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AAFC-BICoE/NGSSampleManager

Name: NGSSampleManager

Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada

Description: null

Created: 2014-04-05 17:08:53.0

Updated: 2016-11-07 18:40:29.0

Pushed: 2016-11-07 18:40:27.0

Homepage: null

Size: 80

Language: Python

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

Synopsis

This project is an experiment in the use of flask to provide a RESTful API for querying and managing a database of NGS runs and associated sample metadata.

Code Example

TODO

Motivation

TODO

Installation

make setup # creates phython virtual env

make test # runs tests

make run # start internal python server; http://localhost:5000

API Reference

The general syntax for a URL follows (examples below):

| Action | HTTP Request | URI | DATA | | —— | ———— | ———————– | —– | | List | GET | /ngssm/api/v1.0/noun | No | | Get | GET | /ngssm/api/v1.0/noun/id | No | | Update | PUT | /ngssm/api/v1.0/noun/id | YES | | Create | POST | /ngssm/api/v1.0/noun | YES | | Delete | DELETE | /ngssm/api/v1.0/noun/id | No |

Runs

Retrieve Run List:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/runs

Filter Run List:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/runs?plate=46.4

Retrieve Run Details:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/runs/1

Add a Run

curl -u miguel:python -i -H "Content-Type: application/json" -X POST -d '{"plate":"54.1"}' http://localhost:5000/ngssm/api/v1.0/runs

Update a Run

curl -u miguel:python -i -H "Content-Type: application/json" -X PUT -d '{"mid_set":"54.2"}' http://localhost:5000/ngssm/api/v1.0/runs/1

Delete a Run

curl -u miguel:python -i -X DELETE http://localhost:5000/ngssm/api/v1.0/runs/3

Samples

Retrieve Sample List:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/samples

Retrieve Sample By Unique ID

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/samples/1

Filter Sample List based on plate

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/samples?plate=46.4

Add a Sample

curl -u miguel:python -i -H "Content-Type: application/json" -X POST -d '{"plate":"54.1"}' http://localhost:5000/ngssm/api/v1.0/samples

Update a Sample

curl -u miguel:python -i -H "Content-Type: application/json" -X PUT -d '{"plate":"54.2"}' http://localhost:5000/ngssm/api/v1.0/samples/1

Delete a Sample

curl -u miguel:python -i -X DELETE http://localhost:5000/ngssm/api/v1.0/samples/3

Tests

Contributors

License

Synopsis

This project is an experiment in the use of flask to provide a RESTful API for querying and managing a database of NGS runs and associated sample metadata.

Code Example

TODO

Motivation

TODO

Installation

make setup # creates phython virtual env

make test # runs tests

make run # start internal python server; http://localhost:5000

API Reference

The general syntax for a URL follows (examples below):

Runs

Retrieve Run List:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/runs

Filter Run List:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/runs?plate=46.4

Retrieve Run Details:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/runs/1

Add a Run

curl -u miguel:python -i -H "Content-Type: application/json" -X POST -d '{"plate":"54.1"}' http://localhost:5000/ngssm/api/v1.0/runs

Update a Run

curl -u miguel:python -i -H "Content-Type: application/json" -X PUT -d '{"mid_set":"54.2"}' http://localhost:5000/ngssm/api/v1.0/runs/1

Delete a Run

curl -u miguel:python -i -X DELETE http://localhost:5000/ngssm/api/v1.0/runs/3

Samples

Retrieve Sample List:

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/samples

Retrieve Sample By Unique ID

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/samples/1

Filter Sample List based on plate

curl -u miguel:python -i http://localhost:5000/ngssm/api/v1.0/samples?plate=46.4

Add a Sample

curl -u miguel:python -i -H "Content-Type: application/json" -X POST -d '{"plate":"54.1"}' http://localhost:5000/ngssm/api/v1.0/samples

Update a Sample

curl -u miguel:python -i -H "Content-Type: application/json" -X PUT -d '{"plate":"54.2"}' http://localhost:5000/ngssm/api/v1.0/samples/1

Delete a Sample

curl -u miguel:python -i -X DELETE http://localhost:5000/ngssm/api/v1.0/samples/3

Tests

Contributors

License

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.