CSV

This generator outputs the classes of the LinkML schema in CSV format. Each row contains the identifier, mappings and description of each class in the schema.

This generator does not output a CSV that is configured based on the template. If fillable template spreadsheets are required, consider using [gen-excel](https://linkml.io/linkml/generators/excel.html) or [DataHarmonizer](https://github.com/cidgoh/DataHarmonizer).

Auto-generated docs

Code

Generate CSVs

class linkml.generators.csvgen.CsvGenerator(schema: str | ~typing.TextIO | ~linkml_runtime.linkml_model.meta.SchemaDefinition | ~linkml.utils.generator.Generator | ~pathlib.Path, schemaview: ~linkml_runtime.utils.schemaview.SchemaView | None = None, format: str | None = None, metadata: bool = True, useuris: bool | None = None, log_level: int | None = 30, mergeimports: bool | None = True, source_file_date: str | None = None, source_file_size: int | None = None, logger: ~logging.Logger | None = None, verbose: bool | None = None, output: str | None = None, namespaces: ~linkml_runtime.utils.namespaces.Namespaces | None = None, directory_output: bool = False, base_dir: str = None, metamodel_name_map: dict[str, str] = None, importmap: str | ~collections.abc.Mapping[str, str] | None = None, emit_prefixes: set[str] = <factory>, metamodel: ~linkml.utils.schemaloader.SchemaLoader = None, stacktrace: bool = False, include: str | ~pathlib.Path | ~linkml_runtime.linkml_model.meta.SchemaDefinition | None = None, sep: str | None = None, closure: set[~linkml_runtime.linkml_model.meta.ClassDefinitionName] | None = None, writer: ~csv.DictWriter | None = None, _str_io: ~io.StringIO | None = None)

Generates CSV summaries

Note: this generator is not widely used, and has largely been supplanted by schemasheets

closure: set[ClassDefinitionName] | None = None

List of classes to include in output

end_schema(**kwargs) → str

Visited once at the end of generation

@param kwargs: Arguments passed through from CLI – implementation dependent

generate_header() → str

generatorname: ClassVar[str] = 'csvgen.py'

Name of the generator. Override with os.path.basename(__file__)

generatorversion: ClassVar[str] = '0.1.1'

Version of the generator. Consider deprecating and instead use overall linkml version

requires_metamodel: ClassVar[bool] = False

Generator queries an instance of the metamodel

sep: str | None = None

Separator for columns

uses_schemaloader: ClassVar[bool] = True

Old-style generator that uses the SchemaLoader and visitor pattern

valid_formats: ClassVar[list[str]] = ['csv', 'tsv']

Allowed formats - first format is default

visit_class(cls: ClassDefinition) → bool

Visited once per schema class

@param cls: class being visited @return: Visit slots and end class. False means skip and go on

visit_schema(classes: list[ClassDefinitionName] = None, **_) → None

Visited once at the beginning of generation

@param kwargs: Arguments passed through from CLI – implementation dependent

writer: DictWriter | None = None

Python dictwriter

Command Line

Note: The output from this command needs to be piped in order to create a CSV file.

gen-csv

Generate CSV/TSV file from LinkML model

gen-csv [OPTIONS] YAMLFILE

Options

-V, --version

Show the version and exit.

-r, --root <root>

Class(es) to transform

-f, --format <format>

Output format

Default:

'csv'

Options:

csv | tsv

--metadata, --no-metadata

Include metadata in output

Default:

True

--useuris, --metauris

Use class and slot URIs over model uris

Default:

True

-im, --importmap <importmap>

Import mapping file

--log_level <log_level>

Logging level

Default:

'WARNING'

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG

-v, --verbose

Verbosity. Takes precedence over –log_level.

--mergeimports, --no-mergeimports

Merge imports into source file (default=mergeimports)

--stacktrace, --no-stacktrace

Print a stack trace when an error occurs

Default:

False

Arguments

YAMLFILE

Required argument