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Input parameter schema.
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‎.gitignore‎

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@@ -153,6 +153,7 @@ doc/build
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doc/schema.md
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doc/source/admin/config_logging_default_yaml.rst
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doc/source/dev/schema.md
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doc/source/dev/plantuml.jar
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client/docs/dist
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# Webpack stats

‎doc/source/dev/image.Makefile‎

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MINDMAPS := $(wildcard *.mindmap.yml)
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INPUTS := $(wildcard *.plantuml.txt)
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OUTPUTS := $(INPUTS:.txt=.svg)
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all: plantuml.jar $(MINDMAPS) $(OUTPUTS)
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$(OUTPUTS): $(INPUTS) $(MINDMAPS)
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java -jar plantuml.jar -c plantuml_options.txt -tsvg $(INPUTS)
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plantuml.jar:
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wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar || curl --output plantuml.jar http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar

‎doc/source/dev/plantuml_options.txt‎

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' skinparam handwritten true
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' skinparam roundcorner 20
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skinparam class {
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ArrowFontColor DarkOrange
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BackgroundColor #FFEFD5
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ArrowColor Orange
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BorderColor DarkOrange
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}
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skinparam object {
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ArrowFontColor DarkOrange
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BackgroundColor #FFEFD5
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BackgroundColor #FFEFD5
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ArrowColor Orange
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BorderColor DarkOrange
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}
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skinparam ComponentBackgroundColor #FFEFD5
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skinparam ComponentBorderColor DarkOrange
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skinparam DatabaseBackgroundColor #FFEFD5
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skinparam DatabaseBorderColor DarkOrange
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skinparam StorageBackgroundColor #FFEFD5
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skinparam StorageBorderColor DarkOrange
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skinparam QueueBackgroundColor #FFEFD5
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skinparam QueueBorderColor DarkOrange
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skinparam note {
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BackgroundColor #FFEFD5
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BorderColor #BF5700
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}
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skinparam sequence {
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ArrowColor Orange
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ArrowFontColor DarkOrange
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ActorBorderColor DarkOrange
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ActorBackgroundColor #FFEFD5
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ParticipantBorderColor DarkOrange
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ParticipantBackgroundColor #FFEFD5
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LifeLineBorderColor DarkOrange
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LifeLineBackgroundColor #FFEFD5
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DividerBorderColor DarkOrange
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GroupBorderColor DarkOrange
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}
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‎doc/source/dev/plantuml_style.txt‎

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<style>
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mindmapDiagram {
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node {
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BackgroundColor #FFEFD5
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BorderColor DarkOrange
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LineColor Orange
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}
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}
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</style>

‎doc/source/dev/tool_state.md‎

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‎doc/source/dev/tool_state_api.plantuml.txt‎

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@startuml
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'!include plantuml_options.txt
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participant "API Request" as apireq
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boundary "Jobs API" as api
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participant "Job Service" as service
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database Database as database
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queue TaskQueue as queue
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apireq -> api : HTTP JSON
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api -> service : To boundary
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service -> service : Build RequestToolState
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service -> service : Validate RequestToolState (pydantic)
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service -> service : decode() RequestToolState \ninto RequestInternalToolState
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service -> database : Serialize RequestInternalToolState
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service -> queue : Queue QueueJobs with reference to\npersisted RequestInternalToolState
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service -> api : JobCreateResponse\n (pydantic model)
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api -> apireq : JobCreateResponse\n (as json)
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@enduml

‎doc/source/dev/tool_state_state_classes.plantuml.txt‎

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@startuml
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!include plantuml_options.txt
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package galaxy.tool_util.parameters.state {
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class ToolState {
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state_representation: str
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input_state: Dict[str, Any]
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+ validate(input_models: ToolParameterBundle)
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+ {abstract} _to_base_model(input_models: ToolParameterBundle): Optional[Type[BaseModel]]
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}
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class RequestToolState {
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state_representation = "request"
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+ _to_base_model(input_models: ToolParameterBundle): Type[BaseModel]
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}
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note bottom: Object references of the form \n{src: "hda", id: <encoded_id>}.\n Allow mapping/reduce constructs.
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class RequestInternalToolState {
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state_representation = "request_internal"
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+ _to_base_model(input_models: ToolParameterBundle): Type[BaseModel]
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}
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note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs.
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class JobInternalToolState {
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state_representation = "job_internal"
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+ _to_base_model(input_models: ToolParameterBundle): Type[BaseModel]
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}
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note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Mapping constructs expanded out.\n (Defaults are inserted?)
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ToolState <|-- RequestToolState
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ToolState <|-- RequestInternalToolState
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ToolState <|-- JobInternalToolState
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RequestToolState - RequestInternalToolState : decode >
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RequestInternalToolState o-- JobInternalToolState : expand >
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}
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@enduml

‎lib/galaxy/config/schemas/tool_shed_config_schema.yml‎

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the repositories and tools within the Tool Shed given that you specify
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the following two config options.
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tool_state_cache_dir:
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type: str
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default: database/tool_state_cache
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required: false
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desc: |
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Cache directory for tool state.
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repo_name_boost:
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type: float
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default: 0.9

‎lib/galaxy/tool_util/cwl/parser.py‎

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tool_id = tool_id[1:]
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return tool_id
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@abstractmethod
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def input_fields(self) -> list:
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"""Return InputInstance objects describing mapping to Galaxy inputs."""
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@abstractmethod
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def input_instances(self):
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"""Return InputInstance objects describing mapping to Galaxy inputs."""
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else:
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return ""
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def input_fields(self):
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def input_fields(self) -> list:
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input_records_schema = self._eval_schema(self._tool.inputs_record_schema)
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if input_records_schema["type"] != "record":
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raise Exception("Unhandled CWL tool input structure")

‎lib/galaxy/tool_util/parameters/__init__.py‎

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from .convert import (
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decode,
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encode,
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)
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from .factory import (
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from_input_source,
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input_models_for_pages,
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input_models_for_tool_source,
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input_models_from_json,
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tool_parameter_bundle_from_json,
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)
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from .json import to_json_schema_string
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from .models import (
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BooleanParameterModel,
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ColorParameterModel,
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ConditionalParameterModel,
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ConditionalWhen,
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CwlBooleanParameterModel,
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CwlDirectoryParameterModel,
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CwlFileParameterModel,
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CwlFloatParameterModel,
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CwlIntegerParameterModel,
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CwlNullParameterModel,
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CwlStringParameterModel,
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CwlUnionParameterModel,
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DataCollectionParameterModel,
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DataParameterModel,
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FloatParameterModel,
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HiddenParameterModel,
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IntegerParameterModel,
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LabelValue,
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RepeatParameterModel,
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RulesParameterModel,
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SelectParameterModel,
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TextParameterModel,
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ToolParameterBundle,
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ToolParameterBundleModel,
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ToolParameterModel,
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ToolParameterT,
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validate_against_model,
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validate_internal_job,
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validate_internal_request,
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validate_request,
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validate_test_case,
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)
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from .state import (
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JobInternalToolState,
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RequestInternalToolState,
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RequestToolState,
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TestCaseToolState,
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ToolState,
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)
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from .visitor import visit_input_values
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__all__ = (
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"from_input_source",
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"input_models_for_pages",
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"input_models_for_tool_source",
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"tool_parameter_bundle_from_json",
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"input_models_from_json",
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"JobInternalToolState",
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"ToolParameterBundle",
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"ToolParameterBundleModel",
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"ToolParameterModel",
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"IntegerParameterModel",
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"BooleanParameterModel",
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"CwlFileParameterModel",
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"CwlFloatParameterModel",
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"CwlIntegerParameterModel",
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"CwlStringParameterModel",
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"CwlNullParameterModel",
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"CwlUnionParameterModel",
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"CwlBooleanParameterModel",
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"CwlDirectoryParameterModel",
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"TextParameterModel",
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"FloatParameterModel",
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"HiddenParameterModel",
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"ColorParameterModel",
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"RulesParameterModel",
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"DataParameterModel",
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"DataCollectionParameterModel",
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"LabelValue",
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"SelectParameterModel",
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"ConditionalParameterModel",
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"ConditionalWhen",
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"RepeatParameterModel",
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"validate_against_model",
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"validate_internal_job",
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"validate_internal_request",
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"validate_request",
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"validate_test_case",
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"ToolState",
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"TestCaseToolState",
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"ToolParameterT",
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"to_json_schema_string",
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"RequestToolState",
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"RequestInternalToolState",
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"visit_input_values",
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"decode",
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"encode",
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)

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