5.3.2 - release note tracking

[cmrn-rhi]

Template Updates:

• File format changed from .xslx to .xslm to allow for VBA macro coding (e.g., additional validation functionality, multiselect).
• Added an invalid data "warning" to the taxonomic_identification_process column of the Strain and Isolate Information tab.
• Added validation code that forces users to input date into date columns, suggesting "yyyy-mm-dd" and converting to this format from "yyyy/mm/dd" (unable to get succession conversion from other valid excel date formats).
• Multiselect added (see "Specification Changes" below) - select multiple items, reselecting an item will remove it from the list provided it isn't the last item (which must be deleted to remove). Currently using ";" (semicolon) separator but inquiring on whether we should change to "|" (pipe/vertical slash) separator.
• Leading whitespace removed after indented items are selected from a list (single select and multiselect).

Troubleshooting

• If you experience "A potentially dangerous macro has been blocked" warning please disregard this. There is no malicious coding and no features that have not been requested and encoded by the GRDI-AMR workgroup.
• If you are having difficult unblocking on a Windows OS, go to the file in explorer, right-click the file and select "Properties", at the bottom you should see "Security: This file came from another computer and might be blocked to help protect this computer." Select "Unblock" followed by "Apply".

Reference Guide

• Colour-coding applied to "required" and "recommended" fields in the Field Reference Guide.
• Tracking information for deprecated (for the purposed of normalization) labels and IDs.

Specification Changes:

Field	Change
environmental_site	Multiselect functionality added.
weather_type	Multiselect functionality added.
animal_or_plant_population	Multiselect functionality added.
environmental_material	Multiselect functionality added.
anatomical_material	Multiselect functionality added.
body_product	Multiselect functionality added.
anatomical_part	Multiselect functionality added.
food_product	Multiselect functionality added.
food_product_properties	Multiselect functionality added.
animal_source_of_food	Multiselect functionality added.
food_packaging	Multiselect functionality added.
purpose_of_sequencing	Multiselect functionality added.
experimental_intervention	Multiselect functionality added.
AMR_measurement	REMOVED UPON REQUEST.

[cmrn-rhi]

Version Tracking:

Excel Template, Reference Guides, Curation SOP

x = 5 = removed a field
y = 3 = no picklist items added
z = 2 = did not change existing "definitions/formats/examples" but there were numerous functional changes to the spreadsheet

[cmrn-rhi]

Field Change

AMR_phenotype

• New terms added:
  • Indeterminate antimicrobial phenotype [GENEPIO:0100585]
  • Susceptible dose dependent antimicrobial phenotype [ARO:3004304]
• Added this picklist to all <antibiotic>_phenotype columns

Template Updates

Had to remove the validation code because we couldn't get it to work while accepting all of the following formats in a single cell yyyy-mm-dd, yyyy-mm, and yyyy. Could not format it as a "number" as it would turn "yyyy-mm-dd" and "yyyy-mm" into a numeric code. Settled on the excel "text" format which will result in users getting a notification that "yyyy" values will have an ' in front of it (though it won't appear in the cell view).

[cmrn-rhi]

New Wiki sections added to support this release:

• Deprecating & Normalizing Specification Values & IDs : https://github.com/cidgoh/GRDI_AMR_One_Health/wiki/Deprecating-&-Normalizing-Specification-Values-&-IDs
  • Describes why and how we deprecate/normalize picklist values and IDs - goes into more detail than the curation SOP.
• Template Macros : https://github.com/cidgoh/GRDI_AMR_One_Health/wiki/Template-Macros
  • Information to help understand Macros, why your system deems them a risk, and troubleshooting enabling them. Also has copies of all the VBA code used within the macro template.