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Alan Christie
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feat: New schema to cover variables (majority of features)
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‎decoder/job-definition-schema.yaml‎

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@@ -95,6 +95,8 @@ definitions:
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type: string
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minLength: 1
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maxLength: 4096
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variables:
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$ref: '#/definitions/job-variables'
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tests:
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$ref: '#/definitions/job-test'
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replaces:
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- type: boolean
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additionalProperties: false
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# Job Variables.
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# Consists of inputs, options and variables (not are required)
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job-variables:
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type: object
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additionalProperties: false
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properties:
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inputs:
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$ref: '#/definitions/job-input-variables'
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options:
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$ref: '#/definitions/job-option-variables'
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order:
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$ref: '#/definitions/job-order-variables'
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outputs:
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$ref: '#/definitions/job-output-variables'
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# Variable ordering (inputs, options, outputs)
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job-order-variables:
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type: object
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additionalProperties: false
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properties:
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inputs:
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type: array
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items:
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type: string
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options:
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type: array
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items:
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type: string
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outputs:
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type: array
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items:
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type: string
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# Variables (inputs)
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job-input-variables:
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type: object
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additionalProperties: false
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properties:
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type:
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type: string
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enum:
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- object
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required:
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type: array
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items:
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type: string
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properties:
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$ref: '#/definitions/job-input-properties'
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required:
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- type
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- properties
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job-input-properties:
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type: object
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additionalProperties: false
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patternProperties:
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'^[a-zA-Z]{1}[a-zA-Z0-9-_]{0,79}$':
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$ref: '#/definitions/job-input-property'
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job-input-property:
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type: object
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additionalProperties: false
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properties:
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title:
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type: string
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mime-types:
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type: array
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items:
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type: string
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type:
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type: string
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enum:
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- file
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- molecules-smi
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multiple:
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type: boolean
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required:
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- title
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- type
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# Variables (outputs)
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job-output-variables:
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type: object
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additionalProperties: false
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properties:
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type:
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type: string
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enum:
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- object
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properties:
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$ref: '#/definitions/job-output-properties'
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required:
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- type
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- properties
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job-output-properties:
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type: object
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additionalProperties: false
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patternProperties:
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'^[a-zA-Z]{1}[a-zA-Z0-9-_]{0,79}$':
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$ref: '#/definitions/job-output-property'
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job-output-property:
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type: object
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additionalProperties: false
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properties:
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title:
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type: string
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mime-types:
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type: array
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items:
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type: string
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creates:
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type: string
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type:
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type: string
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enum:
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- file
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annotation-properties:
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type: object
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additionalProperties: true
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required:
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- title
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- creates
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- type
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# Variables (options)
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job-option-variables:
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type: object
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additionalProperties: false
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properties:
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type:
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type: string
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enum:
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- object
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required:
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type: array
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items:
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type: string
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properties:
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$ref: '#/definitions/job-option-properties'
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required:
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- type
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- properties
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job-option-properties:
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type: object
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additionalProperties: false
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patternProperties:
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'^[a-zA-Z]{1}[a-zA-Z0-9-_]{0,79}$':
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$ref: '#/definitions/job-option-property'
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job-option-property:
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type: object
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additionalProperties: false
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properties:
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title:
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type: string
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type:
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type: string
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enum:
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- string
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- integer
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- number
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- boolean
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- array
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pattern:
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type: string
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minimum:
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type: number
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maximum:
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type: number
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default:
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oneOf:
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- type: string
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- type: number
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- type: boolean
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enum:
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type: array
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items:
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anyOf:
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- type: string
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- type: number
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- type: boolean
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items:
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type: object
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additionalProperties: true
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required:
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- title
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- type
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# An individual Test.
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# Consists of a identity (i.e. 'test-filter-molecules')
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# followed by a Test object.

‎example-definitions/bad/README.txt‎

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Any '.yaml' files here are expected NOT to comply with the Job Definition schema

‎example-definitions/good/README.txt‎

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Any '.yaml' files here are expected to comply with the Job Definition schema

‎example-definitions/good/virtual-screening-dmpk.yaml‎

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---
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kind: DataManagerJobDefinition
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kind-version: '2021.1'
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name: DMPK tools
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collection: im-dmpk
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jobs:
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pk-tmax-cmax-sim:
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name: Estimation of absorption
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description: >-
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Estimation of absorption from t1/2 and Tmax after po administration (one-compartment)
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version: '1.0.0'
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category: dmpk
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keywords:
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- dmpk
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- absorption
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- cmax
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- kel
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image:
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name: informaticsmatters/vs-dmpk
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tag: 'stable'
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project-directory: /data
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working-directory: /data
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fix-permissions: true
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command: >-
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python -m dmpk.pk_tmax_cmax_sim
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--half-life {{ halfLife }}
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--absorption {{ absorption }}
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--dose {{ dose }}
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--auc {{ auc }}
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--time {{ time }}
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--output '{{ outputBaseName }}'
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{% if plotWidth is defined %}--plot-width {{ plotWidth }}{% endif %}
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{% if plotHeight is defined %}--plot-height {{ plotHeight }}{% endif %}
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{% if fontSize is defined %}--font-size {{ fontSize }}{% endif %}
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variables:
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order:
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options:
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- outputBaseName
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- halfLife
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- absorption
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- dose
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- auc
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- time
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- plotWidth
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- plotHeight
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- fontSize
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outputs:
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type: object
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properties:
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pngFile:
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title: PNG file
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mime-types:
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- image/png
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creates: '{{ outputBaseName }}.png'
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type: file
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txtFile:
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title: Text file
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mime-types:
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- text/plain
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creates: '{{ outputBaseName }}.txt'
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type: file
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options:
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type: object
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required:
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- outputBaseName
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- halfLife
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- absorption
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- dose
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- auc
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- time
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properties:
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outputBaseName:
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title: Output file base name
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type: string
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pattern: "^[A-Za-z0-9_/\\.\\-]+$"
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default: output
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halfLife:
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title: Half life (hours)
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type: number
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absorption:
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title: Half life absorption (hours)
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type: number
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dose:
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title: Initial dose (mg)
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type: number
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auc:
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title: AUC (mg/L*hr)
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type: number
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time:
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title: Time (h)
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type: number
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plotWidth:
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title: Plot width (inches)
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type: integer
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default: 10
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plotHeight:
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title: Plot height (inches)
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type: integer
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default: 4
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fontSize:
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title: Find size (points)
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type: integer
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default: 12
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tests:
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simple-execution:
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options:
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outputBaseName: foo/output
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halfLife: 0.79
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absorption: 0.5
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dose: 0.14
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auc: 0.88
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time: 8
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plotWidth: 10
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plotHeight: 4
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checks:
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exitCode: 0
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outputs:
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- name: foo/output.png
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checks:
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- exists: true
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- name: foo/output.txt
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checks:
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- exists: true
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- lineCount: 12

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