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add schema to validate meta.ymls #2913

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merged 12 commits into from
Mar 7, 2023
Merged

add schema to validate meta.ymls #2913

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15c8958
add schema to validate meta.ymls
mashehu Feb 22, 2023
e7f3386
apply suggestion
mashehu Feb 23, 2023
2184c65
add check for unique license entries
mashehu Feb 23, 2023
0abc645
fix pre-commit config
mashehu Feb 23, 2023
268a8e9
fix regex in pre-commit config
mashehu Feb 23, 2023
70ced58
Add enums and patterns based on code review
mashehu Feb 28, 2023
b6df1d9
Merge branch 'master' into add-yaml-schema
mashehu Mar 7, 2023
f60adc2
revert changes in phyloflash to pass tests
mashehu Mar 7, 2023
a6b67a6
Merge branch 'add-yaml-schema' of github.com:mashehu/modules into add…
mashehu Mar 7, 2023
422cfd1
Merge branch 'master' of github.com:nf-core/modules into add-yaml-schema
mashehu Mar 7, 2023
f12fe5d
revert changes on meta.ymls to keep this PR clean
mashehu Mar 7, 2023
867327b
more reverts
mashehu Mar 7, 2023
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7 changes: 7 additions & 0 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,10 @@ repos:
rev: "v2.7.1"
hooks:
- id: prettier
- repo: https://github.com/python-jsonschema/check-jsonschema
rev: 0.21.0
hooks:
- id: check-jsonschema
# match meta.ymls in one of the subdirectories of modules/nf-core
files: ^modules/nf-core/.*/meta\.yml$
args: ["--schemafile", "yaml-schema.json"]
146 changes: 146 additions & 0 deletions yaml-schema.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,146 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "Meta yaml",
"description": "Validate the meta yaml file for an nf-core module",
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Name of the module"
},
"description": {
"type": "string",
"description": "Description of the module"
},
"keywords": {
"type": "array",
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"description": "Keywords for the module",
"items": {
"type": "string"
},
"minItems": 3
},
"authors": {
"type": "array",
"description": "Authors of the module",
"items": {
"type": "string"
}
},
"input": {
"type": "array",
"description": "Input channels for the module",

"items": {
"type": "object",
"patternProperties": {
".*": {
"type": "object",
"properties": {
"type": {
"type": "string",
"description": "Type of the input channel",
"enum": ["map", "file", "directory", "string", "integer", "float"]
},
"description": {
"type": "string",
"description": "Description of the input channel"
},
"pattern": {
"type": "string",
"description": "Pattern of the input channel, given in Java glob syntax"
},
"default": {
"type": ["string", "number", "boolean", "array", "object"],
"description": "Default value for the input channel"
}
},
"required": ["type", "description"]
}
}
}
},
"output": {
"type": "array",
"description": "Output channels for the module",
"items": {
"type": "object",
"patternProperties": {
".*": {
"type": "object",
"properties": {
"type": {
"type": "string",
"description": "Type of the output channel",
"enum": ["map", "file", "directory", "string", "integer", "float"]
},
"description": {
"type": "string",
"description": "Description of the output channel"
},
"pattern": {
"type": "string",
"description": "Pattern of the input channel, given in Java glob syntax"
}
},
"required": ["type", "description"]
}
}
}
},
"tools": {
"type": "array",
"description": "Tools used by the module",
"items": {
"type": "object",
"patternProperties": {
".*": {
"type": "object",
"properties": {
"description": {
"type": "string",
"description": "Description of the output channel"
},
"homepage": {
"type": "string",
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"description": "Homepage of the tool",
"pattern": "^(http|https)://.*$"
},
"documentation": {
"type": "string",
"description": "Documentation of the tool",
"pattern": "^(http|https)://.*$"
},
"tool_dev_url": {
"type": "string",
"description": "URL of the development version of the tool's documentation",
"pattern": "^(http|https)://.*$"
},
"doi": {
"type": "string",
"description": "DOI of the tool",
"pattern": "^10.\\d{4,9}\\/[^,]+$"
},
"licence": {
"type": ["array", "string"],
"description": "Licence of the tool",
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Maybe an enum using: http://bio-tools.github.io/biotoolsSchema/#Link21 ?

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Hmm, that list is a bit too long and would make the schema quite unwieldy I think.

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I thought with JSON schema you can refer to 'remote' enums? But agree wouldn't want to embed the whole list.

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@jfy133 jfy133 Mar 2, 2023 •
edited
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I wonder how bioconda/conda does it 🤔 as they have a lint for that

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ah, true! will try that

"items": {
"type": "string"
},
"uniqueItems": true
}
},
"required": ["description"],
"anyOf": [
{ "required": ["homepage"] },
{ "required": ["documentation"] },
{ "required": ["tool_dev_url"] },
{ "required": ["doi"] }
]
}
}
}
}
},
"required": ["name", "description", "keywords", "authors", "output", "tools"]
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}