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draft schema for paramter restrictions extension
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mr-c committed May 6, 2022
1 parent 11b3f46 commit 72e56ba
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1 change: 1 addition & 0 deletions MANIFEST.in
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Expand Up @@ -57,6 +57,7 @@ include cwltool/cwlNodeEngineJSConsole.js
include cwltool/cwlNodeEngineWithContext.js
include cwltool/extensions.yml
include cwltool/extensions-v1.1.yml
include cwltool/extensions-v1.2.yml
include cwltool/jshint/jshint_wrapper.js
include cwltool/jshint/jshint.js
include cwltool/hello.simg
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272 changes: 272 additions & 0 deletions cwltool/extensions-v1.2.yml
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@@ -0,0 +1,272 @@
$base: http://commonwl.org/cwltool#
$namespaces:
cwl: "https://w3id.org/cwl/cwl#"
cwltool: "http://commonwl.org/cwltool#"
$graph:
- $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml

- name: Secrets
type: record
inVocab: false
extends: cwl:ProcessRequirement
fields:
class:
type: string
doc: "Always 'Secrets'"
jsonldPredicate:
"_id": "@type"
"_type": "@vocab"
secrets:
type: string[]
doc: |
List one or more input parameters that are sensitive (such as passwords)
which will be deliberately obscured from logging.
jsonldPredicate:
"_type": "@id"
refScope: 0


- name: ProcessGenerator
type: record
inVocab: true
extends: cwl:Process
documentRoot: true
fields:
- name: class
jsonldPredicate:
"_id": "@type"
"_type": "@vocab"
type: string
- name: run
type: [string, cwl:Process]
jsonldPredicate:
_id: "cwl:run"
_type: "@id"
subscope: run
doc: |
Specifies the process to run.
- name: MPIRequirement
type: record
inVocab: false
extends: cwl:ProcessRequirement
doc: |
Indicates that a process requires an MPI runtime.
fields:
- name: class
type: string
doc: "Always 'MPIRequirement'"
jsonldPredicate:
"_id": "@type"
"_type": "@vocab"
- name: processes
type: [int, cwl:Expression]
doc: |
The number of MPI processes to start. If you give a string,
this will be evaluated as a CWL Expression and it must
evaluate to an integer.
- name: CUDARequirement
type: record
extends: cwl:ProcessRequirement
inVocab: false
doc: |
Require support for NVIDA CUDA (GPU hardware acceleration).
fields:
class:
type: string
doc: 'cwltool:CUDARequirement'
jsonldPredicate:
_id: "@type"
_type: "@vocab"
cudaVersionMin:
type: string
doc: |
Minimum CUDA version to run the software, in X.Y format. This
corresponds to a CUDA SDK release. When running directly on
the host (not in a container) the host must have a compatible
CUDA SDK (matching the exact version, or, starting with CUDA
11.3, matching major version). When run in a container, the
container image should provide the CUDA runtime, and the host
driver is injected into the container. In this case, because
CUDA drivers are backwards compatible, it is possible to
use an older SDK with a newer driver across major versions.
See https://docs.nvidia.com/deploy/cuda-compatibility/ for
details.
cudaComputeCapability:
type:
- 'string'
- 'string[]'
doc: |
CUDA hardware capability required to run the software, in X.Y
format.
* If this is a single value, it defines only the minimum
compute capability. GPUs with higher capability are also
accepted.
* If it is an array value, then only select GPUs with compute
capabilities that explicitly appear in the array.
cudaDeviceCountMin:
type: ['null', int, cwl:Expression]
default: 1
doc: |
Minimum number of GPU devices to request. If not specified,
same as `cudaDeviceCountMax`. If neither are specified,
default 1.
cudaDeviceCountMax:
type: ['null', int, cwl:Expression]
doc: |
Maximum number of GPU devices to request. If not specified,
same as `cudaDeviceCountMin`.
- name: intervalBase
type: record
abstract: true
fields:
low:
type: [int, float, double]
default: -.inf # negative infinity
jsonldPredicate: "cwltool:low"
high:
type: [int, float, double]
default: .inf # positive infinity
jsonldPredicate: "cwltool:high"

- name: intInterval
type: record
extends: intervalBase
doc: |
Integer number interval specification. All integer intervals are inclusive.
fields:
class:
type:
type: enum
name: intInterval_class
symbols:
- cwltool:intInterval
jsonldPredicate:
_id: "@type"
_type: "@vocab"
low:
type: int
default: -.inf # negative infinity
jsonldPredicate: "cwltool:low"
high:
type: int
default: .inf # positive infinity
jsonldPredicate: "cwltool:high"
# compact form proposal
# doc: |
# Examples:
# "[0,3)" any real number between 0 (inclusive) and 3 (exclusive)
# "[6,)" any real number greater than or equal to 6
# "(0,1)" any real number between 0 and 1 (exclusive)


- name: realInterval
type: record
extends: intervalBase
doc: |
Integer number interval
fields:
class:
type:
type: enum
name: realInterval_class
symbols:
- cwltool:realInterval
jsonldPredicate:
_id: "@type"
_type: "@vocab"
low_inclusive:
type: boolean
default: true
high_inclusive:
type: boolean
default: true
# compact form proposal
# doc: |
# Use "(" or "[" to indicate an exclusive or inclusive beginning,
# and ")" or "]" to indicate an exclusive or inclusive end.
# Default is inclusive.
# Examples:
# "[0,3)" any real number between 0 (inclusive) and 3 (exclusive)
# "[6,)" any real number greater than or equal to 6
# "(0,1)" any real number between 0 and 1 (exclusive)

- name: regex
type: record
doc: |
Regular Expression
TODO: what type of regex?
fields:
class:
type:
type: enum
name: regex_class
symbols:
- cwltool:regex
jsonldPredicate:
_id: "@type"
_type: "@vocab"
rpattern:
type: string


- name: Restrictions
type: record
fields:
input:
type: string
jsonldPredicate:
"_type": "@id"
refScope: 2
constraints:
type:
type: array
items:
- string
- int
- float
- double
- regex
- cwl:Expression
- intInterval
- realInterval

- name: ParameterRestrictions
type: record
extends: cwl:ProcessRequirement
inVocab: false
doc: |
Prototype of input value restrictions construct.
fields:
class:
type:
type: enum
name: ParameterRestrictions_class
symbols:
- cwltool:ParameterRestrictions
jsonldPredicate:
_id: "@type"
_type: "@vocab"
restrictions:
type: Restrictions[]
jsonldPredicate:
_id: "cwltool:restrictions"
mapSubject: input
mapPredicate: constraints
doc: |
(Only applicable for string, int, long, float and double parameters)
List of restrictions that apply to the input parameter "id".
A given parameter value should be accepted if any of the restrictions
match the input. Restrictions can be
single values (applies to all types),
ranges of the same type (applies to int, float and double),
regular expressions (for string parameters)
or Expressions (if an expression is provided, the expression must
return a boolean representing a match).
If the parameter is an array type, every value has to match at least
one of the restrictions.
4 changes: 3 additions & 1 deletion cwltool/main.py
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Expand Up @@ -661,9 +661,11 @@ def setup_schema(
ext10 = res.read().decode("utf-8")
with pkg_resources.resource_stream(__name__, "extensions-v1.1.yml") as res:
ext11 = res.read().decode("utf-8")
with pkg_resources.resource_stream(__name__, "extensions-v1.2.yml") as res:
ext12 = res.read().decode("utf-8")
use_custom_schema("v1.0", "http://commonwl.org/cwltool", ext10)
use_custom_schema("v1.1", "http://commonwl.org/cwltool", ext11)
use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext11)
use_custom_schema("v1.2", "http://commonwl.org/cwltool", ext12)
use_custom_schema("v1.2.0-dev1", "http://commonwl.org/cwltool", ext11)
use_custom_schema("v1.2.0-dev2", "http://commonwl.org/cwltool", ext11)
use_custom_schema("v1.2.0-dev3", "http://commonwl.org/cwltool", ext11)
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1 change: 1 addition & 0 deletions cwltool/process.py
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Expand Up @@ -121,6 +121,7 @@ def filter(self, record: logging.LogRecord) -> bool:
"http://commonwl.org/cwltool#LoadListingRequirement",
"http://commonwl.org/cwltool#InplaceUpdateRequirement",
"http://commonwl.org/cwltool#CUDARequirement",
"http://commonwl.org/cwltool#ParameterRestrictions",
]

cwl_files = (
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40 changes: 40 additions & 0 deletions tests/parameter_restrictions.cwl
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cwlVersion: v1.2
class: CommandLineTool

doc: |
Tests of paramater restrictions extension

inputs:
one: double
two: string


hints:
cwltool:ParameterRestrictions:
restrictions:
one:
- class: cwltool:realInterval
low: 0
high: 3
high_inclusive: false
- class: cwltool:realInterval
low: 6
# high should be the default of positive infinity
high_inclusive: false
two:
- class: cwltool:regex
rpattern: "foo.*bar"


baseCommand: echo

arguments:
- $(inputs.one)
- $(inputs.two)

outputs:
result: stdout

$namespaces:
cwltool: "http://commonwl.org/cwltool#"

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