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30 changes: 30 additions & 0 deletions
30
lib/galaxy/model/dataset_collections/types/sample_sheet.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| from galaxy.exceptions import RequestParameterMissingException | ||
| from galaxy.model import DatasetCollectionElement | ||
| from . import BaseDatasetCollectionType | ||
| from .sample_sheet_util import validate_row | ||
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| class SampleSheetDatasetCollectionType(BaseDatasetCollectionType): | ||
| """A flat list of named elements starting rows with column metadata.""" | ||
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| collection_type = "sample_sheet" | ||
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| def generate_elements(self, dataset_instances, **kwds): | ||
| rows = kwds.get("rows", None) | ||
| column_definitions = kwds.get("column_definitions", None) | ||
| if rows is None: | ||
| raise RequestParameterMissingException( | ||
| "Missing or null parameter 'rows' required for 'sample_sheet' collection types." | ||
| ) | ||
| if len(dataset_instances) != len(rows): | ||
| self._validation_failed("Supplied element do not match 'rows'.") | ||
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| for identifier, element in dataset_instances.items(): | ||
| columns = rows[identifier] | ||
| validate_row(columns, column_definitions) | ||
| association = DatasetCollectionElement( | ||
| element=element, | ||
| element_identifier=identifier, | ||
| columns=columns, | ||
| ) | ||
| yield association |
101 changes: 101 additions & 0 deletions
101
lib/galaxy/model/dataset_collections/types/sample_sheet_util.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| from typing import ( | ||
| List, | ||
| Optional, | ||
| Union, | ||
| ) | ||
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| from pydantic import ( | ||
| BaseModel, | ||
| ConfigDict, | ||
| RootModel, | ||
| TypeAdapter, | ||
| ) | ||
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| from galaxy.exceptions import RequestParameterInvalidException | ||
| from galaxy.schema.schema import ( | ||
| SampleSheetColumnDefinition, | ||
| SampleSheetColumnDefinitions, | ||
| SampleSheetColumnType, | ||
| SampleSheetColumnValueT, | ||
| SampleSheetRow, | ||
| ) | ||
| from galaxy.tool_util.parser.parameter_validators import ( | ||
| AnySafeValidatorModel, | ||
| DiscriminatedAnySafeValidatorModel, | ||
| parse_dict_validators, | ||
| UnsafeValidatorConfiguredInUntrustedContext, | ||
| ) | ||
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| class SampleSheetColumnDefinitionModel(BaseModel): | ||
| model_config = ConfigDict(extra="forbid") | ||
| type: SampleSheetColumnType | ||
| validators: Optional[List[AnySafeValidatorModel]] = None | ||
| restrictions: Optional[List[SampleSheetColumnValueT]] = None | ||
| suggestions: Optional[List[SampleSheetColumnValueT]] = None | ||
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| SampleSheetColumnDefinitionsModel = RootModel[List[SampleSheetColumnDefinitionModel]] | ||
| SampleSheetColumnDefinitionDictOrModel = Union[SampleSheetColumnDefinition, SampleSheetColumnDefinitionModel] | ||
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| def sample_sheet_column_definition_to_model( | ||
| column_definition: SampleSheetColumnDefinitionDictOrModel, | ||
| ) -> SampleSheetColumnDefinitionModel: | ||
| if isinstance(column_definition, SampleSheetColumnDefinitionModel): | ||
| return column_definition | ||
| else: | ||
| return SampleSheetColumnDefinitionModel.model_validate(column_definition) | ||
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| def validate_column_definitions(column_definitions: Optional[SampleSheetColumnDefinitions]): | ||
| for column_definition in column_definitions or []: | ||
| _validate_column_definition(column_definition) | ||
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| def _validate_column_definition(column_definition: SampleSheetColumnDefinition): | ||
| # we should do most of this with pydantic but I just wanted to especially make sure | ||
| # we were only using safe validators | ||
| return SampleSheetColumnDefinitionModel(**column_definition) | ||
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| def validate_row(row: SampleSheetRow, column_definitions: Optional[SampleSheetColumnDefinitions]): | ||
| if column_definitions is None: | ||
| return | ||
| if len(row) != len(column_definitions): | ||
| raise RequestParameterInvalidException( | ||
| "Sample sheet row validation failed, incorrect number of columns specified." | ||
| ) | ||
| for column_value, column_definition in zip(row, column_definitions): | ||
| validate_column_value(column_value, column_definition) | ||
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| def validate_column_value( | ||
| column_value: SampleSheetColumnValueT, column_definition: SampleSheetColumnDefinitionDictOrModel | ||
| ): | ||
| column_definition_model = sample_sheet_column_definition_to_model(column_definition) | ||
| column_type = column_definition_model.type | ||
| if column_type == "int": | ||
| if not isinstance(column_value, int): | ||
| raise RequestParameterInvalidException(f"{column_value} was not an integer as expected") | ||
| elif column_type == "float": | ||
| if not isinstance(column_value, (float, int)): | ||
| raise RequestParameterInvalidException(f"{column_value} was not a number as expected") | ||
| elif column_type == "string": | ||
| if not isinstance(column_value, (str,)): | ||
| raise RequestParameterInvalidException(f"{column_value} was not a string as expected") | ||
| elif column_type == "boolean": | ||
| if not isinstance(column_value, (bool,)): | ||
| raise RequestParameterInvalidException(f"{column_value} was not a boolean as expected") | ||
| restrictions = column_definition_model.restrictions | ||
| if restrictions is not None: | ||
| if column_value not in restrictions: | ||
| raise RequestParameterInvalidException( | ||
| f"{column_value} was not in specified list of valid values as expected" | ||
| ) | ||
| validators = column_definition_model.validators or [] | ||
| for validator in validators: | ||
| try: | ||
| validator.statically_validate(column_value) | ||
| except ValueError as e: | ||
| raise RequestParameterInvalidException(str(e)) |
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