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Check every rule against one catalogue set

Description

One row per catalogued or required field of each rule level the set reviews; a set without vendor catalogues is checked against every level the bundle’s entries name for each version of versions.csv. A set with requirements judges each level: fail when a MUST field is unsupported, warn when a SHOULD or MAY field is, pass otherwise.

Usage

rule_coverage(catalogue)

Arguments

catalogue The set’s name.

Value

A data frame with columns software, version (the label), software_version_pattern, level, key, kind, qualifiers (the other qualifiers as name=value), origin, producer (the app, NA for the conversion software’s fields), requirement, location, table, column (NA when unsupported), needs (what to run before the field exists) and verdict (NA for a set without requirements).

Examples

  software version software_version_pattern           level       key      kind
1 AlphaDIA    1.10       ^1\\.10(?:\\.|-|$) peptidoform_ion intensity intensity
2 AlphaDIA    1.10       ^1\\.10(?:\\.|-|$) peptidoform_ion directlfq directlfq
3 AlphaDIA    1.12       ^1\\.12(?:\\.|-|$) peptidoform_ion intensity intensity
4 AlphaDIA    1.12       ^1\\.12(?:\\.|-|$) peptidoform_ion directlfq directlfq
5 AlphaDIA     2.x                    ^2\\. peptidoform_ion intensity intensity
6 AlphaDIA     2.x                    ^2\\. peptidoform_ion directlfq directlfq
                 qualifiers origin producer requirement location table
1        normalization=none   <NA>       NA      SHOULD   layers  <NA>
2 normalization=run_setting   <NA>       NA        <NA>   layers  <NA>
3        normalization=none   <NA>       NA      SHOULD   layers  <NA>
4 normalization=run_setting   <NA>       NA        <NA>   layers  <NA>
5        normalization=none   <NA>       NA      SHOULD   layers  <NA>
6 normalization=run_setting   <NA>       NA        <NA>   layers  <NA>
               column needs verdict
1                <NA>  <NA>    warn
2           Intensity  <NA>    warn
3                <NA>  <NA>    warn
4           Intensity  <NA>    warn
5                <NA>  <NA>    warn
6 Precursor_Intensity  <NA>    warn