This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.datatypes._schema

from typing import (

from pydantic import (

class CompositeFileInfo(BaseModel):
    name: str = Field(..., title="Name", description="The name of this composite file")  # Mark this field as required
    optional: bool = Field(title="Optional", description="")  # TODO add description
    mimetype: Optional[str] = Field(title="MIME type", description="The MIME type of this file")
    description: Optional[str] = Field(
        title="Description", description="Summary description of the purpouse of this file"
    substitute_name_with_metadata: Optional[str] = Field(
        title="Substitute name with metadata", description=""  # TODO add description
    is_binary: bool = Field(title="Is binary", description="Whether this file is a binary file")
    to_posix_lines: bool = Field(title="To posix lines", description="")  # TODO add description
    space_to_tab: bool = Field(title="Spaces to tabulation", description="")  # TODO add description

[docs]class DatatypeDetails(BaseModel): extension: str = Field( ..., # Mark this field as required title="Extension", description="The data type’s Dataset file extension", example="bed", ) description: Optional[str] = Field(title="Description", description="A summary description for this data type") description_url: Optional[HttpUrl] = Field( title="Description URL", description="The URL to a detailed description for this datatype", example="https://wiki.galaxyproject.org/Learn/Datatypes#Bed", ) display_in_upload: bool = Field( default=False, title="Display in upload", description="If True, the associated file extension will be displayed in the `File Format` select list in the `Upload File from your computer` tool in the `Get Data` tool section of the tool panel", ) composite_files: Optional[List[CompositeFileInfo]] = Field( default=None, title="Composite files", description="A collection of files composing this data type" )
[docs]class DatatypesMap(BaseModel): ext_to_class_name: Dict[str, str] = Field( ..., # Mark this field as required title="Extension Map", description="Dictionary mapping datatype's extensions with implementation classes", ) class_to_classes: Dict[str, Dict[str, bool]] = Field( ..., # Mark this field as required title="Classes Map", description="Dictionary mapping datatype's classes with their base classes", )
[docs]class DatatypesCombinedMap(BaseModel): datatypes: List[str] = Field( ..., # Mark this field as required title="Datatypes", description="List of datatypes extensions", ) datatypes_mapping: DatatypesMap = Field( ..., # Mark this field as required title="Datatypes Mapping", description="Dictionaries for mapping datatype's extensions/classes with their implementation classes", )
class DatatypeConverter(BaseModel): source: str = Field( ..., # Mark this field as required title="Source", description="Source type for conversion", example="bam", ) target: str = Field( ..., # Mark this field as required title="Target", description="Target type for conversion", example="bai", ) tool_id: str = Field( ..., # Mark this field as required title="Tool identifier", description="The converter tool identifier", example="CONVERTER_Bam_Bai_0", )
[docs]class DatatypeConverterList(BaseModel): __root__: List[DatatypeConverter] = Field(title="List of data type converters", default=[])
class DatatypeEDAMDetails(BaseModel): prefix_IRI: str = Field( ..., # Mark this field as required title="Prefix IRI", description="The EDAM prefixed Resource Identifier", example="format_1782", ) label: Optional[str] = Field( title="Label", description="The EDAM label", example="NCBI gene report format", ) definition: Optional[str] = Field( title="Definition", description="The EDAM definition", example="Entry (gene) format of the NCBI database.", )
[docs]class DatatypesEDAMDetailsDict(BaseModel): __root__: Dict[str, DatatypeEDAMDetails] = Field( title="Dict of EDAM details for formats", default={}, )