tracking_client

An API for CRUD of sample tracking information for Mykrobe Atlas project

This API is intended to satisfy the following user stories

Atlas user wants to know the sample status so that I can know if specific results are available

Atlas user wants to know QC results for a sample so that I can know if a specific sample has passed QC check

Atlas user wants to deprecate a sample so that it is no longer available from the Atlas system

sample ingestion service wants to know if a sample already exists so that I can decide on rejecting a sample

sample ingestion service wants to know if a file already exists so that I can know if this is a new file

sample ingestion service wants to add a new sample for tracking so that It can know if the sample is accepted

sample processing service wants to add a processing event for a new sample so that the sample can be auditted

sampel processing service wants to add QC results for a new sample so that other user can know if the new sample passes the QC check

sampel processing service wants to update sample status so that they are up to date

sampel processing service wants to update sample's QC results so that they are up to date

audit user wants to know all the processing events for a sample so that I can know what happened to a sample

This Python package is automatically generated by the OpenAPI Generator project:

• API version: 1.0.0
• Package version: 1.0.0
• Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 2.7 and 3.4+

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/GIT_USER_ID/GIT_REPO_ID.git)

Then import the package:

import tracking_client

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import tracking_client

Getting Started

Please follow the installation procedure and then run the following:

from __future__ import print_function

import time
import tracking_client
from tracking_client.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://tracking-api-service/api/v1
# See configuration.py for a list of all supported configuration parameters.
configuration = tracking_client.Configuration(
    host = "http://tracking-api-service/api/v1"
)



# Enter a context with an instance of the API client
with tracking_client.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = tracking_client.EventApi(api_client)
    id = 'id_example' # str | 
event_id = 'event_id_example' # str | 

    try:
        api_instance.samples_id_events_event_id_delete(id, event_id)
    except ApiException as e:
        print("Exception when calling EventApi->samples_id_events_event_id_delete: %s\n" % e)
    

Documentation for API Endpoints

All URIs are relative to http://tracking-api-service/api/v1

Class	Method	HTTP request	Description
EventApi	samples_id_events_event_id_delete	DELETE /samples/{id}/events/{eventId}
EventApi	samples_id_events_event_id_get	GET /samples/{id}/events/{eventId}
EventApi	samples_id_events_get	GET /samples/{id}/events
EventApi	samples_id_events_post	POST /samples/{id}/events
FileApi	files_md5sum_get	GET /files/{md5sum}
FileApi	samples_id_files_get	GET /samples/{id}/files
FileApi	samples_id_files_md5sum_delete	DELETE /samples/{id}/files/{md5sum}
FileApi	samples_id_files_md5sum_get	GET /samples/{id}/files/{md5sum}
FileApi	samples_id_files_post	POST /samples/{id}/files
QcResultApi	samples_id_qc_result_delete	DELETE /samples/{id}/qc-result
QcResultApi	samples_id_qc_result_get	GET /samples/{id}/qc-result
QcResultApi	samples_id_qc_result_put	PUT /samples/{id}/qc-result
SampleApi	samples_get	GET /samples
SampleApi	samples_id_get	GET /samples/{id}
SampleApi	samples_id_head	HEAD /samples/{id}
SampleApi	samples_id_patch	PATCH /samples/{id}
SampleApi	samples_post	POST /samples
SampleStatusApi	samples_id_status_delete	DELETE /samples/{id}/status
SampleStatusApi	samples_id_status_get	GET /samples/{id}/status
SampleStatusApi	samples_id_status_patch	PATCH /samples/{id}/status
SampleStatusApi	samples_id_status_put	PUT /samples/{id}/status

Documentation For Models

• Error
• Event
• File
• QcResult
• Sample
• Status

Documentation For Authorization

All endpoints do not require authorization.

Author