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draft schema for paramter restrictions extension
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‎MANIFEST.in‎

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@@ -57,6 +57,7 @@ include cwltool/cwlNodeEngineJSConsole.js
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include cwltool/cwlNodeEngineWithContext.js
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include cwltool/extensions.yml
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include cwltool/extensions-v1.1.yml
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include cwltool/extensions-v1.2.yml
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include cwltool/jshint/jshint_wrapper.js
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include cwltool/jshint/jshint.js
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include cwltool/hello.simg

‎cwltool/extensions-v1.2.yml‎

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$base: http://commonwl.org/cwltool#
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$namespaces:
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cwl: "https://w3id.org/cwl/cwl#"
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cwltool: "http://commonwl.org/cwltool#"
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$graph:
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- $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml
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- name: Secrets
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type: record
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inVocab: false
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extends: cwl:ProcessRequirement
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fields:
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class:
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type: string
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doc: "Always 'Secrets'"
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jsonldPredicate:
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"_id": "@type"
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"_type": "@vocab"
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secrets:
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type: string[]
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doc: |
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List one or more input parameters that are sensitive (such as passwords)
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which will be deliberately obscured from logging.
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jsonldPredicate:
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"_type": "@id"
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refScope: 0
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- name: ProcessGenerator
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type: record
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inVocab: true
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extends: cwl:Process
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documentRoot: true
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fields:
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- name: class
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jsonldPredicate:
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"_id": "@type"
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"_type": "@vocab"
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type: string
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- name: run
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type: [string, cwl:Process]
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jsonldPredicate:
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_id: "cwl:run"
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_type: "@id"
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subscope: run
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doc: |
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Specifies the process to run.
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- name: MPIRequirement
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type: record
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inVocab: false
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extends: cwl:ProcessRequirement
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doc: |
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Indicates that a process requires an MPI runtime.
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fields:
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- name: class
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type: string
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doc: "Always 'MPIRequirement'"
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jsonldPredicate:
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"_id": "@type"
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"_type": "@vocab"
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- name: processes
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type: [int, cwl:Expression]
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doc: |
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The number of MPI processes to start. If you give a string,
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this will be evaluated as a CWL Expression and it must
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evaluate to an integer.
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- name: CUDARequirement
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type: record
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extends: cwl:ProcessRequirement
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inVocab: false
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doc: |
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Require support for NVIDA CUDA (GPU hardware acceleration).
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fields:
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class:
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type: string
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doc: 'cwltool:CUDARequirement'
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jsonldPredicate:
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_id: "@type"
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_type: "@vocab"
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cudaVersionMin:
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type: string
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doc: |
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Minimum CUDA version to run the software, in X.Y format. This
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corresponds to a CUDA SDK release. When running directly on
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the host (not in a container) the host must have a compatible
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CUDA SDK (matching the exact version, or, starting with CUDA
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11.3, matching major version). When run in a container, the
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container image should provide the CUDA runtime, and the host
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driver is injected into the container. In this case, because
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CUDA drivers are backwards compatible, it is possible to
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use an older SDK with a newer driver across major versions.
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See https://docs.nvidia.com/deploy/cuda-compatibility/ for
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details.
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cudaComputeCapability:
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type:
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- 'string'
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- 'string[]'
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doc: |
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CUDA hardware capability required to run the software, in X.Y
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format.
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* If this is a single value, it defines only the minimum
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compute capability. GPUs with higher capability are also
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accepted.
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* If it is an array value, then only select GPUs with compute
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capabilities that explicitly appear in the array.
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cudaDeviceCountMin:
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type: ['null', int, cwl:Expression]
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default: 1
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doc: |
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Minimum number of GPU devices to request. If not specified,
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same as `cudaDeviceCountMax`. If neither are specified,
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default 1.
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cudaDeviceCountMax:
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type: ['null', int, cwl:Expression]
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doc: |
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Maximum number of GPU devices to request. If not specified,
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same as `cudaDeviceCountMin`.
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- name: intervalBase
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type: record
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abstract: true
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fields:
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low:
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type: [int, float, double]
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default: -.inf # negative infinity
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jsonldPredicate: "cwltool:low"
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high:
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type: [int, float, double]
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default: .inf # positive infinity
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jsonldPredicate: "cwltool:high"
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- name: intInterval
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type: record
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extends: intervalBase
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doc: |
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Integer number interval specification. All integer intervals are inclusive.
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fields:
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class:
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type:
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type: enum
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name: intInterval_class
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symbols:
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- cwltool:intInterval
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jsonldPredicate:
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_id: "@type"
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_type: "@vocab"
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low:
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type: int
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default: -.inf # negative infinity
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jsonldPredicate: "cwltool:low"
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high:
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type: int
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default: .inf # positive infinity
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jsonldPredicate: "cwltool:high"
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# compact form proposal
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# doc: |
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# Examples:
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# "[0,3)" any real number between 0 (inclusive) and 3 (exclusive)
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# "[6,)" any real number greater than or equal to 6
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# "(0,1)" any real number between 0 and 1 (exclusive)
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- name: realInterval
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type: record
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extends: intervalBase
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doc: |
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Integer number interval
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fields:
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class:
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type:
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type: enum
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name: realInterval_class
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symbols:
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- cwltool:realInterval
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jsonldPredicate:
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_id: "@type"
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_type: "@vocab"
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low_inclusive:
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type: boolean
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default: true
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high_inclusive:
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type: boolean
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default: true
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# compact form proposal
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# doc: |
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# Use "(" or "[" to indicate an exclusive or inclusive beginning,
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# and ")" or "]" to indicate an exclusive or inclusive end.
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# Default is inclusive.
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# Examples:
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# "[0,3)" any real number between 0 (inclusive) and 3 (exclusive)
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# "[6,)" any real number greater than or equal to 6
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# "(0,1)" any real number between 0 and 1 (exclusive)
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- name: regex
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type: record
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doc: |
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Regular Expression
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TODO: what type of regex?
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fields:
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class:
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type:
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type: enum
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name: regex_class
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symbols:
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- cwltool:regex
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jsonldPredicate:
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_id: "@type"
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_type: "@vocab"
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rpattern:
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type: string
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- name: Restrictions
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type: record
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fields:
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input:
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type: string
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jsonldPredicate:
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"_type": "@id"
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refScope: 2
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constraints:
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type:
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type: array
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items:
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- string
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- int
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- float
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- double
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- regex
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- cwl:Expression
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- intInterval
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- realInterval
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- name: ParameterRestrictions
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type: record
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extends: cwl:ProcessRequirement
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inVocab: false
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doc: |
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Prototype of input value restrictions construct.
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fields:
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class:
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type:
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type: enum
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name: ParameterRestrictions_class
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symbols:
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- cwltool:ParameterRestrictions
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jsonldPredicate:
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_id: "@type"
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_type: "@vocab"
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restrictions:
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type: Restrictions[]
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jsonldPredicate:
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_id: "cwltool:restrictions"
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mapSubject: input
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mapPredicate: constraints
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doc: |
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(Only applicable for string, int, long, float and double parameters)
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List of restrictions that apply to the input parameter "id".
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A given parameter value should be accepted if any of the restrictions
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match the input. Restrictions can be
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single values (applies to all types),
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ranges of the same type (applies to int, float and double),
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regular expressions (for string parameters)
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or Expressions (if an expression is provided, the expression must
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return a boolean representing a match).
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If the parameter is an array type, every value has to match at least
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one of the restrictions.

‎cwltool/main.py‎

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@@ -661,9 +661,11 @@ def setup_schema(
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ext10 = res.read().decode("utf-8")
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with pkg_resources.resource_stream(__name__, "extensions-v1.1.yml") as res:
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ext11 = res.read().decode("utf-8")
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with pkg_resources.resource_stream(__name__, "extensions-v1.2.yml") as res:
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ext12 = res.read().decode("utf-8")
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use_custom_schema("v1.0", "http://commonwl.org/cwltool", ext10)
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use_custom_schema("v1.1", "http://commonwl.org/cwltool", ext11)
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use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext11)
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use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext12)
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use_custom_schema("v1.2.0-dev1", "http://commonwl.org/cwltool", ext11)
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use_custom_schema("v1.2.0-dev2", "http://commonwl.org/cwltool", ext11)
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use_custom_schema("v1.2.0-dev3", "http://commonwl.org/cwltool", ext11)

‎cwltool/process.py‎

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@@ -121,6 +121,7 @@ def filter(self, record: logging.LogRecord) -> bool:
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"http://commonwl.org/cwltool#LoadListingRequirement",
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"http://commonwl.org/cwltool#InplaceUpdateRequirement",
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"http://commonwl.org/cwltool#CUDARequirement",
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"http://commonwl.org/cwltool#ParameterRestrictions",
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]
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cwl_files = (

‎tests/parameter_restrictions.cwl‎

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cwlVersion: v1.2
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class: CommandLineTool
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doc: |
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Tests of paramater restrictions extension
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inputs:
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one: double
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two: string
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hints:
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cwltool:ParameterRestrictions:
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restrictions:
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one:
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- class: cwltool:realInterval
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low: 0
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high: 3
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high_inclusive: false
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- class: cwltool:realInterval
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low: 6
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# high should be the default of positive infinity
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high_inclusive: false
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two:
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- class: cwltool:regex
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rpattern: "foo.*bar"
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baseCommand: echo
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arguments:
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- $(inputs.one)
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- $(inputs.two)
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outputs:
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result: stdout
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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