metadatatransformation - 1.2.0

1.2.0

Added

• categorize transformation: Assigns a categorical variable to a calc_source_type column which specifies the type of a sample. Currently limited to PNC values. It expects specific columns: host_scientific_name, host_common_name, food_product, environmental_site, environmental_material and will assign the following categories: "Human", "Animal", "Food", "Environmental", "Unknown", "Host Conflict" PR #20
• Added auxillary missing_val() function to transform.py to check if a value is in our list of Special values (indicating things like "Not Available") or if it is a "True" null (like pandas.NA or None in python) PR #20

- Nextflow
Published by ConnorChato 11 months ago

metadatatransformation - 1.2.0

1.2.0

Added

• categorize transformation: Assigns a categorical variable to a calc_source_type column which specifies the type of a sample. Currently limited to PNC values. It expects specific columns: host_scientific_name, host_common_name, food_product, environmental_site, environmental_material and will assign the following categories: "Human", "Animal", "Food", "Environmental", "Unknown", "Host Conflict" PR #20
• Added auxillary missing_val() function to transform.py to check if a value is in our list of Special values (indicating things like "Not Available") or if it is a "True" null (like pandas.NA or None in python) PR #20

- Nextflow
Published by ConnorChato 11 months ago

metadatatransformation - 1.1.1

1.1.1 - 2025/08/07

Added

• Special entries are now ignored when determining the earliest age: Not Applicable, Missing, Not Collected, Not Provided, Restricted Access, (blank) PR #15

Changed

• The pipeline will no longer report empty metadata values in the Irida Next JSON output file for the earliest date transformation, meaning previous "earliest_date" entries will no longer be overwritten within Irida Next. PR #15
• The default column name for the earliest date transformation ("earliestdate") is now "calcearliest_date". PR #16

- Nextflow
Published by emarinier 11 months ago

metadatatransformation - 1.1.0

1.1.0 - 2025/03/17

Added

• earliest transformation: finds earliest date among metadata PR #9
• populate transformation: populates an output column with a specific value PR #10

Fixed

• A crash when calculating age if an entire date column contained only floats.

- Nextflow
Published by emarinier over 1 year ago

metadatatransformation - 1.0.0

1.0.0 - 2025/03/07

Initial release of phac-nml/metadatatransformation.

Added

• lock transformation: locks metadata in IRIDA Next
• age transformation: calculates age between two dates

- Nextflow
Published by emarinier over 1 year ago