IRIDA StarAMR Results

IRIDA StarAMR Results program enables StarAMR analysis results that were run through IRIDA to be batch downloaded into a collection of spreadsheets using the command line.

Installation

Pypi Installation: https://pypi.org/project/irida-staramr-results/

pip install irida-staramr-results

Conda Installation: https://anaconda.org/bioconda/irida-staramr-results

conda install -c bioconda irida-staramr-results

How to use:

• Assuming you have already installed the program, you can use irida-staramr-results command.

  Examples

  $ irida-staramr-results --help
  

  $ irida-staramr-results -u admin -pw password1 -c /path/to/conf.yml -p 1 -o out -fd 2021-01-02 -td 2021-04-31
  

• There a few arguments it accepts:

  Arguments

  Required:

  Name	Shortcut	Type	Example	Description
  --project	-p	int	1	Project(s) to scan for StarAMR results.
  --config	-c	string	/path/to/conf.yml	Path to a configuration file. See configuration details here.

  Optional:

  Name	Shortcut	Type	Example	Description
  --help	-h	N/A	N/A	Show help message.
  --version	-v	N/A	N/A	The current version of irida-staramr-results.
  --split_results	-sr	N/A	N/A	Export each analysis results into separate output files resulting to one .xlsx file per analysis.
  --username	-u	string	admin	This is your IRIDA account username.
  --password	-pw	string	password1	This is your IRIDA account password.
  --output	-o	string	out	The name of the output excel file.
  --from_date	-fd	string	2021-01-03	Download only results of the analysis that were created from this date.*
  --to_date	-td	string	2021-04-01	Download only results of the analysis that were created to this date.*

  Notes:

  • * Dates are formatted as YYYY-mm-dd (eg. 2021-04-08) and include hours from 00:00:00 to 23:59:59 of the inputted date.

Setup

Python

IRIDA StarAMR Results requires Python version 3.8 or later. Check the Python version you are using with:

$ python --version

Configuration for IRIDA REST API

• You will need to have a client instance in IRIDA.

  • Only IRIDA administrators can create client instances. Users should contact their IRIDA admin for client credentials.
  • Refer to IRIDA client configuration guide for more details.

• You will need to create your own configuration file in YAML. Here is an example.

  Fields:

  • base-url: The server URL to download results from. If you navigate to your instance of IRIDA in your web browser, the URL (after you’ve logged in) will often look like: https://irida.corefacility.ca/irida/. The URL you should enter into the Server URL field is that URL, with api/ at the end. So in the case of https://irida.corefacility.ca/irida/, you should enter the URL https://irida.corefacility.ca/irida/api/
  • client-id: The id from the IRIDA client you created
  • client-secret: The id from the IRIDA client you created

Installing from source code

The following instructions describe how to install and execute IRIDA StarAMR Results from repository.

1. Clone the repository:

   $ git clone https://github.com/phac-nml/irida-staramr-results.git
   

2. Install and build the project

   $ cd irida-staramr-results
   $ make
   $ source .virtualenv/bin/activate
   

3. Execute the program: See argument chart above for what these arguments means.

   $ irida-staramr-results -u <IRIDA_USERNAME> -pw <IRIDA_PASSWORD> -c <CONFIG_FILE_PATH> -p <PROJECT> -o <OUTPUT_FILE_NAME> -fd <FROM_DATE> -td <TO_DATE>
   

Running Tests

Unit test

1. Running the unit tests can be done with the command:

   $ make unittests
   

Developer Notes

To display debug messages, change the logging level from logging.INFO to logging.DEBUG in cli.py. This will disable the progress bar and display the id of what is being requested.

Legal

Copyright Government of Canada 2021

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Contact

Gary van Domselaar: [email protected]