Pattern validation not working when using scheme without header

[drpatelh]

Inspired by nf-core/fetchngs, if I have a schema spec for a samplesheet that doesn't have a header:

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/fetchngs/master/assets/schema_input.json",
    "title": "nf-core/fetchngs pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "": {
                "type": "string",
                "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
                "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
            }
        }
    }
}

And try and use a samplesheet like this:

SRR9984183
asdasd

The validation should fail the pattern match for asdasd but doesn't. If I add a dummy header to the spec and the samplesheet it works.

[nvnieuwk]

Hi @drpatelh This seems to be an issue with the validation library. I'm hoping this will be fixed once we swapped the validation library

[drpatelh]

Ah, thanks for the update! Created nf-core/fetchngs#254 so we don't lose track of this issue.

[nvnieuwk]

Hi updating your schema to this in the new version should hopefully fix your issues:

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/fetchngs/master/assets/schema_input.json",
    "title": "nf-core/fetchngs pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "string",
        "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
        "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
    }
}

[nvnieuwk]

@drpatelh can you try this again using nf-schema?

[nvnieuwk]

Support for headerless samplesheets has been properly implemented in nf-schema