mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-14 10:44:28 +00:00
246 lines
9.3 KiB
Python
246 lines
9.3 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 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()
|
|
|
|
# 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 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)
|
|
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:
|
|
if hdmf_only:
|
|
shutil.rmtree(yaml_path / "linkml" / "hdmf_common")
|
|
shutil.rmtree(yaml_path / "linkml" / "hdmf_experimental")
|
|
shutil.rmtree(pydantic_path / "pydantic" / "hdmf_common")
|
|
shutil.rmtree(pydantic_path / "pydantic" / "hdmf_experimental")
|
|
shutil.move(tmp_dir / "linkml" / "hdmf_common", yaml_path / "linkml")
|
|
shutil.move(tmp_dir / "linkml" / "hdmf_experimental", yaml_path / "linkml")
|
|
shutil.move(tmp_dir / "pydantic" / "hdmf_common", pydantic_path / "pydantic")
|
|
shutil.move(tmp_dir / "pydantic" / "hdmf_experimental", pydantic_path / "pydantic")
|
|
else:
|
|
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").glob("v*"), 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 *")
|
|
|
|
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_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("--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()
|
|
if args.hdmf:
|
|
repo = GitRepo(HDMF_COMMON_REPO)
|
|
else:
|
|
repo = GitRepo(NWB_CORE_REPO)
|
|
|
|
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()
|