nwb-linkml/scripts/generate_core.py

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")

                    # first load the core namespace
                    core_ns = io.load_namespace_adapter(repo.namespace_file)
                    if repo.namespace == NWB_CORE_REPO:
                        # 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 = 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").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 *")

            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()