@delta-infra/cli 1.0.73 → 1.0.74

package/skills/delta-science/scripts/invoke.py

@@ -1,189 +1,329 @@
-#!/usr/bin/env python3
-"""Invoke one Delta Science operation strictly through delta-cli."""
-
-from __future__ import annotations
-
-import argparse
-import json
-import os
-from pathlib import Path
-import shutil
-import subprocess
-import sys
-import time
-from typing import Any
-
-
-SKILL_DIR = Path(__file__).resolve().parents[1]
-
-
-def _json_object(raw: str | None, flag: str) -> dict[str, Any] | None:
-    if raw is None:
-        return None
-    try:
-        value = json.loads(raw)
-    except json.JSONDecodeError as exc:
-        raise ValueError(f"{flag} is not valid JSON: {exc}") from exc
-    if not isinstance(value, dict):
-        raise ValueError(f"{flag} must decode to a JSON object")
-    return value
-
-
-def _runtime_config() -> dict[str, Any]:
-    path = SKILL_DIR / "runtime.local.json"
-    if not path.is_file():
-        return {}
-    try:
-        value = json.loads(path.read_text(encoding="utf-8"))
-    except (OSError, json.JSONDecodeError):
-        return {}
-    return value if isinstance(value, dict) else {}
-
-
-def _resolve_cli(explicit: str | None, runtime: dict[str, Any]) -> str:
-    candidates: list[str | None] = [
-        explicit,
-        os.environ.get("DELTA_CLI_PATH"),
-        runtime.get("cli_path"),
-        shutil.which("delta-cli"),
-        shutil.which("delta-cli.exe"),
-    ]
-    package_root = SKILL_DIR.parents[1]
-    exe_name = "delta-cli.exe" if os.name == "nt" else "delta-cli"
-    candidates.append(str(package_root / "bin" / exe_name))
-    for candidate in candidates:
-        if candidate and Path(candidate).is_file():
-            return str(Path(candidate).resolve())
-    raise FileNotFoundError(
-        "delta-cli not found; install @delta-infra/cli, set DELTA_CLI_PATH, "
-        "or add cli_path to delta-science/runtime.local.json"
-    )
-
-
-def _unwrap(stdout: str) -> tuple[Any, int]:
-    try:
-        root = json.loads(stdout)
-    except json.JSONDecodeError as exc:
-        raise RuntimeError(f"CLI stdout is not JSON: {exc}") from exc
-    if not isinstance(root, dict):
-        raise RuntimeError("CLI stdout root is not an object")
-    if root.get("ok") is not True:
-        raise RuntimeError(json.dumps(root.get("error", root), ensure_ascii=False))
-    if "data" not in root:
-        raise RuntimeError("CLI success envelope is missing data")
-
-    value: Any = root["data"]
-    depth = 0
-    while isinstance(value, dict):
-        if "status_code" in value and "data" in value:
-            status_code = value.get("status_code")
-            if not isinstance(status_code, int) or not 200 <= status_code < 300:
-                raise RuntimeError(json.dumps(value, ensure_ascii=False))
-            value = value["data"]
-        elif (
-            "code" in value
-            and "data" in value
-            and set(value).intersection({"message", "msg"})
-        ):
-            code = value.get("code")
-            if code not in (0, "0", None):
-                raise RuntimeError(json.dumps(value, ensure_ascii=False))
-            value = value["data"]
-        else:
-            break
-        depth += 1
-        if depth > 4:
-            raise RuntimeError("too many nested service envelopes")
-    if isinstance(value, dict) and value.get("valid") is False:
-        raise RuntimeError(json.dumps({
-            "valid": False,
-            "error": value.get("error"),
-            "warnings": value.get("warnings"),
-        }, ensure_ascii=False))
-    return value, depth
-
-
-def _parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(description=__doc__)
-    parser.add_argument("--tool", required=True)
-    parser.add_argument("--endpoint", required=True)
-    body = parser.add_mutually_exclusive_group()
-    body.add_argument("--data-json")
-    body.add_argument("--params-json")
-    parser.add_argument("--cli")
-    parser.add_argument("--science-base-url")
-    parser.add_argument("--timeout", type=float, default=120.0)
-    return parser
-
-
-def main() -> int:
-    args = _parser().parse_args()
-    started = time.perf_counter()
-    stage = "arguments"
-    try:
-        data = _json_object(args.data_json, "--data-json")
-        params = _json_object(args.params_json, "--params-json")
-        runtime = _runtime_config()
-        stage = "cli-resolution"
-        cli = _resolve_cli(args.cli, runtime)
-
-        command = [
-            cli, "science", "invoke",
-            "--tool", args.tool,
-            "--endpoint", args.endpoint,
-        ]
-        if data is not None:
-            command.extend(["--data", json.dumps(data, ensure_ascii=False, separators=(",", ":"))])
-        if params is not None:
-            command.extend(["--params", json.dumps(params, ensure_ascii=False, separators=(",", ":"))])
-
-        env = os.environ.copy()
-        base_url = args.science_base_url or runtime.get("science_base_url")
-        if base_url:
-            env["DELTA_INFRA_SCIENCE_BASE_URL"] = str(base_url)
-
-        stage = "delta-cli"
-        completed = subprocess.run(
-            command,
-            capture_output=True,
-            text=True,
-            encoding="utf-8",
-            errors="replace",
-            env=env,
-            timeout=args.timeout,
-            check=False,
-        )
-        if completed.returncode != 0:
-            detail = completed.stderr.strip() or completed.stdout.strip()
-            raise RuntimeError(f"exit_code={completed.returncode}: {detail}")
-        stage = "response-validation"
-        native, depth = _unwrap(completed.stdout)
-        result = {
-            "ok": True,
-            "transport": "delta-cli",
-            "tool": args.tool,
-            "endpoint": args.endpoint,
-            "elapsed_seconds": round(time.perf_counter() - started, 3),
-            "envelope_depth": depth,
-            "native": native,
-        }
-        print(json.dumps(result, ensure_ascii=False))
-        return 0
-    except subprocess.TimeoutExpired:
-        error = f"timeout after {args.timeout}s"
-    except (OSError, ValueError, RuntimeError) as exc:
-        error = str(exc)
-    print(json.dumps({
-        "ok": False,
-        "transport": "delta-cli",
-        "tool": args.tool,
-        "endpoint": args.endpoint,
-        "stage": stage,
-        "elapsed_seconds": round(time.perf_counter() - started, 3),
-        "error": error[:2000],
-    }, ensure_ascii=False))
-    return 1
-
-
-if __name__ == "__main__":
-    sys.exit(main())
+#!/usr/bin/env python3
+"""Invoke one Delta Science operation strictly through delta-cli."""
+
+from __future__ import annotations
+
+import argparse
+import json
+import os
+from pathlib import Path
+import shutil
+import subprocess
+import sys
+import time
+from typing import Any
+from urllib.parse import urlsplit
+
+
+SKILL_DIR = Path(__file__).resolve().parents[1]
+
+LEGACY_TOOL_ALIASES = {
+    "antbo": "antbo-service",
+    "synbo": "synbo-service",
+}
+
+LEGACY_ENDPOINTS = {
+    "pubchem": {
+        "health": "chem_pubchem_health",
+        "compound-resolve-cids": "chem_pubchem_compound_resolve-cids",
+        "compound-properties": "chem_pubchem_compound_properties",
+        "compound-synonyms": "chem_pubchem_compound_synonyms",
+        "compound-summary": "chem_pubchem_compound_summary",
+        "compound-batch-summary": "chem_pubchem_compound_batch-summary",
+    },
+    "rdkit": {
+        "health": "chem_rdkit_health",
+        "parse": "chem_rdkit_parse",
+        "descriptors": "chem_rdkit_descriptors",
+        "batch-descriptors": "chem_rdkit_batch-descriptors",
+        "batch-parse-describe": "chem_rdkit_batch-parse-describe",
+        "render": "chem_rdkit_render",
+        "fingerprint": "chem_rdkit_fingerprint",
+        "similarity": "chem_rdkit_similarity",
+        "similarity-matrix": "chem_rdkit_similarity-matrix",
+        "substructure": "chem_rdkit_substructure",
+    },
+    "pymatgen": {
+        "health": "chem_pymatgen_health",
+        "composition-parse": "chem_pymatgen_composition_parse",
+        "structure-parse": "chem_pymatgen_structure_parse",
+        "structure-summary": "chem_pymatgen_structure_summary",
+        "structure-convert": "chem_pymatgen_structure_convert",
+        "structure-symmetry": "chem_pymatgen_structure_symmetry",
+    },
+    "gsasii": {
+        "health": "chem_gsasii_health",
+        "powder-simulate": "chem_gsasii_powder_simulate",
+        "powder-refine": "chem_gsasii_powder_refine",
+    },
+    "lammps": {
+        "health": "chem_lammps_health",
+        "lj-melt-example": "chem_lammps_examples_lj-melt",
+        "run": "chem_lammps_run",
+    },
+    "delta-bo": {
+        "commands": "chem_delta-bo_commands",
+        "generate": "chem_delta-bo_generate",
+    },
+    "ldm-bo": {
+        "health": "chem_ldm-bo_health",
+        "recommend": "chem_ldm-bo_recommend",
+        "trajectory": "chem_ldm-bo_trajectory",
+    },
+    "synbo": {
+        "health": "chem_synbo_health",
+        "initialize": "chem_synbo_initialize",
+        "optimize": "chem_synbo_optimize",
+    },
+    "antbo": {
+        "health": "biology_antbo_health",
+        "run-default-job": "biology_antbo_run_default_job",
+        "run": "biology_antbo_run",
+        "log": "biology_antbo_log",
+        "jobs": "biology_antbo_jobs",
+        "stop": "biology_antbo_stop",
+    },
+}
+
+
+def _json_object(raw: str | None, flag: str) -> dict[str, Any] | None:
+    if raw is None:
+        return None
+    try:
+        value = json.loads(raw)
+    except json.JSONDecodeError as exc:
+        raise ValueError(f"{flag} is not valid JSON: {exc}") from exc
+    if not isinstance(value, dict):
+        raise ValueError(f"{flag} must decode to a JSON object")
+    return value
+
+
+def _runtime_config() -> dict[str, Any]:
+    path = SKILL_DIR / "runtime.local.json"
+    if not path.is_file():
+        return {}
+    try:
+        value = json.loads(path.read_text(encoding="utf-8"))
+    except (OSError, json.JSONDecodeError):
+        return {}
+    return value if isinstance(value, dict) else {}
+
+
+def _resolve_cli(explicit: str | None, runtime: dict[str, Any]) -> str:
+    candidates: list[str | None] = [
+        explicit,
+        os.environ.get("DELTA_CLI_PATH"),
+        runtime.get("cli_path"),
+        shutil.which("delta-cli"),
+        shutil.which("delta-cli.exe"),
+    ]
+    package_root = SKILL_DIR.parents[1]
+    exe_name = "delta-cli.exe" if os.name == "nt" else "delta-cli"
+    candidates.append(str(package_root / "bin" / exe_name))
+    for candidate in candidates:
+        if candidate and Path(candidate).is_file():
+            return str(Path(candidate).resolve())
+    raise FileNotFoundError(
+        "delta-cli not found; install @delta-infra/cli, set DELTA_CLI_PATH, "
+        "or add cli_path to delta-science/runtime.local.json"
+    )
+
+
+def _cli_science_base_url(cli: str, env: dict[str, str], timeout: float) -> str:
+    explicit = env.get("DELTA_INFRA_SCIENCE_BASE_URL", "").strip()
+    if explicit:
+        return explicit
+    completed = subprocess.run(
+        [cli, "config", "show"],
+        capture_output=True,
+        text=True,
+        encoding="utf-8",
+        errors="replace",
+        env=env,
+        timeout=min(timeout, 15.0),
+        check=False,
+    )
+    if completed.returncode != 0:
+        return ""
+    try:
+        root = json.loads(completed.stdout)
+        value = root.get("data", {}).get("science_base_url", "")
+    except (AttributeError, json.JSONDecodeError):
+        return ""
+    return str(value).strip()
+
+
+def _catalog_profile(base_url: str, requested: str) -> str:
+    if requested != "auto":
+        return requested
+    try:
+        path = urlsplit(base_url).path.rstrip("/").lower()
+    except ValueError:
+        path = ""
+    return "legacy" if path.endswith("/science_tool") else "canonical"
+
+
+def _resolve_catalog_names(tool: str, endpoint: str, profile: str) -> tuple[str, str]:
+    if profile == "canonical":
+        return tool, endpoint
+    canonical_tool = tool.removesuffix("-service") if tool in {"antbo-service", "synbo-service"} else tool
+    resolved_tool = LEGACY_TOOL_ALIASES.get(canonical_tool, canonical_tool)
+    if endpoint.startswith(("chem_", "biology_")):
+        return resolved_tool, endpoint
+    resolved_endpoint = LEGACY_ENDPOINTS.get(canonical_tool, {}).get(endpoint)
+    if not resolved_endpoint:
+        raise ValueError(
+            f"no legacy science_tool mapping for {canonical_tool}/{endpoint}"
+        )
+    return resolved_tool, resolved_endpoint
+
+
+def _unwrap(stdout: str) -> tuple[Any, int]:
+    try:
+        root = json.loads(stdout)
+    except json.JSONDecodeError as exc:
+        raise RuntimeError(f"CLI stdout is not JSON: {exc}") from exc
+    if not isinstance(root, dict):
+        raise RuntimeError("CLI stdout root is not an object")
+    if root.get("ok") is not True:
+        raise RuntimeError(json.dumps(root.get("error", root), ensure_ascii=False))
+    if "data" not in root:
+        raise RuntimeError("CLI success envelope is missing data")
+
+    value: Any = root["data"]
+    depth = 0
+    while isinstance(value, dict):
+        if "status_code" in value and "data" in value:
+            status_code = value.get("status_code")
+            if not isinstance(status_code, int) or not 200 <= status_code < 300:
+                raise RuntimeError(json.dumps(value, ensure_ascii=False))
+            value = value["data"]
+        elif (
+            "code" in value
+            and "data" in value
+            and set(value).intersection({"message", "msg"})
+        ):
+            code = value.get("code")
+            if code not in (0, "0", None):
+                raise RuntimeError(json.dumps(value, ensure_ascii=False))
+            value = value["data"]
+        else:
+            break
+        depth += 1
+        if depth > 4:
+            raise RuntimeError("too many nested service envelopes")
+    if isinstance(value, dict) and value.get("valid") is False:
+        raise RuntimeError(json.dumps({
+            "valid": False,
+            "error": value.get("error"),
+            "warnings": value.get("warnings"),
+        }, ensure_ascii=False))
+    return value, depth
+
+
+def _parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--tool", required=True)
+    parser.add_argument("--endpoint", required=True)
+    body = parser.add_mutually_exclusive_group()
+    body.add_argument("--data-json")
+    body.add_argument("--params-json")
+    parser.add_argument("--cli")
+    parser.add_argument("--science-base-url")
+    parser.add_argument(
+        "--catalog-profile",
+        choices=("auto", "canonical", "legacy"),
+        default="auto",
+    )
+    parser.add_argument("--timeout", type=float, default=120.0)
+    return parser
+
+
+def main() -> int:
+    args = _parser().parse_args()
+    started = time.perf_counter()
+    stage = "arguments"
+    profile = "unknown"
+    resolved_tool = args.tool
+    resolved_endpoint = args.endpoint
+    try:
+        data = _json_object(args.data_json, "--data-json")
+        params = _json_object(args.params_json, "--params-json")
+        runtime = _runtime_config()
+        stage = "cli-resolution"
+        cli = _resolve_cli(args.cli, runtime)
+
+        env = os.environ.copy()
+        base_url = args.science_base_url or runtime.get("science_base_url")
+        if base_url:
+            env["DELTA_INFRA_SCIENCE_BASE_URL"] = str(base_url)
+        configured_base_url = _cli_science_base_url(cli, env, args.timeout)
+        requested_profile = str(runtime.get("catalog_profile", args.catalog_profile))
+        if requested_profile not in {"auto", "canonical", "legacy"}:
+            raise ValueError("catalog_profile must be auto, canonical, or legacy")
+        profile = _catalog_profile(configured_base_url, requested_profile)
+        resolved_tool, resolved_endpoint = _resolve_catalog_names(
+            args.tool, args.endpoint, profile
+        )
+
+        command = [
+            cli, "science", "invoke",
+            "--tool", resolved_tool,
+            "--endpoint", resolved_endpoint,
+        ]
+        if data is not None:
+            command.extend(["--data", json.dumps(data, ensure_ascii=False, separators=(",", ":"))])
+        if params is not None:
+            command.extend(["--params", json.dumps(params, ensure_ascii=False, separators=(",", ":"))])
+
+        stage = "delta-cli"
+        completed = subprocess.run(
+            command,
+            capture_output=True,
+            text=True,
+            encoding="utf-8",
+            errors="replace",
+            env=env,
+            timeout=args.timeout,
+            check=False,
+        )
+        if completed.returncode != 0:
+            detail = completed.stderr.strip() or completed.stdout.strip()
+            raise RuntimeError(f"exit_code={completed.returncode}: {detail}")
+        stage = "response-validation"
+        native, depth = _unwrap(completed.stdout)
+        result = {
+            "ok": True,
+            "transport": "delta-cli",
+            "tool": args.tool,
+            "endpoint": args.endpoint,
+            "resolved_tool": resolved_tool,
+            "resolved_endpoint": resolved_endpoint,
+            "catalog_profile": profile,
+            "elapsed_seconds": round(time.perf_counter() - started, 3),
+            "envelope_depth": depth,
+            "native": native,
+        }
+        print(json.dumps(result, ensure_ascii=False))
+        return 0
+    except subprocess.TimeoutExpired:
+        error = f"timeout after {args.timeout}s"
+    except (OSError, ValueError, RuntimeError) as exc:
+        error = str(exc)
+    print(json.dumps({
+        "ok": False,
+        "transport": "delta-cli",
+        "tool": args.tool,
+        "endpoint": args.endpoint,
+        "resolved_tool": resolved_tool,
+        "resolved_endpoint": resolved_endpoint,
+        "catalog_profile": profile,
+        "stage": stage,
+        "elapsed_seconds": round(time.perf_counter() - started, 3),
+        "error": error[:2000],
+    }, ensure_ascii=False))
+    return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())