"""
Generate CSVs
"""
import os
from csv import DictWriter
from dataclasses import dataclass
from io import StringIO
from typing import Optional
import click
from linkml_runtime.linkml_model.meta import ClassDefinition, ClassDefinitionName
from linkml_runtime.utils.formatutils import be, underscore
from linkml._version import __version__
from linkml.utils.generator import Generator, shared_arguments
[docs]@dataclass
class CsvGenerator(Generator):
"""
Generates CSV summaries
Note: this generator is not widely used,
and has largely been supplanted by schemasheets
"""
# ClassVars
generatorname = os.path.basename(__file__)
generatorversion = "0.1.1"
valid_formats = ["csv", "tsv"]
uses_schemaloader = True
requires_metamodel = False
# ObjectVars
sep: Optional[str] = None
"""Separator for columns"""
closure: Optional[set[ClassDefinitionName]] = None
"""List of classes to include in output"""
writer: Optional[DictWriter] = None
"""Python dictwriter"""
_str_io: Optional[StringIO] = None
"""String that the writer outputs to"""
def __post_init__(self):
super().__post_init__()
self._str_io = None
self.generate_header() # TODO: don't do this in initialization
[docs] def visit_schema(self, classes: list[ClassDefinitionName] = None, **_) -> None:
# Note: classes comes from the "root" argument
self.closure = set()
if classes is None:
classes = []
# Validate the supplied list of classes
for clsname in classes:
if clsname not in self.schema.classes:
raise ValueError(f"Unrecognized class: {clsname}")
else:
self.closure.update(self.ancestors(self.schema.classes[clsname]))
self._str_io = StringIO()
dialect: str = "excel" if self.format == "csv" else "excel-tab"
self.writer = DictWriter(self._str_io, ["id", "mappings", "description"], dialect=dialect)
self.writer.writeheader()
[docs] def visit_class(self, cls: ClassDefinition) -> bool:
# TODO: find out what to do with mappings
if not self.closure or cls.name in self.closure:
self.writer.writerow(
{
"id": underscore(cls.name),
# 'mappings': "|".join(cls.mappings),
"mappings": "",
"description": be(cls.description),
}
)
return True
return False
[docs] def end_schema(self, **kwargs) -> str:
return self._str_io.getvalue()
@shared_arguments(CsvGenerator)
@click.command(name="csv")
@click.version_option(__version__, "-V", "--version")
@click.option("--root", "-r", multiple=True, help="Class(es) to transform")
def cli(yamlfile, root=None, **args):
"""Generate CSV/TSV file from LinkML model"""
print(CsvGenerator(yamlfile, **args).serialize(classes=root, **args))
if __name__ == "__main__":
cli()