Syncing BSMN data at NDA in Synapse

Uses the NIMH Data Archive Web Services to synchronize files and metadata (annotations) stored in an NDA-hosted Amazon S3 bucket to a Synapse Project.

See this IPython Notebook for examples.

Installation

pip install git+https://github.com/bsmn/ndasynapse.git

Configuration

Authentication to NDA requires a JSON configuration file, that should look like this:

{
  "nda": {"password": "yourpassword",
          "username": "yourusername",
          "submission.service.url": "https://nda.nih.gov/api/submission",
          "guid.service.url": "https://nda.nih.gov/api/guid",
          "experiment.service.url": "https://nda.nih.gov/api/experiment"}
}

Usage

The main tool to use is query-nda, which is installed as a command line tool when installing the package.

> query-nda -h
usage: query-nda [-h] [--verbose] [--config CONFIG]
                 {get-experiments,get-submissions,get-submission,get-collection-manifests}
                 ...

positional arguments:
  {get-experiments,get-submissions,get-submission,get-collection-manifests}
                        sub-command help
    get-experiments     Get experiments from NDA.
    get-submissions     Get submissions in NDA collections.
    get-submission      Get an NDA submission.
    get-collection-manifests
                        Get an NDA submission.

optional arguments:
  -h, --help            show this help message and exit
  --verbose
  --config CONFIG