nwb-linkml/scripts/generate_core.py

202 lines
7.5 KiB
Python

import pdb
import shutil
import os
import traceback
from argparse import ArgumentParser
from pathlib import Path
from linkml_runtime.dumpers import yaml_dumper
from rich.live import Live
from rich.panel import Panel
from rich.console import Group
from rich.progress import Progress, SpinnerColumn, BarColumn, TextColumn, Column
from rich import print
from nwb_linkml.generators.pydantic import NWBPydanticGenerator
from nwb_linkml.providers import LinkMLProvider, PydanticProvider
from nwb_linkml.providers.git import NWB_CORE_REPO, GitRepo
from nwb_linkml.io import schema as io
def generate_core_yaml(output_path:Path, dry_run:bool=False):
"""Just build the latest version of the core schema"""
core = io.load_nwb_core()
built_schemas = core.build().schemas
for schema in built_schemas:
output_file = output_path / (schema.name + '.yaml')
if not dry_run:
yaml_dumper.dump(schema, output_file)
def generate_core_pydantic(yaml_path:Path, output_path:Path, dry_run:bool=False):
"""Just generate the latest version of the core schema"""
for schema in yaml_path.glob('*.yaml'):
python_name = schema.stem.replace('.', '_').replace('-', '_')
pydantic_file = (output_path / python_name).with_suffix('.py')
generator = NWBPydanticGenerator(
str(schema),
pydantic_version='2',
emit_metadata=True,
gen_classvars=True,
gen_slots=True
)
gen_pydantic = generator.serialize()
if not dry_run:
with open(pydantic_file, 'w') as pfile:
pfile.write(gen_pydantic)
def generate_versions(yaml_path:Path, pydantic_path:Path, dry_run:bool=False):
"""
Generate linkml models for all versions
"""
repo = GitRepo(NWB_CORE_REPO)
#repo.clone(force=True)
repo.clone()
# use a directory underneath this one as the temporary directory rather than
# the default hidden one
tmp_dir = Path(__file__).parent / '__tmp__'
if tmp_dir.exists():
shutil.rmtree(tmp_dir)
tmp_dir.mkdir()
linkml_provider = LinkMLProvider(path=tmp_dir, verbose=False)
pydantic_provider = PydanticProvider(path=tmp_dir, verbose=False)
failed_versions = {}
overall_progress = Progress()
overall_task = overall_progress.add_task('All Versions', total=len(NWB_CORE_REPO.versions))
build_progress = Progress(
TextColumn("[bold blue]{task.fields[name]} - [bold green]{task.fields[action]}",
table_column=Column(ratio=1)),
BarColumn(table_column=Column(ratio=1), bar_width=None)
)
panel = Panel(Group(build_progress, overall_progress))
try:
with Live(panel) as live:
# make pbar tasks
linkml_task = None
pydantic_task = None
for version in NWB_CORE_REPO.versions:
# build linkml
try:
# check out the version (this should also refresh the hdmf-common schema)
linkml_task = build_progress.add_task('', name=version, action='Checkout Version', total=3)
repo.tag = version
build_progress.update(linkml_task, advance=1, action="Load Namespaces")
# first load the core namespace
core_ns = io.load_namespace_adapter(repo.namespace_file)
# then the hdmf-common namespace
hdmf_common_ns = io.load_namespace_adapter(repo.temp_directory / 'hdmf-common-schema' / 'common' / 'namespace.yaml')
core_ns.imported.append(hdmf_common_ns)
build_progress.update(linkml_task, advance=1, action="Build LinkML")
linkml_res = linkml_provider.build(core_ns)
build_progress.update(linkml_task, advance=1, action="Built LinkML")
# build pydantic
ns_files = [res['namespace'] for res in linkml_res.values()]
pydantic_task = build_progress.add_task('', name=version, action='', total=len(ns_files))
for schema in ns_files:
pbar_string = ' - '.join([schema.parts[-3], schema.parts[-2], schema.parts[-1]])
build_progress.update(pydantic_task, action=pbar_string)
pydantic_provider.build(schema, versions=core_ns.versions, split=True)
build_progress.update(pydantic_task, advance=1)
build_progress.update(pydantic_task, action='Built Pydantic')
except Exception as e:
build_progress.stop_task(linkml_task)
if linkml_task is not None:
build_progress.update(linkml_task, action='[bold red]LinkML Build Failed')
build_progress.stop_task(linkml_task)
if pydantic_task is not None:
build_progress.update(pydantic_task, action='[bold red]LinkML Build Failed')
build_progress.stop_task(pydantic_task)
failed_versions[version] = traceback.format_exception(e)
finally:
overall_progress.update(overall_task, advance=1)
linkml_task = None
pydantic_task = None
if not dry_run:
shutil.rmtree(yaml_path / 'linkml')
shutil.rmtree(pydantic_path / 'pydantic')
shutil.move(tmp_dir / 'linkml', yaml_path)
shutil.move(tmp_dir / 'pydantic', pydantic_path)
# import the most recent version of the schemaz we built
latest_version = sorted((pydantic_path / 'pydantic' / 'core').iterdir(), key=os.path.getmtime)[-1]
# make inits to use the schema! we don't usually do this in the
# provider class because we directly import the files there.
with open(pydantic_path / 'pydantic' / '__init__.py', 'w') as initfile:
initfile.write(' ')
with open(pydantic_path / '__init__.py', 'w') as initfile:
initfile.write(f'from .pydantic.core.{latest_version.name}.namespace import *')
finally:
if len(failed_versions) > 0:
print('Failed Building Versions:')
print(failed_versions)
def parser() -> ArgumentParser:
parser = ArgumentParser('Generate all available versions of NWB core schema')
parser.add_argument(
'--yaml',
help="directory to export linkML schema to",
type=Path,
default=Path(__file__).parent.parent / 'nwb_linkml' / 'src' / 'nwb_linkml' / 'schema'
)
parser.add_argument(
'--pydantic',
help="directory to export pydantic models",
type=Path,
default=Path(__file__).parent.parent / 'nwb_linkml' / 'src' / 'nwb_linkml' / 'models'
)
parser.add_argument(
'--latest',
help="Only generate the latest version of the core schemas.",
action="store_true"
)
parser.add_argument(
'--dry-run',
help="Generate schema and pydantic models without moving them into the target directories, for testing purposes",
action='store_true'
)
return parser
def main():
args = parser().parse_args()
if not args.dry_run:
args.yaml.mkdir(exist_ok=True)
args.pydantic.mkdir(exist_ok=True)
if args.latest:
generate_core_yaml(args.yaml, args.dry_run)
generate_core_pydantic(args.yaml, args.pydantic, args.dry_run)
else:
generate_versions(args.yaml, args.pydantic, args.dry_run)
if __name__ == "__main__":
main()