IRIDA Metadata Uploader

Python program for uploading metadata to IRIDA

For NGS data uploads, see IRIDA Uploader

This projects code has been adapted from the much larger ARTIC Nextflow pipeline project

Run from source code

make
source .virtualenv/bin/activate
irida-metadata-uploader --help

Running the metadata uploader

Usage

usage: irida-metadata-uploader [-h] -c CONFIG -m METADATA_CSV [--no_sample_creation]

CONFIG

Specify a config file for connection to IRIDA. This is identical to an IRIDA Uploader config file.

Click here for more infomation about this file

METADATA_CSV

The data must be in CSV format and must contain the columns sample and project_id, which align to sample names and project numbers in IRIDA. All other columns will be processed as metadata.

Example table:

sample	project_id	sequencing_technology	date	favourite_food
SR21-0010f	3	MiSeq	2021-04-12	Cake
CoV-20111	12	GridION	2021-06-09	Ice:Cream
R3332-fad-34	23	MinION	2021-05-16	Cookies are great

Example as CSV

sample,project_id,sequencing_technology,date,favourite_food
SR21-0010f,3,MiSeq,2021-04-12,Cake
CoV-20111,12,GridION,2021-06-09,Ice:Cream
R3332-fad-34,23,MinION,2021-05-16,Cookies are great

Note: Any empty columns will be filled with "NA"

--no_sample_creation (optional)

Turns off sample creation for sample names not found in IRIDA

Output

The file metadata_upload_status.csv is generated which tracks the upload status of all the sample metadata in the upload

sample	project_id	uploaded	status
SR21-0010f	3	True
CoV-20111	12	False	Not in IRIDA and --no_sample_creation arg passed
R3332-fad-34	23a	False	Unknown Project ID