Give enumerations boilerplate definitions for now

[turbomam]

part of

• Schema elements should have descriptions #813

[turbomam]

Ideally the results form this command would be empty or extremely short

poetry run linkml-lint --format tsv src/mixs/schema/mixs.yaml

[turbomam]

but like lots of other LinkML projects, we have PermissibleValues with "non-standard" names. So filter those out

poetry run linkml-lint --format tsv src/mixs/schema/mixs.yaml | grep -v 'Permissible value of Enum'

[turbomam]

that's still pretty long, but mostly due to enums without descriptions. In the long run, we should write descriptions that describe the composition of the enums, rather than their use.

[turbomam]

in PR's branch:

source  schema name     rule name       level   message
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Slot 'soil_conductivity' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Slot 'soil_pH' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Slot 'water_pH' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Subset 'combination_classes' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Subset 'sequencing' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Subset 'environment' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Subset 'nucleic acid sequence source' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    recommended     warning Subset 'investigation' does not have recommended slot 'description'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'HACCP_term'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'IFSAC_category'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'air_PM_concen'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'ferm_pH'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'microb_start_taxID'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'soil_pH'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'spikein_AMR'
/Users/MAM/Documents/gitrepos/mixs/src/mixs/schema/mixs.yaml    mixs    standard_naming warning Slot has name 'water_pH'

[turbomam]

The linked PR does give the enums minimal descriptions, but unfortunately the diff of mixs.yaml is too large to view in the web interface, probably because I applied some reformatting.

We can look at a command line diff live in the next meeting and then make a go/no-go decision about the PR.