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Add numeric input range validation + tests
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@nx10
nx10 committed Nov 17, 2023
1 parent 311b38c commit 6756c53
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Showing 9 changed files with 510 additions and 185 deletions.
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ exclude = [
"node_modules",
"venv",
]
line-length = 88
line-length = 120
indent-width = 4
src=["src"]

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68 changes: 17 additions & 51 deletions src/styx/boutiques/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,7 @@ class ContainerImageItem1(BaseModel):
extra="forbid",
)
type: Type1
url: constr(min_length=1) = Field(
..., description="URL where the image is available."
)
url: constr(min_length=1) = Field(..., description="URL where the image is available.")
working_directory: Optional[Any] = Field(None, alias="working-directory")
container_hash: Optional[Any] = Field(None, alias="container-hash")

Expand Down Expand Up @@ -95,9 +93,7 @@ class EnvironmentVariable(BaseModel):
description='The environment variable name (identifier) containing only alphanumeric characters and underscores. Example: "PROGRAM_PATH".',
)
value: str = Field(..., description="The value of the environment variable.")
description: Optional[str] = Field(
None, description="Description of the environment variable."
)
description: Optional[str] = Field(None, description="Description of the environment variable.")


class Group(BaseModel):
Expand All @@ -108,12 +104,8 @@ class Group(BaseModel):
...,
description='A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: "outfile_group".',
)
name: constr(min_length=1) = Field(
..., description="A human-readable name for the input group."
)
description: Optional[str] = Field(
None, description="Description of the input group."
)
name: constr(min_length=1) = Field(..., description="A human-readable name for the input group.")
description: Optional[str] = Field(None, description="Description of the input group.")
members: List[constr(pattern=r"^[0-9,_,a-z,A-Z]*$", min_length=1)] = Field(
..., description="IDs of the inputs belonging to this group."
)
Expand Down Expand Up @@ -172,9 +164,7 @@ class Inputs(Input):
...,
description='A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: "data_file".',
)
name: constr(min_length=1) = Field(
..., description="A human-readable input name. Example: 'Data file'."
)
name: constr(min_length=1) = Field(..., description="A human-readable input name. Example: 'Data file'.")
type: Type4 = Field(..., description="Input type.")
description: Optional[str] = Field(None, description="Input description.")
value_key: Optional[str] = Field(
Expand Down Expand Up @@ -279,9 +269,7 @@ class Inputs1(Input1):
...,
description='A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: "data_file".',
)
name: constr(min_length=1) = Field(
..., description="A human-readable input name. Example: 'Data file'."
)
name: constr(min_length=1) = Field(..., description="A human-readable input name. Example: 'Data file'.")
type: Type4 = Field(..., description="Input type.")
description: Optional[str] = Field(None, description="Input description.")
value_key: Optional[str] = Field(
Expand Down Expand Up @@ -384,9 +372,7 @@ class Test(BaseModel):


class OutputFile(BaseModel):
file_template: Optional[List[str]] = Field(
None, alias="file-template", min_length=1
)
file_template: Optional[List[str]] = Field(None, alias="file-template", min_length=1)
list: Optional[ListModel] = None


Expand All @@ -410,9 +396,7 @@ class OutputFiles(OutputFile):
...,
description='A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: "data_file"',
)
name: constr(min_length=1) = Field(
..., description="A human-readable output name. Example: 'Data file'"
)
name: constr(min_length=1) = Field(..., description="A human-readable output name. Example: 'Data file'")
description: Optional[str] = Field(None, description="Output description.")
value_key: Optional[str] = Field(
None,
Expand All @@ -436,9 +420,7 @@ class OutputFiles(OutputFile):
description='List of file extensions that will be stripped from the input values before being substituted in the path template. Example: [".nii",".nii.gz"].',
)
list: Optional[bool] = Field(None, description="True if output is a list of value.")
optional: Optional[bool] = Field(
None, description="True if output may not be produced by the tool."
)
optional: Optional[bool] = Field(None, description="True if output may not be produced by the tool.")
command_line_flag: Optional[str] = Field(
None,
alias="command-line-flag",
Expand Down Expand Up @@ -470,9 +452,7 @@ class OutputFiles1(OutputFile1):
...,
description='A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: "data_file"',
)
name: constr(min_length=1) = Field(
..., description="A human-readable output name. Example: 'Data file'"
)
name: constr(min_length=1) = Field(..., description="A human-readable output name. Example: 'Data file'")
description: Optional[str] = Field(None, description="Output description.")
value_key: Optional[str] = Field(
None,
Expand All @@ -496,9 +476,7 @@ class OutputFiles1(OutputFile1):
description='List of file extensions that will be stripped from the input values before being substituted in the path template. Example: [".nii",".nii.gz"].',
)
list: Optional[bool] = Field(None, description="True if output is a list of value.")
optional: Optional[bool] = Field(
None, description="True if output may not be produced by the tool."
)
optional: Optional[bool] = Field(None, description="True if output may not be produced by the tool.")
command_line_flag: Optional[str] = Field(
None,
alias="command-line-flag",
Expand Down Expand Up @@ -561,27 +539,21 @@ class Tool(BaseModel):
extra="forbid",
)
name: constr(min_length=1) = Field(..., description="Tool name.")
tool_version: constr(min_length=1) = Field(
..., alias="tool-version", description="Tool version."
)
tool_version: constr(min_length=1) = Field(..., alias="tool-version", description="Tool version.")
description: constr(min_length=1) = Field(..., description="Tool description.")
deprecated_by_doi: Optional[Union[constr(min_length=1), bool]] = Field(
None,
alias="deprecated-by-doi",
description="doi of the tool that deprecates the current one. May be set to 'true' if the current tool is deprecated but no specific tool deprecates it.",
)
author: Optional[constr(min_length=1)] = Field(
None, description="Tool author name(s)."
)
author: Optional[constr(min_length=1)] = Field(None, description="Tool author name(s).")
url: Optional[constr(min_length=1)] = Field(None, description="Tool URL.")
descriptor_url: Optional[constr(min_length=1)] = Field(
None,
alias="descriptor-url",
description="Link to the descriptor itself (e.g. the GitHub repo where it is hosted).",
)
doi: Optional[constr(min_length=1)] = Field(
None, description="DOI of the descriptor (not of the tool itself)."
)
doi: Optional[constr(min_length=1)] = Field(None, description="DOI of the descriptor (not of the tool itself).")
shell: Optional[constr(min_length=1)] = Field(
None,
description="Absolute path of the shell interpreter to use in the container (defaults to /bin/sh).",
Expand All @@ -595,9 +567,7 @@ class Tool(BaseModel):
description='A string that describes the tool command line, where input and output values are identified by "keys". At runtime, command-line keys are substituted with flags and values.',
)
container_image: Optional[ContainerImage] = Field(None, alias="container-image")
schema_version: SchemaVersion = Field(
..., alias="schema-version", description="Version of the schema used."
)
schema_version: SchemaVersion = Field(..., alias="schema-version", description="Version of the schema used.")
environment_variables: Optional[List[EnvironmentVariable]] = Field(
None,
alias="environment-variables",
Expand All @@ -616,13 +586,9 @@ class Tool(BaseModel):
alias="online-platform-urls",
description="Online platform URLs from which the tool can be executed.",
)
output_files: Optional[List[Union[OutputFiles, OutputFiles1]]] = Field(
None, alias="output-files", min_length=1
)
output_files: Optional[List[Union[OutputFiles, OutputFiles1]]] = Field(None, alias="output-files", min_length=1)
invocation_schema: Optional[Dict[str, Any]] = Field(None, alias="invocation-schema")
suggested_resources: Optional[SuggestedResources] = Field(
None, alias="suggested-resources"
)
suggested_resources: Optional[SuggestedResources] = Field(None, alias="suggested-resources")
tags: Optional[Dict[str, List[str]]] = Field(
None,
description="A set of key-value pairs specifying tags describing the pipeline. The tag names are open, they might be more constrained in the future.",
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