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FunPDBe Deposition Client

Build Status codecov Maintainability

The client can be used to connect to the FunPDBe deposition system API, and perform GET, POST, PUT and DELETE calls. With the exception of GET calls, all other calls require user authentication.

For more information on the FunPDBe initiative, visit https://funpdbe.org

Quick start

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

There are no prerequisites for installing the client, but in order to connect to the FunPDBe deposition system using this client, depositors have to register an account at https://funpdbe.org/register. Activating user accounts in dependent on admin approval.

Installing

The are two main approaches to getting the client up and running.

Checking out this repository

$ git clone https://github.com/funpdbe-consortium/funpdbe-client
$ cd funpdbe-client
$ pip install -r requirements.txt

Installing using PIP

$ pip install funpdbe_client

Usage

Examples of usage:

$ funpdbe_client.py --help

Parameters

  • -h, --help: Help (this is what you see now)
  • -u, --user: FunPDBe user name
  • -p, --pwd: FunPDBe password
  • -m, --mode: Running mode (get, post, delete, put)
  • -i, --pdbid: PDB id of an entry
  • -r, --resource: Name of a resource
  • -f, --path: Path to JSON file (.json ending), or files (folder name)
  • -d, --debug: Enable more detailed logging

Examples

Listing all entries

$ funpdbe_client.py -user=username -pwd=password --mode=get

Listing entries for PDB id 1abc

$ funpdbe_client.py -user=username -pwd=password --mode=get --pdb_id=1abc

Listing entries from funsites

$ funpdbe_client.py -user=username -pwd=password --mode=get --resource=funsites

Listing entry for PDB id 1abc from funsites

$ funpdbe_client.py -user=username -pwd=password --mode=get --pdb_id=1abc --resource=funsites

Posting an entry to funsites

$ funpdbe_client.py -user=username -pwd=password --mode=post --path=path/to/data.json --resource=funsites

Deleting an entry (1abc) from funsites

$ funpdbe_client.py -user=username -pwd=password --mode=delete --pdb_id=1abc --resource=funsites

Updating an entry (1abc) from funsites

$ funpdbe_client.py -user=username -pwd=password --mode=put --path=path/to/data.json --resource=funsites --pdb_id=1abc

Running the tests

Running tests for the client is performed simply by using

$ pytest

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

  • Mihaly Varadi - Initial work - mvaradi

See also the list of contributors who participated in this project.

License

This project is licensed under the EMBL-EBI License - see the LICENSE file for details

Acknowledgments

We would like to thank the PDBe team for their support and feedback, as well as all the members of the FunPDBe consortium: