From 825bbbb0b1f94261c233394c7703564e836aa8b3 Mon Sep 17 00:00:00 2001 From: hadley Date: Fri, 30 Nov 2018 16:45:05 -0500 Subject: [PATCH] pipeline_steps.step_number pipeline_steps.step_number is an integer in the schema but the spec text has it as a string apply #49 --- description-domain.md | 2 +- schemas/description_domain.json | 301 +++++++++++++++----------------- 2 files changed, 146 insertions(+), 157 deletions(-) diff --git a/description-domain.md b/description-domain.md index ed3612f..e1bde78 100644 --- a/description-domain.md +++ b/description-domain.md @@ -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" diff --git a/schemas/description_domain.json b/schemas/description_domain.json index 92f4e11..8483c7e 100644 --- a/schemas/description_domain.json +++ b/schemas/description_domain.json @@ -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" + } } - } } - } } - } } - } }