8000 Adds the remainder of requirements (mostly spec'd) · illusional/python-cwlgen@ea22ec6 · GitHub
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Adds the remainder of requirements (mostly spec'd)
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‎cwlgen/requirements.py

Lines changed: 292 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -42,17 +42,208 @@ def get_dict(self):
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return base
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class SchemaDefRequirement(Requirement):
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"""
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This field consists of an array of type definitions which must be used when interpreting the inputs and
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outputs fields. When a type field contain a IRI, the implementation must check if the type is defined
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in schemaDefs and use that definition. If the type is not found in schemaDefs, it is an error.
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The entries in schemaDefs must be processed in the order listed such that later schema definitions
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may refer to earlier schema definitions.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#SchemaDefRequirement
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"""
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def __init__(self, types):
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"""
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:param types: The list of type definitions.
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:type types: list[InputRecordSchema | InputEnumSchema | InputArraySchema]
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"""
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Requirement.__init__(self, "SchemaDefRequirement")
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self.types = types
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< 8000 span class=pl-k>def get_dict(self):
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base = Requirement.get_dict(self)
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base['types'] = [t.get_dict() for t in self.types]
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# class InputRecordSchema(object):
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# """
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# Documentation: https://www.commonwl.org/v1.0/Workflow.html#InputRecordSchema
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# """
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# def __init__(self, label=None, name=None):
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# """
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# :param fields: Defines the fields of the record.
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# :type fields: array<InputRecordField>
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# :param label: A short, human-readable label of this object.
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# :param name: NF (Name of the InputRecord)
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# """
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# self.fields = []
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# self.label = label
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# self.name = name
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#
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# def get_dict(self):
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# schema = {"type": "record"}
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# if self.fields:
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# schema["fields"] = {f.name: f.get_dict() for f in self.fields}
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# if self.label:
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# schema["label"] = self.label
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# if self.name:
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# schema["name"] = self.name
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# return schema
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class SoftwareRequirement(Requirement):
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"""
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A list of software packages that should be configured in the environment of the defined process.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#SoftwareRequirement
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"""
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def __init__(self):
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Requirement.__init__(self, "SoftwareRequirement")
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self.packages = [] # list[SoftwarePackage]
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def get_dict(self):
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base = Requirement.get_dict(self)
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base["packages"] = [p.get_dict() for p in self.packages]
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class SoftwarePackage(object):
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"""
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#SoftwarePackage
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"""
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def __init__(self, package, version=None, specs=None):
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"""
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:param package: The name of the software to be made available. If the name is common, inconsistent,
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or otherwise ambiguous it should be combined with one or more identifiers in the specs field
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:param version: The (optional) versions of the software that are known to be compatible.
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:param specs: One or more IRIs identifying resources for installing or enabling the software in 'package'
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"""
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self.package = package
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self.version = version
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self.specs = version
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def get_dict(self):
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base = {"package": self.package}
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if self.version:
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base["version"] = self.version
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if self.specs:
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base["specs"] = self.specs
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class InitialWorkDirRequirement(Requirement):
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"""
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Define a list of files and subdirectories that must be created by the workflow
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platform in the designated output directory prior to executing the command line tool.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#InitialWorkDirRequirement
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"""
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def __init__(self, listing):
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"""
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:param listing: The list of files or subdirectories that must be placed in the
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designated output directory prior to executing the command line tool.
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:type listing: array<File | Directory | Dirent | string | Expression> | string | Expression
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"""
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Requirement.__init__(self, "InitialWorkDirRequirement")
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self.listing = listing
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def get_dict(self):
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base = Requirement.get_dict(self)
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if isinstance(self.listing, str):
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base["listing"] = self.listing
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elif isinstance(self.listing, list):
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if len(self.listing) == 1:
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raise Exception("InitialWorkDirRequirement.listing must have at least one element")
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base["listing"] = [r if isinstance(r, str) else r.get_dict() for r in self.listing]
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else:
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raise Exception("Couldn't recognise type of '{list_type}', expected: array<File | Directory | Dirent | "
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"string| Expression> | string | Expression".format(list_type=type(self.listing)))
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return base
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class Dirent(object):
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"""
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Define a file or subdirectory that must be placed in the designated output directory
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prior to executing the command line tool. May be the result of executing an expression,
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such as building a configuration file from a template.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#Dirent
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"""
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def __init__(self, entry, entryname=None, writable=None):
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self.entry = entry
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self.entryname = entryname
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self.writable = writable
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def get_dict(self):
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return {k: v for k, v in vars(self).items() if v is not None}
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class SubworkflowFeatureRequirement(Requirement):
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"""
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Indicates that the workflow platform must support nested workflows in the run field of WorkflowStep.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#SubworkflowFeatureRequirement
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"""
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def __init__(self):
187+
Requirement.__init__(self, 'SubworkflowFeatureRequirement')
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def get_dict(self):
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return Requirement.get_dict(self)
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class ScatterFeatureRequirement(Requirement):
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"""
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Indicates that the workflow platform must support the scatter and scatterMethod fields of WorkflowStep.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#ScatterFeatureRequirement
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"""
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def __init__(self):
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Requirement.__init__(self, 'ScatterFeatureRequirement')
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def get_dict(self):
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return Requirement.get_dict(self)
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class MultipleInputFeatureRequirement(Requirement):
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"""
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Indicates that the workflow platform must support multiple
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inbound data links listed in the source field of WorkflowStepInput.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement
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"""
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def __init__(self):
216+
Requirement.__init__(self, 'MultipleInputFeatureRequirement')
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def get_dict(self):
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return Requirement.get_dict(self)
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class StepInputExpressionRequirement(Requirement):
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"""
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Indicate that the workflow platform must support the valueFrom field of WorkflowStepInput.
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Documentation: https://www.commonwl.org/v1.0/Workflow.html#StepInputExpressionRequirement
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"""
228+
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def __init__(self):
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Requirement.__init__(self, 'StepInputExpressionRequirement')
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def get_dict(self):
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return Requirement.get_dict(self)
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47236
class DockerRequirement(Requirement):
48-
'''
49-
Workflow component should be run in a Docker container.
50-
This class specifies how to fetch or build the image.
51-
'''
237+
"""
238+
Indicates that a workflow component should be run in a Docker container,
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and specifies how to fetch or build the image.
240+
241+
Documentation: https://www.commonwl.org/v1.0/CommandLineTool.html#DockerRequirement
242+
"""
52243

53244
def __init__(self, docker_pull=None, docker_load=None, docker_file=None,
54245
docker_import=None, docker_image_id=None, docker_output_dir=None):
55-
'''
246+
"""
56247
:param docker_pull: image to retrive with docker pull
57248
:type docker_pull: STRING
58249
:param docker_load: HTTP URL from which to download Docker image
@@ -65,7 +256,7 @@ def __init__(self, docker_pull=None, docker_load=None, docker_file=None,
65256
:type docker_image_id: STRING
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:param docker_output_dir: designated output dir inside the Docker container
67258
:type docker_output_dir: STRING
68-
'''
259+
"""
69260
Requirement.__init__(self, 'DockerRequirement')
70261
self.dockerPull = docker_pull
71262
self.dockerLoad = docker_load
@@ -74,19 +265,106 @@ def __init__(self, docker_pull=None, docker_load=None, docker_file=None,
74265
self.dockerImageId = docker_image_id
75266
self.dockerOutputDir = docker_output_dir
76267

77-
def _to_dict(self):
268+
def get_dict(self):
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base = Requirement.get_dict(self)
270+
base.update({p: v for p, v in vars(self).items() if p.startswith('docker') and v is not None})
271+
return base
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class EnvVarRequirement(Requirement):
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"""
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Define a list of environment variables which will be set in the execution environment of the tool.
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See EnvironmentDef for details.
278+
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Documentation: https://www.commonwl.org/v1.0/CommandLineTool.html#EnvVarRequirement
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"""
281+
def __init__(self, env_def):
78282
"""
79-
Add this requirement to a dictionary description of a
80-
tool generated in an export method.
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:param env_def: The list of environment variables.
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:type env_def: list[EnvironmentDef]
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"""
286+
Requirement.__init__(self, 'ShellCommandRequirement')
287+
self.envDef = env_def
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289+
def get_dict(self):
290+
base = Requirement.get_dict(self)
291+
base["envDef"] = [e.get_dict() for e in self.envDef]
81292

293+
class EnvironmentDef(object):
82294
"""
83-
return {p: v for p, v in vars(self).items() if p.startswith('docker') and v is not None}
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Define an environment variable that will be set in the runtime environment
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by the workflow platform when executing the command line tool.
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May be the result of executing an expression, such as getting a parameter from input.
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Documentation: https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef
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"""
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def __init__(self, env_name, env_value):
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"""
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:param env_name: The environment variable name
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:type env_name: STRING
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:param env_value: The environment variable value
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:type env_value: STRING
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"""
308+
self.envName = env_name
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self.envValue = env_value
85310

86-
class SubworkflowFeatureRequirement(Requirement):
311+
def get_dict(self):
312+
return {"envName": self.envName, "envValue": self.envValue}
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314+
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class ShellCommandRequirement(Requirement):
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"""
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Modify the behavior of CommandLineTool to generate a single string containing a shell command line.
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Documentation: https://www.commonwl.org/v1.0/CommandLineTool.html#ShellCommandRequirement
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"""
87321

88322
def __init__(self):
89-
Requirement.__init__(self, 'SubworkflowFeatureRequirement')
323+
Requirement.__init__(self, 'ShellCommandRequirement')
324+
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def get_dict(self):
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return Requirement.get_dict(self)
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328+
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class ResourceRequirement(Requirement):
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"""
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Specify basic hardware resource requirements.
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Documentation: https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement
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"""
90335

91-
def _to_dict(self):
92-
return dict()
336+
def __init__(self, cores_min=None, cores_max=None, ram_min=None, ram_max=None, tmpdir_min=None, tmpdir_max=None,
337+
outdir_min=None, outdir_max=None):
338+
"""
339+
:param cores_min: Minimum reserved number of CPU cores
340+
:type cores_min: string | float
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:param cores_max: Maximum reserved number of CPU cores
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:type cores_max: string | float
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:param ram_min: Minimum reserved RAM in mebibytes (2**20)
344+
:type ram_min: string | float
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:param ram_max: Maximum reserved RAM in mebibytes (2**20)
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:type ram_max: string | float
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:param tmpdir_min: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
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:type tmpdir_min: string | float
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:param tmpdir_max: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
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:type tmpdir_max: string | float
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:param outdir_min: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
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:type outdir_min: string | float
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:param outdir_max: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
354+
:type outdir_max: string | float
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"""
356+
Requirement.__init__(self, 'ResourceRequirement')
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358+
self.coresMin = cores_min
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self.coresMax = cores_max
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self.ramMin = ram_min
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self.ramMax = ram_max
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self.tmpdirMin = tmpdir_min
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self.tmpdirMax = tmpdir_max
364+
self.outdirMin = outdir_min
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self.outdirMax = outdir_max
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367+
def get_dict(self):
368+
base = Requirement.get_dict(self)
369+
base.update({p: v for p, v in vars(self).items() if v is not None})
370+
return base

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