nwb-linkml/scripts/generate_core.py

252 lines
8.8 KiB
Python

import shutil
import os
import sys
import traceback
from pdb import post_mortem
import subprocess
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, HDMF_COMMON_REPO, GitRepo
from nwb_linkml.io import schema as io
def generate_core_yaml(output_path: Path, dry_run: bool = False, hdmf_only: bool = False):
"""Just build the latest version of the core schema"""
core = io.load_nwb_core(hdmf_only=hdmf_only)
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 make_tmp_dir(clear: bool = False) -> Path:
# 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() and clear:
for p in tmp_dir.iterdir():
if p.is_dir() and not p.name == "git":
shutil.rmtree(p)
tmp_dir.mkdir(exist_ok=True)
return tmp_dir
def generate_versions(
yaml_path: Path,
pydantic_path: Path,
dry_run: bool = False,
repo: GitRepo = NWB_CORE_REPO,
hdmf_only=False,
pdb=False,
):
"""
Generate linkml models for all versions
"""
# repo.clone(force=True)
repo.clone()
tmp_dir = make_tmp_dir()
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 repo.namespace.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")
if repo.namespace == NWB_CORE_REPO:
# first load HDMF common
hdmf_common_ns = io.load_namespace_adapter(
repo.temp_directory / "hdmf-common-schema" / "common" / "namespace.yaml"
)
# then load nwb core
core_ns = io.load_namespace_adapter(
repo.namespace_file, imported=[hdmf_common_ns]
)
else:
# otherwise just load HDMF
core_ns = io.load_namespace_adapter(repo.namespace_file)
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 = schema.parts[-3]
build_progress.update(pydantic_task, action=pbar_string)
pydantic_provider.build(
schema, versions=core_ns.versions, split=True, parallel=True
)
build_progress.update(pydantic_task, advance=1)
build_progress.update(pydantic_task, action="Built Pydantic")
except Exception as e:
if pdb:
live.stop()
post_mortem()
sys.exit(1)
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.copytree(tmp_dir / "linkml", yaml_path, dirs_exist_ok=True)
shutil.copytree(tmp_dir / "pydantic", pydantic_path, dirs_exist_ok=True)
shutil.rmtree(tmp_dir / "linkml")
shutil.rmtree(tmp_dir / "pydantic")
# 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 / "__init__.py", "w") as initfile:
initfile.write(" ")
subprocess.run(["black", "."])
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_models"
/ "src"
/ "nwb_models"
/ "schema"
/ "linkml",
)
parser.add_argument(
"--pydantic",
help="directory to export pydantic models",
type=Path,
default=Path(__file__).parent.parent
/ "nwb_models"
/ "src"
/ "nwb_models"
/ "models"
/ "pydantic",
)
parser.add_argument("--hdmf", help="Only generate the HDMF namespaces", action="store_true")
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",
)
parser.add_argument("--pdb", help="Launch debugger on an error", action="store_true")
return parser
def main():
args = parser().parse_args()
tmp_dir = make_tmp_dir(clear=True)
git_dir = tmp_dir / "git"
git_dir.mkdir(exist_ok=True)
if args.hdmf:
repo = GitRepo(HDMF_COMMON_REPO, path=git_dir)
else:
repo = GitRepo(NWB_CORE_REPO, path=git_dir)
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, args.hdmf)
generate_core_pydantic(args.yaml, args.pydantic, args.dry_run)
else:
generate_versions(args.yaml, args.pydantic, args.dry_run, repo, args.hdmf, pdb=args.pdb)
if __name__ == "__main__":
main()