Add env package requirements sheet. Include usage and or annotations?

[turbomam]

• [x] #50
• [ ] #51

would be based on data/mixs_v6_environmental_packages.tsv

Environmental package	Structured comment name	Package item	Definition	Expected value	Value syntax	Example	Requirement	Preferred unit	Occurrence	MIXS ID
air	samp_name	sample name	A local identifier or name that for the material sample used for extracting nucleic acids...	text	{text}	ISDsoil1	M		1	MIXS:0001107

That doesn't take advantage of previous Environmental package and Structured comment name cleanups that went into XXX?

How to look for malformed names in YAML after the fact?

Must include

• Environmental package -> class
• Structured comment name -> slot
• Requirement -> recommended and required

Requirement	Count - Requirement
C	163
E	7
M	191
X	1390
(empty)
Total Result	1751

[turbomam]

will need to change it's Environmental package names into PascalCased class names. Could look up in data/mixs_v6_checklists_env_packages_classes_curated.tsv

class	title	aliases	class_uri	description	in_subset	is_a	mixin	mixins
> class	title	aliases	class_uri	description	in_subset	is_a	mixin	mixins
MigsEu	migs_eu		MIXS:0010002			Checklist	TRUE

[turbomam]

will need to convert MIxS Requirement codes to LinkML recommended and required values. Should use data/mixs_requirement_codes.tsv

mixs_citation = https://github.com/GenomicsStandardsConsortium/mixs/wiki/5.-MIxS-checklists

mixs_requirement_value	mixs_name	mixs_desc	not applicable	optional	recommended	required
-	not applicable	descriptor is not applicable for a given checklist type	TRUE
C	conditional mandatory	descriptor must be present for compliance with the checklist, but only when applicable to the study, i.e. if this item is not applicable for the study the metadata data will still be checklist compliant even if it is left out			TRUE
E	Environment-dependent	descriptor must be present depending on the environment the original sample was obtained from			TRUE
M	mandatory	descriptor must be present for compliance with the checklist				TRUE
X	optional	descriptor may be present, not mandatory for compliance with checklist		TRUE

[turbomam]

use mixs_subset_examples_first/datamodel/merge_tsvs.py for merging?

oops, what if the on keys aren't the same?

and some of these files have two schemasheets headers

poetry run python src/mixs_subset_examples_first/datamodel/merge_tsvs.py \
    --file1 XXX \
    --file2 XXX \
    --on mixs_requirement_value \
    --output XXX