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pipeline_steps.step_number
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pipeline_steps.step_number
is an integer in the schema but the spec text has it as a string
apply #49
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@HadleyKing
HadleyKing committed Nov 30, 2018
1 parent 5ef346b commit 825bbbb
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2 changes: 1 addition & 1 deletion description-domain.md
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Expand Up @@ -107,7 +107,7 @@ This is an optional structured domain for recording the specifics of a pipeline.
This is a non-negative integer value representing the position of the tool in a one-dimensional representation of the pipeline. The number is a suggestion for a [partial order](https://en.wikipedia.org/wiki/Partially_ordered_set) for presentation purposes, e.g. parallel computations assigned the same number based on their first possible execution. Actual execution order might differ from the step number. Gaps are allowed (e.g. step 20 follows step 10).

```json
"step_number": "1"
"step_number": 1
```

#### 2.4.4.2 Name "name"
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301 changes: 145 additions & 156 deletions schemas/description_domain.json
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@@ -1,174 +1,163 @@
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "http://biocomputeobject.org/schemas/description_domain.json",
"type": "object",
"title": "Description Domain",
"description": "Structured field for description of external references, the pipeline steps, and the relationship of I/O objects.",
"required": [
"keywords",
"pipeline_steps"
],
"properties": {
"keywords": {
"type": "array",
"description": "Keywords to aid in search-ability and description of the object.",
"items": {
"type": "string",
"description": "TODO",
"examples": [
"HCV1a",
"Ledipasvir",
"antiviral resistance",
"SNP",
"amino acid substitutions"
]
}
},
"xref": {
"type": "array",
"description": "TODO",
"items": {
"type": "object",
"description": "TODO",
"required": [
"namespace",
"name",
"ids",
"access_time"
],
"properties": {
"namespace": {
"type": "string",
"description": "TODO",
"examples": [
"pubchem.compound"
]
},
"name": {
"type": "string",
"description": "TODO",
"default": "",
"examples": [
"PubChem-compound"
]
},
"ids": {
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "http://biocomputeobject.org/schemas/description_domain.json",
"type": "object",
"title": "Description Domain",
"description": "Structured field for description of external references, the pipeline steps, and the relationship of I/O objects.",
"required": [
"keywords",
"pipeline_steps"
],
"properties": {
"keywords": {
"type": "array",
"description": "TODO",
"description": "Keywords to aid in search-ability and description of the object.",
"items": {
"type": "string",
"description": "TODO",
"examples": [
"67505836"
]
}
},
"access_time": {
"type": "string",
"description": "TODO",
"format": "date-time"
}
}
}
},
"platform": {
"type": "array",
"description": "reference to a particular deployment of an existing platform where this BCO can be reproduced.",
"items": {
"type": "string",
"examples": [ "hive" ]
}
},
"pipeline_steps": {
"type": "object",
"description": "TODO",
"required": [
"tool"
],
"properties": {
"tool": {
"type": "array",
"description": "TODO",
"items": {
"type": "object",
"description": "TODO",
"required": [
"step_number",
"name",
"description",
"version",
"input_list",
"output_list"
],
"properties": {
"step_number": {
"type": "integer",
"description": "TODO"
},
"name": {
"type": "string",
"description": "this is a recognized name of the software tool",
"examples": [
"HIVE-hexagon"
]
},
"description": {
"type": "string",
"description": "TODO",
"examples": [
"Alignment of reads to a set of references"
"HCV1a",
"Ledipasvir",
"antiviral resistance",
"SNP",
"amino acid substitutions"
]
},
"version": {
"type": "string",
}
},
"xref": {
"type": "array",
"description": "TODO",
"items": {
"type": "object",
"description": "TODO",
"examples": [
"1.3"
]
},
"prerequisite": {
"type": "array",
"description": "reference or required prereqs",
"items": {
"type": "object",
"description": "TODO",
"required": [
"required": [
"namespace",
"name",
"uri"
],
"properties": {
"ids",
"access_time"
],
"properties": {
"namespace": {
"type": "string",
"description": "TODO",
"examples": [
"pubchem.compound"
]
},
"name": {
"type": "string",
"description": "Public searchable name for reference or prereq",
"default": "",
"examples": [
"Hepatitis C virus genotype 1"
]
"type": "string",
"description": "TODO",
"default": "",
"examples": [
"PubChem-compound"
]
},
"ids": {
"type": "array",
"description": "TODO",
"items": {
"type": "string",
"description": "TODO",
"examples": [
"67505836"
]
}
},
"uri": {
"$ref": "biocomputeobject.json#/definitions/uri"
"access_time": {
"type": "string",
"description": "TODO",
"format": "date-time"
}
}
}
},
"input_list": {
"type": "array",
"description": "TODO",
"items": {
"$ref": "biocomputeobject.json#/definitions/uri"
}
},
"output_list": {
"type": "array",
"description": "TODO",
"items": {
"$ref": "biocomputeobject.json#/definitions/uri"
}
},
"platform": {
"type": "array",
"description": "reference to a particular deployment of an existing platform where this BCO can be reproduced.",
"items": {
"type": "string",
"examples": [
"hive"
]
}
},
"pipeline_steps": {
"type": "object",
"description": "TODO",
"required": [
"step_number",
"name",
"description",
"version",
"input_list",
"output_list"
],
"properties": {
"step_number": {
"type": "integer",
"description": "TODO"
},
"name": {
"type": "string",
"description": "this is a recognized name of the software tool",
"examples": [
"HIVE-hexagon"
]
},
"description": {
"type": "string",
"description": "TODO",
"examples": [
"Alignment of reads to a set of references"
]
},
"version": {
"type": "string",
"description": "TODO",
"examples": [
"1.3"
]
},
"prerequisite": {
"type": "array",
"description": "reference or required prereqs",
"items": {
"type": "object",
"description": "TODO",
"required": [
"name",
"uri"
],
"properties": {
"name": {
"type": "string",
"description": "Public searchable name for reference or prereq",
"default": "",
"examples": [
"Hepatitis C virus genotype 1"
]
},
"uri": {
"$ref": "biocomputeobject.json#/definitions/uri"
}
}
}
},
"input_list": {
"type": "array",
"description": "TODO",
"items": {
"$ref": "biocomputeobject.json#/definitions/uri"
}
},
"output_list": {
"type": "array",
"description": "TODO",
"items": {
"$ref": "biocomputeobject.json#/definitions/uri"
}
}
}
}
}
}
}
}
}
}

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