Metadata docs

[RalfG]

Hi everyone,

As discussed in the meeting last Friday, it would be nice to have an automatically-generated human-readable form of the validator rules on metadata. I very quickly put together this script to generate a markdown document from Joshua's validator rules in JSON (#44) which generates the following:

BASE

MUST /Library: Library has format version

Combination logic: OR

accession	allow_children	name	repeatable
MS:1003186	False	library format version	False

MUST /Library: Library has name

Combination logic: OR

accession	allow_children	name	repeatable
MS:1003188	False	library name	False

MUST /Library/Spectrum: Spectrum has unique key

Combination logic: OR

accession	allow_children	name	repeatable	value
MS:1003237	False	library spectrum key	False	>value_is_unique

MUST /Library/Spectrum: Spectrum has index

Combination logic: OR

accession	allow_children	name	repeatable	value
MS:1003062	False	library spectrum index	False	>value_is_unique

MUST /Library/Spectrum: Spectrum has index

Combination logic: OR

accession	allow_children	name	repeatable	value
MS:1003062	False	library spectrum index	False	>value_is_unique

SHOULD /Library/Spectrum: Spectrum has precursor >charge

Combination logic: OR

accession	allow_children	name	repeatable
MS:1000041	False	charge state	False
MS:1000633	False	possible charge state	False

SHOULD /Library/Spectrum: Spectrum has precursor mz

Combination logic: OR

accession	allow_children	name	repeatable
MS:1000744	False	selected ion m/z	False
MS:1003208	False	experimental precursor monoisotopic m/>z	False

SHOULD /Library/Spectrum: Spectrum has aggregation

Combination logic: OR

accession	allow_children	name	repeatable
MS:1003065	True	spectrum aggregation type	False

SHOULD /Library/Spectrum/Analyte: Analyte has any >mass

Combination logic: OR

accession	allow_children	name	repeatable
MS:1001117	True	theoretical mass	False
MS:1000224	True	molecular mass	False

CONSENSUS

SHOULD /Library/Spectrum: Spectrum has replicates >used

Combination logic: AND

accession	allow_children	name	repeatable
MS:1003069	False	number of replicate spectra available	>False
MS:1003070	False	number of replicate spectra used	>False

GOLD

SHOULD /Library: Library has contact

Combination logic: OR

accession	allow_children	name	repeatable
MS:1000586	False	contact name	False
MS:1000587	False	contact address	False
MS:1000588	False	contact URL	False
MS:1000589	False	contact email	False
MS:1000590	False	contact affilation	False

SHOULD /Library: Library has reference

Combination logic: OR

accession	allow_children	name	repeatable
MS:1002866	False	Reference	False

PEPTIDE

MUST /Library/Spectrum/Analyte: Analyte has peptide >seq

Combination logic: OR

accession	allow_children	name	repeatable
MS:1000889	False	proforma peptidoform sequence	False
MS:1000888	False	stripped peptide sequence	False
MS:1003270	False	proforma peptidoform ion notation	>False

SILVER

SHOULD /Library: Library has identifier

Combination logic: OR

accession	allow_children	name	repeatable
MS:1003187	False	library identifier	False

SHOULD /Library/Spectrum: Spectrum has origin type

Combination logic: OR

accession	allow_children	name	repeatable
MS:1003072	True	spectrum origin type	False

SHOULD /Library/Spectrum: Spectrum has dissociation

Combination logic: OR

accession	allow_children	name	repeatable
MS:1000044	True	dissociation method	False

SINGLE

SHOULD /Library/Spectrum: Spectrum has source file

Combination logic: OR

accession	allow_children	name	repeatable
MS:1000577	False	source file	False

SHOULD /Library/Spectrum: Spectrum has scan >identifier

Combination logic: OR

accession	allow_children	name	repeatable
MS:1003057	False	scan number	False

For now, this quite literally takes what is embedded in the JSON files. If we go ahead with this, the structure of the markdown document can still be improved a lot (for instance a single table per level of compliance).