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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.

Project description

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.

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:

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
    

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: gary.vandomselaar@phac-aspc.gc.ca

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