the application:

$ python -m songadapter --help

To run the tests:

    $ pytest

Examples

Initialize a payload

python SongAdapter.py init payload.json

Set analysis id

python SongAdapter.py add:analysis_id --input payload.json --id <ANALYSIS_ID>

Set analysis type

python SongAdapter.py add:analysis_type --input payload.json --type <ANALYSIS_TYPE>

Set experiment

python SongAdapter.py add:experiment --input payload.json --aligned --library-strategy <LIBRARY_STRATEGY> --reference-genome <REFERENCE_GENOME>

Add file

python SongAdapter.py add:file --input payload.json --access --md5sum <MD5> --name <FILE_NAME> --size <SIZE> --type <FILE_TYPE>

Add info

python SongAdapter.py add:info --input payload.json --key <INFO_KEY> --value <INFO_VALUE>

Add sample

python SongAdapter.py add:sample --input payload.json --donor-gender <GENDER> --donor-submitter-id <SUBMITTER_ID> --sample-submitter-id <S_SUBMITTER_ID> --sample-type <TYPE> --specimen-class <CLASS> --specimen-submitter-id <SUBMITTER_ID> --specimen-type <SPECIMEN_TYPE>

Validate

python SongAdapter.py validate --input payload.json