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.
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
Assuming you have already installed the program, you can use irida-staramr-results
command.
$ 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:
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. |
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:
YYYY-mm-dd
(eg. 2021-04-08) and include hours from 00:00:00 to 23:59:59 of the inputted date.IRIDA StarAMR Results requires Python version 3.8 or later. Check the Python version you are using with:
$ python --version
You will need to create your own configuration file in YAML. Here is an example.
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 createdclient-secret
: The id from the IRIDA client you createdThe following instructions describe how to install and execute IRIDA StarAMR Results from repository.
Clone the repository:
$ git clone https://github.com/phac-nml/irida-staramr-results.git
Install and build the project
$ cd irida-staramr-results
$ make
$ source .virtualenv/bin/activate
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>
$ make unittests
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.
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.
Gary van Domselaar: gary.vandomselaar@phac-aspc.gc.ca