diff --git a/.gitignore b/.gitignore index d41950258..59387d51f 100644 --- a/.gitignore +++ b/.gitignore @@ -37,6 +37,8 @@ pip-log.txt .tox .ruff_cache .mypy_cache +workernode + # Eclipse .project diff --git a/diracx-api/pyproject.toml b/diracx-api/pyproject.toml index 511998916..d37f95429 100644 --- a/diracx-api/pyproject.toml +++ b/diracx-api/pyproject.toml @@ -13,6 +13,7 @@ classifiers = [ "Topic :: System :: Distributed Computing", ] dependencies = [ + "cwl-utils", "diracx-client", "diracx-core", "httpx", diff --git a/diracx-api/src/diracx/api/job_report.py b/diracx-api/src/diracx/api/job_report.py new file mode 100644 index 000000000..711a5152f --- /dev/null +++ b/diracx-api/src/diracx/api/job_report.py @@ -0,0 +1,66 @@ +"""All classes related to job reports.""" + +from __future__ import annotations + +from datetime import datetime, timezone + +from diracx.client.aio import AsyncDiracClient # type: ignore[attr-defined] +from diracx.core.models.job import JobMinorStatus, JobStatus, JobStatusUpdate + + +class JobReport: + """JobReport.""" + + def __init__(self, job_id: int, source: str, client: AsyncDiracClient) -> None: + """Initialize Job Report. + + :param job_id: the job ID + :param source: source for the reports + :param client: DiracX client instance + """ + self.job_status_info: dict[ + str, dict[str, str] + ] = {} # where job status updates are cumulated + self.job_id = job_id + self.source = source + self._client = client + + def set_job_status( + self, + status: JobStatus | None = None, + minor_status: JobMinorStatus | None = None, + application_status: str | None = None, + ) -> None: + """Add a new job status to the job report. + + :param status: job status + :param minor_status: job minor status + :param application_status: application status + """ + timestamp = str(datetime.now(timezone.utc)) + # add job status record + self.job_status_info.update( + { + timestamp: JobStatusUpdate( + Status=status, + MinorStatus=minor_status, + ApplicationStatus=application_status, + Source=self.source, + ).model_dump() + } + ) + + async def send_stored_status_info(self): + """Send all the accumulated job status information.""" + if not self.job_status_info: + return + body = {self.job_id: self.job_status_info} + ret = await self._client.jobs.set_job_statuses(body) + if ret.success: + self.job_status_info = {} + else: + raise RuntimeError(f"Could not set job statuses: {ret}") + + async def commit(self): + """Send all the accumulated information.""" + await self.send_stored_status_info() diff --git a/diracx-api/src/diracx/api/job_wrapper.py b/diracx-api/src/diracx/api/job_wrapper.py new file mode 100644 index 000000000..98a0ca2fe --- /dev/null +++ b/diracx-api/src/diracx/api/job_wrapper.py @@ -0,0 +1,699 @@ +#!/usr/bin/env python +"""Job wrapper for executing CWL workflows with DIRAC.""" + +from __future__ import annotations + +import asyncio +import json +import logging +import random +import re +import shutil +import sys +import time +from pathlib import Path +from typing import Any, Sequence, cast + +from cwl_utils.parser import ( + save, +) +from cwl_utils.parser.cwl_v1_2 import ( + CommandLineTool, + ExpressionTool, + File, + Saveable, + Workflow, +) +from DIRACCommon.Core.Utilities.ReturnValues import ( # type: ignore[import-untyped] + returnValueOrRaise, +) +from ruamel.yaml import YAML + +from diracx.api.job_report import JobReport +from diracx.api.jobs import create_sandbox, download_sandbox +from diracx.client.aio import AsyncDiracClient # type: ignore[attr-defined] +from diracx.core.exceptions import WorkflowProcessingError +from diracx.core.models.commands import ( + PostProcessCommand, + PreProcessCommand, + StoreOutputDataCommand, +) +from diracx.core.models.cwl import JobHint +from diracx.core.models.cwl_submission import JobInputModel, JobModel +from diracx.core.models.job import JobMinorStatus, JobStatus + +# cwltool lifecycle patterns worth reporting as ApplicationStatus. +# Anchored to a log-level prefix to avoid false positives from user output. +# Group 1 captures from the bracket onward, stripping the prefix. +_CWLTOOL_STATUS_RE = re.compile( + r"(?:INFO|WARNING|ERROR) " + r"(\[(?:job |step )?[^\]]+\]" + r" (?:completed \w+|start(?:ing \S+)?|will be skipped" + r"|exited with status: \d+|was terminated by signal: \w+" + r"|Iteration \d+ completed \w+))" +) + +# ----------------------------------------------------------------------------- +# JobWrapper +# ----------------------------------------------------------------------------- + +logger = logging.getLogger(__name__) + + +class JobWrapper: + """Job Wrapper for the execution hook.""" + + def __init__(self, job_id: int) -> None: + """Initialize the job wrapper.""" + self._preprocess_commands: list[PreProcessCommand] = [] + self._postprocess_commands: list[PostProcessCommand] = [] + self._output_sandbox: list[str] = [] + self._input_data_sources: list[str] = [] + self._input_sandbox_sources: list[str] = [] + self._replica_map_path: Path | None = None + self._job_path: Path = Path() + self._job_id = job_id + src = "JobWrapper" + self._diracx_client: AsyncDiracClient = AsyncDiracClient() + self._job_report: JobReport = JobReport(self._job_id, src, self._diracx_client) + self._job_report.set_job_status( + JobStatus.RUNNING, JobMinorStatus.JOB_INITIALIZATION + ) + + async def __download_input_sandbox( + self, inputs: JobInputModel, job_hint: JobHint, job_path: Path + ) -> dict[str, Path]: + """Download input sandbox files and return SB: → local path mappings. + + Parses SB: prefixed paths from CWL input values (identified via the + hint's input_sandbox source references), downloads and extracts sandbox + tars (cached per unique SB: reference), and returns a mapping of full + SB: URIs to their local extracted file paths for replica map injection. + + :param inputs: The job input model containing CWL input values. + :param job_hint: The dirac:Job hint with input_sandbox config. + :param job_path: Path to the job working directory. + :return: Dict mapping SB: URI strings to local file Paths. + """ + sandbox_mappings: dict[str, Path] = {} + if not job_hint.input_sandbox: + return sandbox_mappings + + self._job_report.set_job_status( + minor_status=JobMinorStatus.DOWNLOADING_INPUT_SANDBOX + ) + + # Cache: download each sandbox tar only once + downloaded_sb_refs: set[str] = set() + + for ref in job_hint.input_sandbox: + cwl_value = inputs.cwl.get(ref.source) + if cwl_value is None: + continue + + # Extract file paths from CWL value + file_paths = self.__extract_file_paths_from_cwl_value(cwl_value) + for file_path in file_paths: + if not file_path.startswith("SB:"): + logger.warning( + "Skipping non-SB: path in input_sandbox: %s", file_path + ) + continue + sb_ref, rel_path = self.parse_sb_path(file_path) + # Download + extract once per unique sandbox reference + if sb_ref not in downloaded_sb_refs: + await download_sandbox(sb_ref, job_path) + downloaded_sb_refs.add(sb_ref) + # Map the full SB: URI to the local extracted file + sandbox_mappings[file_path] = job_path / rel_path + + logger.info("Input sandbox files downloaded successfully") + return sandbox_mappings + + @staticmethod + def __extract_file_paths_from_cwl_value(cwl_value: Any) -> list[str]: + """Extract file paths/sandbox IDs from a CWL input value.""" + paths: list[str] = [] + if not isinstance(cwl_value, list): + cwl_value = [cwl_value] + for item in cwl_value: + path = None + if isinstance(item, dict): + path = item.get("path") or item.get("location") + elif hasattr(item, "path"): + path = item.path + if path and isinstance(path, str): + paths.append(path) + return paths + + @staticmethod + def parse_sb_path(path: str) -> tuple[str, str]: + """Parse an SB: URI into sandbox reference and relative path. + + Format: SB:|# + + The SB: prefix is preserved in the returned reference — it is + the canonical form used by the DiracX API for sandbox operations. + + :param path: Full SB: URI string (e.g. ``SB:SandboxSE|/S3/...#file.sh``) + :return: Tuple of (sb_ref, relative_path) where sb_ref includes ``SB:`` + :raises ValueError: If path is not a valid SB: reference + """ + if not path.startswith("SB:"): + raise ValueError(f"Not an SB: path: {path}") + if "#" not in path: + raise ValueError(f"SB: path missing '#' fragment separator: {path}") + sb_ref, rel_path = path.split("#", 1) + return sb_ref, rel_path + + async def __upload_output_sandbox( + self, + outputs: dict[str, str | Path | Sequence[str | Path]], + ): + outputs_to_sandbox = [] + for output_name, src_path in outputs.items(): + if self._output_sandbox and output_name in self._output_sandbox: + if isinstance(src_path, (Path, str)): + src_path = [Path(src_path)] + for path in src_path: + outputs_to_sandbox.append(Path(path)) + if outputs_to_sandbox: + self._job_report.set_job_status( + JobStatus.COMPLETING, + minor_status=JobMinorStatus.UPLOADING_OUTPUT_SANDBOX, + ) + sb_ref = await create_sandbox(outputs_to_sandbox) + logger.info( + "Successfully stored output %s in Sandbox %s", + self._output_sandbox, + sb_ref, + ) + await self._diracx_client.jobs.assign_sandbox_to_job( + self._job_id, f'"{sb_ref}"' + ) + self._job_report.set_job_status( + JobStatus.COMPLETING, + minor_status=JobMinorStatus.OUTPUT_SANDBOX_UPLOADED, + ) + + async def __download_input_data( + self, inputs: JobInputModel, job_path: Path + ) -> dict[str, Path | list[Path]]: + """Download LFNs into the job working directory and build a replica map. + + Uses ``self._input_data_sources`` (from the dirac:Job hint) to identify + which CWL inputs contain LFN references, then resolves the actual LFN + paths from the CWL input values. + + :param inputs: The job input model containing CWL input values. + :param job_path: Path to the job working directory. + :return: Mapping of input names to downloaded local file paths. + """ + from DIRAC.DataManagementSystem.Client.DataManager import ( + DataManager, # type: ignore[import-untyped] + ) + + if not self._input_data_sources: + return {} + + new_paths: dict[str, Path | list[Path]] = {} + self._job_report.set_job_status( + minor_status=JobMinorStatus.INPUT_DATA_RESOLUTION + ) + + datamanager = DataManager() + + # Extract LFNs from CWL inputs using the hint's source references + lfns_by_input: dict[str, list[str]] = {} + for source_id in self._input_data_sources: + cwl_value = inputs.cwl.get(source_id) + if cwl_value is None: + continue + lfns = self.__extract_lfns_from_cwl_value(cwl_value) + if lfns: + lfns_by_input[source_id] = lfns + + if not lfns_by_input: + return {} + + # Collect all LFNs for replica map generation + all_lfns = [lfn for lfns in lfns_by_input.values() for lfn in lfns] + if all_lfns: + self.__build_replica_map(datamanager, all_lfns, job_path) + + # Download files + for input_name, lfns in lfns_by_input.items(): + res = returnValueOrRaise(datamanager.getFile(lfns, str(job_path))) + if res["Failed"]: + raise RuntimeError(f"Could not get files: {res['Failed']}") + paths = res["Successful"] + if paths: + downloaded = [ + Path(paths[lfn]).relative_to(job_path.resolve()) + for lfn in lfns + if lfn in paths + ] + if len(downloaded) == 1: + new_paths[input_name] = downloaded[0] + else: + new_paths[input_name] = downloaded + + return new_paths + + @staticmethod + def __extract_lfns_from_cwl_value(cwl_value: Any) -> list[str]: + """Extract LFN paths from a CWL input value. + + CWL File values can be: + - {"class": "File", "path": "LFN:/path/to/file"} + - [{"class": "File", "path": "LFN:/path/to/file"}, ...] + - A cwl_utils File object with a .path attribute + """ + lfns: list[str] = [] + if not isinstance(cwl_value, list): + cwl_value = [cwl_value] + for item in cwl_value: + path = None + if isinstance(item, dict): + path = item.get("path") or item.get("location") + elif hasattr(item, "path"): + path = item.path + if path and isinstance(path, str): + if not path.startswith("LFN:"): + logger.warning("Skipping non-LFN path in input_data: %s", path) + continue + lfns.append(path.removeprefix("LFN:")) + return lfns + + def __build_replica_map(self, datamanager, lfns: list[str], job_path: Path) -> None: + """Query replica info and write a replica_map.json for dirac-cwl-run. + + Uses DataManager's FileCatalog to get replicas and file metadata, + then builds a ReplicaMap model matching dirac-cwl's expected format. + """ + from diracx.core.models.replica_map import ReplicaMap + + # Get active replicas with URLs: {lfn: {se: pfn_url}} + replica_result = returnValueOrRaise( + datamanager.getActiveReplicas(lfns, getUrl=True) + ) + successful_replicas = replica_result.get("Successful", {}) + + if not successful_replicas: + return + + # Get file metadata (size, checksum, GUID) + metadata_result = datamanager.fileCatalog.getFileMetadata( + list(successful_replicas.keys()) + ) + metadata = {} + if metadata_result["OK"]: + metadata = metadata_result["Value"].get("Successful", {}) + + entries: dict[str, dict] = {} + for lfn, se_pfn_map in successful_replicas.items(): + replicas = [{"url": pfn, "se": se} for se, pfn in se_pfn_map.items()] + if not replicas: + continue + + entry: dict[str, Any] = {"replicas": replicas} + + lfn_meta = metadata.get(lfn, {}) + if "Size" in lfn_meta: + entry["size_bytes"] = lfn_meta["Size"] + checksum: dict[str, str] = {} + if "Checksum" in lfn_meta: + checksum["adler32"] = lfn_meta["Checksum"] + if "GUID" in lfn_meta: + checksum["guid"] = lfn_meta["GUID"] + if checksum: + entry["checksum"] = checksum + + entries[lfn] = entry + + if entries: + replica_map = ReplicaMap.model_validate(entries) + replica_map_path = job_path / "replica_map.json" + with open(replica_map_path, "w") as f: + f.write(replica_map.model_dump_json(indent=2)) + self._replica_map_path = replica_map_path + logger.info("Built replica map with %d entries", len(entries)) + + def _add_sandbox_entries_to_replica_map( + self, sandbox_mappings: dict[str, Path], job_path: Path + ) -> None: + """Inject sandbox file mappings into the replica map JSON. + + Each entry maps an SB: path to a local file:// URL so the CWL executor + can resolve sandbox files through the same replica map as LFN files. + + :param sandbox_mappings: Dict of SB: path → local extracted file Path + :param job_path: Job working directory + """ + from diracx.core.models.replica_map import ReplicaMap + + # Load existing replica map or start fresh + entries: dict[str, dict] = {} + if self._replica_map_path and self._replica_map_path.exists(): + existing = ReplicaMap.model_validate_json( + self._replica_map_path.read_text() + ) + entries = { + k: json.loads(v.model_dump_json()) for k, v in existing.root.items() + } + + # Add sandbox entries + for sb_path, local_path in sandbox_mappings.items(): + entries[sb_path] = { + "replicas": [{"url": local_path.resolve().as_uri(), "se": "local"}], + } + + if entries: + replica_map = ReplicaMap.model_validate(entries) + replica_map_path = job_path / "replica_map.json" + with open(replica_map_path, "w") as f: + f.write(replica_map.model_dump_json(indent=2)) + self._replica_map_path = replica_map_path + logger.info( + "Added %d sandbox entries to replica map", len(sandbox_mappings) + ) + + def __update_inputs( + self, inputs: JobInputModel, updates: dict[str, Path | list[Path]] + ): + """Update CWL job inputs with new file paths. + + This method updates the `inputs.cwl` object by replacing or adding + file paths for each input specified in `updates`. It supports both + single files and lists of files. + + :param inputs: The job input model whose `cwl` dictionary will be updated. + :type inputs: JobInputModel + :param updates: Dictionary mapping input names to their corresponding local file + paths. Each value can be a single `Path` or a list of `Path` objects. + :type updates: dict[str, Path | list[Path]] + + .. note:: + This method is typically called after downloading LFNs + using `download_lfns` to ensure that the CWL job inputs reference + the correct local files. + """ + for _, value in inputs.cwl.items(): + files = value if isinstance(value, list) else [value] + for file in files: + if isinstance(file, File) and file.path: + file.path = Path(file.path).name + for input_name, path in updates.items(): + if isinstance(path, Path): + inputs.cwl[input_name] = File(path=str(path)) + else: + inputs.cwl[input_name] = [] + for p in path: + inputs.cwl[input_name].append(File(path=str(p))) + + def __parse_output_filepaths( + self, stdout: str + ) -> dict[str, str | Path | Sequence[str | Path]]: + """Get the outputted filepaths per output. + + :param str stdout: + The console output of the the job + + :return dict[str, list[str]]: + The dict of the list of filepaths for each output + """ + outputted_files: dict[str, str | Path | Sequence[str | Path]] = {} + outputs = json.loads(stdout) + for output, files in outputs.items(): + if not files: + continue + if not isinstance(files, list): + files = [files] + file_paths = [] + for file in files: + if file: + file_paths.append(str(file["path"])) + outputted_files[output] = file_paths + return outputted_files + + async def pre_process( + self, + executable: CommandLineTool | Workflow | ExpressionTool, + arguments: JobInputModel | None, + job_hint: JobHint, + ) -> None: + """Pre-process the job before execution. + + Writes the CWL task and parameters to disk, downloads input sandbox + and input data as declared in the dirac:Job hint. + """ + logger = logging.getLogger("JobWrapper - Pre-process") + + # Write CWL task to file + logger.info("Preparing the task...") + task_dict = save(executable) + task_path = self._job_path / "task.cwl" + with open(task_path, "w") as task_file: + YAML().dump(task_dict, task_file) + + if arguments: + # Download input sandbox and collect SB: → local path mappings + sandbox_mappings: dict[str, Path] = {} + if job_hint.input_sandbox: + logger.info("Downloading input sandbox files...") + sandbox_mappings = await self.__download_input_sandbox( + arguments, job_hint, self._job_path + ) + + # Download input data (LFNs) using hint source references + if job_hint.input_data: + updates = await self.__download_input_data(arguments, self._job_path) + self.__update_inputs(arguments, updates) + + # Inject sandbox entries into replica map + if sandbox_mappings: + self._add_sandbox_entries_to_replica_map( + sandbox_mappings, self._job_path + ) + + # Write input parameters to file + logger.info("Preparing the parameters...") + parameter_dict = save(cast(Saveable, arguments.cwl)) + parameter_path = self._job_path / "parameter.cwl" + with open(parameter_path, "w") as parameter_file: + YAML().dump(parameter_dict, parameter_file) + + if self._preprocess_commands: + await self.__run_preprocess_commands(self._job_path) + + await self._job_report.commit() + + async def post_process( + self, + status: int, + stdout: str, + stderr: str, + ): + """Post-process the job after execution. + + :return: True if the job is post-processed successfully, False otherwise + """ + logger = logging.getLogger("JobWrapper - Post-process") + if status != 0: + raise RuntimeError(f"Error {status} during the task execution.") + + logger.info(stdout) + logger.info(stderr) + + outputs = self.__parse_output_filepaths(stdout) + + success = True + + if self._postprocess_commands: + success = await self.__run_postprocess_commands( + self._job_path, outputs=outputs + ) + + await self.__upload_output_sandbox(outputs=outputs) + await self._job_report.commit() + return success + + async def __run_preprocess_commands(self, job_path: Path, **kwargs: Any) -> None: + """Run all pre-process commands.""" + for cmd in self._preprocess_commands: + try: + await cmd.execute(job_path, **kwargs) + except Exception as e: + msg = f"Command '{type(cmd).__name__}' failed during the pre-process stage: {e}" + logger.exception(msg) + raise WorkflowProcessingError(msg) from e + + async def __run_postprocess_commands( + self, + job_path: Path, + outputs: dict[str, str | Path | Sequence[str | Path]] = {}, + **kwargs: Any, + ) -> bool: + """Run all post-process commands.""" + for cmd in self._postprocess_commands: + try: + await cmd.execute(job_path, outputs=outputs, **kwargs) + except Exception as e: + msg = f"Command '{type(cmd).__name__}' failed during the post-process stage: {e}" + logger.exception(msg) + raise WorkflowProcessingError(msg) from e + return True + + def _build_commands_from_hint(self, job_hint: JobHint) -> None: + """Build pre/post-process commands from the dirac:Job hint. + + The ``type`` field determines which commands are attached. + I/O config from the hint is used to configure commands. + """ + # Extract input I/O config from the hint + self._input_data_sources = [ref.source for ref in job_hint.input_data] + self._input_sandbox_sources = [ref.source for ref in job_hint.input_sandbox] + self._output_sandbox = [ref.source for ref in job_hint.output_sandbox] + + # Extract output I/O config from the hint + output_paths = { + entry.source: entry.output_path for entry in job_hint.output_data + } + output_se = [] + for entry in job_hint.output_data: + output_se.extend(entry.output_se) + output_se = list(set(output_se)) + + # Build post-process commands — output storage + if output_paths: + self._postprocess_commands.append( + StoreOutputDataCommand(output_paths=output_paths, output_se=output_se) + ) + + async def run_job(self, job: JobModel) -> bool: + """Execute a given CWL workflow using dirac-cwl-run via subprocess. + + This is the equivalent of the DIRAC JobWrapper. + + :param job: The job model containing workflow and inputs. + :return: True if the job is executed successfully, False otherwise. + """ + logger = logging.getLogger("JobWrapper") + + # Extract dirac:Job hint and build commands from type + I/O config + job_hint = JobHint.from_cwl(job.task) + self._build_commands_from_hint(job_hint) + + # Isolate the job in a specific directory + self._job_path = Path(".") / "workernode" / f"{random.randint(1000, 9999)}" # noqa: S311 + self._job_path.mkdir(parents=True, exist_ok=True) + + try: + # Pre-process the job + logger.info("Pre-processing Task...") + await self.pre_process(job.task, job.input, job_hint) + logger.info("Task pre-processed successfully!") + + # Build dirac-cwl-run command (different interface from cwltool) + task_file = self._job_path / "task.cwl" + param_file = self._job_path / "parameter.cwl" + command = ["dirac-cwl-run", str(task_file.name)] + if param_file.exists(): + command.append(str(param_file.name)) + if self._replica_map_path and self._replica_map_path.exists(): + command.extend(["--replica-map", str(self._replica_map_path.name)]) + + # Execute the task + logger.info("Executing Task: %s", command) + self._job_report.set_job_status(minor_status=JobMinorStatus.APPLICATION) + await self._job_report.commit() + proc = await asyncio.create_subprocess_exec( # noqa: S603 + *command, + stdout=asyncio.subprocess.PIPE, + stderr=asyncio.subprocess.PIPE, + cwd=self._job_path, + ) + assert proc.stderr is not None # guaranteed by stderr=PIPE + assert proc.stdout is not None # guaranteed by stdout=PIPE + + # Stream stderr line-by-line while collecting stdout concurrently + async def _collect_stdout() -> bytes: + assert proc.stdout is not None + return await proc.stdout.read() + + stdout_task = asyncio.create_task(_collect_stdout()) + + stderr_lines: list[str] = [] + last_commit = time.monotonic() + async for raw in proc.stderr: + line = raw.decode().rstrip("\n") + stderr_lines.append(line) + # Always re-emit to stderr for Watchdog peek + print(line, file=sys.stderr, flush=True) + # Only report lifecycle transitions as ApplicationStatus + match = _CWLTOOL_STATUS_RE.search(line) + if match: + self._job_report.set_job_status(application_status=match.group(1)) + now = time.monotonic() + if now - last_commit >= 2.0: + try: + await self._job_report.commit() + except Exception: + logger.warning( + "Failed to commit status update", + exc_info=True, + ) + last_commit = now + + # Flush any remaining status updates + try: + await self._job_report.commit() + except Exception: + logger.warning("Failed to commit final status update", exc_info=True) + + stdout_bytes = await stdout_task + stdout_text = stdout_bytes.decode() + await proc.wait() + + if proc.returncode != 0: + logger.error( + "Error in executing workflow:\n%s", "\n".join(stderr_lines) + ) + self._job_report.set_job_status( + JobStatus.COMPLETING, + minor_status=JobMinorStatus.APP_ERRORS, + application_status=f"failed (exit {proc.returncode})", + ) + self._job_report.set_job_status(JobStatus.FAILED) + return False + logger.info("Task executed successfully!") + self._job_report.set_job_status( + JobStatus.COMPLETING, + minor_status=JobMinorStatus.APP_SUCCESS, + ) + # Post-process the job + logger.info("Post-processing Task...") + if await self.post_process( + proc.returncode, + stdout_text, + "\n".join(stderr_lines), + ): + logger.info("Task post-processed successfully!") + self._job_report.set_job_status( + JobStatus.DONE, JobMinorStatus.EXEC_COMPLETE + ) + return True + logger.error("Failed to post-process Task") + self._job_report.set_job_status(JobStatus.FAILED) + return False + + except Exception: + logger.exception("JobWrapper: Failed to execute workflow") + self._job_report.set_job_status(JobStatus.FAILED) + return False + finally: + # Commit all stored job reports + await self._job_report.commit() + # Clean up + if self._job_path.exists(): + shutil.rmtree(self._job_path) diff --git a/diracx-api/src/diracx/api/jobs.py b/diracx-api/src/diracx/api/jobs.py index 181b7b9b7..0631ba764 100644 --- a/diracx-api/src/diracx/api/jobs.py +++ b/diracx-api/src/diracx/api/jobs.py @@ -14,8 +14,8 @@ import httpx import zstandard -from diracx.client.aio import AsyncDiracClient -from diracx.client.models import SandboxInfo +from diracx.client.aio import AsyncDiracClient # type: ignore[attr-defined] +from diracx.client.models import SandboxInfo # type: ignore[attr-defined] from .utils import with_client diff --git a/diracx-api/src/diracx/api/utils.py b/diracx-api/src/diracx/api/utils.py index 8e70be70e..fcfa21f19 100644 --- a/diracx-api/src/diracx/api/utils.py +++ b/diracx-api/src/diracx/api/utils.py @@ -4,7 +4,7 @@ from functools import wraps -from diracx.client.aio import AsyncDiracClient +from diracx.client.aio import AsyncDiracClient # type: ignore[attr-defined] def with_client(func): diff --git a/diracx-api/tests/test_job_wrapper.py b/diracx-api/tests/test_job_wrapper.py new file mode 100644 index 000000000..c51809e43 --- /dev/null +++ b/diracx-api/tests/test_job_wrapper.py @@ -0,0 +1,336 @@ +"""Tests for JobWrapper command building, output parsing, and replica map wiring.""" + +from __future__ import annotations + +import json +from pathlib import Path + +from diracx.api.job_wrapper import JobWrapper +from diracx.core.models.commands import StoreOutputDataCommand +from diracx.core.models.cwl import IOSource, JobHint, OutputDataEntry + +# --------------------------------------------------------------------------- +# Helper to create a bare JobWrapper instance (bypasses __init__) +# --------------------------------------------------------------------------- + + +def _make_wrapper() -> object: + """Create a bare JobWrapper without calling __init__.""" + w = JobWrapper.__new__(JobWrapper) + w._preprocess_commands = [] + w._postprocess_commands = [] + w._output_sandbox = [] + w._input_data_sources = [] + w._input_sandbox_sources = [] + w._replica_map_path = None + return w + + +# --------------------------------------------------------------------------- +# Tests: _build_commands_from_hint +# --------------------------------------------------------------------------- + + +class TestBuildCommandsFromHint: + """Test _build_commands_from_hint populates commands and I/O source lists.""" + + def test_no_io_no_commands(self): + """Hint with no I/O should produce no commands.""" + w = _make_wrapper() + hint = JobHint() + w._build_commands_from_hint(hint) + + assert w._preprocess_commands == [] + assert w._postprocess_commands == [] + assert w._input_data_sources == [] + assert w._input_sandbox_sources == [] + assert w._output_sandbox == [] + + def test_output_data_creates_store_command(self): + """output_data in hint creates a StoreOutputDataCommand.""" + w = _make_wrapper() + hint = JobHint( + output_data=[ + OutputDataEntry( + source="my_output", + output_path="/lhcb/user/a/auser/output.dst", + output_se=["CERN-DST"], + ) + ] + ) + w._build_commands_from_hint(hint) + + assert len(w._postprocess_commands) == 1 + cmd = w._postprocess_commands[0] + assert isinstance(cmd, StoreOutputDataCommand) + assert cmd._output_paths == {"my_output": "/lhcb/user/a/auser/output.dst"} + assert cmd._output_se == ["CERN-DST"] + + def test_multiple_output_data_single_command(self): + """Multiple output_data entries produce a single command with all paths.""" + w = _make_wrapper() + hint = JobHint( + output_data=[ + OutputDataEntry( + source="out1", + output_path="/lhcb/user/a/auser/file1.dst", + output_se=["CERN-DST"], + ), + OutputDataEntry( + source="out2", + output_path="/lhcb/user/a/auser/file2.dst", + output_se=["CERN-DST"], + ), + ] + ) + w._build_commands_from_hint(hint) + + assert len(w._postprocess_commands) == 1 + cmd = w._postprocess_commands[0] + assert isinstance(cmd, StoreOutputDataCommand) + assert "out1" in cmd._output_paths + assert "out2" in cmd._output_paths + assert cmd._output_paths["out1"] == "/lhcb/user/a/auser/file1.dst" + assert cmd._output_paths["out2"] == "/lhcb/user/a/auser/file2.dst" + + def test_multiple_output_data_se_deduplicated(self): + """output_se values across multiple output_data entries are deduplicated.""" + w = _make_wrapper() + hint = JobHint( + output_data=[ + OutputDataEntry( + source="out1", + output_path="/lhcb/user/a/auser/file1.dst", + output_se=["CERN-DST", "IN2P3-DST"], + ), + OutputDataEntry( + source="out2", + output_path="/lhcb/user/a/auser/file2.dst", + output_se=["CERN-DST"], + ), + ] + ) + w._build_commands_from_hint(hint) + + cmd = w._postprocess_commands[0] + assert sorted(cmd._output_se) == sorted(["CERN-DST", "IN2P3-DST"]) + + def test_input_data_sources_extracted(self): + """input_data sources are extracted into _input_data_sources.""" + w = _make_wrapper() + hint = JobHint( + input_data=[ + IOSource(source="data_file"), + IOSource(source="another_file"), + ] + ) + w._build_commands_from_hint(hint) + + assert w._input_data_sources == ["data_file", "another_file"] + assert w._postprocess_commands == [] + + def test_input_sandbox_sources_extracted(self): + """input_sandbox sources are extracted into _input_sandbox_sources.""" + w = _make_wrapper() + hint = JobHint( + input_sandbox=[ + IOSource(source="helper_script"), + IOSource(source="config_file"), + ] + ) + w._build_commands_from_hint(hint) + + assert w._input_sandbox_sources == ["helper_script", "config_file"] + + def test_output_sandbox_sources_extracted(self): + """output_sandbox sources are extracted into _output_sandbox.""" + w = _make_wrapper() + hint = JobHint( + output_sandbox=[ + IOSource(source="log_output"), + ] + ) + w._build_commands_from_hint(hint) + + assert w._output_sandbox == ["log_output"] + + def test_all_io_together(self): + """All I/O fields together populate all lists and create one command.""" + w = _make_wrapper() + hint = JobHint( + input_data=[IOSource(source="data_in")], + input_sandbox=[IOSource(source="script")], + output_sandbox=[IOSource(source="logs")], + output_data=[ + OutputDataEntry( + source="result", + output_path="/lhcb/user/a/auser/result.root", + ) + ], + ) + w._build_commands_from_hint(hint) + + assert w._input_data_sources == ["data_in"] + assert w._input_sandbox_sources == ["script"] + assert w._output_sandbox == ["logs"] + assert len(w._postprocess_commands) == 1 + cmd = w._postprocess_commands[0] + assert isinstance(cmd, StoreOutputDataCommand) + assert "result" in cmd._output_paths + + +# --------------------------------------------------------------------------- +# Tests: __parse_output_filepaths (private — accessed via name-mangling) +# --------------------------------------------------------------------------- + + +class TestParseOutputFilepaths: + """Test __parse_output_filepaths parses cwltool JSON stdout.""" + + def _parse(self, wrapper, stdout: str): + """Call the name-mangled private method.""" + return wrapper._JobWrapper__parse_output_filepaths(stdout) + + def test_single_output_file(self): + """Single output file is parsed into a list with one path.""" + w = _make_wrapper() + stdout = json.dumps( + { + "my_output": { + "class": "File", + "path": "/tmp/workdir/output.dst", + "location": "file:///tmp/workdir/output.dst", + } + } + ) + result = self._parse(w, stdout) + + assert "my_output" in result + assert result["my_output"] == ["/tmp/workdir/output.dst"] + + def test_multiple_named_outputs(self): + """Multiple named outputs are all parsed.""" + w = _make_wrapper() + stdout = json.dumps( + { + "output_a": {"class": "File", "path": "/tmp/a.dst"}, + "output_b": {"class": "File", "path": "/tmp/b.root"}, + } + ) + result = self._parse(w, stdout) + + assert "output_a" in result + assert "output_b" in result + assert result["output_a"] == ["/tmp/a.dst"] + assert result["output_b"] == ["/tmp/b.root"] + + def test_array_of_output_files(self): + """Array of output files produces a list with all paths.""" + w = _make_wrapper() + stdout = json.dumps( + { + "output_files": [ + {"class": "File", "path": "/tmp/file1.root"}, + {"class": "File", "path": "/tmp/file2.root"}, + {"class": "File", "path": "/tmp/file3.root"}, + ] + } + ) + result = self._parse(w, stdout) + + assert "output_files" in result + assert result["output_files"] == [ + "/tmp/file1.root", + "/tmp/file2.root", + "/tmp/file3.root", + ] + + def test_null_output_skipped(self): + """Null/None output values are skipped (not added to result).""" + w = _make_wrapper() + stdout = json.dumps( + { + "present_output": {"class": "File", "path": "/tmp/present.root"}, + "null_output": None, + } + ) + result = self._parse(w, stdout) + + assert "present_output" in result + assert "null_output" not in result + + def test_empty_outputs(self): + """Empty JSON object produces empty dict.""" + w = _make_wrapper() + result = self._parse(w, "{}") + assert result == {} + + def test_false_output_skipped(self): + """Falsy (but not None) output values like False are also skipped.""" + w = _make_wrapper() + stdout = json.dumps( + { + "valid": {"class": "File", "path": "/tmp/valid.root"}, + "falsy": False, + } + ) + result = self._parse(w, stdout) + + assert "valid" in result + assert "falsy" not in result + + +# --------------------------------------------------------------------------- +# Tests: replica map wiring +# --------------------------------------------------------------------------- + + +class TestReplicaMapWiring: + """Test that _replica_map_path controls --replica-map in the command.""" + + def _build_command(self, wrapper, job_path: Path) -> list[str]: + """Replicate the command-building logic from run_job().""" + task_file = job_path / "task.cwl" + param_file = job_path / "parameter.cwl" + # Create the files so .exists() checks pass + task_file.write_text("class: CommandLineTool\n") + param_file.write_text("{}\n") + + command = ["dirac-cwl-run", str(task_file.name)] + if param_file.exists(): + command.append(str(param_file.name)) + if wrapper._replica_map_path and wrapper._replica_map_path.exists(): + command.extend(["--replica-map", str(wrapper._replica_map_path.name)]) + return command + + def test_no_replica_map_not_in_command(self, tmp_path): + """When _replica_map_path is None, --replica-map is absent.""" + w = _make_wrapper() + w._replica_map_path = None + + command = self._build_command(w, tmp_path) + + assert "--replica-map" not in command + + def test_replica_map_path_set_and_exists_in_command(self, tmp_path): + """When _replica_map_path is set and file exists, --replica-map is present.""" + w = _make_wrapper() + replica_map_path = tmp_path / "replica_map.json" + replica_map_path.write_text('{"replicas": []}') + w._replica_map_path = replica_map_path + + command = self._build_command(w, tmp_path) + + assert "--replica-map" in command + idx = command.index("--replica-map") + assert command[idx + 1] == "replica_map.json" + + def test_replica_map_path_set_but_missing_not_in_command(self, tmp_path): + """When _replica_map_path is set but file doesn't exist, --replica-map is absent.""" + w = _make_wrapper() + # Point to a non-existent file + w._replica_map_path = tmp_path / "missing_replica_map.json" + + command = self._build_command(w, tmp_path) + + assert "--replica-map" not in command diff --git a/diracx-api/tests/test_job_wrapper_integration.py b/diracx-api/tests/test_job_wrapper_integration.py new file mode 100644 index 000000000..268c4c864 --- /dev/null +++ b/diracx-api/tests/test_job_wrapper_integration.py @@ -0,0 +1,498 @@ +"""Integration tests for JobWrapper: full pre_process -> run_job -> post_process chain. + +This test exercises the complete JobWrapper lifecycle with: +- A real CWL CommandLineTool (executed via dirac-cwl-run) +- Mocked external services (DataManager, sandbox download/upload, JobReport, client) +- Real cwl_utils and ruamel.yaml +""" + +from __future__ import annotations + +import json +import shutil +import sys +import types +from pathlib import Path +from unittest.mock import AsyncMock, MagicMock, patch + +# --------------------------------------------------------------------------- +# Direct imports — all dependencies are available in the test environment +# --------------------------------------------------------------------------- +import cwl_utils.parser.cwl_v1_2 as _cwl_v1_2 # noqa: E402 +import pytest + +import diracx.api.job_wrapper as _jw_mod # noqa: E402 +from diracx.api.job_wrapper import JobWrapper # noqa: E402 + +CommandLineTool = _cwl_v1_2.CommandLineTool + + +def _build_cwl_tool() -> CommandLineTool: + """Build a minimal CWL CommandLineTool for the integration test. + + The tool runs ``cat `` and captures stdout. + The dirac:Job hint declares: + - input_data: input_file (an LFN) + - input_sandbox: helper_script (an SB: reference) + - output_sandbox: stdout_log + """ + return CommandLineTool( + cwlVersion="v1.2", + baseCommand=["cat"], + label="integration-test", + hints=[ + { + "class": "dirac:Job", + "schema_version": "1.0", + "type": "User", + "input_data": [{"source": "input_file"}], + "input_sandbox": [{"source": "helper_script"}], + "output_sandbox": [{"source": "stdout_log"}], + } + ], + inputs=[ + { + "id": "input_file", + "type": "File", + "inputBinding": {"position": 1}, + }, + { + "id": "helper_script", + "type": "File", + }, + ], + outputs=[ + { + "id": "stdout_log", + "type": "stdout", + } + ], + stdout="stdout.log", + id=None, + requirements=None, + ) + + +# --------------------------------------------------------------------------- +# Fixtures +# --------------------------------------------------------------------------- + + +@pytest.fixture() +def job_files(tmp_path): + """Create test data files and return their paths.""" + data_file = tmp_path / "input.txt" + data_file.write_text("Hello from LFN data file\n") + + helper_script = tmp_path / "helper.sh" + helper_script.write_text("#!/bin/bash\necho 'helper executed'\n") + helper_script.chmod(0o755) + + return { + "data_file": data_file, + "helper_script": helper_script, + "tmp": tmp_path, + } + + +# --------------------------------------------------------------------------- +# Integration test +# --------------------------------------------------------------------------- + + +class TestJobWrapperIntegration: + """Full integration test: run_job with mocked external services.""" + + async def test_run_job_full_chain(self, job_files, monkeypatch, tmp_path): + """Verify run_job() succeeds through the full chain. + + Exercises hint parsing, sandbox download, LFN download, replica map + building, SB injection, real CWL execution, and output parsing. + """ + data_file: Path = job_files["data_file"] + helper_script: Path = job_files["helper_script"] + + # ------------------------------------------------------------------ + # Build the CWL task and job model. + # ------------------------------------------------------------------ + from diracx.core.models.cwl_submission import JobInputModel, JobModel + + task = _build_cwl_tool() + + job_input = JobInputModel( + sandbox=None, + cwl={ + "input_file": { + "class": "File", + "path": "LFN:/test/data/input.txt", + }, + "helper_script": { + "class": "File", + "path": "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh", + }, + }, + ) + job_model = JobModel(task=task, input=job_input) + + # ------------------------------------------------------------------ + # Mock: download_sandbox — copies helper script into job_path + # ------------------------------------------------------------------ + sandbox_calls: list[tuple[str, Path]] = [] + + async def mock_download_sandbox(sb_ref: str, job_path: Path) -> None: + sandbox_calls.append((sb_ref, job_path)) + dest = job_path / "helper.sh" + shutil.copy(helper_script, dest) + + monkeypatch.setattr(_jw_mod, "download_sandbox", mock_download_sandbox) + + # ------------------------------------------------------------------ + # Mock: create_sandbox — returns a fake SB: reference + # ------------------------------------------------------------------ + async def mock_create_sandbox(files) -> str: + return "SB:SandboxSE|/S3/store/sha256:output.tar.zst" + + monkeypatch.setattr(_jw_mod, "create_sandbox", mock_create_sandbox) + + # ------------------------------------------------------------------ + # Mock: DIRAC.DataManagementSystem.Client.DataManager.DataManager + # (imported dynamically inside __download_input_data) + # ------------------------------------------------------------------ + dm_mock = MagicMock() + lfn = "/test/data/input.txt" + + dm_mock.getActiveReplicas.return_value = { + "OK": True, + "Value": { + "Successful": {lfn: {"LocalSE": f"file://{data_file}"}}, + "Failed": {}, + }, + } + dm_mock.fileCatalog.getFileMetadata.return_value = { + "OK": True, + "Value": { + "Successful": { + lfn: { + "Size": data_file.stat().st_size, + "Checksum": "deadbeef", + } + }, + "Failed": {}, + }, + } + + def fake_get_file(lfns, dest_dir): + successful = {} + for _lfn in lfns: + dest = Path(dest_dir).resolve() / data_file.name + shutil.copy(data_file, dest) + successful[_lfn] = str(dest) + return {"OK": True, "Value": {"Successful": successful, "Failed": {}}} + + dm_mock.getFile.side_effect = fake_get_file + + # ------------------------------------------------------------------ + # Mock: JobReport and AsyncDiracClient + # ------------------------------------------------------------------ + job_report_mock = MagicMock() + job_report_mock.set_job_status = MagicMock() + job_report_mock.commit = AsyncMock() + + diracx_client_mock = MagicMock() + diracx_client_mock.jobs.assign_sandbox_to_job = AsyncMock() + + # ------------------------------------------------------------------ + # Redirect CWD to tmp_path so run_job's Path(".") resolves there. + # ------------------------------------------------------------------ + monkeypatch.chdir(tmp_path) + job_path = tmp_path / "workernode" / "1234" + job_path.mkdir(parents=True) + + # Intercept shutil.rmtree to preserve the job dir for inspection + rmtree_calls: list[Path] = [] + + def mock_rmtree(path, **kwargs): + rmtree_calls.append(Path(path)) + + # ------------------------------------------------------------------ + # Install mock DataManager in sys.modules for the dynamic import + # inside __download_input_data + # ------------------------------------------------------------------ + dm_module = types.ModuleType("DIRAC.DataManagementSystem.Client.DataManager") + dm_module.DataManager = MagicMock(return_value=dm_mock) # type: ignore[attr-defined] + sys.modules["DIRAC"] = types.ModuleType("DIRAC") + sys.modules["DIRAC.DataManagementSystem"] = types.ModuleType( + "DIRAC.DataManagementSystem" + ) + sys.modules["DIRAC.DataManagementSystem.Client"] = types.ModuleType( + "DIRAC.DataManagementSystem.Client" + ) + sys.modules["DIRAC.DataManagementSystem.Client.DataManager"] = dm_module + + # ------------------------------------------------------------------ + # Subclass JobWrapper to resolve _job_path to absolute before + # pre_process. run_job creates Path(".") / "workernode" / "", + # which is relative; as_uri() requires an absolute path. + # ------------------------------------------------------------------ + + class _AbsPathWrapper(JobWrapper): + """Subclass that resolves _job_path to absolute before pre_process.""" + + async def pre_process(self, executable, arguments, job_hint): + self._job_path = self._job_path.resolve() + return await super().pre_process(executable, arguments, job_hint) + + # ------------------------------------------------------------------ + # Instantiate and run + # ------------------------------------------------------------------ + with ( + patch.object(_jw_mod, "AsyncDiracClient", return_value=diracx_client_mock), + patch.object(_jw_mod, "JobReport", return_value=job_report_mock), + patch.object(_jw_mod.shutil, "rmtree", mock_rmtree), + patch("random.randint", return_value=1234), + ): + wrapper = _AbsPathWrapper(job_id=42) + result = await wrapper.run_job(job_model) + + # ------------------------------------------------------------------ + # Assertions + # ------------------------------------------------------------------ + assert result is True, "run_job should return True on success" + + # Verify sandbox download was called with the right SB: reference + assert len(sandbox_calls) == 1 + sb_ref_called, _ = sandbox_calls[0] + assert sb_ref_called == "SB:SandboxSE|/S3/store/sha256:abc.tar.zst" + + # Verify DataManager.getFile was called with the correct LFN + dm_mock.getFile.assert_called_once() + call_args = dm_mock.getFile.call_args + assert lfn in call_args[0][0] + + # Verify JobReport methods were called + assert job_report_mock.set_job_status.call_count > 0 + assert job_report_mock.commit.call_count > 0 + + # Verify cleanup was triggered + assert len(rmtree_calls) == 1 + + # Inspect job directory (preserved since rmtree was mocked) + assert job_path.exists(), "job_path should still exist (rmtree mocked)" + assert (job_path / "task.cwl").exists(), "task.cwl must be written" + assert (job_path / "parameter.cwl").exists(), "parameter.cwl must be written" + + # replica_map.json must exist with both LFN and SB: entries + replica_map_path = job_path / "replica_map.json" + assert replica_map_path.exists(), "replica_map.json must be created" + + replica_map = json.loads(replica_map_path.read_text()) + assert lfn in replica_map, f"replica_map must contain LFN {lfn}" + sb_key = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + assert sb_key in replica_map, f"replica_map must contain SB key {sb_key}" + + # Output file (stdout.log) must exist in job dir + assert (job_path / "stdout.log").exists(), "stdout.log output file must exist" + + # Verify stderr lines were streamed as ApplicationStatus + app_status_calls = [ + call + for call in job_report_mock.set_job_status.call_args_list + if call.kwargs.get("application_status") is not None + and call.args == () + and set(call.kwargs.keys()) == {"application_status"} + ] + # cwltool emits lifecycle lines; at least one should have been relayed + assert len(app_status_calls) > 0, ( + "cwltool lifecycle lines should be relayed as ApplicationStatus" + ) + # Verify no log level prefixes leak into ApplicationStatus + for call in app_status_calls: + status = call.kwargs["application_status"] + assert status.startswith("["), ( + f"ApplicationStatus should start with '[', got: {status!r}" + ) + + async def test_stderr_lines_stored_as_application_status( + self, job_files, monkeypatch, tmp_path + ): + """Verify that each stderr line from the subprocess is stored as ApplicationStatus. + + Uses a mocked Popen to emit known stderr lines and checks that + set_job_status is called with each line as application_status, and + commit() is called after each line. + """ + data_file: Path = job_files["data_file"] + helper_script: Path = job_files["helper_script"] + + from diracx.core.models.cwl_submission import JobInputModel, JobModel + + task = _build_cwl_tool() + job_input = JobInputModel( + sandbox=None, + cwl={ + "input_file": { + "class": "File", + "path": "LFN:/test/data/input.txt", + }, + "helper_script": { + "class": "File", + "path": "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh", + }, + }, + ) + job_model = JobModel(task=task, input=job_input) + + # Mock download_sandbox and create_sandbox + async def mock_download_sandbox(sb_ref, job_path): + shutil.copy(helper_script, job_path / "helper.sh") + + monkeypatch.setattr(_jw_mod, "download_sandbox", mock_download_sandbox) + + async def mock_create_sandbox(files): + return "SB:SandboxSE|/S3/store/sha256:output.tar.zst" + + monkeypatch.setattr(_jw_mod, "create_sandbox", mock_create_sandbox) + + # Mock DataManager + dm_mock = MagicMock() + lfn = "/test/data/input.txt" + dm_mock.getActiveReplicas.return_value = { + "OK": True, + "Value": { + "Successful": {lfn: {"LocalSE": f"file://{data_file}"}}, + "Failed": {}, + }, + } + dm_mock.fileCatalog.getFileMetadata.return_value = { + "OK": True, + "Value": { + "Successful": { + lfn: {"Size": data_file.stat().st_size, "Checksum": "deadbeef"} + }, + "Failed": {}, + }, + } + + def fake_get_file(lfns, dest_dir): + successful = {} + for _lfn in lfns: + dest = Path(dest_dir).resolve() / data_file.name + shutil.copy(data_file, dest) + successful[_lfn] = str(dest) + return {"OK": True, "Value": {"Successful": successful, "Failed": {}}} + + dm_mock.getFile.side_effect = fake_get_file + + dm_module = types.ModuleType("DIRAC.DataManagementSystem.Client.DataManager") + dm_module.DataManager = MagicMock(return_value=dm_mock) # type: ignore[attr-defined] + sys.modules["DIRAC"] = types.ModuleType("DIRAC") + sys.modules["DIRAC.DataManagementSystem"] = types.ModuleType( + "DIRAC.DataManagementSystem" + ) + sys.modules["DIRAC.DataManagementSystem.Client"] = types.ModuleType( + "DIRAC.DataManagementSystem.Client" + ) + sys.modules["DIRAC.DataManagementSystem.Client.DataManager"] = dm_module + + # Mock JobReport and client + job_report_mock = MagicMock() + job_report_mock.set_job_status = MagicMock() + job_report_mock.commit = AsyncMock() + + diracx_client_mock = MagicMock() + diracx_client_mock.jobs.assign_sandbox_to_job = AsyncMock() + + monkeypatch.chdir(tmp_path) + job_path = tmp_path / "workernode" / "1234" + job_path.mkdir(parents=True) + + # Mock async subprocess to emit known stderr lines. + # Mix lifecycle lines (matched by _STATUS_RE) with noise lines (not matched). + known_stderr = [ + "INFO Resolved '/tmp/task.cwl' to 'file:///tmp/task.cwl'", + "INFO [job echo_job] /tmp/xyz$ echo hello", + "INFO [job echo_job] completed success", + "INFO Final process status is success", + ] + # Only lifecycle lines become ApplicationStatus, with log prefix stripped + expected_statuses = [ + "[job echo_job] completed success", + ] + + class _FakeStderr: + """Async iterator that yields encoded stderr lines.""" + + def __init__(self, lines: list[bytes]): + self._iter = iter(lines) + + def __aiter__(self): + return self + + async def __anext__(self): + try: + return next(self._iter) + except StopIteration: + raise StopAsyncIteration from None + + class _FakeStdout: + """Async reader that returns encoded stdout.""" + + def __init__(self, data: bytes): + self._data = data + + async def read(self) -> bytes: + return self._data + + fake_proc = MagicMock() + fake_proc.stderr = _FakeStderr([f"{line}\n".encode() for line in known_stderr]) + fake_proc.stdout = _FakeStdout( + b'{"stdout_log": {"class": "File", "path": "stdout.log"}}' + ) + fake_proc.returncode = 0 + fake_proc.wait = AsyncMock(return_value=0) + + # Create the expected output file when subprocess is spawned + async def mock_create_subprocess(*args, **kwargs): + cwd = kwargs.get("cwd") + if cwd: + (Path(cwd) / "stdout.log").write_text("Hello from LFN data file\n") + return fake_proc + + class _AbsPathWrapper(JobWrapper): + async def pre_process(self, executable, arguments, job_hint): + self._job_path = self._job_path.resolve() + return await super().pre_process(executable, arguments, job_hint) + + with ( + patch.object(_jw_mod, "AsyncDiracClient", return_value=diracx_client_mock), + patch.object(_jw_mod, "JobReport", return_value=job_report_mock), + patch.object(_jw_mod.shutil, "rmtree", lambda p, **kw: None), + patch("random.randint", return_value=1234), + patch.object( + _jw_mod.asyncio, + "create_subprocess_exec", + side_effect=mock_create_subprocess, + ), + ): + wrapper = _AbsPathWrapper(job_id=42) + result = await wrapper.run_job(job_model) + + assert result is True, "run_job should return True with mocked Popen" + + # Extract application_status calls that came from the streaming loop + # (these have only application_status kwarg and no positional args) + streamed_statuses = [ + call.kwargs["application_status"] + for call in job_report_mock.set_job_status.call_args_list + if call.kwargs.get("application_status") is not None + and call.args == () + and set(call.kwargs.keys()) == {"application_status"} + ] + assert streamed_statuses == expected_statuses, ( + f"Expected lifecycle lines {expected_statuses} as ApplicationStatus, " + f"got {streamed_statuses}" + ) + + # commit() is called in pre_process, after the streaming loop (flush), + # and in post_process — at least once for the flush + assert job_report_mock.commit.call_count >= 1 diff --git a/diracx-api/tests/test_job_wrapper_sandbox.py b/diracx-api/tests/test_job_wrapper_sandbox.py new file mode 100644 index 000000000..6e2ac7906 --- /dev/null +++ b/diracx-api/tests/test_job_wrapper_sandbox.py @@ -0,0 +1,95 @@ +"""Tests for JobWrapper SB: path parsing and replica map injection.""" + +from __future__ import annotations + +import json + +import pytest + +from diracx.api.job_wrapper import JobWrapper +from diracx.core.models.replica_map import ReplicaMap + +# --------------------------------------------------------------------------- +# Tests +# --------------------------------------------------------------------------- + + +class TestParseSBPath: + """Test the SB: path parsing logic.""" + + def test_parse_sb_path(self): + """Parse SB: path into sandbox reference and relative path.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc123.tar.zst#helper.sh" + sb_ref, rel_path = JobWrapper.parse_sb_path(sb_path) + assert sb_ref == "SB:SandboxSE|/S3/store/sha256:abc123.tar.zst" + assert rel_path == "helper.sh" + + def test_parse_sb_path_nested(self): + """Parse SB: path with nested relative path.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:def456.tar.zst#config/db.yaml" + sb_ref, rel_path = JobWrapper.parse_sb_path(sb_path) + assert sb_ref == "SB:SandboxSE|/S3/store/sha256:def456.tar.zst" + assert rel_path == "config/db.yaml" + + def test_parse_sb_path_no_fragment(self): + """SB: path without # fragment should raise ValueError.""" + with pytest.raises(ValueError, match="missing '#' fragment"): + JobWrapper.parse_sb_path("SB:SandboxSE|/S3/store/sha256:abc.tar.zst") + + def test_parse_sb_path_no_prefix(self): + """Non-SB: path should raise ValueError.""" + with pytest.raises(ValueError, match="Not an SB: path"): + JobWrapper.parse_sb_path("/some/local/file.txt") + + +class TestAddSandboxEntriesToReplicaMap: + """Test injecting sandbox entries into the replica map JSON.""" + + def test_creates_new_replica_map(self, tmp_path): + """When no replica map exists, create one with sandbox entries.""" + sandbox_mappings = { + "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh": tmp_path + / "helper.sh", + } + (tmp_path / "helper.sh").write_text("#!/bin/bash") + + wrapper = JobWrapper.__new__(JobWrapper) + wrapper._replica_map_path = None + wrapper._add_sandbox_entries_to_replica_map(sandbox_mappings, tmp_path) + + assert wrapper._replica_map_path is not None + replica_map = ReplicaMap.model_validate_json( + wrapper._replica_map_path.read_text() + ) + key = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + assert key in replica_map.root + entry = replica_map[key] + assert len(entry.replicas) == 1 + assert entry.replicas[0].se == "local" + assert "helper.sh" in str(entry.replicas[0].url) + + def test_extends_existing_replica_map(self, tmp_path): + """When a replica map already exists (from LFN resolution), add sandbox entries.""" + existing = { + "/lhcb/data/file.dst": { + "replicas": [ + {"url": "root://eoslhcb.cern.ch//data/file.dst", "se": "CERN-DST"} + ], + } + } + map_path = tmp_path / "replica_map.json" + map_path.write_text(json.dumps(existing)) + + sandbox_mappings = { + "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#script.py": tmp_path + / "script.py", + } + (tmp_path / "script.py").write_text("print('hello')") + + wrapper = JobWrapper.__new__(JobWrapper) + wrapper._replica_map_path = map_path + wrapper._add_sandbox_entries_to_replica_map(sandbox_mappings, tmp_path) + + replica_map = ReplicaMap.model_validate_json(map_path.read_text()) + assert "/lhcb/data/file.dst" in replica_map.root + assert "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#script.py" in replica_map.root diff --git a/diracx-cli/pyproject.toml b/diracx-cli/pyproject.toml index 9c93c35b5..64be80527 100644 --- a/diracx-cli/pyproject.toml +++ b/diracx-cli/pyproject.toml @@ -14,6 +14,7 @@ classifiers = [ ] dependencies = [ "diraccfg", # TODO: Should this be an extra + "cwltool", "diracx-api", "diracx-client", "diracx-core", @@ -35,9 +36,10 @@ types = [ [project.scripts] dirac = "diracx.cli:app" +dirac-cwl-run = "diracx.cli.executor.__main__:cli" [project.entry-points."diracx.cli"] -jobs = "diracx.cli.jobs:app" +job = "diracx.cli.job:app" config = "diracx.cli.config:app" [project.entry-points."diracx.cli.hidden"] diff --git a/diracx-cli/src/diracx/cli/__init__.py b/diracx-cli/src/diracx/cli/__init__.py index 632c1ff13..15a3a6b8a 100644 --- a/diracx-cli/src/diracx/cli/__init__.py +++ b/diracx-cli/src/diracx/cli/__init__.py @@ -6,7 +6,6 @@ __all__ = ("app",) - # Load all the sub commands cli_names = set( [ diff --git a/diracx-cli/src/diracx/cli/_submission/__init__.py b/diracx-cli/src/diracx/cli/_submission/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/diracx-cli/src/diracx/cli/_submission/confirm.py b/diracx-cli/src/diracx/cli/_submission/confirm.py new file mode 100644 index 000000000..2535528e7 --- /dev/null +++ b/diracx-cli/src/diracx/cli/_submission/confirm.py @@ -0,0 +1,58 @@ +# diracx-cli/src/diracx/cli/_submission/confirm.py +from __future__ import annotations + +__all__ = ("needs_confirmation", "build_summary", "prompt_confirmation") + + +def _fmt_bytes(n: int) -> str: + """Format bytes as human-readable string.""" + if n >= 1024**3: + return f"{n / 1024**3:.1f} GB" + elif n >= 1024**2: + return f"{n / 1024**2:.1f} MB" + elif n >= 1024: + return f"{n / 1024:.1f} KB" + return f"{n} B" + + +def needs_confirmation(num_jobs: int, yes: bool = False) -> bool: + """Check if submission needs user confirmation.""" + if yes: + return False + return num_jobs > 100 + + +def build_summary( + *, + workflow_name: str, + workflow_path: str, + num_jobs: int, + source: str, + num_unique_sandboxes: int, + total_sandbox_bytes: int, + num_lfn_inputs: int, +) -> str: + """Build a human-readable submission summary string.""" + lines = [ + "Submission summary:", + f" Workflow: {workflow_path} ({workflow_name})", + f" Jobs: {num_jobs:,}", + f" Source: {source}", + ] + + if num_unique_sandboxes > 0: + lines.append( + f" Sandboxes: {num_unique_sandboxes} unique ({_fmt_bytes(total_sandbox_bytes)})" + ) + + if num_lfn_inputs > 0: + lines.append(f" LFN inputs: {num_lfn_inputs:,}") + + return "\n".join(lines) + + +def prompt_confirmation(summary: str) -> bool: + """Display summary and prompt for confirmation. Returns True if user confirms.""" + print(summary) + response = input("\nProceed? [y/N] ").strip().lower() + return response in ("y", "yes") diff --git a/diracx-cli/src/diracx/cli/_submission/inputs.py b/diracx-cli/src/diracx/cli/_submission/inputs.py new file mode 100644 index 000000000..2c0d8c539 --- /dev/null +++ b/diracx-cli/src/diracx/cli/_submission/inputs.py @@ -0,0 +1,101 @@ +"""Input parsing utilities for CWL job submission.""" + +from __future__ import annotations + +import argparse +import json +from pathlib import Path +from typing import Any + +import yaml + + +def parse_input_files(files: list[Path]) -> list[dict[str, Any]]: + """Parse job input sets from YAML or JSON files. + + YAML files support multi-document format (--- separators). + JSON files are treated as a single input set. + Multiple files are concatenated into a flat list of job inputs. + """ + results: list[dict[str, Any]] = [] + for path in files: + if not path.exists(): + raise FileNotFoundError(f"Input file not found: {path}") + content = path.read_text() + if path.suffix.lower() == ".json": + results.append(json.loads(content)) + else: + # YAML — may be multi-document + docs = list(yaml.safe_load_all(content)) + results.extend(doc for doc in docs if doc is not None) + return results + + +def parse_range(range_str: str) -> tuple[str, int, int, int]: + """Parse a --range argument of the form PARAM=END, PARAM=START:END, or PARAM=START:END:STEP. + + Returns (param, start, end, step). + """ + if "=" not in range_str: + raise ValueError( + f"Invalid range format {range_str!r}: expected PARAM=END, " + "PARAM=START:END, or PARAM=START:END:STEP" + ) + param, _, spec = range_str.partition("=") + parts = spec.split(":") + try: + if len(parts) == 1: + return param, 0, int(parts[0]), 1 + elif len(parts) == 2: + return param, int(parts[0]), int(parts[1]), 1 + elif len(parts) == 3: + return param, int(parts[0]), int(parts[1]), int(parts[2]) + else: + raise ValueError( + f"Invalid range format {range_str!r}: too many ':' separators" + ) + except (TypeError, ValueError) as exc: + raise ValueError(f"Invalid range format {range_str!r}: {exc}") from exc + + +def _file_type(value: str) -> dict[str, str]: + """Argparse type converter for CWL File inputs.""" + return {"class": "File", "path": value} + + +def parse_cli_args(cwl_inputs: list[dict[str, Any]], args: list[str]) -> dict[str, Any]: + """Parse CLI arguments against CWL workflow input declarations. + + Builds an argparse parser dynamically from the CWL ``inputs`` list. + Returns a dict of {input_id: value}, omitting inputs that were not + provided (i.e. still ``None`` / empty list after parsing). + """ + if not args: + return {} + + parser = argparse.ArgumentParser(add_help=False) + + for inp in cwl_inputs: + inp_id: str = inp["id"] + inp_type: str = inp["type"] + flag = f"--{inp_id}" + + if inp_type == "boolean": + parser.add_argument(flag, dest=inp_id, action="store_true", default=None) + elif inp_type == "File": + parser.add_argument(flag, dest=inp_id, type=_file_type, default=None) + elif inp_type == "File[]": + parser.add_argument( + flag, + dest=inp_id, + type=_file_type, + action="append", + default=None, + ) + else: + type_map: dict[str, type] = {"string": str, "int": int, "float": float} + py_type = type_map.get(inp_type, str) + parser.add_argument(flag, dest=inp_id, type=py_type, default=None) + + namespace = parser.parse_args(args) + return {k: v for k, v in vars(namespace).items() if v is not None} diff --git a/diracx-cli/src/diracx/cli/_submission/pipeline.py b/diracx-cli/src/diracx/cli/_submission/pipeline.py new file mode 100644 index 000000000..645dd2d11 --- /dev/null +++ b/diracx-cli/src/diracx/cli/_submission/pipeline.py @@ -0,0 +1,153 @@ +from __future__ import annotations + +__all__ = ("submit_cwl",) + +import logging +from pathlib import Path + +import yaml + +from diracx.client.aio import AsyncDiracClient # type: ignore[attr-defined] +from diracx.client.models import CWLJobSubmission # type: ignore[attr-defined] + +from .confirm import build_summary, needs_confirmation, prompt_confirmation +from .inputs import parse_cli_args, parse_input_files, parse_range +from .sandbox import ( + group_jobs_by_sandbox, + rewrite_sandbox_refs, + scan_file_references, +) + +logger = logging.getLogger(__name__) + + +def _extract_cwl_inputs(cwl: dict) -> list[dict]: + """Extract input declarations from a parsed CWL document.""" + inputs = cwl.get("inputs", []) + if isinstance(inputs, dict): + return [{"id": k, **v} for k, v in inputs.items()] + return inputs + + +def _extract_label(cwl: dict) -> str: + """Extract the workflow label, falling back to 'unnamed'.""" + return cwl.get("label", "unnamed") + + +async def _upload_sandboxes( + jobs: list[dict], + sandbox_groups: list[tuple[frozenset[Path], list[int]]], + client: AsyncDiracClient, +) -> list[dict]: + """Upload sandboxes and rewrite File references in job inputs.""" + from diracx.api.jobs import create_sandbox + + sb_ref_map: dict[Path, str] = {} + for file_set, _job_indices in sandbox_groups: + paths = sorted(file_set) + sb_ref = await create_sandbox(paths, client=client) + for p in paths: + sb_ref_map[p] = sb_ref + + return [rewrite_sandbox_refs(job, sb_ref_map) for job in jobs] + + +async def submit_cwl( + *, + workflow: Path, + input_files: list[Path], + cli_args: list[str], + range_spec: str | None, + yes: bool, +) -> list: + """Shared CWL submission pipeline. + + 1. Parse CWL and inputs + 2. Validate + 3. Process sandboxes + 4. Confirm if needed + 5. Submit via API + 6. Return results + """ + # 1. Parse CWL + cwl_yaml = workflow.read_text() + cwl = yaml.safe_load(cwl_yaml) + cwl_inputs = _extract_cwl_inputs(cwl) + label = _extract_label(cwl) + + # 2. Parse inputs + jobs: list[dict] = parse_input_files(input_files) + + # Merge CLI args if provided + if cli_args: + cli_input = parse_cli_args(cwl_inputs, cli_args) + if jobs: + jobs = [{**job, **cli_input} for job in jobs] + else: + jobs = [cli_input] + + # 3. Handle range — server-side expansion + if range_spec: + param, start, end, step = parse_range(range_spec) + base_inputs = jobs[0] if jobs else None + + async with AsyncDiracClient() as client: + body = CWLJobSubmission( + workflow=cwl_yaml, + range_param=param, + range_start=start, + range_end=end, + range_step=step, + base_inputs=base_inputs, + ) + return await client.jobs.submit_cwl_jobs(body) + + # 4. Sandbox processing + if not jobs: + jobs = [{}] + + sandbox_groups = group_jobs_by_sandbox(jobs) + + # Determine source description for summary + if len(input_files) > 0: + source = f"{len(input_files)} input file(s)" + else: + source = "no inputs" + + # Count LFNs across all jobs + total_lfns = 0 + for job in jobs: + _, lfns = scan_file_references(job) + total_lfns += len(lfns) + + # Compute sandbox sizes (approximate from local files) + total_sandbox_bytes = 0 + for file_set, _ in sandbox_groups: + for f in file_set: + if f.exists(): + total_sandbox_bytes += f.stat().st_size + + # 5. Confirm if needed + if needs_confirmation(len(jobs), yes=yes): + summary = build_summary( + workflow_name=label, + workflow_path=str(workflow), + num_jobs=len(jobs), + source=source, + num_unique_sandboxes=len(sandbox_groups), + total_sandbox_bytes=total_sandbox_bytes, + num_lfn_inputs=total_lfns, + ) + if not prompt_confirmation(summary): + raise SystemExit("Submission cancelled.") + + # 6. Upload sandboxes and submit + async with AsyncDiracClient() as client: + if sandbox_groups: + jobs = await _upload_sandboxes(jobs, sandbox_groups, client) + + body = CWLJobSubmission( + workflow=cwl_yaml, + inputs=jobs if jobs != [{}] else [], + ) + return await client.jobs.submit_cwl_jobs(body) diff --git a/diracx-cli/src/diracx/cli/_submission/sandbox.py b/diracx-cli/src/diracx/cli/_submission/sandbox.py new file mode 100644 index 000000000..32667e367 --- /dev/null +++ b/diracx-cli/src/diracx/cli/_submission/sandbox.py @@ -0,0 +1,116 @@ +"""Sandbox scanning, grouping, and path rewriting for CWL job submission.""" + +from __future__ import annotations + +from pathlib import Path +from typing import Any + + +def _is_file_obj(value: Any) -> bool: + """Return True if value is a CWL File object dict.""" + return isinstance(value, dict) and value.get("class") == "File" + + +def _classify_path(path_str: str) -> tuple[Path | None, str | None]: + """Classify a CWL File path string. + + Returns (local_path, lfn) where exactly one is set, or both None for SB: paths. + """ + if path_str.startswith("LFN:"): + return None, path_str + if path_str.startswith("SB:"): + return None, None + return Path(path_str), None + + +def scan_file_references(inputs: dict) -> tuple[list[Path], list[str]]: + """Walk an input dict and classify CWL File references. + + Returns: + local_files: paths to local files (no LFN: or SB: prefix) + lfns: LFN: prefixed path strings + SB: paths are silently ignored (already uploaded). + Non-File values are skipped. + + """ + local_files: list[Path] = [] + lfns: list[str] = [] + + for value in inputs.values(): + if _is_file_obj(value): + path_str: str = value["path"] + local, lfn = _classify_path(path_str) + if local is not None: + local_files.append(local) + elif lfn is not None: + lfns.append(lfn) + elif isinstance(value, list): + for item in value: + if _is_file_obj(item): + path_str = item["path"] + local, lfn = _classify_path(path_str) + if local is not None: + local_files.append(local) + elif lfn is not None: + lfns.append(lfn) + + return local_files, lfns + + +def group_jobs_by_sandbox( + jobs: list[dict], +) -> list[tuple[frozenset[Path], list[int]]]: + """Group jobs by their unique set of local files. + + Jobs with no local files are excluded from all groups. + + Returns: + List of (file_set, job_indices) tuples, one per unique file set. + + """ + groups: dict[frozenset[Path], list[int]] = {} + + for idx, job in enumerate(jobs): + local_files, _ = scan_file_references(job) + if not local_files: + continue + key = frozenset(local_files) + groups.setdefault(key, []).append(idx) + + return list(groups.items()) + + +def _rewrite_file_obj(file_obj: dict, sb_ref_map: dict[Path, str]) -> dict: + """Return a new File dict with the path rewritten if found in sb_ref_map.""" + path_str: str = file_obj["path"] + if path_str.startswith("LFN:") or path_str.startswith("SB:"): + return file_obj + local = Path(path_str) + if local in sb_ref_map: + # Append #filename so the wrapper can extract the file from the archive + return {**file_obj, "path": f"{sb_ref_map[local]}#{local.name}"} + return file_obj + + +def rewrite_sandbox_refs(inputs: dict, sb_ref_map: dict[Path, str]) -> dict: + """Return a new inputs dict with local File paths replaced by SB: references. + + LFN: and SB: paths pass through unchanged. + Non-File values pass through unchanged. + The original dict is not mutated. + """ + result: dict = {} + for key, value in inputs.items(): + if _is_file_obj(value): + result[key] = _rewrite_file_obj(value, sb_ref_map) + elif isinstance(value, list): + new_list = [] + for item in value: + if _is_file_obj(item): + new_list.append(_rewrite_file_obj(item, sb_ref_map)) + else: + new_list.append(item) + result[key] = new_list + else: + result[key] = value + return result diff --git a/diracx-cli/src/diracx/cli/_submission/simple.py b/diracx-cli/src/diracx/cli/_submission/simple.py new file mode 100644 index 000000000..c06228b85 --- /dev/null +++ b/diracx-cli/src/diracx/cli/_submission/simple.py @@ -0,0 +1,68 @@ +from __future__ import annotations + +__all__ = ("detect_sandbox_files", "generate_cwl") + +import shlex +from pathlib import Path + + +def detect_sandbox_files(command: str) -> list[Path]: + """Detect local files referenced in a command string. + + Tokenizes the command and checks each token against the filesystem. + Only includes files that are: + - Regular files (not directories) + - Not symlinks + - Relative paths (not absolute) + """ + tokens = shlex.split(command) + result: list[Path] = [] + for token in tokens: + p = Path(token) + if not p.is_absolute() and p.exists() and p.is_file() and not p.is_symlink(): + result.append(p) + return result + + +def generate_cwl( + command: str, + sandbox_files: list[Path], +) -> dict: + """Generate a minimal CWL CommandLineTool from a shell command.""" + tokens = shlex.split(command) + label = tokens[0] if tokens else "command" + if len(tokens) > 1 and not tokens[1].startswith("-"): + label = Path(tokens[1]).stem + + cwl: dict = { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "label": label, + "hints": [ + { + "class": "dirac:Job", + "schema_version": "1.0", + "type": "User", + } + ], + "baseCommand": ["bash", "-c", command], + "stdout": "stdout.log", + "stderr": "stderr.log", + "inputs": [], + "outputs": [ + {"id": "stdout_log", "type": "stdout"}, + {"id": "stderr_log", "type": "stderr"}, + ], + "$namespaces": {"dirac": "https://diracgrid.org/cwl#"}, + } + + if sandbox_files: + cwl["hints"][0]["input_sandbox"] = [{"source": "sandbox_files"}] + cwl["inputs"].append( + { + "id": "sandbox_files", + "type": {"type": "array", "items": "File"}, + } + ) + + return cwl diff --git a/diracx-cli/src/diracx/cli/auth.py b/diracx-cli/src/diracx/cli/auth.py index 1ed22586b..9f8c84024 100644 --- a/diracx-cli/src/diracx/cli/auth.py +++ b/diracx-cli/src/diracx/cli/auth.py @@ -11,7 +11,7 @@ import typer -from diracx.client.aio import AsyncDiracClient +from diracx.client.aio import AsyncDiracClient # type: ignore[attr-defined] # See https://github.com/DIRACGrid/diracx/issues/578 from diracx.client.models import DeviceFlowErrorResponse # type: ignore [attr-defined] diff --git a/diracx-cli/src/diracx/cli/executor/__init__.py b/diracx-cli/src/diracx/cli/executor/__init__.py new file mode 100644 index 000000000..df80fca8a --- /dev/null +++ b/diracx-cli/src/diracx/cli/executor/__init__.py @@ -0,0 +1,18 @@ +"""DIRAC CWL Executor package. + +This package provides custom executors for running CWL workflows with DIRAC-specific +functionality, including replica map management. +""" + +# Install the mypyc compatibility hook before any cwltool import. +# executor.py imports cwltool.executors which transitively imports +# cwltool.command_line_tool — the hook must be in place first. +from __future__ import annotations + +from ._mypyc_compat import install as _install_pure_python_hook + +_install_pure_python_hook() + +from .executor import DiracExecutor, dirac_executor_factory # noqa: E402 + +__all__ = ["DiracExecutor", "dirac_executor_factory"] diff --git a/diracx-cli/src/diracx/cli/executor/__main__.py b/diracx-cli/src/diracx/cli/executor/__main__.py new file mode 100644 index 000000000..d6c747012 --- /dev/null +++ b/diracx-cli/src/diracx/cli/executor/__main__.py @@ -0,0 +1,161 @@ +"""CLI tool for running CWL workflows with the DIRAC executor. + +Invoked as ``dirac-cwl-run`` on the worker node. Handles mypyc +compatibility, replica map management, and cwltool integration. +""" + +from __future__ import annotations + +import logging +import sys +from datetime import datetime, timezone +from pathlib import Path + +import typer + +logger = logging.getLogger("dirac-cwl-run") + +app = typer.Typer( + context_settings={"allow_extra_args": True, "ignore_unknown_options": True} +) + + +@app.command() +def main( # noqa: B008 + ctx: typer.Context, + workflow: Path = typer.Argument( # noqa: B008 + ..., help="Path to CWL workflow file", exists=True + ), + inputs: Path | None = typer.Argument( # noqa: B008 + None, help="Path to inputs YAML file (optional)" + ), + outdir: Path | None = typer.Option(None, help="Output directory"), # noqa: B008 + tmpdir_prefix: Path | None = typer.Option(None, help="Temporary directory prefix"), # noqa: B008 + leave_tmpdir: bool = typer.Option(False, help="Keep temporary directories"), # noqa: B008 + replica_map: Path | None = typer.Option( # noqa: B008 + None, help="Path to global replica map JSON file" + ), + preserve_environment: list[str] = typer.Option( # noqa: B008 + [], + "--preserve-environment", + help="Preserve specific environment variable when running CommandLineTools.", + ), + preserve_entire_environment: bool = typer.Option( # noqa: B008 + False, + "--preserve-entire-environment", + help="Preserve entire host environment when running CommandLineTools.", + ), + debug: bool = typer.Option(False, help="Enable debug logging"), # noqa: B008 +): + """Run a CWL workflow with the DIRAC executor.""" + # UTC logging + logging.Formatter.converter = lambda *_: datetime.now(timezone.utc).timetuple() + + start_time = datetime.now(timezone.utc) + workflow_params = ctx.args or [] + + # Build cwltool arguments + cwltool_args = [ + "--outdir", + str(outdir) if outdir else ".", + "--disable-color", + ] + + if tmpdir_prefix: + cwltool_args.extend(["--tmpdir-prefix", str(tmpdir_prefix)]) + if leave_tmpdir: + cwltool_args.append("--leave-tmpdir") + if debug: + cwltool_args.append("--debug") + if preserve_entire_environment: + cwltool_args.append("--preserve-entire-environment") + else: + for envvar in preserve_environment: + cwltool_args.extend(["--preserve-environment", envvar]) + + cwltool_args.append(str(workflow)) + if inputs: + cwltool_args.append(str(inputs)) + if workflow_params: + cwltool_args.extend(workflow_params) + + try: + # mypyc patch is applied by __init__.py before these imports + from cwltool.context import LoadingContext + from cwltool.main import main as cwltool_main + + from . import DiracExecutor + from .tool import dirac_make_tool + + dirac_executor = DiracExecutor(global_map_path=replica_map) + + logger.info("Workflow: %s", workflow.resolve()) + if inputs: + logger.info("Inputs: %s", inputs.resolve()) + if replica_map: + logger.info("Replica map: %s", replica_map) + + # Prevent our logger from duplicating cwltool output. + # Use stderr so that only the cwltool JSON output goes to stdout, + # allowing the caller to reliably parse it with json.loads(). + logger.propagate = False + handler = logging.StreamHandler(sys.stderr) + handler.setFormatter(logging.Formatter("%(message)s")) + logger.addHandler(handler) + logger.setLevel(logging.INFO) + + loading_context = LoadingContext() + loading_context.construct_tool_object = dirac_make_tool # type: ignore[assignment] + + exit_code = cwltool_main( + argsl=cwltool_args, + executor=dirac_executor, + loadingContext=loading_context, # type: ignore[arg-type] + ) + + end_time = datetime.now(timezone.utc) + duration = end_time - start_time + + # Write final replica map + if exit_code == 0 and dirac_executor.global_map: + output_dir = Path(outdir).resolve() if outdir else Path.cwd() + final_map_path = output_dir / "replica_map.json" + try: + final_map_path.write_text( + dirac_executor.global_map.model_dump_json(indent=2) + ) + logger.info( + "Replica map written: %s (%d entries)", + final_map_path, + len(dirac_executor.global_map.root), + ) + except Exception as e: + logger.warning("Could not write final replica map: %s", e) + + if exit_code == 0: + logger.info( + "Workflow completed successfully in %s", str(duration).split(".")[0] + ) + else: + logger.error( + "Workflow failed with exit code %d after %s", + exit_code, + str(duration).split(".")[0], + ) + + sys.exit(exit_code) + + except SystemExit: + raise + except Exception as e: + logger.exception("Error executing workflow: %s", e) + sys.exit(1) + + +def cli(): + """Entry point for the CLI when installed as a script.""" + app() + + +if __name__ == "__main__": + cli() diff --git a/diracx-cli/src/diracx/cli/executor/_mypyc_compat.py b/diracx-cli/src/diracx/cli/executor/_mypyc_compat.py new file mode 100644 index 000000000..c6bb519fe --- /dev/null +++ b/diracx-cli/src/diracx/cli/executor/_mypyc_compat.py @@ -0,0 +1,54 @@ +"""Force pure Python import for specific mypyc-compiled cwltool modules. + +mypyc compiles cwltool modules to .so files. The compiled CommandLineTool.job() +resolves self.make_path_mapper() as a direct C call, bypassing Python's MRO. +This prevents both monkey-patching and subclassing from working. + +By forcing the .py source to load instead of .so, normal Python dispatch is +restored and subclass method overrides work correctly. +""" + +from __future__ import annotations + +import importlib.abc +import importlib.util +import logging +import os +import sys + +logger = logging.getLogger("dirac-cwl-run") + +# Modules that must be loaded from .py for method dispatch to work +_FORCE_PURE_PYTHON = frozenset({"cwltool.command_line_tool"}) + + +class _PurePythonFinder(importlib.abc.MetaPathFinder): + """Meta path finder that forces .py over .so for specific modules.""" + + def find_spec(self, fullname, path, target=None): + """Find a pure Python (.py) module spec, ignoring mypyc .so files.""" + if fullname not in _FORCE_PURE_PYTHON or path is None: + return None + + # path is the parent package's __path__, provided by Python for + # submodule imports (e.g. cwltool.__path__ for cwltool.command_line_tool) + module_name = fullname.rsplit(".", 1)[-1] + + for search_path in path: + py_file = os.path.join(search_path, module_name + ".py") + if os.path.isfile(py_file): + logger.debug( + "Forcing pure Python import: %s from %s", fullname, py_file + ) + return importlib.util.spec_from_file_location( + fullname, + py_file, + submodule_search_locations=None, + ) + return None + + +def install(): + """Install the import hook. Must be called before any cwltool import.""" + if not any(isinstance(f, _PurePythonFinder) for f in sys.meta_path): + sys.meta_path.insert(0, _PurePythonFinder()) diff --git a/diracx-cli/src/diracx/cli/executor/executor.py b/diracx-cli/src/diracx/cli/executor/executor.py new file mode 100644 index 000000000..243b01266 --- /dev/null +++ b/diracx-cli/src/diracx/cli/executor/executor.py @@ -0,0 +1,305 @@ +"""Custom executor for DIRAC CWL workflows with replica map management.""" + +from __future__ import annotations + +import functools +import logging +from collections.abc import MutableMapping +from pathlib import Path +from typing import cast + +from cwltool.context import RuntimeContext +from cwltool.errors import WorkflowException +from cwltool.executors import SingleJobExecutor +from cwltool.job import CommandLineJob +from cwltool.process import Process +from cwltool.stdfsaccess import StdFsAccess +from cwltool.utils import CWLOutputType +from cwltool.workflow_job import WorkflowJob + +from diracx.core.models.replica_map import ReplicaMap + +from .fs_access import DiracReplicaMapFsAccess + +logger = logging.getLogger("dirac-cwl-run") + + +class DiracExecutor(SingleJobExecutor): + """Custom executor that handles replica map management between steps. + + This executor overrides run_jobs() to intercept each CommandLineJob execution + and manage replica maps before and after the job runs. + """ + + def __init__(self, global_map_path: Path | None = None): + """Initialize executor with optional global replica map path.""" + super().__init__() + self.global_map_path = global_map_path + self.global_map: ReplicaMap | None = None + + def run_jobs( + self, + process: Process, + job_order_object: MutableMapping[str, CWLOutputType | None], + logger_arg: logging.Logger, + runtime_context: RuntimeContext, + ) -> None: + """Override run_jobs to intercept each job execution. + + This method is called once at the top level and iterates through ALL jobs + including nested CommandLineTools within subworkflows. The generator pattern + flattens the workflow hierarchy so we see every CommandLineJob here. + """ + # Load replica map once at the start + if self.global_map is None: + if self.global_map_path and self.global_map_path.exists(): + self.global_map = ReplicaMap.model_validate_json( + self.global_map_path.read_text() + ) + logger.info( + "Loaded replica map with %d file(s)", len(self.global_map.root) + ) + else: + self.global_map = ReplicaMap(root={}) + logger.debug("Initialized empty replica map") + + # Set up custom filesystem access that can resolve LFNs via replica map + # we create a partial function that binds the replica map to our custom + # fs access class + runtime_context.make_fs_access = cast( + type[StdFsAccess], + functools.partial(DiracReplicaMapFsAccess, replica_map=self.global_map), + ) + + # Store the replica map on the runtime context so DiracCommandLineTool + # can pass it to DiracPathMapper in make_path_mapper() + runtime_context.replica_map = self.global_map # type: ignore[attr-defined] + + # Get job iterator - this yields ALL jobs including nested ones + jobiter = process.job(job_order_object, self.output_callback, runtime_context) + + try: + for job in jobiter: + if job is not None: + # Standard setup from SingleJobExecutor.run_jobs + if runtime_context.builder is not None and hasattr(job, "builder"): + job.builder = runtime_context.builder + if job.outdir is not None: + self.output_dirs.add(job.outdir) + + # Validation mode (from SingleJobExecutor.run_jobs) + if runtime_context.validate_only is True: + if isinstance(job, WorkflowJob): + name = job.tool.lc.filename + else: + name = getattr(job, "name", str(job)) + print( + f"{name} is valid CWL. No errors detected in the inputs.", + file=runtime_context.validate_stdout, + ) + return + + # CUSTOM: Intercept CommandLineJob to manage replica maps + if isinstance(job, CommandLineJob): + # job_name = getattr(job, "name", "unknown") + self._prepare_job_replica_map(job, runtime_context) + + # Execute the job + job.run(runtime_context) + + # CUSTOM: Update replica map after CommandLineJob completes + if isinstance(job, CommandLineJob): + self._update_replica_map_from_job(job, runtime_context) + else: + logger.error("Workflow cannot make any more progress.") + break + except WorkflowException: + raise + except Exception as err: + logger.exception("Got workflow error") + raise WorkflowException(str(err)) from err + + def _prepare_job_replica_map( + self, job: CommandLineJob, runtime_context: RuntimeContext + ): + """Prepare replica map for a specific CommandLineJob. + + Args: + job: The CommandLineJob about to be executed + runtime_context: Runtime context containing execution settings + + """ + job_name = getattr(job, "name", "unknown") + + # Extract LFNs from job inputs + # job.builder.job contains the actual input dictionary + job_inputs = job.builder.job if hasattr(job, "builder") else {} + step_lfns = self._extract_lfns_from_inputs(job_inputs) + + # Filter global map for this step's inputs + if step_lfns and self.global_map: + step_replica_map = ReplicaMap( + root={ + lfn: entry + for lfn, entry in self.global_map.root.items() + if lfn in step_lfns + } + ) + found = len(step_replica_map.root) + if found > 0: + logger.info("%s: Found %d input files in replica map", job_name, found) + else: + logger.warning( + "%s: Expected input files not found in replica map: %s", + job_name, + step_lfns, + ) + step_replica_map = ReplicaMap(root={}) + elif step_lfns: + logger.warning( + "%s: Input files requested but no replica map available: %s", + job_name, + step_lfns, + ) + step_replica_map = ReplicaMap(root={}) + else: + # Create empty replica map for steps with no LFN inputs (e.g., simulation) + step_replica_map = ReplicaMap(root={}) + + # Write step replica map to job's output directory + if job.outdir: + step_replica_map_path = Path(job.outdir) / "replica_map.json" + step_replica_map_path.write_text(step_replica_map.model_dump_json(indent=2)) + else: + logger.warning( + "%s: Job has no output directory, cannot write replica map", job_name + ) + + def _update_replica_map_from_job( + self, job: CommandLineJob, runtime_context: RuntimeContext + ): + """Update replica map from job outputs. + + After a job completes, the application may have added new LFNs + to the step replica map. Merge those back into the global map. + + Args: + job: The completed CommandLineJob + runtime_context: Runtime context containing execution settings + + """ + job_name = getattr(job, "name", "unknown") + + if not job.outdir: + logger.warning( + "%s: Job has no output directory, cannot update replica map", job_name + ) + return + + step_replica_map_path = Path(job.outdir) / "replica_map.json" + if not step_replica_map_path.exists(): + logger.debug("%s: No step replica map found, skipping update", job_name) + return + + try: + step_replica_map = ReplicaMap.model_validate_json( + step_replica_map_path.read_text() + ) + + if self.global_map is None: + self.global_map = ReplicaMap(root={}) + + # Only register files that are NOT already in the global map + # This filters out input files that were copied to the step replica map + new_entries = [] + updated_entries = [] + for lfn, entry in step_replica_map.root.items(): + if lfn in self.global_map.root: + # File already exists - check if it was updated + existing_entry = self.global_map.root[lfn] + # If the entry has changed (e.g., new replicas added), update it + if existing_entry != entry: + self.global_map.root[lfn] = entry + updated_entries.append(lfn) + logger.debug( + "%s: Updated replica map entry for %s", job_name, lfn + ) + # Otherwise skip - this is an input file that hasn't changed + else: + # This is a new file (output from this job) + self.global_map.root[lfn] = entry + new_entries.append(lfn) + + if new_entries: + logger.info( + "%s: Registered %d new output file(s) (replica map total: %d)", + job_name, + len(new_entries), + len(self.global_map.root), + ) + if updated_entries: + logger.info( + "%s: Updated %d existing replica map entries", + job_name, + len(updated_entries), + ) + except Exception as e: + logger.exception("%s: Failed to update replica map - %s", job_name, e) + + def _extract_lfns_from_inputs( + self, job_order: MutableMapping[str, CWLOutputType | None] + ) -> list[str]: + """Extract LFN paths from job inputs. + + Recursively searches through the job order dictionary to find File objects + with paths that look like LFNs (start with "LFN:"). + + Args: + job_order: Job input dictionary + + Returns: + List of LFN paths found in the inputs (with LFN: prefix stripped) + + """ + lfns = [] + + def extract_recursive(obj): + if isinstance(obj, dict): + # Check if this looks like a File with an LFN path + if "class" in obj and obj["class"] == "File": + # Check both "path" and "location" fields + for field in ["path", "location"]: + value = obj.get(field, "") + if value.startswith("LFN:"): + # Strip LFN: prefix for replica map lookup + lfn = value[4:] + if lfn not in lfns: + lfns.append(lfn) + break + else: + for value in obj.values(): + extract_recursive(value) + elif isinstance(obj, list): + for item in obj: + extract_recursive(item) + + extract_recursive(job_order) + return lfns + + +def dirac_executor_factory(global_map_path: Path | None = None): + """Create a DiracExecutor with configuration. + + Args: + global_map_path: Path to master replica map JSON file + + Returns: + Executor function compatible with cwltool + + """ + + def executor(process, job_order, runtime_context, logger_arg): + dirac_exec = DiracExecutor(global_map_path) + return dirac_exec(process, job_order, runtime_context, logger_arg) + + return executor diff --git a/diracx-cli/src/diracx/cli/executor/fs_access.py b/diracx-cli/src/diracx/cli/executor/fs_access.py new file mode 100644 index 000000000..cd72b3d81 --- /dev/null +++ b/diracx-cli/src/diracx/cli/executor/fs_access.py @@ -0,0 +1,130 @@ +"""Custom filesystem access for DIRAC file references using replica map.""" + +from __future__ import annotations + +import os +from typing import Any + +from cwltool.stdfsaccess import StdFsAccess + +from diracx.core.models.replica_map import ReplicaMap + + +def _is_ref(path: str) -> bool: + """Check if a path is an LFN: or SB: reference.""" + return path.startswith("LFN:") or path.startswith("SB:") + + +class DiracReplicaMapFsAccess(StdFsAccess): + """Use replica map to resolve LFN: and SB: paths to physical file locations. + + This class extends StdFsAccess to handle LFN: and SB: prefixed paths by + looking them up in the replica map and using the physical file path instead. + + Key difference: LFN keys are stored WITHOUT prefix, SB keys are stored WITH prefix. + """ + + def __init__(self, basedir: str, replica_map: ReplicaMap | None = None): + """Initialize with optional replica map. + + Args: + basedir: Base directory for relative paths + replica_map: ReplicaMap instance for path resolution + + """ + super().__init__(basedir) + self.replica_map = replica_map or ReplicaMap(root={}) + + def _resolve_path(self, path: str) -> tuple[str, bool]: + """Resolve an LFN or SB reference to a physical file path. + + Args: + path: File reference (LFN:/path or SB:pfn#relpath) + + Returns: + Tuple of (physical path/URL, is_remote) + + """ + # SB: keys are stored with prefix; LFN keys without + if path.startswith("SB:"): + key = path + else: + key = path.removeprefix("LFN:") + + if key in self.replica_map.root: + entry = self.replica_map[key] + if entry.replicas: + url = entry.replicas[0].url + is_remote = url.scheme != "file" + return str(url) if is_remote else (url.path or ""), is_remote + + # Not in replica map — return cleaned path for LFN, original for SB + if path.startswith("SB:"): + return path, False + return key, False + + def _abs(self, p: str) -> str: + """Resolve path, handling LFN/SB references via replica map.""" + if _is_ref(p): + p, is_remote = self._resolve_path(p) + if is_remote: + return p + return super()._abs(p) + + def glob(self, pattern: str) -> list[str]: + """Glob with LFN/SB support.""" + if _is_ref(pattern): + resolved, is_remote = self._resolve_path(pattern) + if is_remote: + return [pattern] + if os.path.exists(resolved): + return [pattern] + return [] + return super().glob(pattern) + + def open(self, fn: str, mode: str) -> Any: + """Open file with LFN/SB resolution.""" + if _is_ref(fn): + fn, is_remote = self._resolve_path(fn) + if is_remote: + raise ValueError(f"Cannot open remote file: {fn}") + return super().open(fn, mode) + + def exists(self, fn: str) -> bool: + """Check if file exists, with LFN/SB resolution.""" + if _is_ref(fn): + fn, is_remote = self._resolve_path(fn) + if is_remote: + return True + return super().exists(fn) + + def isfile(self, fn: str) -> bool: + """Check if path is a file, with LFN/SB resolution.""" + if _is_ref(fn): + fn, is_remote = self._resolve_path(fn) + if is_remote: + return True + return super().isfile(fn) + + def isdir(self, fn: str) -> bool: + """Check if path is a directory, with LFN/SB resolution.""" + if _is_ref(fn): + return False + return super().isdir(fn) + + def size(self, fn: str) -> int: + """Get file size, with LFN/SB resolution.""" + if _is_ref(fn): + # Try to get size from replica map first + if fn.startswith("SB:"): + key = fn + else: + key = fn.removeprefix("LFN:") + if key in self.replica_map.root: + entry = self.replica_map[key] + if entry.size_bytes is not None: + return entry.size_bytes + fn, is_remote = self._resolve_path(fn) + if is_remote: + raise ValueError(f"Cannot determine size of remote file: {fn}") + return super().size(fn) diff --git a/diracx-cli/src/diracx/cli/executor/pathmapper.py b/diracx-cli/src/diracx/cli/executor/pathmapper.py new file mode 100644 index 000000000..a870f6b35 --- /dev/null +++ b/diracx-cli/src/diracx/cli/executor/pathmapper.py @@ -0,0 +1,177 @@ +"""Custom PathMapper for handling DIRAC LFNs in CWL workflows.""" +# ruff: noqa: N803 + +from __future__ import annotations + +import logging +from typing import List, Optional, cast + +from cwltool.pathmapper import MapperEnt, PathMapper, uri_file_path +from cwltool.utils import CWLObjectType + +from diracx.core.models.replica_map import ReplicaMap + +logger = logging.getLogger("dirac-cwl-run") + + +class DiracPathMapper(PathMapper): + """PathMapper that can resolve LFN: URIs using a replica map. + + This extends PathMapper to intercept files with LFN: URIs and resolve them + to physical file paths using the replica map before processing. + """ + + def __init__( + self, + referenced_files: List[CWLObjectType], + basedir: str, + stagedir: str, + separateDirs: bool = True, + replica_map: Optional[ReplicaMap] = None, + ): + """Initialize with optional replica map. + + Args: + referenced_files: Files referenced in the CWL workflow + basedir: Base directory for relative paths + stagedir: Staging directory for files + separateDirs: Whether to separate directories + replica_map: ReplicaMap for LFN resolution + + """ + self.replica_map = replica_map or ReplicaMap(root={}) + super().__init__(referenced_files, basedir, stagedir, separateDirs) + + def visit( + self, + obj: CWLObjectType, + stagedir: str, + basedir: str, + copy: bool = False, + staged: bool = False, + ) -> None: + """Visit a file object, handling LFN: URIs. + + LFN: URIs are resolved to their physical file locations (PFNs) using the + replica map. The PFN can be: + - A local file path (file://...) + - A remote URL (root://... for xrootd, etc.) + + CWL will use these paths/URLs directly without staging (copying/linking). + The files are either already downloaded locally or will be accessed via + network protocols like xrootd. + """ + tgt = str(obj.get("location", "")) + logger.debug("DiracPathMapper.visit: processing location=%s", tgt) + + # Check if this is an LFN or SB: reference that we need to resolve + if (tgt.startswith("LFN:") or tgt.startswith("SB:")) and obj.get( + "class" + ) == "File": + # For LFN: entries, the replica map key is the bare path (without "LFN:" prefix). + # For SB: entries, the replica map key is the full "SB:..." string. + if tgt.startswith("LFN:"): + lookup_key = tgt[4:] # Remove "LFN:" prefix + else: + lookup_key = tgt # SB: key includes the prefix + logger.debug("DiracPathMapper.visit: Found LFN/SB key=%s", lookup_key) + + # Look up in replica map to resolve to PFN + if lookup_key in self.replica_map.root: + entry = self.replica_map[lookup_key] + if entry.replicas: + # Get the first replica's URL (can be file:// or root:// or https:// etc.) + pfn = str(entry.replicas[0].url) + logger.info("DiracPathMapper: Resolved %s -> %s", lookup_key, pfn) + + # cwltool uses MapperEnt.target as the path passed to the command + # (set via file_o["path"] = pathmapper.mapper(location)[1]). + # For local file:// URLs we must convert to a plain filesystem path; + # for remote protocols (root://, https://) the URL is used as-is. + if pfn.startswith("file://"): + target = uri_file_path(pfn) + else: + target = pfn + + self._pathmap[tgt] = MapperEnt( + resolved=pfn, # The physical URL/path + target=target, # Local path for file://, URL for remote protocols + type="File", + staged=False, # We're not staging/copying this file + ) + + # Add size from replica map if available + if entry.size_bytes is not None and "size" not in obj: + obj["size"] = entry.size_bytes + + # Store checksum if available + if entry.checksum and "checksum" not in obj: + if entry.checksum.adler32: + # Format: "adler32$788c5caa" + obj["checksum"] = f"adler32${entry.checksum.adler32}" + + # Handle secondary files if any + self.visitlisting( + cast(List[CWLObjectType], obj.get("secondaryFiles", [])), + stagedir, + basedir, + copy=copy, + staged=staged, + ) + + # Don't call parent visit - we've handled this completely + return + + else: + logger.warning( + "DiracPathMapper: %s in replica map but has no replicas", + lookup_key, + ) + else: + # LFN/SB not in replica map - this will likely fail later + logger.error( + "DiracPathMapper: %s NOT in replica map! Available keys: %s", + lookup_key, + list(self.replica_map.root.keys())[:5], + ) + + # Handle remote protocol URLs (root://, https://, etc.) that should not be staged + if obj.get("class") == "File" and any( + tgt.startswith(scheme) + for scheme in ("root://", "xroot://", "https://", "http://") + ): + logger.info("DiracPathMapper: Using remote URL directly: %s", tgt) + self._pathmap[tgt] = MapperEnt( + resolved=tgt, + target=tgt, + type="File", + staged=False, + ) + self.visitlisting( + cast(List[CWLObjectType], obj.get("secondaryFiles", [])), + stagedir, + basedir, + copy=copy, + staged=staged, + ) + return + + # For non-LFN files or when LFN resolution failed, delegate to parent class + super().visit(obj, stagedir, basedir, copy, staged) + + def mapper(self, src: str) -> MapperEnt: + """Return the MapperEnt for a given source URI. + + Extends the base implementation to handle DIRAC-specific URI schemes + (LFN:, SB:) that may contain ``#`` fragment identifiers. cwltool's base + ``mapper()`` treats ``#`` as a separator and tries to look up the prefix + before appending the fragment to the target path, which is incorrect for + SB: keys where the full key (including fragment) is stored in _pathmap. + We intercept those cases and return the stored entry directly. + """ + # If the full key is already present, return it directly (handles SB: keys + # with '#' fragments that are stored under the full key). + if src in self._pathmap: + return self._pathmap[src] + # Fall back to cwltool's default fragment-stripping logic for all other URIs. + return super().mapper(src) diff --git a/diracx-cli/src/diracx/cli/executor/tool.py b/diracx-cli/src/diracx/cli/executor/tool.py new file mode 100644 index 000000000..4f35128ff --- /dev/null +++ b/diracx-cli/src/diracx/cli/executor/tool.py @@ -0,0 +1,66 @@ +"""Custom CWL tool classes for DIRAC executor. + +Provides DiracCommandLineTool (a CommandLineTool subclass that supports custom +path mappers) and dirac_make_tool (a factory for cwltool's construct_tool_object). +""" +# ruff: noqa: N803 + +from __future__ import annotations + +import logging + +from cwltool.command_line_tool import CommandLineTool +from cwltool.context import LoadingContext +from cwltool.pathmapper import PathMapper +from cwltool.process import Process +from cwltool.utils import CWLObjectType +from cwltool.workflow import default_make_tool +from ruamel.yaml.comments import CommentedMap + +from .pathmapper import DiracPathMapper + +logger = logging.getLogger("dirac-cwl-run") + + +class DiracCommandLineTool(CommandLineTool): + """CommandLineTool that uses DiracPathMapper for LFN resolution. + + Overrides make_path_mapper to create a DiracPathMapper when a replica_map + is available on the runtimeContext (set by DiracExecutor.run_jobs), + falling back to the default PathMapper otherwise. + """ + + @staticmethod + def make_path_mapper( + reffiles: list[CWLObjectType], + stagedir: str, + runtimeContext, + separateDirs: bool, + ) -> PathMapper: + """Create a PathMapper, using DiracPathMapper when a replica map is available.""" + replica_map = getattr(runtimeContext, "replica_map", None) + if replica_map is not None: + return DiracPathMapper( + reffiles, + runtimeContext.basedir, + stagedir, + separateDirs, + replica_map=replica_map, + ) + return PathMapper(reffiles, runtimeContext.basedir, stagedir, separateDirs) + + +def dirac_make_tool( + toolpath_object: CommentedMap, loadingContext: LoadingContext +) -> Process: + """Create a CWL tool instance, using DiracCommandLineTool for CommandLineTools. + + Delegate to cwltool's default_make_tool for everything else (Workflow, + ExpressionTool, etc.). + """ + if ( + isinstance(toolpath_object, dict) + and toolpath_object.get("class") == "CommandLineTool" + ): + return DiracCommandLineTool(toolpath_object, loadingContext) + return default_make_tool(toolpath_object, loadingContext) diff --git a/diracx-cli/src/diracx/cli/internal/job_wrapper.py b/diracx-cli/src/diracx/cli/internal/job_wrapper.py new file mode 100755 index 000000000..427957d05 --- /dev/null +++ b/diracx-cli/src/diracx/cli/internal/job_wrapper.py @@ -0,0 +1,138 @@ +#!/usr/bin/env python +"""Job wrapper template for executing CWL jobs.""" + +from __future__ import annotations + +import asyncio +import json +import logging +import os +import sys +from pathlib import Path +from typing import Any + +from cwl_utils.parser import load_document_by_uri +from cwl_utils.parser.cwl_v1_2_utils import load_inputfile +from ruamel.yaml import YAML + +from diracx.api.job_wrapper import JobWrapper +from diracx.core.models.cwl_submission import JobModel + + +async def main(): + """Execute the job wrapper for a given job model. + + Fetches the CWL workflow definition and input parameters from the + diracX API using the WorkflowID stored in the job config JSON. + """ + if len(sys.argv) < 2: + logging.error("Usage: job_wrapper.py ") + sys.exit(1) + + job_id = int(sys.argv[-1]) + + # Fetch workflow_id, CWL, and params from diracX API using the job_id + from diracx.client.aio import AsyncDiracClient + from diracx.core.models.search import ScalarSearchOperator, ScalarSearchSpec + + async with AsyncDiracClient() as client: + # Get workflow_id and params from job attributes + results = await client.jobs.search( + parameters=["JobID", "WorkflowID", "WorkflowParams"], + search=[ + ScalarSearchSpec( + parameter="JobID", + operator=ScalarSearchOperator.EQUAL, + value=str(job_id), + ) + ], + ) + if not results: + logging.error("Job %d not found", job_id) + sys.exit(1) + + job_attrs = results[0] + workflow_id = job_attrs.get("WorkflowID") + workflow_params = job_attrs.get("WorkflowParams") + + if not workflow_id: + logging.error("Job %d has no WorkflowID", job_id) + sys.exit(1) + + # Fetch CWL definition + workflow_response = await client.jobs.get_workflow(workflow_id) + cwl_yaml = workflow_response["cwl"] + + # Parse CWL + yaml_doc = YAML() + task_dict = yaml_doc.load(cwl_yaml) + + cwl_path = Path.cwd() / f"{workflow_id[:8]}.cwl" + with open(cwl_path, "w") as f: + YAML().dump(task_dict, f) + + task_obj = load_document_by_uri(str(cwl_path)) + + # Build job model + job_model_dict: dict[str, Any] = {"task": task_obj, "input": None} + + # If workflow_params were stored, use them as CWL inputs + if workflow_params: + cwl_inputs_obj = load_inputfile(workflow_params) + job_model_dict["input"] = {"sandbox": None, "cwl": cwl_inputs_obj} + + job = JobModel.model_validate(job_model_dict) + job_wrapper = JobWrapper(job_id) + + res = await job_wrapper.run_job(job) + if res: + logging.info("Job done.") + return 0 + else: + logging.info("Job failed.") + return 1 + + +def setup_diracx() -> None: + """Get a DiracX client instance with the current user's credentials.""" + from pathlib import Path + + import DIRAC # type: ignore[import-untyped] + + DIRAC.initialize() + + from DIRAC import gConfig + from DIRAC.Core.Security.DiracX import ( + diracxTokenFromPEM, # type: ignore[import-untyped] + ) + from DIRAC.Core.Security.Locations import ( + getDefaultProxyLocation, # type: ignore[import-untyped] + ) + + diracx_url = gConfig.getValue("/DiracX/URL") + if not diracx_url: + raise ValueError("Missing mandatory /DiracX/URL configuration") + + os.environ["DIRACX_URL"] = diracx_url + + proxy_location = getDefaultProxyLocation() + diracx_token = diracxTokenFromPEM(proxy_location) + if not diracx_token: + raise ValueError(f"No diracx token in the proxy file {proxy_location}") + + token_file = Path.home() / ".cache" / "diracx" / "credentials.json" + token_file.parent.mkdir(parents=True, exist_ok=True) + with open( + token_file, + "w", + encoding="utf-8", + opener=lambda p, f: os.open(p, f | os.O_TRUNC, 0o600), + ) as f: + json.dump(diracx_token, f) + + +if __name__ == "__main__": + logging.basicConfig(level=logging.INFO) + + setup_diracx() + sys.exit(asyncio.run(main())) diff --git a/diracx-cli/src/diracx/cli/job/__init__.py b/diracx-cli/src/diracx/cli/job/__init__.py new file mode 100644 index 000000000..c23423657 --- /dev/null +++ b/diracx-cli/src/diracx/cli/job/__init__.py @@ -0,0 +1,14 @@ +from __future__ import annotations + +__all__ = ("app",) + +from ..utils import AsyncTyper +from .sandbox import app as sandbox_app +from .submit import app as submit_app + +app = AsyncTyper(help="Job operations.") +app.add_typer(submit_app, name="submit") +app.add_typer(sandbox_app, name="sandbox") + +# Import submodules to register commands +from . import search as _search # noqa: F401, E402 diff --git a/diracx-cli/src/diracx/cli/job/sandbox.py b/diracx-cli/src/diracx/cli/job/sandbox.py new file mode 100644 index 000000000..5b414b0f0 --- /dev/null +++ b/diracx-cli/src/diracx/cli/job/sandbox.py @@ -0,0 +1,198 @@ +"""Commands for exploring and retrieving job output sandboxes.""" + +from __future__ import annotations + +__all__: list[str] = [] + +import io +import sys +import tarfile +from pathlib import Path +from typing import Annotated + +import httpx +import typer +import zstandard +from rich.console import Console +from rich.syntax import Syntax +from rich.table import Table + +from diracx.client.aio import AsyncDiracClient +from diracx.client.models import SandboxType + +from ..utils import AsyncTyper + +app = AsyncTyper(help="Output sandbox operations.") + + +async def _get_output_sb_refs(job_id: int) -> list[str]: + """Return the list of SB: references for a job's output sandbox.""" + async with AsyncDiracClient() as client: + refs = await client.jobs.get_job_sandbox(job_id, SandboxType.OUTPUT) + return [r for r in (refs or []) if r is not None] + + +async def _download_sandbox_bytes(sb_ref: str) -> bytes: + """Download a sandbox tar archive and return the raw bytes.""" + async with AsyncDiracClient() as client: + # Strip SB:SE| prefix — the server accepts just the /S3/... path, + # and the generated client regex has a typo that rejects "SB:" + pfn = sb_ref.split("|", 1)[-1] if "|" in sb_ref else sb_ref + res = await client.jobs.get_sandbox_file(pfn=pfn) + async with httpx.AsyncClient() as http_client: + response = await http_client.get(res.url) + response.raise_for_status() + return response.content + + +def _open_tar(data: bytes) -> tarfile.TarFile: + """Open a (possibly zstd-compressed) tar archive from bytes.""" + fh = io.BytesIO(data) + magic = fh.read(4) + fh.seek(0) + if magic.startswith(b"\x28\xb5\x2f\xfd"): + dctx = zstandard.ZstdDecompressor() + decompressed = dctx.decompress(data) + return tarfile.open(fileobj=io.BytesIO(decompressed), mode="r") + return tarfile.open(fileobj=fh, mode="r") + + +def _guess_syntax(filename: str) -> str | None: + """Return a rich Syntax lexer name from filename, or None.""" + ext = Path(filename).suffix.lower() + return { + ".py": "python", + ".sh": "bash", + ".yaml": "yaml", + ".yml": "yaml", + ".json": "json", + ".xml": "xml", + ".log": "text", + ".txt": "text", + ".cwl": "yaml", + }.get(ext) + + +@app.async_command(name="list") +async def list_files( + job_id: Annotated[int, typer.Argument(help="Job ID")], +): + """List files in the output sandbox of a job.""" + sb_refs = await _get_output_sb_refs(job_id) + if not sb_refs: + print("No output sandbox found for this job.") + return + + console = Console() + for sb_ref in sb_refs: + data = await _download_sandbox_bytes(sb_ref) + tf = _open_tar(data) + table = Table( + "Name", "Size", title=f"Sandbox: {sb_ref.split('/')[-1].split('.')[0][:12]}" + ) + for member in sorted(tf.getmembers(), key=lambda m: m.name): + if member.isfile(): + size = member.size + if size < 1024: + size_str = f"{size} B" + elif size < 1024 * 1024: + size_str = f"{size / 1024:.1f} KB" + else: + size_str = f"{size / (1024 * 1024):.1f} MB" + table.add_row(member.name, size_str) + console.print(table) + + +@app.async_command() +async def peek( + job_id: Annotated[int, typer.Argument(help="Job ID")], + filename: Annotated[str, typer.Argument(help="File to display (e.g. stdout.log)")], + lines: Annotated[ + int, typer.Option("--lines", "-n", help="Number of lines to show (0=all)") + ] = 50, +): + """Display the contents of a file from the output sandbox.""" + sb_refs = await _get_output_sb_refs(job_id) + if not sb_refs: + print("No output sandbox found for this job.", file=sys.stderr) + raise typer.Exit(1) + + for sb_ref in sb_refs: + data = await _download_sandbox_bytes(sb_ref) + tf = _open_tar(data) + try: + member = tf.getmember(filename) + except KeyError: + continue + + fobj = tf.extractfile(member) + if fobj is None: + print(f"{filename} is not a regular file.", file=sys.stderr) + raise typer.Exit(1) + + content = fobj.read().decode(errors="replace") + if lines > 0: + content_lines = content.splitlines() + if len(content_lines) > lines: + content = "\n".join(content_lines[:lines]) + content += f"\n... ({len(content_lines) - lines} more lines)" + + console = Console() + lexer = _guess_syntax(filename) + if lexer and lexer != "text": + console.print(Syntax(content, lexer)) + else: + console.print(content) + return + + print(f"File '{filename}' not found in any output sandbox.", file=sys.stderr) + raise typer.Exit(1) + + +@app.async_command() +async def get( + job_id: Annotated[int, typer.Argument(help="Job ID")], + output_dir: Annotated[ + Path, typer.Option("--output", "-o", help="Directory to extract files into") + ] = Path("."), + filename: Annotated[ + str | None, typer.Argument(help="Specific file to extract (default: all)") + ] = None, +): + """Download output sandbox files to a local directory.""" + sb_refs = await _get_output_sb_refs(job_id) + if not sb_refs: + print("No output sandbox found for this job.", file=sys.stderr) + raise typer.Exit(1) + + output_dir.mkdir(parents=True, exist_ok=True) + extracted: list[str] = [] + + for sb_ref in sb_refs: + data = await _download_sandbox_bytes(sb_ref) + tf = _open_tar(data) + + if filename: + try: + member = tf.getmember(filename) + except KeyError: + continue + tf.extract(member, path=output_dir, filter="data") + extracted.append(member.name) + else: + for member in tf.getmembers(): + if member.isfile(): + tf.extract(member, path=output_dir, filter="data") + extracted.append(member.name) + + if not extracted: + if filename: + print( + f"File '{filename}' not found in any output sandbox.", file=sys.stderr + ) + else: + print("No files extracted.", file=sys.stderr) + raise typer.Exit(1) + + for name in extracted: + print(f" {output_dir / name}") diff --git a/diracx-cli/src/diracx/cli/jobs.py b/diracx-cli/src/diracx/cli/job/search.py similarity index 89% rename from diracx-cli/src/diracx/cli/jobs.py rename to diracx-cli/src/diracx/cli/job/search.py index 1102bd7e8..d9d77c06c 100644 --- a/diracx-cli/src/diracx/cli/jobs.py +++ b/diracx-cli/src/diracx/cli/job/search.py @@ -1,8 +1,6 @@ -# Can't using PEP-604 with typer: https://github.com/tiangolo/typer/issues/348 -# from __future__ import annotations from __future__ import annotations -__all__ = ("app",) +__all__: list[str] = [] import json import re @@ -10,7 +8,7 @@ from rich.console import Console from rich.table import Table -from typer import FileText, Option +from typer import Option from diracx.client.aio import AsyncDiracClient from diracx.core.models.search import ( @@ -20,10 +18,7 @@ ) from diracx.core.preferences import OutputFormats, get_diracx_preferences -from .utils import AsyncTyper - -app = AsyncTyper() - +from . import app available_operators = ( f"Scalar operators: {', '.join([op.value for op in ScalarSearchOperator])}. " @@ -49,42 +44,6 @@ def parse_condition(value: str) -> SearchSpec: raise ValueError(f"Unknown operator {operator}") -@app.async_command() -async def search( - parameter: list[str] = [ - "JobID", - "Status", - "MinorStatus", - "ApplicationStatus", - "JobGroup", - "Site", - "JobName", - "Owner", - "LastUpdateTime", - ], - condition: Annotated[ - list[str], Option(help=f'Example: "JobID eq 1000". {available_operators}') - ] = [], - all: bool = False, - page: int = 1, - per_page: int = 10, -): - search_specs = [parse_condition(cond) for cond in condition] - async with AsyncDiracClient() as api: - jobs, content_range = await api.jobs.search( - parameters=None if all else parameter, - search=search_specs if search_specs else None, - page=page, - per_page=per_page, - cls=lambda _, jobs, headers: ( - jobs, - ContentRange(headers.get("Content-Range", "jobs")), - ), - ) - - display(jobs, cast(ContentRange, content_range)) - - class ContentRange: unit: str | None = None start: int | None = None @@ -154,9 +113,36 @@ def display_rich(data, content_range: ContentRange) -> None: @app.async_command() -async def submit(jdl: list[FileText]): +async def search( + parameter: list[str] = [ + "JobID", + "Status", + "MinorStatus", + "ApplicationStatus", + "JobGroup", + "Site", + "JobName", + "Owner", + "LastUpdateTime", + ], + condition: Annotated[ + list[str], Option(help=f'Example: "JobID eq 1000". {available_operators}') + ] = [], + all: bool = False, + page: int = 1, + per_page: int = 10, +): + search_specs = [parse_condition(cond) for cond in condition] async with AsyncDiracClient() as api: - jobs = await api.jobs.submit_jdl_jobs([x.read() for x in jdl]) - print( - f"Inserted {len(jobs)} jobs with ids: {','.join(map(str, (job.job_id for job in jobs)))}" - ) + jobs, content_range = await api.jobs.search( + parameters=None if all else parameter, + search=search_specs if search_specs else None, + page=page, + per_page=per_page, + cls=lambda _, jobs, headers: ( + jobs, + ContentRange(headers.get("Content-Range", "jobs")), + ), + ) + + display(jobs, cast(ContentRange, content_range)) diff --git a/diracx-cli/src/diracx/cli/job/submit/__init__.py b/diracx-cli/src/diracx/cli/job/submit/__init__.py new file mode 100644 index 000000000..f23a2a19c --- /dev/null +++ b/diracx-cli/src/diracx/cli/job/submit/__init__.py @@ -0,0 +1,12 @@ +from __future__ import annotations + +__all__ = ("app",) + +from ...utils import AsyncTyper + +app = AsyncTyper(help="Submit jobs to the grid.") + +# Import submodules to register commands +from . import cmd as _cmd # noqa: F401, E402 +from . import cwl as _cwl # noqa: F401, E402 +from . import jdl as _jdl # noqa: F401, E402 diff --git a/diracx-cli/src/diracx/cli/job/submit/cmd.py b/diracx-cli/src/diracx/cli/job/submit/cmd.py new file mode 100644 index 000000000..86edfd85e --- /dev/null +++ b/diracx-cli/src/diracx/cli/job/submit/cmd.py @@ -0,0 +1,78 @@ +from __future__ import annotations + +__all__: list[str] = [] + +import tempfile +from pathlib import Path +from typing import Annotated + +import typer +import yaml + +from ..._submission.pipeline import submit_cwl +from ..._submission.simple import detect_sandbox_files, generate_cwl +from . import app + + +@app.async_command( + help="""Submit a simple command to the grid. + +Runs COMMAND on a worker node. Local files referenced in the command +are automatically detected and shipped as input sandboxes. + +Use --sandbox for additional files not mentioned in the command. + +Examples: + dirac job submit cmd "python my_script.py" + dirac job submit cmd "python my_script.py" --sandbox config.json +""", +) +async def cmd( + command: Annotated[str, typer.Argument(help="Shell command to run on the grid")], + sandbox: Annotated[ + list[Path], + typer.Option("--sandbox", help="Additional local files to ship"), + ] = [], + yes: Annotated[ + bool, typer.Option("-y", "--yes", help="Skip confirmation prompt") + ] = False, +): + """Submit a simple command to the grid.""" + # Auto-detect files from command + auto_files = detect_sandbox_files(command) + all_sandbox = list(set(auto_files + sandbox)) + + # Generate CWL + cwl = generate_cwl(command=command, sandbox_files=all_sandbox) + + # Write CWL to temp file (pipeline expects a Path) + with tempfile.NamedTemporaryFile(mode="w", suffix=".cwl", delete=False) as f: + yaml.dump(cwl, f) + cwl_path = Path(f.name) + + try: + # Build sandbox inputs if files exist + input_files: list[Path] = [] + if all_sandbox: + sandbox_input = { + "sandbox_files": [ + {"class": "File", "path": str(p)} for p in all_sandbox + ] + } + with tempfile.NamedTemporaryFile( + mode="w", suffix=".yaml", delete=False + ) as inp_f: + yaml.dump(sandbox_input, inp_f) + input_files = [Path(inp_f.name)] + + results = await submit_cwl( + workflow=cwl_path, + input_files=input_files, + cli_args=[], + range_spec=None, + yes=yes, + ) + job_ids = [str(r.job_id) for r in results] + print(f"Submitted {len(results)} job(s): {', '.join(job_ids)}") + finally: + cwl_path.unlink(missing_ok=True) diff --git a/diracx-cli/src/diracx/cli/job/submit/cwl.py b/diracx-cli/src/diracx/cli/job/submit/cwl.py new file mode 100644 index 000000000..474207924 --- /dev/null +++ b/diracx-cli/src/diracx/cli/job/submit/cwl.py @@ -0,0 +1,68 @@ +from __future__ import annotations + +__all__: list[str] = [] + +from pathlib import Path +from typing import Annotated + +import typer + +from ..._submission.pipeline import submit_cwl +from . import app + + +@app.async_command( + context_settings={"allow_extra_args": True, "ignore_unknown_options": True}, + help="""Submit a CWL workflow to the grid. + +WORKFLOW is a CWL file (.cwl). INPUTS are optional YAML/JSON files +providing input values (one job per file, or one job per YAML document). + +Workflow inputs can also be passed as CLI arguments after a -- separator. +These are parsed against the workflow's declared input parameters: + + dirac job submit cwl workflow.cwl -- --message "hello" --count 42 + +Combine file inputs with CLI overrides: + + dirac job submit cwl workflow.cwl base.yaml -- --message "override" +""", +) +async def cwl( + ctx: typer.Context, + workflow: Annotated[Path, typer.Argument(help="CWL workflow file (.cwl)")], + range: Annotated[ + str | None, + typer.Option( + "--range", + help="Parametric range: PARAM=END, PARAM=START:END, or PARAM=START:END:STEP", + ), + ] = None, + yes: Annotated[ + bool, typer.Option("-y", "--yes", help="Skip confirmation prompt") + ] = False, +): + """Submit a CWL workflow to the grid.""" + # ctx.args contains: extra positional paths (input files) and + # unknown options passed after -- (cli args for the workflow). + # Positional file args appear before any --option args. + input_files: list[Path] = [] + cli_args: list[str] = [] + in_cli = False + for arg in ctx.args: + if arg.startswith("-"): + in_cli = True + if in_cli: + cli_args.append(arg) + else: + input_files.append(Path(arg)) + + results = await submit_cwl( + workflow=workflow, + input_files=input_files, + cli_args=cli_args, + range_spec=range, + yes=yes, + ) + job_ids = [str(r.job_id) for r in results] + print(f"Submitted {len(results)} job(s): {', '.join(job_ids)}") diff --git a/diracx-cli/src/diracx/cli/job/submit/jdl.py b/diracx-cli/src/diracx/cli/job/submit/jdl.py new file mode 100644 index 000000000..5d8c11fb5 --- /dev/null +++ b/diracx-cli/src/diracx/cli/job/submit/jdl.py @@ -0,0 +1,28 @@ +from __future__ import annotations + +__all__: list[str] = [] + +from typer import FileText + +from diracx.client.aio import AsyncDiracClient + +from . import app + + +@app.async_command( + help="""Submit jobs in JDL format. + +JDL is one or more JDL file paths. + +Examples: + dirac job submit jdl job.jdl + dirac job submit jdl job1.jdl job2.jdl +""", +) +async def jdl(jdl: list[FileText]): + """Submit jobs in JDL format.""" + async with AsyncDiracClient() as api: + jobs = await api.jobs.submit_jdl_jobs([x.read() for x in jdl]) + print( + f"Inserted {len(jobs)} jobs with ids: {','.join(map(str, (job.job_id for job in jobs)))}" + ) diff --git a/diracx-cli/tests/test_cwl_submit.py b/diracx-cli/tests/test_cwl_submit.py new file mode 100644 index 000000000..d70464748 --- /dev/null +++ b/diracx-cli/tests/test_cwl_submit.py @@ -0,0 +1,87 @@ +from __future__ import annotations + +from pathlib import Path +from unittest.mock import AsyncMock, MagicMock, patch + +import yaml +from typer.testing import CliRunner + +from diracx.cli.job import app as job_app + +runner = CliRunner() + + +@staticmethod +def cwl_file(tmp_path: Path) -> Path: + cwl = { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "label": "test-tool", + "hints": [ + { + "class": "dirac:Job", + "schema_version": "1.0", + "type": "User", + } + ], + "inputs": [{"id": "message", "type": "string"}], + "outputs": [], + "baseCommand": ["echo"], + "$namespaces": {"dirac": "https://diracgrid.org/cwl#"}, + } + f = tmp_path / "workflow.cwl" + f.write_text(yaml.dump(cwl)) + return f + + +class TestCWLSubmitCommand: + def test_basic_submit(self, tmp_path): + wf = cwl_file(tmp_path) + inputs_f = tmp_path / "inputs.yaml" + inputs_f.write_text("message: hello\n") + + with patch( + "diracx.cli.job.submit.cwl.submit_cwl", new_callable=AsyncMock + ) as mock_submit: + mock_submit.return_value = [MagicMock(job_id=1001, status="Submitting")] + result = runner.invoke( + job_app, + ["submit", "cwl", str(wf), str(inputs_f), "-y"], + ) + assert result.exit_code == 0, result.output + assert "1001" in result.output + mock_submit.assert_called_once() + call_kwargs = mock_submit.call_args[1] + assert call_kwargs["workflow"] == wf + assert call_kwargs["input_files"] == [inputs_f] + assert call_kwargs["yes"] is True + + def test_range_submit(self, tmp_path): + wf = cwl_file(tmp_path) + with patch( + "diracx.cli.job.submit.cwl.submit_cwl", new_callable=AsyncMock + ) as mock_submit: + mock_submit.return_value = [ + MagicMock(job_id=i, status="Submitting") for i in range(10) + ] + result = runner.invoke( + job_app, + ["submit", "cwl", str(wf), "--range", "message=0:10", "-y"], + ) + assert result.exit_code == 0, result.output + call_kwargs = mock_submit.call_args[1] + assert call_kwargs["range_spec"] == "message=0:10" + + def test_cli_args_after_separator(self, tmp_path): + wf = cwl_file(tmp_path) + with patch( + "diracx.cli.job.submit.cwl.submit_cwl", new_callable=AsyncMock + ) as mock_submit: + mock_submit.return_value = [MagicMock(job_id=1001, status="Submitting")] + result = runner.invoke( + job_app, + ["submit", "cwl", str(wf), "-y", "--", "--message", "hello"], + ) + assert result.exit_code == 0, result.output + call_kwargs = mock_submit.call_args[1] + assert call_kwargs["cli_args"] == ["--message", "hello"] diff --git a/diracx-cli/tests/test_executor.py b/diracx-cli/tests/test_executor.py new file mode 100644 index 000000000..3aa7d0f2d --- /dev/null +++ b/diracx-cli/tests/test_executor.py @@ -0,0 +1,477 @@ +"""Unit tests for DiracExecutor, DiracPathMapper, and DiracCommandLineTool.""" +# ruff: noqa: N803, N818 # Stub classes mirror cwltool's camelCase API + +from __future__ import annotations + +import types +from unittest.mock import MagicMock, patch + +import diracx.cli.executor.tool as _tool_mod +from diracx.cli.executor.executor import DiracExecutor +from diracx.cli.executor.fs_access import DiracReplicaMapFsAccess # noqa: F401 +from diracx.cli.executor.pathmapper import DiracPathMapper +from diracx.cli.executor.tool import DiracCommandLineTool, dirac_make_tool +from diracx.core.models.replica_map import ReplicaMap + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + + +def _make_replica_map(*lfns_with_urls) -> ReplicaMap: + """Create a ReplicaMap from (lfn, url) pairs.""" + root = {} + for lfn, url in lfns_with_urls: + root[lfn] = {"replicas": [{"url": url, "se": "TEST-SE"}]} + return ReplicaMap(root=root) + + +def _make_replica_map_with_meta(lfn, url, size_bytes=None, adler32=None) -> ReplicaMap: + entry = {"replicas": [{"url": url, "se": "TEST-SE"}]} + if size_bytes is not None: + entry["size_bytes"] = size_bytes + if adler32 is not None: + entry["checksum"] = {"adler32": adler32} + return ReplicaMap(root={lfn: entry}) + + +# --------------------------------------------------------------------------- +# Tests: DiracExecutor._extract_lfns_from_inputs +# --------------------------------------------------------------------------- + + +class TestExtractLfnsFromInputs: + """Test the static method that finds LFNs in CWL job inputs.""" + + def test_single_file_with_lfn_location(self): + """A File object with LFN: location should yield its LFN (without prefix).""" + executor = DiracExecutor.__new__(DiracExecutor) + inputs = { + "input_file": { + "class": "File", + "location": "LFN:/lhcb/data/2024/file.dst", + } + } + result = executor._extract_lfns_from_inputs(inputs) + assert result == ["/lhcb/data/2024/file.dst"] + + def test_single_file_with_lfn_path(self): + """A File with LFN: in the 'path' field should also be extracted.""" + executor = DiracExecutor.__new__(DiracExecutor) + inputs = { + "f": { + "class": "File", + "path": "LFN:/lhcb/data/2024/other.dst", + } + } + result = executor._extract_lfns_from_inputs(inputs) + assert result == ["/lhcb/data/2024/other.dst"] + + def test_array_of_files(self): + """An array of File objects should yield all their LFNs.""" + executor = DiracExecutor.__new__(DiracExecutor) + inputs = { + "files": [ + {"class": "File", "location": "LFN:/lhcb/data/a.dst"}, + {"class": "File", "location": "LFN:/lhcb/data/b.dst"}, + {"class": "File", "location": "LFN:/lhcb/data/c.dst"}, + ] + } + result = executor._extract_lfns_from_inputs(inputs) + assert sorted(result) == [ + "/lhcb/data/a.dst", + "/lhcb/data/b.dst", + "/lhcb/data/c.dst", + ] + + def test_no_lfn_inputs_returns_empty(self): + """Inputs without LFN: paths should return an empty list.""" + executor = DiracExecutor.__new__(DiracExecutor) + inputs = { + "param": "hello", + "count": 42, + } + result = executor._extract_lfns_from_inputs(inputs) + assert result == [] + + def test_sb_references_not_extracted(self): + """SB: references are sandbox files, not LFNs — must not appear in result.""" + executor = DiracExecutor.__new__(DiracExecutor) + inputs = { + "script": { + "class": "File", + "location": "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#run.sh", + } + } + result = executor._extract_lfns_from_inputs(inputs) + assert result == [] + + def test_mixed_lfn_and_non_lfn(self): + """Only LFN: files are extracted; other inputs are ignored.""" + executor = DiracExecutor.__new__(DiracExecutor) + inputs = { + "data": {"class": "File", "location": "LFN:/lhcb/data/file.dst"}, + "script": { + "class": "File", + "location": "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#run.sh", + }, + "config": {"class": "File", "location": "file:///local/config.yaml"}, + "count": 5, + } + result = executor._extract_lfns_from_inputs(inputs) + assert result == ["/lhcb/data/file.dst"] + + def test_deduplication(self): + """The same LFN appearing twice should be returned only once.""" + executor = DiracExecutor.__new__(DiracExecutor) + inputs = { + "a": {"class": "File", "location": "LFN:/lhcb/data/file.dst"}, + "b": {"class": "File", "location": "LFN:/lhcb/data/file.dst"}, + } + result = executor._extract_lfns_from_inputs(inputs) + assert result == ["/lhcb/data/file.dst"] + + +# --------------------------------------------------------------------------- +# Tests: DiracExecutor._prepare_job_replica_map +# --------------------------------------------------------------------------- + + +class TestPrepareJobReplicaMap: + """Test filtering the global replica map for a single job step.""" + + def _make_executor_with_map(self, replica_map: ReplicaMap) -> DiracExecutor: + executor = DiracExecutor.__new__(DiracExecutor) + executor.global_map = replica_map + executor.global_map_path = None + executor.output_dirs = set() + return executor + + def _make_job(self, inputs: dict, outdir: str) -> object: + """Create a minimal CommandLineJob-like object.""" + job = types.SimpleNamespace( + name="test_job", + outdir=outdir, + builder=types.SimpleNamespace(job=inputs), + ) + return job + + def test_filters_global_map_for_step(self, tmp_path): + """Only the LFNs referenced by a step should appear in its replica map.""" + global_map = _make_replica_map( + ("/lhcb/data/a.dst", "file:///storage/a.dst"), + ("/lhcb/data/b.dst", "file:///storage/b.dst"), + ("/lhcb/data/c.dst", "file:///storage/c.dst"), + ) + executor = self._make_executor_with_map(global_map) + job = self._make_job( + {"f": {"class": "File", "location": "LFN:/lhcb/data/a.dst"}}, + str(tmp_path), + ) + runtime_context = types.SimpleNamespace() + executor._prepare_job_replica_map(job, runtime_context) + + step_map = ReplicaMap.model_validate_json( + (tmp_path / "replica_map.json").read_text() + ) + assert "/lhcb/data/a.dst" in step_map.root + assert "/lhcb/data/b.dst" not in step_map.root + assert "/lhcb/data/c.dst" not in step_map.root + + def test_empty_lfns_produces_empty_map(self, tmp_path): + """A step with no LFN inputs should get an empty replica map written.""" + global_map = _make_replica_map( + ("/lhcb/data/a.dst", "file:///storage/a.dst"), + ) + executor = self._make_executor_with_map(global_map) + job = self._make_job({"param": "hello"}, str(tmp_path)) + executor._prepare_job_replica_map(job, types.SimpleNamespace()) + + step_map = ReplicaMap.model_validate_json( + (tmp_path / "replica_map.json").read_text() + ) + assert step_map.root == {} + + def test_missing_lfn_silently_skipped(self, tmp_path): + """LFNs requested by a step but absent from the global map are silently skipped.""" + global_map = _make_replica_map( + ("/lhcb/data/a.dst", "file:///storage/a.dst"), + ) + executor = self._make_executor_with_map(global_map) + job = self._make_job( + { + "f1": {"class": "File", "location": "LFN:/lhcb/data/a.dst"}, + "f2": {"class": "File", "location": "LFN:/lhcb/data/MISSING.dst"}, + }, + str(tmp_path), + ) + executor._prepare_job_replica_map(job, types.SimpleNamespace()) + + step_map = ReplicaMap.model_validate_json( + (tmp_path / "replica_map.json").read_text() + ) + assert "/lhcb/data/a.dst" in step_map.root + assert "/lhcb/data/MISSING.dst" not in step_map.root + + +# --------------------------------------------------------------------------- +# Tests: DiracExecutor._update_replica_map_from_job +# --------------------------------------------------------------------------- + + +class TestUpdateReplicaMapFromJob: + """Test merging step output back into the global replica map.""" + + def _make_executor(self, initial_map: ReplicaMap | None = None) -> DiracExecutor: + executor = DiracExecutor.__new__(DiracExecutor) + executor.global_map = initial_map or ReplicaMap(root={}) + executor.global_map_path = None + executor.output_dirs = set() + return executor + + def test_new_entries_added_to_global_map(self, tmp_path): + """New LFNs written by a job must appear in the global replica map.""" + executor = self._make_executor() + + step_map = _make_replica_map(("/lhcb/out/result.dst", "file:///out/result.dst")) + (tmp_path / "replica_map.json").write_text(step_map.model_dump_json()) + + job = types.SimpleNamespace(name="step1", outdir=str(tmp_path)) + executor._update_replica_map_from_job(job, types.SimpleNamespace()) + + assert "/lhcb/out/result.dst" in executor.global_map.root + + def test_existing_entries_preserved(self, tmp_path): + """Pre-existing entries in the global map must not be overwritten with identical data.""" + initial = _make_replica_map( + ("/lhcb/data/input.dst", "file:///storage/input.dst") + ) + executor = self._make_executor(initial) + + # Step map contains the same input entry (unchanged) plus a new output + step_map = _make_replica_map( + ("/lhcb/data/input.dst", "file:///storage/input.dst"), + ("/lhcb/out/output.dst", "file:///out/output.dst"), + ) + (tmp_path / "replica_map.json").write_text(step_map.model_dump_json()) + + job = types.SimpleNamespace(name="step1", outdir=str(tmp_path)) + executor._update_replica_map_from_job(job, types.SimpleNamespace()) + + assert "/lhcb/data/input.dst" in executor.global_map.root + assert "/lhcb/out/output.dst" in executor.global_map.root + + def test_no_replica_map_file_is_safe(self, tmp_path): + """If no replica_map.json exists in outdir, the update is a safe no-op.""" + executor = self._make_executor() + job = types.SimpleNamespace(name="step_no_map", outdir=str(tmp_path)) + # Should not raise + executor._update_replica_map_from_job(job, types.SimpleNamespace()) + assert executor.global_map.root == {} + + def test_no_outdir_is_safe(self): + """If job.outdir is None, the update is a safe no-op.""" + executor = self._make_executor() + job = types.SimpleNamespace(name="step_no_outdir", outdir=None) + executor._update_replica_map_from_job(job, types.SimpleNamespace()) + assert executor.global_map.root == {} + + +# --------------------------------------------------------------------------- +# Tests: DiracPathMapper.visit +# --------------------------------------------------------------------------- + + +class TestDiracPathMapper: + """Test LFN resolution logic in DiracPathMapper.visit.""" + + def _make_mapper(self, replica_map: ReplicaMap) -> DiracPathMapper: + """Instantiate DiracPathMapper without calling super().__init__ (avoids file scanning).""" + mapper = DiracPathMapper.__new__(DiracPathMapper) + mapper._pathmap = {} + mapper.replica_map = replica_map + return mapper + + def test_lfn_resolved_to_pfn(self): + """LFN: location should be mapped to its PFN in _pathmap.""" + replica_map = _make_replica_map( + ("/lhcb/data/file.dst", "file:///storage/file.dst") + ) + mapper = self._make_mapper(replica_map) + obj = {"class": "File", "location": "LFN:/lhcb/data/file.dst"} + mapper.visit(obj, "/stagedir", "/basedir") + assert "LFN:/lhcb/data/file.dst" in mapper._pathmap + entry = mapper._pathmap["LFN:/lhcb/data/file.dst"] + assert "/storage/file.dst" in entry.resolved + + def test_multiple_replicas_picks_first(self): + """When multiple replicas exist, the first one is used.""" + root = { + "/lhcb/data/file.dst": { + "replicas": [ + {"url": "file:///first/file.dst", "se": "SE-1"}, + {"url": "file:///second/file.dst", "se": "SE-2"}, + ] + } + } + replica_map = ReplicaMap(root=root) + mapper = self._make_mapper(replica_map) + obj = {"class": "File", "location": "LFN:/lhcb/data/file.dst"} + mapper.visit(obj, "/stagedir", "/basedir") + entry = mapper._pathmap["LFN:/lhcb/data/file.dst"] + assert "first" in entry.resolved + + def test_size_set_from_replica_map(self): + """visit() should annotate obj with size_bytes from the replica map.""" + replica_map = _make_replica_map_with_meta( + "/lhcb/data/file.dst", + "file:///storage/file.dst", + size_bytes=1048576, + ) + mapper = self._make_mapper(replica_map) + obj = {"class": "File", "location": "LFN:/lhcb/data/file.dst"} + mapper.visit(obj, "/stagedir", "/basedir") + assert obj.get("size") == 1048576 + + def test_checksum_set_from_replica_map(self): + """visit() should annotate obj with checksum from the replica map.""" + replica_map = _make_replica_map_with_meta( + "/lhcb/data/file.dst", + "file:///storage/file.dst", + adler32="788c5caa", + ) + mapper = self._make_mapper(replica_map) + obj = {"class": "File", "location": "LFN:/lhcb/data/file.dst"} + mapper.visit(obj, "/stagedir", "/basedir") + assert obj.get("checksum") == "adler32$788c5caa" + + def test_existing_size_not_overwritten(self): + """visit() should not overwrite size if already present on obj.""" + replica_map = _make_replica_map_with_meta( + "/lhcb/data/file.dst", + "file:///storage/file.dst", + size_bytes=1048576, + ) + mapper = self._make_mapper(replica_map) + obj = {"class": "File", "location": "LFN:/lhcb/data/file.dst", "size": 9999} + mapper.visit(obj, "/stagedir", "/basedir") + # Existing size is preserved + assert obj["size"] == 9999 + + def test_remote_url_mapped_directly(self): + """root:// URLs should be mapped directly without staging.""" + mapper = self._make_mapper(ReplicaMap(root={})) + obj = { + "class": "File", + "location": "root://eoslhcb.cern.ch//eos/lhcb/data/file.dst", + } + mapper.visit(obj, "/stagedir", "/basedir") + loc = "root://eoslhcb.cern.ch//eos/lhcb/data/file.dst" + assert loc in mapper._pathmap + entry = mapper._pathmap[loc] + assert entry.resolved == loc + assert entry.staged is False + + def test_missing_lfn_does_not_add_to_pathmap(self): + """LFN missing from replica map should not be added to _pathmap by DiracPathMapper. + + When the LFN is absent, DiracPathMapper falls through to the parent PathMapper.visit(). + The key invariant is that DiracPathMapper itself did NOT add the LFN key to _pathmap + before delegating to the parent. We verify this by checking the _pathmap state after + the visit call (ignoring any error from the parent's attempt to handle the unknown path). + """ + mapper = self._make_mapper(ReplicaMap(root={})) + obj = {"class": "File", "location": "LFN:/lhcb/data/MISSING.dst"} + try: + mapper.visit(obj, "/stagedir", "/basedir") + except Exception: + pass # Parent may raise for unknown paths — that's OK + # DiracPathMapper must NOT have added the LFN key itself + assert "LFN:/lhcb/data/MISSING.dst" not in mapper._pathmap + + def test_staged_false_for_lfn(self): + """LFN-resolved entries should have staged=False (no local copy needed).""" + replica_map = _make_replica_map( + ("/lhcb/data/file.dst", "file:///storage/file.dst") + ) + mapper = self._make_mapper(replica_map) + obj = {"class": "File", "location": "LFN:/lhcb/data/file.dst"} + mapper.visit(obj, "/stagedir", "/basedir") + entry = mapper._pathmap["LFN:/lhcb/data/file.dst"] + assert entry.staged is False + + +# --------------------------------------------------------------------------- +# Tests: DiracCommandLineTool.make_path_mapper +# --------------------------------------------------------------------------- + + +class TestDiracCommandLineTool: + """Test DiracCommandLineTool.make_path_mapper and dirac_make_tool.""" + + def _make_runtime_context(self, replica_map=None): + ctx = types.SimpleNamespace(basedir="/base", replica_map=replica_map) + return ctx + + def test_make_path_mapper_with_replica_map_returns_dirac_mapper(self): + """When replica_map is set on context, make_path_mapper returns DiracPathMapper.""" + replica_map = _make_replica_map( + ("/lhcb/data/file.dst", "file:///storage/file.dst") + ) + ctx = self._make_runtime_context(replica_map=replica_map) + mapper = DiracCommandLineTool.make_path_mapper([], "/stagedir", ctx, True) + assert isinstance(mapper, DiracPathMapper) + + def test_make_path_mapper_without_replica_map_returns_default(self): + """When no replica_map is on context, make_path_mapper returns base PathMapper.""" + ctx = types.SimpleNamespace(basedir="/base") # no replica_map attr + mapper = DiracCommandLineTool.make_path_mapper([], "/stagedir", ctx, True) + # Should NOT be a DiracPathMapper — should be the plain PathMapper + assert not isinstance(mapper, DiracPathMapper) + + def test_make_path_mapper_replica_map_none_returns_default(self): + """replica_map=None on context falls through to plain PathMapper.""" + ctx = self._make_runtime_context(replica_map=None) + mapper = DiracCommandLineTool.make_path_mapper([], "/stagedir", ctx, True) + assert not isinstance(mapper, DiracPathMapper) + + def test_dirac_make_tool_commandlinetool_returns_dirac_instance(self): + """dirac_make_tool should return DiracCommandLineTool for CommandLineTool class. + + We mock DiracCommandLineTool's __init__ so we don't need a full cwltool toolpath. + The test verifies routing: the factory creates a DiracCommandLineTool for + toolpath_objects whose class is 'CommandLineTool'. + """ + toolpath = {"class": "CommandLineTool", "baseCommand": "echo"} + loading_ctx = types.SimpleNamespace() + sentinel = MagicMock(spec=DiracCommandLineTool) + with patch.object( + _tool_mod, "DiracCommandLineTool", return_value=sentinel + ) as mock_cls: + result = dirac_make_tool(toolpath, loading_ctx) + mock_cls.assert_called_once_with(toolpath, loading_ctx) + assert result is sentinel + + def test_dirac_make_tool_delegates_workflow(self): + """dirac_make_tool should delegate non-CommandLineTool classes to default_make_tool.""" + toolpath = {"class": "Workflow", "steps": []} + loading_ctx = types.SimpleNamespace() + sentinel = MagicMock() + with patch.object( + _tool_mod, "default_make_tool", return_value=sentinel + ) as mock_fn: + result = dirac_make_tool(toolpath, loading_ctx) + mock_fn.assert_called_once_with(toolpath, loading_ctx) + assert result is sentinel + + def test_dirac_make_tool_delegates_expression_tool(self): + """dirac_make_tool delegates ExpressionTool to default_make_tool.""" + toolpath = {"class": "ExpressionTool"} + loading_ctx = types.SimpleNamespace() + sentinel = MagicMock() + with patch.object( + _tool_mod, "default_make_tool", return_value=sentinel + ) as mock_fn: + result = dirac_make_tool(toolpath, loading_ctx) + mock_fn.assert_called_once_with(toolpath, loading_ctx) + assert result is sentinel diff --git a/diracx-cli/tests/test_executor_integration.py b/diracx-cli/tests/test_executor_integration.py new file mode 100644 index 000000000..e3cfd9c15 --- /dev/null +++ b/diracx-cli/tests/test_executor_integration.py @@ -0,0 +1,253 @@ +"""Integration tests for the dirac-cwl-run subprocess. + +These tests run ``dirac-cwl-run`` as a real subprocess to prove the full +executor stack works end-to-end: mypyc patch → executor init → replica map +loading → LFN resolution → CWL execution → output files. + +cwltool is required for these tests. If it is not installed the entire module +is skipped. Individual tests are also skipped if ``dirac-cwl-run`` is not on +PATH (e.g. in a virtualenv without the diracx-cli package installed). +""" + +from __future__ import annotations + +import json +import subprocess +from pathlib import Path + +import pytest + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +_COPY_CWL = """\ +cwlVersion: v1.2 +class: CommandLineTool +baseCommand: [cp] + +inputs: + - id: input_file + type: File + inputBinding: + position: 1 + +outputs: + - id: output_file + type: File + outputBinding: + glob: output.txt + +arguments: + - valueFrom: output.txt + position: 2 +""" + + +def _run(args: list[str], cwd: Path, timeout: int = 120) -> subprocess.CompletedProcess: + return subprocess.run( + args, + capture_output=True, + text=True, + cwd=cwd, + timeout=timeout, + ) + + +# --------------------------------------------------------------------------- +# Tests +# --------------------------------------------------------------------------- + + +def test_basic_execution_with_replica_map(tmp_path): + """Run a CWL cp-tool that resolves an LFN via a replica_map.json. + + Proves: mypyc patch → executor init → replica map loading → LFN + resolution → CWL execution → output file produced. + """ + # 1. Create a local input file with known content + input_content = "hello from integration test\n" + local_input = tmp_path / "local_input.txt" + local_input.write_text(input_content) + + # 2. Write the CWL workflow + cwl_file = tmp_path / "task.cwl" + cwl_file.write_text(_COPY_CWL) + + # 3. Write the CWL inputs referencing an LFN + lfn = "/test/data/input.txt" + inputs_yaml = tmp_path / "inputs.yml" + inputs_yaml.write_text(f"input_file:\n class: File\n location: 'LFN:{lfn}'\n") + + # 4. Write the replica_map.json mapping the LFN to the local file + replica_map_data = { + lfn: { + "replicas": [ + {"url": local_input.as_uri(), "se": "local"}, + ], + "size_bytes": len(input_content.encode()), + } + } + replica_map_file = tmp_path / "replica_map.json" + replica_map_file.write_text(json.dumps(replica_map_data)) + + # 5. Create output directory + outdir = tmp_path / "output" + outdir.mkdir() + + # 6. Run dirac-cwl-run + result = _run( + [ + "dirac-cwl-run", + str(cwl_file), + str(inputs_yaml), + "--outdir", + str(outdir), + "--replica-map", + str(replica_map_file), + ], + cwd=tmp_path, + ) + + # Provide debug output on failure + if result.returncode != 0: + pytest.fail( + f"dirac-cwl-run failed with exit code {result.returncode}\n" + f"STDOUT:\n{result.stdout}\n" + f"STDERR:\n{result.stderr}" + ) + + # 7. Assert exit code 0 + assert result.returncode == 0, ( + f"Expected exit code 0, got {result.returncode}\nSTDERR: {result.stderr}" + ) + + # 8. Assert output file exists and content matches + output_file = outdir / "output.txt" + assert output_file.exists(), ( + f"Expected output file {output_file} to exist.\n" + f"outdir contents: {list(outdir.iterdir())}" + ) + assert output_file.read_text() == input_content + + +def test_execution_without_replica_map(tmp_path): + """Run a CWL cp-tool using a plain local file (no LFN, no replica map). + + Proves that baseline CWL execution works through the dirac-cwl-run entry + point even when no replica map is provided. + """ + # 1. Create a local input file + input_content = "baseline cwl execution test\n" + local_input = tmp_path / "local_input.txt" + local_input.write_text(input_content) + + # 2. Write the CWL workflow + cwl_file = tmp_path / "task.cwl" + cwl_file.write_text(_COPY_CWL) + + # 3. Write CWL inputs referencing the local file directly + inputs_yaml = tmp_path / "inputs.yml" + inputs_yaml.write_text( + f"input_file:\n class: File\n location: '{local_input.as_uri()}'\n" + ) + + # 4. Create output directory + outdir = tmp_path / "output" + outdir.mkdir() + + # 5. Run dirac-cwl-run (no --replica-map) + result = _run( + [ + "dirac-cwl-run", + str(cwl_file), + str(inputs_yaml), + "--outdir", + str(outdir), + ], + cwd=tmp_path, + ) + + if result.returncode != 0: + pytest.fail( + f"dirac-cwl-run failed with exit code {result.returncode}\n" + f"STDOUT:\n{result.stdout}\n" + f"STDERR:\n{result.stderr}" + ) + + assert result.returncode == 0 + + output_file = outdir / "output.txt" + assert output_file.exists(), ( + f"Expected output file {output_file} to exist.\n" + f"outdir contents: {list(outdir.iterdir())}" + ) + assert output_file.read_text() == input_content + + +def test_sb_reference_in_replica_map(tmp_path): + """Run a CWL cp-tool where the input is resolved via an SB: reference. + + The SB: key in the replica map is mapped to a local file. Proves that + sandbox references are handled correctly through the replica map. + """ + # 1. Create the real local file the SB: entry will point to + input_content = "sandbox file content for integration test\n" + local_file = tmp_path / "extracted_helper.txt" + local_file.write_text(input_content) + + # 2. Write the CWL workflow + cwl_file = tmp_path / "task.cwl" + cwl_file.write_text(_COPY_CWL) + + # 3. SB: key — use the full reference as it would appear in a job description + sb_key = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.txt" + + # 4. Write CWL inputs with SB: location + inputs_yaml = tmp_path / "inputs.yml" + inputs_yaml.write_text(f"input_file:\n class: File\n location: '{sb_key}'\n") + + # 5. Write replica_map.json with the SB: key + replica_map_data = { + sb_key: { + "replicas": [ + {"url": local_file.as_uri(), "se": "local"}, + ], + } + } + replica_map_file = tmp_path / "replica_map.json" + replica_map_file.write_text(json.dumps(replica_map_data)) + + # 6. Create output directory + outdir = tmp_path / "output" + outdir.mkdir() + + # 7. Run dirac-cwl-run + result = _run( + [ + "dirac-cwl-run", + str(cwl_file), + str(inputs_yaml), + "--outdir", + str(outdir), + "--replica-map", + str(replica_map_file), + ], + cwd=tmp_path, + ) + + if result.returncode != 0: + pytest.fail( + f"dirac-cwl-run failed with exit code {result.returncode}\n" + f"STDOUT:\n{result.stdout}\n" + f"STDERR:\n{result.stderr}" + ) + + assert result.returncode == 0 + + output_file = outdir / "output.txt" + assert output_file.exists(), ( + f"Expected output file {output_file} to exist.\n" + f"outdir contents: {list(outdir.iterdir())}" + ) + assert output_file.read_text() == input_content diff --git a/diracx-cli/tests/test_fs_access.py b/diracx-cli/tests/test_fs_access.py new file mode 100644 index 000000000..962c9ce9d --- /dev/null +++ b/diracx-cli/tests/test_fs_access.py @@ -0,0 +1,145 @@ +"""Tests for DiracReplicaMapFsAccess SB: path resolution.""" + +from __future__ import annotations + +from pathlib import Path + +import pytest + +from diracx.cli.executor.fs_access import DiracReplicaMapFsAccess +from diracx.core.models.replica_map import ReplicaMap + + +@pytest.fixture +def sandbox_file(tmp_path: Path) -> Path: + """Create a local file simulating an extracted sandbox file.""" + f = tmp_path / "helper.sh" + f.write_text("#!/bin/bash\necho hello") + return f + + +@pytest.fixture +def fs_access_with_sb(tmp_path: Path, sandbox_file: Path) -> DiracReplicaMapFsAccess: + """FsAccess with a sandbox entry in the replica map.""" + sb_key = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + replica_map = ReplicaMap( + root={ + sb_key: { + "replicas": [{"url": f"file://{sandbox_file}", "se": "local"}], + } + } + ) + return DiracReplicaMapFsAccess(str(tmp_path), replica_map=replica_map) + + +class TestSBResolution: + def test_resolve_path_sb(self, fs_access_with_sb, sandbox_file): + """SB: path should resolve to local file path via replica map.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + resolved, is_remote = fs_access_with_sb._resolve_path(sb_path) + assert resolved == str(sandbox_file) + assert is_remote is False + + def test_resolve_path_lfn_still_works(self, tmp_path): + """LFN: resolution should still work after rename.""" + lfn_file = tmp_path / "data.dst" + lfn_file.write_text("data") + replica_map = ReplicaMap( + root={ + "/lhcb/data/file.dst": { + "replicas": [{"url": f"file://{lfn_file}", "se": "CERN-DST"}], + } + } + ) + fs = DiracReplicaMapFsAccess(str(tmp_path), replica_map=replica_map) + resolved, is_remote = fs._resolve_path("LFN:/lhcb/data/file.dst") + assert resolved == str(lfn_file) + assert is_remote is False + + def test_abs_resolves_sb(self, fs_access_with_sb, sandbox_file): + """_abs should resolve SB: paths through replica map.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + result = fs_access_with_sb._abs(sb_path) + assert result == str(sandbox_file) + + def test_exists_sb(self, fs_access_with_sb): + """exists() should return True for SB: path with local file.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + assert fs_access_with_sb.exists(sb_path) is True + + def test_isfile_sb(self, fs_access_with_sb): + """isfile() should return True for SB: path.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + assert fs_access_with_sb.isfile(sb_path) is True + + def test_isdir_sb(self, fs_access_with_sb): + """isdir() should return False for SB: paths (always files).""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + assert fs_access_with_sb.isdir(sb_path) is False + + def test_open_sb(self, fs_access_with_sb): + """open() should work for SB: path resolved to local file.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + with fs_access_with_sb.open(sb_path, "r") as f: + content = f.read() + assert "echo hello" in content + + def test_size_sb(self, fs_access_with_sb, sandbox_file): + """size() should return file size for SB: path.""" + sb_path = "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#helper.sh" + assert fs_access_with_sb.size(sb_path) == sandbox_file.stat().st_size + + +@pytest.fixture +def fs_access_with_remote_lfn(tmp_path: Path) -> DiracReplicaMapFsAccess: + """FsAccess with an LFN that resolves to a remote (root://) URL.""" + replica_map = ReplicaMap( + root={ + "/lhcb/data/remote.dst": { + "replicas": [ + { + "url": "root://eoslhcb.cern.ch//eos/lhcb/data/remote.dst", + "se": "CERN-EOS", + } + ], + "size_bytes": 2048, + } + } + ) + return DiracReplicaMapFsAccess(str(tmp_path), replica_map=replica_map) + + +class TestLFNResolution: + def test_resolve_lfn_remote_url(self, fs_access_with_remote_lfn): + """LFN resolving to a root:// URL should be marked as remote.""" + resolved, is_remote = fs_access_with_remote_lfn._resolve_path( + "LFN:/lhcb/data/remote.dst" + ) + assert is_remote is True + assert "root://" in resolved + + def test_exists_remote_lfn_returns_true(self, fs_access_with_remote_lfn): + """exists() should return True for a remote LFN without touching the filesystem.""" + assert fs_access_with_remote_lfn.exists("LFN:/lhcb/data/remote.dst") is True + + def test_size_from_replica_map(self, fs_access_with_remote_lfn): + """size() should return size_bytes from the replica map entry.""" + assert fs_access_with_remote_lfn.size("LFN:/lhcb/data/remote.dst") == 2048 + + def test_lfn_not_in_map_returns_cleaned_path(self, tmp_path: Path): + """Missing LFN should resolve to path without the LFN: prefix.""" + fs = DiracReplicaMapFsAccess(str(tmp_path), replica_map=ReplicaMap(root={})) + resolved, is_remote = fs._resolve_path("LFN:/lhcb/data/missing.dst") + assert resolved == "/lhcb/data/missing.dst" + assert is_remote is False + + def test_glob_remote_lfn_returns_original(self, fs_access_with_remote_lfn): + """glob() should return the original LFN: path for remote LFNs.""" + lfn_path = "LFN:/lhcb/data/remote.dst" + result = fs_access_with_remote_lfn.glob(lfn_path) + assert result == [lfn_path] + + def test_open_remote_lfn_raises(self, fs_access_with_remote_lfn): + """open() should raise ValueError for a remote LFN.""" + with pytest.raises(ValueError, match="Cannot open remote file"): + fs_access_with_remote_lfn.open("LFN:/lhcb/data/remote.dst", "r") diff --git a/diracx-cli/tests/test_no_cwltool_import.py b/diracx-cli/tests/test_no_cwltool_import.py new file mode 100644 index 000000000..0e91e6eae --- /dev/null +++ b/diracx-cli/tests/test_no_cwltool_import.py @@ -0,0 +1,45 @@ +"""Ensure the mypyc compatibility patch is installed before cwltool imports. + +cwltool is mypyc-compiled. The executor's __init__.py must install the +_PurePythonFinder meta path hook BEFORE any cwltool import, so that +cwltool.command_line_tool loads from .py instead of .so. This enables +subclassing CommandLineTool (DiracCommandLineTool). + +If this test fails, the CWL executor will break at runtime due to +mypyc class subclassing errors. +""" + +from __future__ import annotations + +import subprocess +import sys + + +def test_mypyc_patch_installed_before_cwltool(): + """Importing diracx.cli.executor must install the mypyc patch before cwltool loads. + + Runs in a subprocess to guarantee a clean import state. + """ + test_script = ( + "import sys\n" + "import diracx.cli.executor\n" + "# The mypyc patch must be active\n" + "finder_names = [type(f).__name__ for f in sys.meta_path]\n" + "assert '_PurePythonFinder' in finder_names, (\n" + " f'_PurePythonFinder not in sys.meta_path: {finder_names}'\n" + ")\n" + "# cwltool must be loaded (the executor imports it)\n" + "cwl_mods = [m for m in sys.modules if m.startswith('cwltool')]\n" + "assert cwl_mods, 'cwltool was not loaded by diracx.cli.executor'\n" + "print('OK')\n" + ) + result = subprocess.run( + [sys.executable, "-c", test_script], + capture_output=True, + text=True, + ) + assert result.returncode == 0, ( + f"mypyc compatibility patch not properly installed.\n" + f"stdout: {result.stdout}\n" + f"stderr: {result.stderr}" + ) diff --git a/diracx-cli/tests/test_submission_confirm.py b/diracx-cli/tests/test_submission_confirm.py new file mode 100644 index 000000000..86691d79a --- /dev/null +++ b/diracx-cli/tests/test_submission_confirm.py @@ -0,0 +1,64 @@ +# diracx-cli/tests/test_submission_confirm.py +from __future__ import annotations + +from diracx.cli._submission.confirm import ( + build_summary, + needs_confirmation, +) + + +class TestNeedsConfirmation: + def test_under_100_jobs(self): + assert needs_confirmation(num_jobs=50) is False + + def test_exactly_100_jobs(self): + assert needs_confirmation(num_jobs=100) is False + + def test_over_100_jobs(self): + assert needs_confirmation(num_jobs=101) is True + + def test_skip_with_yes(self): + assert needs_confirmation(num_jobs=1000, yes=True) is False + + +class TestBuildSummary: + def test_basic_summary(self): + summary = build_summary( + workflow_name="hello-world", + workflow_path="workflow.cwl", + num_jobs=1000, + source="--range seed=0:1000", + num_unique_sandboxes=1, + total_sandbox_bytes=45 * 1024 * 1024, + num_lfn_inputs=0, + ) + assert "workflow.cwl" in summary + assert "hello-world" in summary + assert "1,000" in summary or "1000" in summary + assert "--range seed=0:1000" in summary + + def test_with_lfn_inputs(self): + summary = build_summary( + workflow_name="lfn-job", + workflow_path="workflow.cwl", + num_jobs=500, + source="--range seed=0:500", + num_unique_sandboxes=0, + total_sandbox_bytes=0, + num_lfn_inputs=1000, + ) + assert "1,000" in summary or "1000" in summary + assert "LFN" in summary + + def test_no_sandboxes_no_lfns(self): + summary = build_summary( + workflow_name="simple", + workflow_path="workflow.cwl", + num_jobs=200, + source="--range seed=0:200", + num_unique_sandboxes=0, + total_sandbox_bytes=0, + num_lfn_inputs=0, + ) + assert "Sandbox" not in summary + assert "LFN" not in summary diff --git a/diracx-cli/tests/test_submission_inputs.py b/diracx-cli/tests/test_submission_inputs.py new file mode 100644 index 000000000..338291f04 --- /dev/null +++ b/diracx-cli/tests/test_submission_inputs.py @@ -0,0 +1,175 @@ +"""Tests for diracx.cli._submission.inputs module.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest + +from diracx.cli._submission.inputs import parse_cli_args, parse_input_files, parse_range + +# --------------------------------------------------------------------------- +# parse_input_files +# --------------------------------------------------------------------------- + + +def test_parse_input_files_single_yaml(tmp_path: Path) -> None: + f = tmp_path / "job.yaml" + f.write_text("foo: bar\nbaz: 42\n") + result = parse_input_files([f]) + assert result == [{"foo": "bar", "baz": 42}] + + +def test_parse_input_files_multi_doc_yaml(tmp_path: Path) -> None: + f = tmp_path / "jobs.yaml" + f.write_text("foo: 1\n---\nfoo: 2\n---\nfoo: 3\n") + result = parse_input_files([f]) + assert result == [{"foo": 1}, {"foo": 2}, {"foo": 3}] + + +def test_parse_input_files_multiple_files(tmp_path: Path) -> None: + f1 = tmp_path / "a.yaml" + f1.write_text("x: 1\n") + f2 = tmp_path / "b.yaml" + f2.write_text("x: 2\n---\nx: 3\n") + result = parse_input_files([f1, f2]) + assert result == [{"x": 1}, {"x": 2}, {"x": 3}] + + +def test_parse_input_files_json(tmp_path: Path) -> None: + f = tmp_path / "job.json" + f.write_text(json.dumps({"key": "value", "num": 7})) + result = parse_input_files([f]) + assert result == [{"key": "value", "num": 7}] + + +def test_parse_input_files_empty_list() -> None: + assert parse_input_files([]) == [] + + +def test_parse_input_files_nonexistent_raises(tmp_path: Path) -> None: + missing = tmp_path / "does_not_exist.yaml" + with pytest.raises(FileNotFoundError): + parse_input_files([missing]) + + +# --------------------------------------------------------------------------- +# parse_range +# --------------------------------------------------------------------------- + + +def test_parse_range_end_only() -> None: + param, start, end, step = parse_range("N=10") + assert param == "N" + assert start == 0 + assert end == 10 + assert step == 1 + + +def test_parse_range_start_end() -> None: + param, start, end, step = parse_range("idx=5:20") + assert param == "idx" + assert start == 5 + assert end == 20 + assert step == 1 + + +def test_parse_range_start_end_step() -> None: + param, start, end, step = parse_range("n=0:100:5") + assert param == "n" + assert start == 0 + assert end == 100 + assert step == 5 + + +def test_parse_range_no_equals_raises() -> None: + with pytest.raises(ValueError, match="Invalid range format"): + parse_range("10") + + +def test_parse_range_bad_numbers_raises() -> None: + with pytest.raises(ValueError): + parse_range("n=abc") + + +def test_parse_range_negative_step() -> None: + param, start, end, step = parse_range("n=10:0:-1") + assert param == "n" + assert start == 10 + assert end == 0 + assert step == -1 + + +# --------------------------------------------------------------------------- +# parse_cli_args +# --------------------------------------------------------------------------- + +CWL_STRING_INPUT = [{"id": "message", "type": "string"}] +CWL_INT_INPUT = [{"id": "count", "type": "int"}] +CWL_FLOAT_INPUT = [{"id": "threshold", "type": "float"}] +CWL_BOOL_INPUT = [{"id": "verbose", "type": "boolean"}] +CWL_FILE_INPUT = [{"id": "infile", "type": "File"}] +CWL_FILE_ARRAY_INPUT = [{"id": "infiles", "type": "File[]"}] +CWL_MULTI_INPUT = [ + {"id": "name", "type": "string"}, + {"id": "count", "type": "int"}, +] + + +def test_parse_cli_args_string() -> None: + result = parse_cli_args(CWL_STRING_INPUT, ["--message", "hello"]) + assert result == {"message": "hello"} + + +def test_parse_cli_args_int() -> None: + result = parse_cli_args(CWL_INT_INPUT, ["--count", "42"]) + assert result == {"count": 42} + + +def test_parse_cli_args_float() -> None: + result = parse_cli_args(CWL_FLOAT_INPUT, ["--threshold", "0.75"]) + assert result["threshold"] == pytest.approx(0.75) + + +def test_parse_cli_args_boolean_flag() -> None: + result = parse_cli_args(CWL_BOOL_INPUT, ["--verbose"]) + assert result == {"verbose": True} + + +def test_parse_cli_args_boolean_absent() -> None: + result = parse_cli_args(CWL_BOOL_INPUT, []) + assert result == {} + + +def test_parse_cli_args_file() -> None: + result = parse_cli_args(CWL_FILE_INPUT, ["--infile", "/data/input.txt"]) + assert result == {"infile": {"class": "File", "path": "/data/input.txt"}} + + +def test_parse_cli_args_file_array() -> None: + result = parse_cli_args( + CWL_FILE_ARRAY_INPUT, + ["--infiles", "/a.txt", "--infiles", "/b.txt"], + ) + assert result == { + "infiles": [ + {"class": "File", "path": "/a.txt"}, + {"class": "File", "path": "/b.txt"}, + ] + } + + +def test_parse_cli_args_multiple_inputs() -> None: + result = parse_cli_args(CWL_MULTI_INPUT, ["--name", "test", "--count", "3"]) + assert result == {"name": "test", "count": 3} + + +def test_parse_cli_args_unknown_arg_raises() -> None: + with pytest.raises(SystemExit): + parse_cli_args(CWL_STRING_INPUT, ["--unknown", "value"]) + + +def test_parse_cli_args_empty_args_returns_empty() -> None: + result = parse_cli_args(CWL_STRING_INPUT, []) + assert result == {} diff --git a/diracx-cli/tests/test_submission_integration.py b/diracx-cli/tests/test_submission_integration.py new file mode 100644 index 000000000..73fd99d75 --- /dev/null +++ b/diracx-cli/tests/test_submission_integration.py @@ -0,0 +1,200 @@ +from __future__ import annotations + +from pathlib import Path +from unittest.mock import AsyncMock, MagicMock, patch + +import yaml + +from diracx.cli._submission.pipeline import submit_cwl + + +@staticmethod +def _cwl_workflow(tmp_path: Path) -> Path: + """CWL with File input + string input.""" + cwl = { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "label": "integration-test", + "hints": [ + { + "class": "dirac:Job", + "schema_version": "1.0", + "type": "User", + "input_sandbox": [{"source": "script"}], + } + ], + "inputs": [ + {"id": "script", "type": "File"}, + {"id": "message", "type": "string"}, + ], + "outputs": [], + "baseCommand": ["python"], + "$namespaces": {"dirac": "https://diracgrid.org/cwl#"}, + } + f = tmp_path / "workflow.cwl" + f.write_text(yaml.dump(cwl)) + return f + + +class TestIntegration: + async def test_submit_with_local_file_sandbox(self, tmp_path): + """Submit a job with a local File input → should upload sandbox and rewrite.""" + workflow = _cwl_workflow(tmp_path) + local_script = tmp_path / "run.py" + local_script.write_text("print('hello')") + + inputs_file = tmp_path / "inputs.yaml" + inputs_file.write_text( + yaml.dump( + { + "script": {"class": "File", "path": str(local_script)}, + "message": "integration test", + } + ) + ) + + mock_client = AsyncMock() + mock_client.jobs.submit_cwl_jobs = AsyncMock( + return_value=[ + MagicMock( + job_id=2001, status="Submitting", minor_status="Initializing Job" + ) + ] + ) + + fake_sb_ref = "SB:SandboxSE|/S3/bucket/sha256:abc123.tar.zst" + + with ( + patch( + "diracx.cli._submission.pipeline.AsyncDiracClient" + ) as mock_client_cls, + patch( + "diracx.api.jobs.create_sandbox", + new_callable=AsyncMock, + return_value=fake_sb_ref, + ), + ): + mock_client_cls.return_value.__aenter__ = AsyncMock( + return_value=mock_client + ) + mock_client_cls.return_value.__aexit__ = AsyncMock(return_value=False) + + results = await submit_cwl( + workflow=workflow, + input_files=[inputs_file], + cli_args=[], + range_spec=None, + yes=True, + ) + + assert len(results) == 1 + call_body = mock_client.jobs.submit_cwl_jobs.call_args[0][0] + submitted_inputs = call_body.inputs[0] + assert submitted_inputs["script"]["path"] == f"{fake_sb_ref}#run.py" + assert submitted_inputs["message"] == "integration test" + + async def test_submit_with_lfn_no_sandbox(self, tmp_path): + """Submit with LFN input → no sandbox upload.""" + workflow = _cwl_workflow(tmp_path) + + inputs_file = tmp_path / "inputs.yaml" + inputs_file.write_text( + yaml.dump( + { + "script": {"class": "File", "path": "LFN:/lhcb/scripts/run.py"}, + "message": "lfn test", + } + ) + ) + + mock_client = AsyncMock() + mock_client.jobs.submit_cwl_jobs = AsyncMock( + return_value=[ + MagicMock( + job_id=2002, status="Submitting", minor_status="Initializing Job" + ) + ] + ) + + with patch( + "diracx.cli._submission.pipeline.AsyncDiracClient" + ) as mock_client_cls: + mock_client_cls.return_value.__aenter__ = AsyncMock( + return_value=mock_client + ) + mock_client_cls.return_value.__aexit__ = AsyncMock(return_value=False) + + await submit_cwl( + workflow=workflow, + input_files=[inputs_file], + cli_args=[], + range_spec=None, + yes=True, + ) + + call_body = mock_client.jobs.submit_cwl_jobs.call_args[0][0] + submitted_inputs = call_body.inputs[0] + assert submitted_inputs["script"]["path"] == "LFN:/lhcb/scripts/run.py" + + async def test_multi_doc_yaml_parametric(self, tmp_path): + """Multi-doc YAML creates multiple jobs sharing one sandbox.""" + workflow = _cwl_workflow(tmp_path) + local_script = tmp_path / "run.py" + local_script.write_text("print('hello')") + + sweep_file = tmp_path / "sweep.yaml" + doc1 = { + "script": {"class": "File", "path": str(local_script)}, + "message": "job 1", + } + doc2 = { + "script": {"class": "File", "path": str(local_script)}, + "message": "job 2", + } + sweep_file.write_text(yaml.dump(doc1) + "---\n" + yaml.dump(doc2)) + + mock_client = AsyncMock() + mock_client.jobs.submit_cwl_jobs = AsyncMock( + return_value=[ + MagicMock( + job_id=3001, status="Submitting", minor_status="Initializing Job" + ), + MagicMock( + job_id=3002, status="Submitting", minor_status="Initializing Job" + ), + ] + ) + + fake_sb_ref = "SB:SandboxSE|/S3/bucket/sha256:shared.tar.zst" + + with ( + patch( + "diracx.cli._submission.pipeline.AsyncDiracClient" + ) as mock_client_cls, + patch( + "diracx.api.jobs.create_sandbox", + new_callable=AsyncMock, + return_value=fake_sb_ref, + ) as mock_create_sb, + ): + mock_client_cls.return_value.__aenter__ = AsyncMock( + return_value=mock_client + ) + mock_client_cls.return_value.__aexit__ = AsyncMock(return_value=False) + + await submit_cwl( + workflow=workflow, + input_files=[sweep_file], + cli_args=[], + range_spec=None, + yes=True, + ) + + # Sandbox uploaded once (both jobs share same local file) + mock_create_sb.assert_called_once() + + # Two jobs submitted + call_body = mock_client.jobs.submit_cwl_jobs.call_args[0][0] + assert len(call_body.inputs) == 2 + assert call_body.inputs[0]["message"] == "job 1" + assert call_body.inputs[1]["message"] == "job 2" diff --git a/diracx-cli/tests/test_submission_pipeline.py b/diracx-cli/tests/test_submission_pipeline.py new file mode 100644 index 000000000..097a7d036 --- /dev/null +++ b/diracx-cli/tests/test_submission_pipeline.py @@ -0,0 +1,107 @@ +from __future__ import annotations + +from pathlib import Path +from unittest.mock import AsyncMock, MagicMock, patch + +import pytest +import yaml + +from diracx.cli._submission.pipeline import submit_cwl + + +@pytest.fixture +def cwl_workflow(tmp_path: Path) -> Path: + """Create a minimal CWL workflow file.""" + cwl = { + "cwlVersion": "v1.2", + "class": "CommandLineTool", + "label": "test-tool", + "hints": [ + { + "class": "dirac:Job", + "schema_version": "1.0", + "type": "User", + } + ], + "inputs": [ + {"id": "message", "type": "string"}, + ], + "outputs": [], + "baseCommand": ["echo"], + "$namespaces": {"dirac": "https://diracgrid.org/cwl#"}, + } + f = tmp_path / "workflow.cwl" + f.write_text(yaml.dump(cwl)) + return f + + +@pytest.fixture +def inputs_file(tmp_path: Path) -> Path: + f = tmp_path / "inputs.yaml" + f.write_text("message: hello\n") + return f + + +@pytest.fixture +def mock_client(): + """Mock AsyncDiracClient for submission.""" + client = AsyncMock() + client.jobs.submit_cwl_jobs = AsyncMock( + return_value=[ + MagicMock(job_id=1001, status="Submitting", minor_status="Initializing Job") + ] + ) + return client + + +class TestSubmitCWL: + @pytest.mark.asyncio + async def test_single_job_submission(self, cwl_workflow, inputs_file, mock_client): + with patch( + "diracx.cli._submission.pipeline.AsyncDiracClient" + ) as mock_client_cls: + mock_client_cls.return_value.__aenter__ = AsyncMock( + return_value=mock_client + ) + mock_client_cls.return_value.__aexit__ = AsyncMock(return_value=False) + + result = await submit_cwl( + workflow=cwl_workflow, + input_files=[inputs_file], + cli_args=[], + range_spec=None, + yes=True, + ) + + assert len(result) == 1 + assert result[0].job_id == 1001 + mock_client.jobs.submit_cwl_jobs.assert_called_once() + call_body = mock_client.jobs.submit_cwl_jobs.call_args[0][0] + assert "cwlVersion" in call_body.workflow + assert call_body.inputs == [{"message": "hello"}] + + @pytest.mark.asyncio + async def test_no_inputs_submission(self, cwl_workflow, mock_client): + with patch( + "diracx.cli._submission.pipeline.AsyncDiracClient" + ) as mock_client_cls: + mock_client_cls.return_value.__aenter__ = AsyncMock( + return_value=mock_client + ) + mock_client_cls.return_value.__aexit__ = AsyncMock(return_value=False) + + await submit_cwl( + workflow=cwl_workflow, + input_files=[], + cli_args=[], + range_spec=None, + yes=True, + ) + + call_body = mock_client.jobs.submit_cwl_jobs.call_args[0][0] + assert call_body.inputs == [] + + @pytest.mark.skip(reason="Range fields added in Task 8") + @pytest.mark.asyncio + async def test_range_submission(self, cwl_workflow, mock_client): + pass diff --git a/diracx-cli/tests/test_submission_sandbox.py b/diracx-cli/tests/test_submission_sandbox.py new file mode 100644 index 000000000..33e942192 --- /dev/null +++ b/diracx-cli/tests/test_submission_sandbox.py @@ -0,0 +1,215 @@ +"""Tests for diracx.cli._submission.sandbox module.""" + +from __future__ import annotations + +from pathlib import Path + +from diracx.cli._submission.sandbox import ( + group_jobs_by_sandbox, + rewrite_sandbox_refs, + scan_file_references, +) + +# --------------------------------------------------------------------------- +# scan_file_references +# --------------------------------------------------------------------------- + + +def test_scan_single_local_file() -> None: + inputs = {"infile": {"class": "File", "path": "/data/input.txt"}} + local_files, lfns = scan_file_references(inputs) + assert local_files == [Path("/data/input.txt")] + assert lfns == [] + + +def test_scan_lfn_passthrough() -> None: + inputs = {"infile": {"class": "File", "path": "LFN:/grid/path/file.root"}} + local_files, lfns = scan_file_references(inputs) + assert local_files == [] + assert lfns == ["LFN:/grid/path/file.root"] + + +def test_scan_sb_ignored() -> None: + inputs = {"infile": {"class": "File", "path": "SB:some-pfn/file.txt"}} + local_files, lfns = scan_file_references(inputs) + assert local_files == [] + assert lfns == [] + + +def test_scan_file_array_mixed_local_and_lfn() -> None: + inputs = { + "files": [ + {"class": "File", "path": "/local/a.txt"}, + {"class": "File", "path": "LFN:/grid/b.root"}, + {"class": "File", "path": "/local/c.txt"}, + ] + } + local_files, lfns = scan_file_references(inputs) + assert sorted(local_files) == [Path("/local/a.txt"), Path("/local/c.txt")] + assert lfns == ["LFN:/grid/b.root"] + + +def test_scan_no_files_scalars_only() -> None: + inputs = {"count": 42, "name": "hello", "flag": True} + local_files, lfns = scan_file_references(inputs) + assert local_files == [] + assert lfns == [] + + +def test_scan_nested_mixed() -> None: + inputs = { + "scalar": 99, + "single": {"class": "File", "path": "/local/file.txt"}, + "multi": [ + {"class": "File", "path": "LFN:/grid/remote.root"}, + ], + } + local_files, lfns = scan_file_references(inputs) + assert local_files == [Path("/local/file.txt")] + assert lfns == ["LFN:/grid/remote.root"] + + +# --------------------------------------------------------------------------- +# group_jobs_by_sandbox +# --------------------------------------------------------------------------- + + +def test_group_all_same_files() -> None: + jobs = [ + {"f": {"class": "File", "path": "/data/a.txt"}}, + {"f": {"class": "File", "path": "/data/a.txt"}}, + {"f": {"class": "File", "path": "/data/a.txt"}}, + ] + groups = group_jobs_by_sandbox(jobs) + assert len(groups) == 1 + file_set, indices = groups[0] + assert file_set == frozenset([Path("/data/a.txt")]) + assert sorted(indices) == [0, 1, 2] + + +def test_group_different_files_per_job() -> None: + jobs = [ + {"f": {"class": "File", "path": "/data/a.txt"}}, + {"f": {"class": "File", "path": "/data/b.txt"}}, + {"f": {"class": "File", "path": "/data/c.txt"}}, + ] + groups = group_jobs_by_sandbox(jobs) + assert len(groups) == 3 + all_indices = sorted(idx for _, indices in groups for idx in indices) + assert all_indices == [0, 1, 2] + + +def test_group_no_local_files_returns_empty() -> None: + jobs = [ + {"f": {"class": "File", "path": "LFN:/grid/a.root"}}, + {"count": 5}, + ] + groups = group_jobs_by_sandbox(jobs) + assert groups == [] + + +def test_group_mixed_local_and_lfn_lfns_dont_affect_grouping() -> None: + # Both jobs have the same local file but different LFNs — should be 1 group. + jobs = [ + { + "local": {"class": "File", "path": "/data/shared.txt"}, + "remote": {"class": "File", "path": "LFN:/grid/a.root"}, + }, + { + "local": {"class": "File", "path": "/data/shared.txt"}, + "remote": {"class": "File", "path": "LFN:/grid/b.root"}, + }, + ] + groups = group_jobs_by_sandbox(jobs) + assert len(groups) == 1 + file_set, indices = groups[0] + assert file_set == frozenset([Path("/data/shared.txt")]) + assert sorted(indices) == [0, 1] + + +# --------------------------------------------------------------------------- +# rewrite_sandbox_refs +# --------------------------------------------------------------------------- + + +def test_rewrite_single_file() -> None: + inputs = {"infile": {"class": "File", "path": "/local/file.txt"}} + sb_ref_map = { + Path("/local/file.txt"): "SB:SandboxSE|/S3/store/sha256:abc123.tar.zst" + } + result = rewrite_sandbox_refs(inputs, sb_ref_map) + assert result == { + "infile": { + "class": "File", + "path": "SB:SandboxSE|/S3/store/sha256:abc123.tar.zst#file.txt", + } + } + + +def test_rewrite_lfn_not_rewritten() -> None: + inputs = {"infile": {"class": "File", "path": "LFN:/grid/file.root"}} + sb_ref_map: dict[Path, str] = {} + result = rewrite_sandbox_refs(inputs, sb_ref_map) + assert result == {"infile": {"class": "File", "path": "LFN:/grid/file.root"}} + + +def test_rewrite_array_mixed() -> None: + inputs = { + "files": [ + {"class": "File", "path": "/local/a.txt"}, + {"class": "File", "path": "LFN:/grid/b.root"}, + {"class": "File", "path": "/local/c.txt"}, + ] + } + sb_ref_map = { + Path("/local/a.txt"): "SB:SandboxSE|/S3/store/sha256:aaa.tar.zst", + Path("/local/c.txt"): "SB:SandboxSE|/S3/store/sha256:ccc.tar.zst", + } + result = rewrite_sandbox_refs(inputs, sb_ref_map) + assert result == { + "files": [ + { + "class": "File", + "path": "SB:SandboxSE|/S3/store/sha256:aaa.tar.zst#a.txt", + }, + {"class": "File", "path": "LFN:/grid/b.root"}, + { + "class": "File", + "path": "SB:SandboxSE|/S3/store/sha256:ccc.tar.zst#c.txt", + }, + ] + } + + +def test_rewrite_sb_not_rewritten() -> None: + inputs = {"infile": {"class": "File", "path": "SB:some-pfn/file.txt"}} + sb_ref_map: dict[Path, str] = {} + result = rewrite_sandbox_refs(inputs, sb_ref_map) + assert result == {"infile": {"class": "File", "path": "SB:some-pfn/file.txt"}} + + +def test_rewrite_non_file_values_preserved() -> None: + inputs = { + "count": 42, + "name": "hello", + "infile": {"class": "File", "path": "/local/file.txt"}, + } + sb_ref_map = {Path("/local/file.txt"): "SB:SandboxSE|/S3/store/sha256:abc.tar.zst"} + result = rewrite_sandbox_refs(inputs, sb_ref_map) + assert result["count"] == 42 + assert result["name"] == "hello" + assert result["infile"] == { + "class": "File", + "path": "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#file.txt", + } + + +def test_rewrite_does_not_mutate_input() -> None: + original = {"infile": {"class": "File", "path": "/local/file.txt"}} + sb_ref_map = {Path("/local/file.txt"): "SB:SandboxSE|/S3/store/sha256:abc.tar.zst"} + result = rewrite_sandbox_refs(original, sb_ref_map) + # Original must be unchanged + assert original["infile"]["path"] == "/local/file.txt" + assert ( + result["infile"]["path"] == "SB:SandboxSE|/S3/store/sha256:abc.tar.zst#file.txt" + ) diff --git a/diracx-cli/tests/test_submit_simple.py b/diracx-cli/tests/test_submit_simple.py new file mode 100644 index 000000000..ae33cf52d --- /dev/null +++ b/diracx-cli/tests/test_submit_simple.py @@ -0,0 +1,130 @@ +from __future__ import annotations + +from pathlib import Path +from unittest.mock import AsyncMock, MagicMock, patch + +from typer.testing import CliRunner + +from diracx.cli._submission.simple import detect_sandbox_files, generate_cwl +from diracx.cli.job import app as job_app + +runner = CliRunner() + + +class TestDetectSandboxFiles: + def test_existing_relative_file(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + (tmp_path / "my_script.py").write_text("print('hello')") + result = detect_sandbox_files("python my_script.py") + assert Path("my_script.py") in result + + def test_ignores_nonexistent(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + result = detect_sandbox_files("python nonexistent.py") + assert result == [] + + def test_ignores_absolute_paths(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + abs_file = tmp_path / "script.py" + abs_file.write_text("print('hello')") + result = detect_sandbox_files(f"python {abs_file}") + assert result == [] + + def test_ignores_directories(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + (tmp_path / "mydir").mkdir() + result = detect_sandbox_files("ls mydir") + assert result == [] + + def test_ignores_symlinks(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + real = tmp_path / "real.py" + real.write_text("print('hello')") + link = tmp_path / "link.py" + link.symlink_to(real) + result = detect_sandbox_files("python link.py") + assert result == [] + + def test_ignores_commands(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + result = detect_sandbox_files("echo hello world") + assert result == [] + + def test_dedup_with_explicit(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + (tmp_path / "script.py").write_text("print('hello')") + auto = detect_sandbox_files("python script.py") + explicit = [Path("script.py")] + combined = list(set(auto + explicit)) + assert len(combined) == 1 + + +class TestGenerateCWL: + def test_basic_generation(self): + cwl = generate_cwl( + command="python my_script.py", + sandbox_files=[Path("my_script.py")], + ) + assert cwl["cwlVersion"] == "v1.2" + assert cwl["class"] == "CommandLineTool" + assert cwl["baseCommand"] == ["bash", "-c", "python my_script.py"] + assert "dirac:Job" in str(cwl["hints"]) + + def test_no_sandbox(self): + cwl = generate_cwl(command="echo hello", sandbox_files=[]) + assert cwl["baseCommand"] == ["bash", "-c", "echo hello"] + + def test_captures_stdout_stderr(self): + """Generated CWL should capture tool stdout/stderr to log files.""" + cwl = generate_cwl(command="echo hello", sandbox_files=[]) + assert cwl["stdout"] == "stdout.log" + assert cwl["stderr"] == "stderr.log" + output_ids = {o["id"] for o in cwl["outputs"]} + assert "stdout_log" in output_ids + assert "stderr_log" in output_ids + + def test_label_derived_from_command(self): + cwl = generate_cwl(command="python my_script.py", sandbox_files=[]) + assert "my_script" in cwl.get("label", "") or "python" in cwl.get("label", "") + + +class TestSubmitCommand: + def test_basic_command(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + (tmp_path / "script.py").write_text("print('hello')") + + with patch( + "diracx.cli.job.submit.cmd.submit_cwl", new_callable=AsyncMock + ) as mock_submit: + mock_submit.return_value = [MagicMock(job_id=1001, status="Submitting")] + result = runner.invoke( + job_app, + ["submit", "cmd", "python script.py", "-y"], + ) + + assert result.exit_code == 0, result.output + assert "1001" in result.output + call_kwargs = mock_submit.call_args[1] + assert call_kwargs["workflow"].suffix == ".cwl" + + def test_explicit_sandbox(self, tmp_path: Path, monkeypatch): + monkeypatch.chdir(tmp_path) + (tmp_path / "config.json").write_text("{}") + + with patch( + "diracx.cli.job.submit.cmd.submit_cwl", new_callable=AsyncMock + ) as mock_submit: + mock_submit.return_value = [MagicMock(job_id=1001, status="Submitting")] + result = runner.invoke( + job_app, + [ + "submit", + "cmd", + "echo hello", + "--sandbox", + str(tmp_path / "config.json"), + "-y", + ], + ) + + assert result.exit_code == 0, result.output diff --git a/diracx-client/src/diracx/client/_generated/aio/operations/_operations.py b/diracx-client/src/diracx/client/_generated/aio/operations/_operations.py index 8aee57b46..7f0f6025a 100644 --- a/diracx-client/src/diracx/client/_generated/aio/operations/_operations.py +++ b/diracx-client/src/diracx/client/_generated/aio/operations/_operations.py @@ -42,11 +42,13 @@ build_jobs_get_job_sandbox_request, build_jobs_get_job_sandboxes_request, build_jobs_get_sandbox_file_request, + build_jobs_get_workflow_request, build_jobs_initiate_sandbox_upload_request, build_jobs_patch_metadata_request, build_jobs_reschedule_jobs_request, build_jobs_search_request, build_jobs_set_job_statuses_request, + build_jobs_submit_cwl_jobs_request, build_jobs_submit_jdl_jobs_request, build_jobs_summary_request, build_jobs_unassign_bulk_jobs_sandboxes_request, @@ -2319,3 +2321,164 @@ async def submit_jdl_jobs(self, body: Union[list[str], IO[bytes]], **kwargs: Any return cls(pipeline_response, deserialized, {}) # type: ignore return deserialized # type: ignore + + @overload + async def submit_cwl_jobs( + self, body: _models.CWLJobSubmission, *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: ~_generated.models.CWLJobSubmission + :keyword content_type: Body Parameter content-type. Content type parameter for JSON body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @overload + async def submit_cwl_jobs( + self, body: IO[bytes], *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: IO[bytes] + :keyword content_type: Body Parameter content-type. Content type parameter for binary body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @distributed_trace_async + async def submit_cwl_jobs( + self, body: Union[_models.CWLJobSubmission, IO[bytes]], **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Is either a CWLJobSubmission type or a IO[bytes] type. Required. + :type body: ~_generated.models.CWLJobSubmission or IO[bytes] + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + _params = kwargs.pop("params", {}) or {} + + content_type: Optional[str] = kwargs.pop("content_type", _headers.pop("Content-Type", None)) + cls: ClsType[list[_models.InsertedJob]] = kwargs.pop("cls", None) + + content_type = content_type or "application/json" + _json = None + _content = None + if isinstance(body, (IOBase, bytes)): + _content = body + else: + _json = self._serialize.body(body, "CWLJobSubmission") + + _request = build_jobs_submit_cwl_jobs_request( + content_type=content_type, + json=_json, + content=_content, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = await self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("[InsertedJob]", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore + + @distributed_trace_async + async def get_workflow(self, workflow_id: str, **kwargs: Any) -> dict[str, str]: + """Get Workflow. + + Retrieve a CWL workflow definition by its content-addressed ID. + + :param workflow_id: Required. + :type workflow_id: str + :return: dict mapping str to str + :rtype: dict[str, str] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = kwargs.pop("headers", {}) or {} + _params = kwargs.pop("params", {}) or {} + + cls: ClsType[dict[str, str]] = kwargs.pop("cls", None) + + _request = build_jobs_get_workflow_request( + workflow_id=workflow_id, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = await self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("{str}", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore diff --git a/diracx-client/src/diracx/client/_generated/models/__init__.py b/diracx-client/src/diracx/client/_generated/models/__init__.py index 14b5195d4..4457a9e9f 100644 --- a/diracx-client/src/diracx/client/_generated/models/__init__.py +++ b/diracx-client/src/diracx/client/_generated/models/__init__.py @@ -16,6 +16,7 @@ BodyAuthRevokeRefreshTokenByRefreshToken, BodyJobsRescheduleJobs, BodyJobsUnassignBulkJobsSandboxes, + CWLJobSubmission, GroupInfo, HTTPValidationError, HeartbeatData, @@ -63,6 +64,7 @@ "BodyAuthRevokeRefreshTokenByRefreshToken", "BodyJobsRescheduleJobs", "BodyJobsUnassignBulkJobsSandboxes", + "CWLJobSubmission", "GroupInfo", "HTTPValidationError", "HeartbeatData", diff --git a/diracx-client/src/diracx/client/_generated/models/_models.py b/diracx-client/src/diracx/client/_generated/models/_models.py index 888ec3b8a..f0fa03b7c 100644 --- a/diracx-client/src/diracx/client/_generated/models/_models.py +++ b/diracx-client/src/diracx/client/_generated/models/_models.py @@ -184,6 +184,79 @@ def __init__(self, *, job_ids: list[int], **kwargs: Any) -> None: self.job_ids = job_ids +class CWLJobSubmission(_serialization.Model): + """Request body for CWL job submission. + + All required parameters must be populated in order to send to server. + + :ivar workflow: Workflow. Required. + :vartype workflow: str + :ivar inputs: Inputs. + :vartype inputs: list[dict[str, any]] + :ivar range_param: Range Param. + :vartype range_param: str + :ivar range_start: Range Start. + :vartype range_start: int + :ivar range_end: Range End. + :vartype range_end: int + :ivar range_step: Range Step. + :vartype range_step: int + :ivar base_inputs: Base Inputs. + :vartype base_inputs: dict[str, any] + """ + + _validation = { + "workflow": {"required": True}, + } + + _attribute_map = { + "workflow": {"key": "workflow", "type": "str"}, + "inputs": {"key": "inputs", "type": "[{object}]"}, + "range_param": {"key": "range_param", "type": "str"}, + "range_start": {"key": "range_start", "type": "int"}, + "range_end": {"key": "range_end", "type": "int"}, + "range_step": {"key": "range_step", "type": "int"}, + "base_inputs": {"key": "base_inputs", "type": "{object}"}, + } + + def __init__( + self, + *, + workflow: str, + inputs: list[dict[str, Any]] = [], + range_param: Optional[str] = None, + range_start: Optional[int] = None, + range_end: Optional[int] = None, + range_step: Optional[int] = None, + base_inputs: Optional[dict[str, Any]] = None, + **kwargs: Any + ) -> None: + """ + :keyword workflow: Workflow. Required. + :paramtype workflow: str + :keyword inputs: Inputs. + :paramtype inputs: list[dict[str, any]] + :keyword range_param: Range Param. + :paramtype range_param: str + :keyword range_start: Range Start. + :paramtype range_start: int + :keyword range_end: Range End. + :paramtype range_end: int + :keyword range_step: Range Step. + :paramtype range_step: int + :keyword base_inputs: Base Inputs. + :paramtype base_inputs: dict[str, any] + """ + super().__init__(**kwargs) + self.workflow = workflow + self.inputs = inputs + self.range_param = range_param + self.range_start = range_start + self.range_end = range_end + self.range_step = range_step + self.base_inputs = base_inputs + + class GroupInfo(_serialization.Model): """GroupInfo. diff --git a/diracx-client/src/diracx/client/_generated/operations/_operations.py b/diracx-client/src/diracx/client/_generated/operations/_operations.py index 11ffdcff7..def675f1f 100644 --- a/diracx-client/src/diracx/client/_generated/operations/_operations.py +++ b/diracx-client/src/diracx/client/_generated/operations/_operations.py @@ -565,6 +565,42 @@ def build_jobs_submit_jdl_jobs_request(**kwargs: Any) -> HttpRequest: return HttpRequest(method="POST", url=_url, headers=_headers, **kwargs) +def build_jobs_submit_cwl_jobs_request(**kwargs: Any) -> HttpRequest: + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + + content_type: Optional[str] = kwargs.pop("content_type", _headers.pop("Content-Type", None)) + accept = _headers.pop("Accept", "application/json") + + # Construct URL + _url = "/api/jobs/" + + # Construct headers + if content_type is not None: + _headers["Content-Type"] = _SERIALIZER.header("content_type", content_type, "str") + _headers["Accept"] = _SERIALIZER.header("accept", accept, "str") + + return HttpRequest(method="POST", url=_url, headers=_headers, **kwargs) + + +def build_jobs_get_workflow_request(workflow_id: str, **kwargs: Any) -> HttpRequest: + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + + accept = _headers.pop("Accept", "application/json") + + # Construct URL + _url = "/api/jobs/workflows/{workflow_id}" + path_format_arguments = { + "workflow_id": _SERIALIZER.url("workflow_id", workflow_id, "str"), + } + + _url: str = _url.format(**path_format_arguments) # type: ignore + + # Construct headers + _headers["Accept"] = _SERIALIZER.header("accept", accept, "str") + + return HttpRequest(method="GET", url=_url, headers=_headers, **kwargs) + + class WellKnownOperations: """ .. warning:: @@ -2818,3 +2854,164 @@ def submit_jdl_jobs(self, body: Union[list[str], IO[bytes]], **kwargs: Any) -> l return cls(pipeline_response, deserialized, {}) # type: ignore return deserialized # type: ignore + + @overload + def submit_cwl_jobs( + self, body: _models.CWLJobSubmission, *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: ~_generated.models.CWLJobSubmission + :keyword content_type: Body Parameter content-type. Content type parameter for JSON body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @overload + def submit_cwl_jobs( + self, body: IO[bytes], *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: IO[bytes] + :keyword content_type: Body Parameter content-type. Content type parameter for binary body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @distributed_trace + def submit_cwl_jobs( + self, body: Union[_models.CWLJobSubmission, IO[bytes]], **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Is either a CWLJobSubmission type or a IO[bytes] type. Required. + :type body: ~_generated.models.CWLJobSubmission or IO[bytes] + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + _params = kwargs.pop("params", {}) or {} + + content_type: Optional[str] = kwargs.pop("content_type", _headers.pop("Content-Type", None)) + cls: ClsType[list[_models.InsertedJob]] = kwargs.pop("cls", None) + + content_type = content_type or "application/json" + _json = None + _content = None + if isinstance(body, (IOBase, bytes)): + _content = body + else: + _json = self._serialize.body(body, "CWLJobSubmission") + + _request = build_jobs_submit_cwl_jobs_request( + content_type=content_type, + json=_json, + content=_content, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("[InsertedJob]", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore + + @distributed_trace + def get_workflow(self, workflow_id: str, **kwargs: Any) -> dict[str, str]: + """Get Workflow. + + Retrieve a CWL workflow definition by its content-addressed ID. + + :param workflow_id: Required. + :type workflow_id: str + :return: dict mapping str to str + :rtype: dict[str, str] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = kwargs.pop("headers", {}) or {} + _params = kwargs.pop("params", {}) or {} + + cls: ClsType[dict[str, str]] = kwargs.pop("cls", None) + + _request = build_jobs_get_workflow_request( + workflow_id=workflow_id, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("{str}", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore diff --git a/diracx-core/pyproject.toml b/diracx-core/pyproject.toml index 720968401..ee7c808b1 100644 --- a/diracx-core/pyproject.toml +++ b/diracx-core/pyproject.toml @@ -16,6 +16,7 @@ dependencies = [ "aiobotocore>=2.15", "botocore>=1.35", "cachetools", + "cwl-utils", "email_validator", "gitpython", "joserfc >=1.5.0", diff --git a/diracx-core/src/diracx/core/config/schema.py b/diracx-core/src/diracx/core/config/schema.py index 62c37b17c..c470dfa82 100644 --- a/diracx-core/src/diracx/core/config/schema.py +++ b/diracx-core/src/diracx/core/config/schema.py @@ -266,7 +266,7 @@ class OperationsConfig(BaseModel): """Configuration for job description defaults and limits.""" Services: ServicesConfig = ServicesConfig() """Configuration for various DIRAC services.""" - SoftwareDistModule: str = "LocalSoftwareDist" + SoftwareDistModule: str = "" """Module used for software distribution.""" Cloud: MutableMapping[str, Any] | None = None diff --git a/diracx-core/src/diracx/core/exceptions.py b/diracx-core/src/diracx/core/exceptions.py index 54d7c240d..6a218a17a 100644 --- a/diracx-core/src/diracx/core/exceptions.py +++ b/diracx-core/src/diracx/core/exceptions.py @@ -100,3 +100,7 @@ def __init__(self, job_id, detail: str | None = None): class NotReadyError(DiracError): """Tried to access a value which is asynchronously loaded but not yet available.""" + + +class WorkflowProcessingError(Exception): + """Workflow exception raised during pre and post processing steps.""" diff --git a/diracx-core/src/diracx/core/models/commands/__init__.py b/diracx-core/src/diracx/core/models/commands/__init__.py new file mode 100644 index 000000000..ed7814c4e --- /dev/null +++ b/diracx-core/src/diracx/core/models/commands/__init__.py @@ -0,0 +1,8 @@ +"""Command classes for workflow pre/post-processing operations.""" + +from __future__ import annotations + +from .core import PostProcessCommand, PreProcessCommand +from .store_output_data import StoreOutputDataCommand + +__all__ = ["PreProcessCommand", "PostProcessCommand", "StoreOutputDataCommand"] diff --git a/diracx-core/src/diracx/core/models/commands/core.py b/diracx-core/src/diracx/core/models/commands/core.py new file mode 100644 index 000000000..e9e3ccdfc --- /dev/null +++ b/diracx-core/src/diracx/core/models/commands/core.py @@ -0,0 +1,39 @@ +"""Core base classes for workflow processing commands.""" + +from __future__ import annotations + +from abc import ABC, abstractmethod +from pathlib import Path + + +class _CommandBase(ABC): + """Base abstract class for pre/post-processing commands. + + New commands **MUST NOT** inherit this class. Instead they should inherit the interface classes + :class:`dirac_cwl.commands.base.PreProcessCommand` and + :class:`dirac_cwl.commands.base.PostProcessCommand` + """ + + @abstractmethod + async def execute(self, job_path: Path, **kwargs) -> None: + """Execute the command in the given job path. + + :param job_path: Path to the job working directory. + :param kwargs: Additional keyword arguments. + :raises NotImplementedError: This method must be implemented by subclasses. + """ + raise NotImplementedError("This method should be implemented by child class") + + +class PreProcessCommand(_CommandBase): + """Interface class for pre-processing commands. + + Every pre-processing command must inherit this class. Used for type validation. + """ + + +class PostProcessCommand(_CommandBase): + """Interface class for post-processing commands. + + Every post-processing command must inherit this class. Used for type validation. + """ diff --git a/diracx-core/src/diracx/core/models/commands/store_output_data.py b/diracx-core/src/diracx/core/models/commands/store_output_data.py new file mode 100644 index 000000000..d2a1bb61c --- /dev/null +++ b/diracx-core/src/diracx/core/models/commands/store_output_data.py @@ -0,0 +1,122 @@ +"""Post-processing command that stores output files to grid storage.""" + +from __future__ import annotations + +import logging +from pathlib import Path +from typing import Any, Sequence + +from diracx.core.models.commands.core import PostProcessCommand + +logger = logging.getLogger(__name__) + + +class StoreOutputDataCommand(PostProcessCommand): + """Store output files to grid storage elements via DataManager. + + Replaces the output storage logic previously in ExecutionHooksBasePlugin. + """ + + def __init__( + self, + output_paths: dict[str, str], + output_se: list[str], + ) -> None: + self._output_paths = output_paths + self._output_se = output_se + self._datamanager = None + + def _get_datamanager(self): + if self._datamanager is None: + from DIRAC.DataManagementSystem.Client.DataManager import ( + DataManager, # type: ignore[import-untyped] + ) + + self._datamanager = DataManager() + return self._datamanager + + async def execute(self, job_path: Path, **kwargs: Any) -> None: + """Store output files to grid storage. + + :param job_path: Path to the job working directory. + :param kwargs: Must include 'outputs' dict mapping output names to file paths. + """ + outputs: dict[str, str | Path | Sequence[str | Path]] = kwargs.get( + "outputs", {} + ) + + for output_name, src_path in outputs.items(): + if not src_path: + raise RuntimeError( + f"src_path parameter required for filesystem storage of {output_name}" + ) + + lfn = self._output_paths.get(output_name, None) + if not lfn: + continue + + logger.info("Storing output %s, with source %s", output_name, src_path) + if isinstance(src_path, (str, Path)): + src_path = [src_path] + + for src in src_path: + # Resolve relative paths against the job working directory + local_path = Path(src) + if not local_path.is_absolute(): + local_path = (job_path / local_path).resolve() + + if not local_path.exists(): + raise RuntimeError( + f"Output file {local_path} does not exist for output '{output_name}'" + ) + + file_lfn = str(Path(lfn) / local_path.name) + + # TODO: Compute Adler32 checksum before upload + # TODO: Extract POOL/ROOT GUID if applicable + # TODO: Prefer local SEs (getSEsForSite) before remote ones + # TODO: Implement retry with exponential backoff on transient failures + # TODO: On complete failure, create a failover Request (RMS) + # for async recovery instead of raising immediately + # TODO: Report upload progress via job status updates + + uploaded = False + last_error = "" + for se in self._output_se: + result = self._get_datamanager().putAndRegister( + file_lfn, str(local_path), se + ) + if not result["OK"]: + last_error = result["Message"] + logger.warning( + "Failed to upload %s to %s: %s", local_path, se, last_error + ) + continue + + # putAndRegister returns {lfn: {'put': ..., 'register': ...}} + lfn_result = result["Value"].get("Successful", {}).get(file_lfn) + if lfn_result: + logger.info( + "Successfully stored %s with LFN %s on %s", + local_path, + file_lfn, + se, + ) + uploaded = True + break + + failed = result["Value"].get("Failed", {}).get(file_lfn, "") + last_error = str(failed) + logger.warning( + "putAndRegister reported failure for %s on %s: %s", + file_lfn, + se, + last_error, + ) + + if not uploaded: + # TODO: Instead of raising, create a failover Request + raise RuntimeError( + f"Could not store {local_path} as {file_lfn} " + f"on any SE {self._output_se}: {last_error}" + ) diff --git a/diracx-core/src/diracx/core/models/cwl.py b/diracx-core/src/diracx/core/models/cwl.py new file mode 100644 index 000000000..e05363e42 --- /dev/null +++ b/diracx-core/src/diracx/core/models/cwl.py @@ -0,0 +1,66 @@ +"""Models for CWL workflow submission via the dirac:Job hint.""" + +from __future__ import annotations + +from typing import Literal + +from pydantic import BaseModel + + +class IOSource(BaseModel): + """Reference to a CWL input or output by its ID.""" + + source: str + + +class OutputDataEntry(BaseModel): + """Output data entry with per-output SE and LFN path.""" + + source: str + output_path: str + output_se: list[str] = ["SE-USER"] + + +class JobHint(BaseModel): + """Unified DIRAC-specific hint for job scheduling and I/O. + + Resource requirements (cores, RAM) are expressed via standard CWL + requirements, not in this hint. + + Execution hooks are determined automatically by ``type``, not + configured by the submitter. + + I/O fields reference CWL input/output IDs via ``source:`` syntax, + consistent with CWL's own referencing conventions. + """ + + schema_version: Literal["1.0"] = "1.0" + + # Scheduling (DIRAC-specific, no CWL equivalent) + priority: int = 5 + cpu_work: int | None = None # HS06-seconds → JDL CPUTime + platform: str | None = None + sites: list[str] | None = None + banned_sites: list[str] | None = None + tags: list[str] | None = None # merged with auto-derived tags + + # Job metadata + type: str = "User" + group: str = "" + log_level: str = "INFO" + + # I/O: reference CWL input/output IDs via source: + input_sandbox: list[IOSource] = [] + input_data: list[IOSource] = [] + output_sandbox: list[IOSource] = [] + output_data: list[OutputDataEntry] = [] + + @classmethod + def from_cwl(cls, cwl_object) -> JobHint: + """Extract a JobHint from a CWL object's hints list.""" + hints = getattr(cwl_object, "hints", []) or [] + for hint in hints: + if isinstance(hint, dict) and hint.get("class") == "dirac:Job": + data = {k: v for k, v in hint.items() if k != "class"} + return cls(**data) + raise ValueError("CWL task is missing required dirac:Job hint") diff --git a/diracx-core/src/diracx/core/models/cwl_submission.py b/diracx-core/src/diracx/core/models/cwl_submission.py new file mode 100644 index 000000000..1fff6759d --- /dev/null +++ b/diracx-core/src/diracx/core/models/cwl_submission.py @@ -0,0 +1,84 @@ +"""Enhanced submission models for DIRAC CWL integration.""" + +from __future__ import annotations + +from typing import Any, Optional + +from cwl_utils.parser import save +from cwl_utils.parser.cwl_v1_2 import ( + CommandLineTool, + ExpressionTool, + Workflow, +) +from pydantic import BaseModel, ConfigDict, field_serializer, model_validator + +from diracx.core.models.cwl import JobHint + +# ----------------------------------------------------------------------------- +# Job models +# ----------------------------------------------------------------------------- + + +class JobInputModel(BaseModel): + """Input data and sandbox files for a job execution.""" + + # Allow arbitrary types to be passed to the model + model_config = ConfigDict(arbitrary_types_allowed=True) + + sandbox: list[str] | None + cwl: dict[str, Any] + + @field_serializer("cwl") + def serialize_cwl(self, value): + """Serialize CWL object to dictionary. + + :param value: CWL object to serialize. + :return: Serialized CWL dictionary. + """ + return save(value) + + +class BaseJobModel(BaseModel): + """Base class for Job definition.""" + + # Allow arbitrary types to be passed to the model + model_config = ConfigDict(arbitrary_types_allowed=True) + + task: CommandLineTool | Workflow | ExpressionTool + + @field_serializer("task") + def serialize_task(self, value): + """Serialize CWL task object to dictionary. + + :param value: CWL task object to serialize. + :return: Serialized task dictionary. + :raises TypeError: If value is not a valid CWL task type. + """ + if isinstance(value, (CommandLineTool, Workflow, ExpressionTool)): + return save(value) + else: + raise TypeError(f"Cannot serialize type {type(value)}") + + @model_validator(mode="before") + @classmethod + def validate_hints(cls, values): + """Validate dirac:Job hint in the task. + + :param values: Model values dictionary. + :return: Validated values dictionary. + """ + task = values.get("task") + JobHint.from_cwl(task) + return values + + +class JobSubmissionModel(BaseJobModel): + """Job definition sent to the router.""" + + inputs: list[JobInputModel] | None = None + + +class JobModel(BaseJobModel): + """Job definition sent to the job wrapper.""" + + input: Optional[JobInputModel] = None diff --git a/diracx-core/src/diracx/core/models/job.py b/diracx-core/src/diracx/core/models/job.py index ec098c2c6..d0cf26673 100644 --- a/diracx-core/src/diracx/core/models/job.py +++ b/diracx-core/src/diracx/core/models/job.py @@ -122,8 +122,45 @@ class JobStatus(StrEnum): class JobMinorStatus(StrEnum): + APPLICATION = "Executing Payload" + APP_ERRORS = "Application Finished With Errors" + APP_NOT_FOUND = "Application not found" + APP_SUCCESS = "Application Finished Successfully" + APP_THREAD_FAILED = "Application thread failed" + APP_THREAD_NOT_COMPLETE = "Application thread did not complete" + DOWNLOADING_INPUT_SANDBOX = "Downloading InputSandbox" + DOWNLOADING_INPUT_SANDBOX_LFN = "Downloading InputSandbox LFN(s)" + EXCEPTION_DURING_EXEC = "Exception During Execution" + EXEC_COMPLETE = "Execution Complete" + FAILED_DOWNLOADING_INPUT_SANDBOX = "Failed Downloading InputSandbox" + FAILED_DOWNLOADING_INPUT_SANDBOX_LFN = "Failed Downloading InputSandbox LFN(s)" + FAILED_SENDING_REQUESTS = "Failed sending requests" + GOING_RESCHEDULE = "Going to reschedule job" + ILLEGAL_JOB_JDL = "Illegal Job JDL" + INPUT_DATA_RESOLUTION = "Resolving Input Data" + INPUT_NOT_AVAILABLE = "Input Data Not Available" + JOB_EXCEEDED_CPU = "Job has reached the CPU limit of the queue" + JOB_EXCEEDED_WALL_CLOCK = "Job has exceeded maximum wall clock time" + JOB_INITIALIZATION = "Initializing Job" + JOB_INSUFFICIENT_DISK = "Job has insufficient disk space to continue" + JOB_WRAPPER_EXECUTION = "JobWrapper execution" + JOB_WRAPPER_INITIALIZATION = "Job Wrapper Initialization" + MARKED_FOR_TERMINATION = "Marked for termination" MAX_RESCHEDULING = "Maximum of reschedulings reached" + NO_CANDIDATE_SITE_FOUND = "No candidate sites available" + OUTPUT_DATA_UPLOADED = "Output Data Uploaded" + OUTPUT_SANDBOX_UPLOADED = "Output Sandbox Uploaded" + PENDING_REQUESTS = "Pending Requests" + PILOT_AGENT_SUBMISSION = "Pilot Agent Submission" + RECEIVED_KILL_SIGNAL = "Received Kill signal" + REQUESTS_DONE = "Requests done" RESCHEDULED = "Job Rescheduled" + RESOLVING_OUTPUT_SANDBOX = "Resolving Output Sandbox" + STALLED_PILOT_NOT_RUNNING = "Job stalled: pilot not running" + UPLOADING_JOB_OUTPUTS = "Uploading Outputs" + UPLOADING_OUTPUT_DATA = "Uploading Output Data" + UPLOADING_OUTPUT_SANDBOX = "Uploading Output Sandbox" + WATCHDOG_STALLED = "Watchdog identified this job as stalled" class JobLoggingRecord(BaseModel): diff --git a/diracx-core/src/diracx/core/models/replica_map.py b/diracx-core/src/diracx/core/models/replica_map.py index e405ebeab..a3523945b 100644 --- a/diracx-core/src/diracx/core/models/replica_map.py +++ b/diracx-core/src/diracx/core/models/replica_map.py @@ -54,10 +54,17 @@ def _validate_lfn(value: str) -> str: - """Validate and normalize Logical File Name. + """Validate and normalize Logical File Name or Sandbox reference. Removes LFN: prefix if present and ensures it's a valid absolute path or a filename without slashes. + SB: prefixed values are sandbox references — stored with prefix as the key. """ + # SB: paths are sandbox references — pass through with prefix + if value.startswith("SB:"): + if len(value) <= 3: + raise ValueError("Sandbox reference cannot be empty") + return value + value = value.removeprefix("LFN:") if not value: raise ValueError("LFN cannot be empty") diff --git a/diracx-core/tests/test_replica_map.py b/diracx-core/tests/test_replica_map.py index aca6e6d79..bb5b1717a 100644 --- a/diracx-core/tests/test_replica_map.py +++ b/diracx-core/tests/test_replica_map.py @@ -1,6 +1,7 @@ from __future__ import annotations import pytest +from pydantic import ValidationError from diracx.core.models.replica_map import ( ReplicaMap, @@ -33,6 +34,48 @@ def test_lfn_prefix_only_raises_error(self): _validate_lfn("LFN:") +class TestValidateSBRef: + """Tests for SB: sandbox reference validation in replica map keys.""" + + def test_sb_ref_accepted_as_key(self): + """SB: prefixed paths should be valid replica map keys.""" + sb_key = "SB:SandboxSE|/S3/diracx-sandbox-store/sha256:abc123.tar.zst#helper.sh" + replica_map = ReplicaMap( + root={ + sb_key: { + "replicas": [{"url": "file:///tmp/job/helper.sh", "se": "local"}], + } + } + ) + assert sb_key in replica_map.root + + def test_sb_ref_empty_rejected(self): + """Empty SB: reference should be rejected.""" + with pytest.raises(ValidationError, match="Sandbox reference cannot be empty"): + ReplicaMap( + root={ + "SB:": { + "replicas": [{"url": "file:///tmp/f.txt", "se": "local"}], + } + } + ) + + def test_sb_ref_preserves_prefix(self): + """SB: prefix should be preserved as part of the key.""" + sb_key = "SB:SandboxSE|/S3/store/sha256:def456.tar.zst#config/app.yaml" + replica_map = ReplicaMap( + root={ + sb_key: { + "replicas": [ + {"url": "file:///tmp/job/config/app.yaml", "se": "local"} + ], + } + } + ) + entry = replica_map[sb_key] + assert str(entry.replicas[0].url) == "file:///tmp/job/config/app.yaml" + + class TestValidatePFN: """Tests for _validate_pfn function.""" diff --git a/diracx-db/src/diracx/db/sql/job/db.py b/diracx-db/src/diracx/db/sql/job/db.py index bb28aa5cf..5a396eef8 100644 --- a/diracx-db/src/diracx/db/sql/job/db.py +++ b/diracx-db/src/diracx/db/sql/job/db.py @@ -24,6 +24,7 @@ JobDBBase, JobJDLs, Jobs, + Workflows, ) @@ -286,3 +287,46 @@ async def get_job_commands(self, job_ids: Iterable[int]) -> list[JobCommand]: JobCommand(job_id=cmd.JobID, command=cmd.Command, arguments=cmd.Arguments) for cmd in commands ] + + async def insert_workflow( + self, workflow_id: str, cwl: str, persistent: bool = False + ) -> bool: + """Insert a workflow if it doesn't already exist. Returns True if inserted.""" + # Check if already exists (content-addressed, immutable) + stmt = select(Workflows.workflow_id).where(Workflows.workflow_id == workflow_id) + result = await self.conn.execute(stmt) + if result.first() is not None: + return False + + await self.conn.execute( + insert(Workflows).values( + WorkflowID=workflow_id, + CWL=cwl, + Persistent=persistent, + CreatedAt=datetime.now(tz=timezone.utc), + ) + ) + return True + + async def get_workflow(self, workflow_id: str) -> str: + """Get the CWL content for a workflow by its ID.""" + stmt = select(Workflows.cwl).where(Workflows.workflow_id == workflow_id) + result = await self.conn.execute(stmt) + row = result.first() + if row is None: + raise InvalidQueryError(f"Workflow {workflow_id} not found") + return row[0] + + async def set_workflow_ref( + self, + job_id: int, + workflow_id: str, + workflow_params: dict | None = None, + ) -> None: + """Set the workflow reference and params on a job.""" + stmt = ( + update(Jobs) + .where(Jobs.job_id == job_id) + .values(WorkflowID=workflow_id, WorkflowParams=workflow_params) + ) + await self.conn.execute(stmt) diff --git a/diracx-db/src/diracx/db/sql/job/schema.py b/diracx-db/src/diracx/db/sql/job/schema.py index a1e3fac82..9130856a1 100644 --- a/diracx-db/src/diracx/db/sql/job/schema.py +++ b/diracx-db/src/diracx/db/sql/job/schema.py @@ -5,10 +5,13 @@ import sqlalchemy.types as types from sqlalchemy import ( + JSON, + Boolean, ForeignKey, Index, String, Text, + text, ) from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column from typing_extensions import Annotated @@ -57,6 +60,17 @@ def process_result_value(self, value, dialect) -> bool | str: raise NotImplementedError(f"Unknown {value=}") +class Workflows(JobDBBase): + __tablename__ = "Workflows" + + workflow_id: Mapped[str] = mapped_column("WorkflowID", String(64), primary_key=True) + cwl: Mapped[str] = mapped_column("CWL", Text) + persistent: Mapped[bool] = mapped_column("Persistent", Boolean, default=False) + created_at: Mapped[datetime] = mapped_column( + "CreatedAt", SmarterDateTime(), server_default=text("(UTC_TIMESTAMP())") + ) + + class Jobs(JobDBBase): __tablename__ = "Jobs" @@ -110,6 +124,14 @@ class Jobs(JobDBBase): accounted_flag: Mapped[bool | str] = mapped_column( "AccountedFlag", AccountedFlagEnum(), default=False ) + workflow_id: Mapped[Optional[str]] = mapped_column( + "WorkflowID", + ForeignKey("Workflows.WorkflowID"), + default=None, + ) + workflow_params: Mapped[Optional[dict]] = mapped_column( + "WorkflowParams", JSON, default=None + ) __table_args__ = ( Index("JobType", "JobType"), @@ -122,6 +144,7 @@ class Jobs(JobDBBase): Index("ApplicationStatus", "ApplicationStatus"), Index("StatusSite", "Status", "Site"), Index("LastUpdateTime", "LastUpdateTime"), + Index("WorkflowID", "WorkflowID"), ) diff --git a/diracx-db/tests/jobs/test_workflow_db.py b/diracx-db/tests/jobs/test_workflow_db.py new file mode 100644 index 000000000..528e484f9 --- /dev/null +++ b/diracx-db/tests/jobs/test_workflow_db.py @@ -0,0 +1,99 @@ +"""Tests for the Workflows table and workflow-related methods on JobDB.""" + +from __future__ import annotations + +import hashlib + +import pytest + +from diracx.core.exceptions import InvalidQueryError +from diracx.db.sql.job.db import JobDB + + +@pytest.fixture +async def job_db(tmp_path): + job_db = JobDB("sqlite+aiosqlite:///:memory:") + async with job_db.engine_context(): + async with job_db.engine.begin() as conn: + if job_db._db_url.startswith("sqlite"): + await conn.exec_driver_sql("PRAGMA foreign_keys=ON") + await conn.run_sync(job_db.metadata.create_all) + yield job_db + + +SAMPLE_CWL = """\ +cwlVersion: v1.2 +class: CommandLineTool +label: test-job +hints: + - class: dirac:Job + schema_version: "1.0" + type: User +inputs: + - id: message + type: string +outputs: [] +""" + + +def _workflow_id(cwl: str) -> str: + return hashlib.sha256(cwl.encode()).hexdigest() + + +async def test_insert_workflow(job_db): + """Test inserting a workflow and retrieving it.""" + wf_id = _workflow_id(SAMPLE_CWL) + + async with job_db as db: + inserted = await db.insert_workflow(wf_id, SAMPLE_CWL) + assert inserted is True + + cwl = await db.get_workflow(wf_id) + assert cwl == SAMPLE_CWL + + +async def test_insert_workflow_idempotent(job_db): + """Inserting the same workflow twice should be a no-op the second time.""" + wf_id = _workflow_id(SAMPLE_CWL) + + async with job_db as db: + first = await db.insert_workflow(wf_id, SAMPLE_CWL) + second = await db.insert_workflow(wf_id, SAMPLE_CWL) + assert first is True + assert second is False + + +async def test_get_workflow_not_found(job_db): + """Getting a non-existent workflow should raise.""" + async with job_db as db: + with pytest.raises(InvalidQueryError): + await db.get_workflow("nonexistent" * 4) + + +async def test_set_workflow_ref(job_db): + """Test linking a job to a workflow with params.""" + wf_id = _workflow_id(SAMPLE_CWL) + + async with job_db as db: + # Create workflow + await db.insert_workflow(wf_id, SAMPLE_CWL) + + # Create a job + job_id = await db.create_job("compressed_jdl") + await db.insert_job_attributes( + {job_id: {"JobID": job_id, "Status": "Received", "VO": "lhcb"}} + ) + + # Link job to workflow + params = {"message": "hello world"} + await db.set_workflow_ref(job_id, wf_id, workflow_params=params) + + +async def test_insert_workflow_persistent(job_db): + """Test inserting a persistent workflow.""" + wf_id = _workflow_id(SAMPLE_CWL) + + async with job_db as db: + await db.insert_workflow(wf_id, SAMPLE_CWL, persistent=True) + cwl = await db.get_workflow(wf_id) + assert cwl == SAMPLE_CWL diff --git a/diracx-logic/pyproject.toml b/diracx-logic/pyproject.toml index 889fe9a55..740df927c 100644 --- a/diracx-logic/pyproject.toml +++ b/diracx-logic/pyproject.toml @@ -14,6 +14,7 @@ classifiers = [ ] dependencies = [ "cachetools", + "cwl-utils", "diraccommon >=9.0.18", "diracx-core", "diracx-db", diff --git a/diracx-logic/src/diracx/logic/jobs/cwl_submission.py b/diracx-logic/src/diracx/logic/jobs/cwl_submission.py new file mode 100644 index 000000000..30b7b5816 --- /dev/null +++ b/diracx-logic/src/diracx/logic/jobs/cwl_submission.py @@ -0,0 +1,320 @@ +"""CWL workflow submission logic. + +Handles parsing CWL + input YAMLs, extracting the dirac:Job hint, +translating to JDL (transition period), and storing workflow references. +""" + +from __future__ import annotations + +import hashlib +import json +import logging +from typing import Any, TypeAlias, Union + +import yaml +from cwl_utils.parser import load_document_by_yaml +from cwl_utils.parser.cwl_v1_2 import ( + CommandLineTool, + CUDARequirement, + ExpressionTool, + MPIRequirement, + ResourceRequirement, + Workflow, +) + +from diracx.core.config import Config +from diracx.core.models.auth import UserInfo +from diracx.core.models.cwl import JobHint +from diracx.core.models.job import InsertedJob +from diracx.db.sql.job.db import JobDB +from diracx.db.sql.job_logging.db import JobLoggingDB + +from .submission import submit_jdl_jobs + +logger = logging.getLogger(__name__) + +CWLTask: TypeAlias = Union[CommandLineTool, Workflow, ExpressionTool] + + +def compute_workflow_id(cwl_yaml: str) -> str: + """Content-address a CWL workflow by its SHA-256 hash. + + The YAML is parsed and re-serialized as sorted JSON before hashing, + so whitespace, comments, and key ordering differences don't produce + distinct workflow IDs. + """ + canonical = json.dumps(yaml.safe_load(cwl_yaml), sort_keys=True) + return hashlib.sha256(canonical.encode()).hexdigest() + + +def parse_cwl(cwl_yaml: str) -> CWLTask: + """Parse a CWL YAML string into a cwl_utils object.""" + doc = yaml.safe_load(cwl_yaml) + return load_document_by_yaml(doc, uri="workflow.cwl") + + +def extract_job_hint(task: CWLTask) -> JobHint: + """Extract the dirac:Job hint from a CWL task, or return defaults if absent.""" + return JobHint.from_cwl(task) + + +def _extract_id(cwl_id: str) -> str: + """Extract short ID from CWL full URI (e.g., 'file.cwl#input1' -> 'input1').""" + return cwl_id.split("#")[-1].split("/")[-1] + + +def _validate_cwl_id( + source: str, + cwl_ids: dict[str, Any], + direction: str, + allowed_types: list[str], +) -> None: + """Validate that a source ID exists in the CWL task's inputs/outputs.""" + if source not in cwl_ids: + available = ", ".join(sorted(cwl_ids.keys())) + raise ValueError( + f"dirac:Job references {direction} '{source}' but CWL task " + f"only has: [{available}]" + ) + + +def expand_range_inputs( + *, + range_param: str, + range_start: int, + range_end: int, + range_step: int, + base_inputs: dict | None, +) -> list[dict]: + """Expand a range spec into a list of input dicts. + + Each dict is base_inputs | {range_param: index}. + """ + base = base_inputs or {} + return [{**base, range_param: i} for i in range(range_start, range_end, range_step)] + + +def cwl_to_jdl( + task: CWLTask, + job_hint: JobHint, + input_params: dict | None, +) -> str: + """Convert a CWL task with dirac:Job hint into a JDL string. + + This is a transition-period function -- once JDL is retired, + job attributes are populated directly from the hint + CWL. + """ + jdl_fields: dict[str, Any] = { + "Executable": "dirac-cwl-exec", + "JobType": job_hint.type, + "Priority": job_hint.priority, + "LogLevel": job_hint.log_level, + } + + if job_hint.cpu_work: + jdl_fields["CPUTime"] = job_hint.cpu_work + if job_hint.platform: + jdl_fields["Platform"] = job_hint.platform + + # Derive JobName from CWL label/id + task_label = getattr(task, "label", None) + task_id = getattr(task, "id", None) + if task_label: + job_name = task_label + elif task_id and task_id != ".": + job_name = task_id.split("#")[-1].split("/")[-1] + else: + job_name = "cwl-job" + + # Append parametric key=value pairs to job name for disambiguation + if input_params: + scalars = [ + f"{k}={v}" + for k, v in input_params.items() + if isinstance(v, (int, float, str)) + ] + if scalars: + job_name = f"{job_name} ({', '.join(scalars)})" + + jdl_fields["JobName"] = job_name + + # Extract from CWL requirements (standard CWL, not dirac:Job) + tags = set(job_hint.tags or []) + for req in getattr(task, "requirements", None) or []: + if isinstance(req, ResourceRequirement): + if req.coresMin: + jdl_fields["MinNumberOfProcessors"] = int(req.coresMin) + if req.coresMax: + jdl_fields["MaxNumberOfProcessors"] = int(req.coresMax) + if req.ramMin: + jdl_fields["MinRAM"] = int(req.ramMin) + if req.ramMax: + jdl_fields["MaxRAM"] = int(req.ramMax) + elif isinstance(req, CUDARequirement): + tags.add("GPU") + elif isinstance(req, MPIRequirement): + raise NotImplementedError( + "MPIRequirement is not yet supported for DIRAC CWL jobs" + ) + + # Auto-derive processor tags + min_proc = jdl_fields.get("MinNumberOfProcessors", 1) + max_proc = jdl_fields.get("MaxNumberOfProcessors") + if min_proc and min_proc > 1: + tags.add("MultiProcessor") + if min_proc and max_proc and min_proc == max_proc: + tags.add(f"{min_proc}Processors") + + if tags: + jdl_fields["Tags"] = list(tags) + + # Sites + if job_hint.sites: + jdl_fields["Site"] = job_hint.sites + if job_hint.banned_sites: + jdl_fields["BannedSites"] = job_hint.banned_sites + + if job_hint.group: + jdl_fields["JobGroup"] = job_hint.group + + # Resolve I/O from CWL input/output source IDs + cwl_input_ids = { + _extract_id(inp.id): inp for inp in (getattr(task, "inputs", None) or []) + } + cwl_output_ids = { + _extract_id(out.id): out for out in (getattr(task, "outputs", None) or []) + } + + # InputSandbox + if job_hint.input_sandbox: + sandbox_files = [] + for ref in job_hint.input_sandbox: + _validate_cwl_id(ref.source, cwl_input_ids, "input", ["File", "File[]"]) + if input_params and ref.source in input_params: + val = input_params[ref.source] + if isinstance(val, dict) and "path" in val: + # Strip #fragment (file-inside-archive) — server only + # knows the sandbox PFN without it + sandbox_files.append(val["path"].split("#")[0]) + elif isinstance(val, list): + sandbox_files.extend( + item["path"].split("#")[0] + for item in val + if isinstance(item, dict) and "path" in item + ) + if sandbox_files: + jdl_fields["InputSandbox"] = sandbox_files + + # InputData + if job_hint.input_data: + lfns = [] + for ref in job_hint.input_data: + _validate_cwl_id(ref.source, cwl_input_ids, "input", ["File", "File[]"]) + if input_params and ref.source in input_params: + val = input_params[ref.source] + if isinstance(val, dict) and "path" in val: + lfns.append(val["path"]) + elif isinstance(val, list): + lfns.extend( + item["path"] + for item in val + if isinstance(item, dict) and "path" in item + ) + if lfns: + jdl_fields["InputData"] = lfns + + # OutputSandbox + sandbox_outputs: list[str] = [] + + # Auto-collect stdout/stderr filenames declared in CWL + if hasattr(task, "stdout") and task.stdout: + sandbox_outputs.append(task.stdout) + if hasattr(task, "stderr") and task.stderr: + sandbox_outputs.append(task.stderr) + + if job_hint.output_sandbox: + for ref in job_hint.output_sandbox: + _validate_cwl_id(ref.source, cwl_output_ids, "output", ["File", "File[]"]) + out = cwl_output_ids[ref.source] + if hasattr(out, "outputBinding") and out.outputBinding: + sandbox_outputs.append(out.outputBinding.glob) + + if sandbox_outputs: + jdl_fields["OutputSandbox"] = sandbox_outputs + + # OutputData (per-output SE and path) + if job_hint.output_data: + output_files = [] + all_ses = set() + for entry in job_hint.output_data: + _validate_cwl_id(entry.source, cwl_output_ids, "output", ["File", "File[]"]) + out = cwl_output_ids[entry.source] + if hasattr(out, "outputBinding") and out.outputBinding: + output_files.append(out.outputBinding.glob) + all_ses.update(entry.output_se) + if output_files: + jdl_fields["OutputData"] = output_files + jdl_fields["OutputPath"] = job_hint.output_data[0].output_path + jdl_fields["OutputSE"] = list(all_ses) + + return _format_as_jdl(jdl_fields) + + +def _format_as_jdl(fields: dict[str, Any]) -> str: + """Format a dict of fields as a JDL string.""" + lines = [] + for key, value in fields.items(): + if isinstance(value, list): + items = ", ".join(f'"{v}"' for v in value) + lines.append(f" {key} = {{{items}}};") + elif isinstance(value, int): + lines.append(f" {key} = {value};") + elif isinstance(value, str): + lines.append(f' {key} = "{value}";') + else: + lines.append(f' {key} = "{value}";') + return "[\n" + "\n".join(lines) + "\n]" + + +async def submit_cwl_jobs( + cwl_yaml: str, + input_yamls: list[dict | None], + job_db: JobDB, + job_logging_db: JobLoggingDB, + user_info: UserInfo, + config: Config, +) -> list[InsertedJob]: + """Submit CWL jobs: store workflow once, create one job per input YAML.""" + workflow_id = compute_workflow_id(cwl_yaml) + + # INSERT IF NOT EXISTS — idempotent, content-addressed + await job_db.insert_workflow(workflow_id, cwl_yaml, persistent=False) + + task = parse_cwl(cwl_yaml) + job_hint = extract_job_hint(task) + + inserted: list[InsertedJob] = [] + for input_params in input_yamls: + # Generate JDL for transition period + jdl = cwl_to_jdl(task, job_hint, input_params) + + # Submit via existing pipeline + jobs = await submit_jdl_jobs( + [jdl], + job_db=job_db, + job_logging_db=job_logging_db, + user_info=user_info, + config=config, + ) + + # Set workflow reference + immutable params on job row + for job in jobs: + await job_db.set_workflow_ref( + job.JobID, + workflow_id=workflow_id, + workflow_params=input_params, + ) + + inserted.extend(jobs) + + return inserted diff --git a/diracx-logic/tests/test_cwl_submission.py b/diracx-logic/tests/test_cwl_submission.py new file mode 100644 index 000000000..5f1c98b28 --- /dev/null +++ b/diracx-logic/tests/test_cwl_submission.py @@ -0,0 +1,326 @@ +"""Tests for CWL submission logic: models, parsing, and cwl_to_jdl translation.""" + +from __future__ import annotations + +import pytest +from pydantic import ValidationError + +from diracx.core.models.cwl import IOSource, JobHint, OutputDataEntry +from diracx.logic.jobs.cwl_submission import ( + compute_workflow_id, + cwl_to_jdl, + extract_job_hint, + parse_cwl, +) + +# --- Model tests --- + + +def test_job_hint_defaults(): + hint = JobHint(schema_version="1.0") + assert hint.priority == 5 + assert hint.type == "User" + assert hint.log_level == "INFO" + assert hint.cpu_work is None + assert hint.sites is None + assert hint.input_sandbox == [] + assert hint.output_data == [] + + +def test_job_hint_full(): + hint = JobHint( + schema_version="1.0", + priority=3, + cpu_work=864000, + platform="x86_64-el9", + sites=["LCG.CERN.cern"], + banned_sites=["LCG.RAL.uk"], + tags=["GPU"], + type="MCSimulation", + group="lhcb_mc", + input_data=[IOSource(source="input_lfns")], + output_data=[ + OutputDataEntry( + source="result", + output_path="/lhcb/mc/output/", + output_se=["SE-TAPE"], + ) + ], + ) + assert hint.cpu_work == 864000 + assert hint.sites == ["LCG.CERN.cern"] + assert len(hint.output_data) == 1 + assert hint.output_data[0].output_se == ["SE-TAPE"] + + +def test_job_hint_default_schema_version(): + hint = JobHint() + assert hint.schema_version == "1.0" + + +def test_job_hint_rejects_invalid_schema_version(): + with pytest.raises(ValidationError): + JobHint(schema_version="99.0") + + +def test_io_source(): + ref = IOSource(source="config_files") + assert ref.source == "config_files" + + +def test_output_data_entry_default_se(): + entry = OutputDataEntry(source="result", output_path="/data/") + assert entry.output_se == ["SE-USER"] + + +# --- Workflow ID tests --- + + +def test_compute_workflow_id_deterministic(): + cwl = "cwlVersion: v1.2\nclass: CommandLineTool\n" + id1 = compute_workflow_id(cwl) + id2 = compute_workflow_id(cwl) + assert id1 == id2 + assert len(id1) == 64 # SHA-256 hex + + +def test_compute_workflow_id_different_content(): + id1 = compute_workflow_id("version1") + id2 = compute_workflow_id("version2") + assert id1 != id2 + + +# --- CWL parsing and hint extraction --- + +MINIMAL_CWL = """\ +cwlVersion: v1.2 +class: CommandLineTool +label: test-job +baseCommand: echo + +hints: + - class: dirac:Job + schema_version: "1.0" + type: User + priority: 3 + cpu_work: 100000 + sites: + - LCG.CERN.cern + banned_sites: + - LCG.RAL.uk + +requirements: + - class: ResourceRequirement + coresMin: 2 + coresMax: 4 + ramMin: 2048 + +inputs: + - id: message + type: string + +outputs: + - id: output_log + type: File + outputBinding: + glob: "output.log" + +$namespaces: + dirac: "https://diracgrid.org/cwl#" +""" + +CWL_WITH_IO = """\ +cwlVersion: v1.2 +class: CommandLineTool +label: analysis-job +baseCommand: echo + +hints: + - class: dirac:Job + schema_version: "1.0" + type: User + input_sandbox: + - source: helper_script + input_data: + - source: input_lfns + output_sandbox: + - source: stderr_log + output_data: + - source: result_file + output_path: "/lhcb/user/output/" + output_se: + - SE-USER + +inputs: + - id: helper_script + type: File + - id: input_lfns + type: + type: array + items: File + - id: config_param + type: string + +outputs: + - id: result_file + type: File + outputBinding: + glob: "result.root" + - id: stderr_log + type: File + outputBinding: + glob: "std.err" + +$namespaces: + dirac: "https://diracgrid.org/cwl#" +""" + +CWL_NO_HINT = """\ +cwlVersion: v1.2 +class: CommandLineTool +baseCommand: echo +inputs: [] +outputs: [] +""" + + +def test_parse_cwl(): + task = parse_cwl(MINIMAL_CWL) + assert task.label == "test-job" + + +def test_extract_job_hint(): + task = parse_cwl(MINIMAL_CWL) + hint = extract_job_hint(task) + assert hint.schema_version == "1.0" + assert hint.type == "User" + assert hint.priority == 3 + assert hint.cpu_work == 100000 + + +def test_extract_job_hint_missing(): + task = parse_cwl(CWL_NO_HINT) + with pytest.raises(ValueError, match="missing required dirac:Job hint"): + extract_job_hint(task) + + +def test_unsupported_schema_version(): + cwl = MINIMAL_CWL.replace('schema_version: "1.0"', 'schema_version: "99.0"') + task = parse_cwl(cwl) + with pytest.raises(ValidationError): + extract_job_hint(task) + + +# --- cwl_to_jdl tests --- + + +def test_cwl_to_jdl_basic(): + task = parse_cwl(MINIMAL_CWL) + hint = extract_job_hint(task) + jdl = cwl_to_jdl(task, hint, None) + + assert 'Executable = "dirac-cwl-exec"' in jdl + assert 'JobType = "User"' in jdl + assert "Priority = 3" in jdl + assert "CPUTime = 100000" in jdl + assert 'JobName = "test-job"' in jdl + assert "MinNumberOfProcessors = 2" in jdl + assert "MaxNumberOfProcessors = 4" in jdl + assert "MinRAM = 2048" in jdl + assert '"LCG.CERN.cern"' in jdl + assert '"LCG.RAL.uk"' in jdl + + +def test_cwl_to_jdl_multiprocessor_tags(): + task = parse_cwl(MINIMAL_CWL) + hint = extract_job_hint(task) + jdl = cwl_to_jdl(task, hint, None) + + assert '"MultiProcessor"' in jdl + + +def test_cwl_to_jdl_output_sandbox(): + task = parse_cwl(CWL_WITH_IO) + hint = extract_job_hint(task) + jdl = cwl_to_jdl(task, hint, None) + + assert '"std.err"' in jdl # output sandbox from stderr_log + + +def test_cwl_to_jdl_output_data(): + task = parse_cwl(CWL_WITH_IO) + hint = extract_job_hint(task) + jdl = cwl_to_jdl(task, hint, None) + + assert '"result.root"' in jdl + assert "OutputPath" in jdl + assert "SE-USER" in jdl + + +def test_cwl_to_jdl_input_data_with_params(): + task = parse_cwl(CWL_WITH_IO) + hint = extract_job_hint(task) + params = { + "input_lfns": [ + {"class": "File", "path": "LFN:/lhcb/data/file1.root"}, + {"class": "File", "path": "LFN:/lhcb/data/file2.root"}, + ], + "helper_script": {"class": "File", "path": "helper.sh"}, + } + jdl = cwl_to_jdl(task, hint, params) + + assert "LFN:/lhcb/data/file1.root" in jdl + assert "LFN:/lhcb/data/file2.root" in jdl + assert "helper.sh" in jdl + + +def test_cwl_to_jdl_bad_source_reference(): + """A source reference to a non-existent CWL input should fail.""" + cwl = CWL_WITH_IO.replace("source: helper_script", "source: nonexistent_input") + task = parse_cwl(cwl) + hint = extract_job_hint(task) + with pytest.raises(ValueError, match="nonexistent_input"): + cwl_to_jdl(task, hint, None) + + +class TestRangeExpansion: + """Tests for server-side range expansion.""" + + def test_basic_range(self): + from diracx.logic.jobs.cwl_submission import expand_range_inputs + + result = expand_range_inputs( + range_param="seed", + range_start=0, + range_end=5, + range_step=1, + base_inputs={"message": "hello"}, + ) + assert len(result) == 5 + assert result[0] == {"message": "hello", "seed": 0} + assert result[4] == {"message": "hello", "seed": 4} + + def test_range_with_step(self): + from diracx.logic.jobs.cwl_submission import expand_range_inputs + + result = expand_range_inputs( + range_param="seed", + range_start=0, + range_end=10, + range_step=2, + base_inputs=None, + ) + assert len(result) == 5 + assert [r["seed"] for r in result] == [0, 2, 4, 6, 8] + + def test_range_no_base_inputs(self): + from diracx.logic.jobs.cwl_submission import expand_range_inputs + + result = expand_range_inputs( + range_param="idx", + range_start=0, + range_end=3, + range_step=1, + base_inputs=None, + ) + assert result == [{"idx": 0}, {"idx": 1}, {"idx": 2}] diff --git a/diracx-routers/src/diracx/routers/jobs/submission.py b/diracx-routers/src/diracx/routers/jobs/submission.py index 818f7e6e0..71c8bbc0d 100644 --- a/diracx-routers/src/diracx/routers/jobs/submission.py +++ b/diracx-routers/src/diracx/routers/jobs/submission.py @@ -4,10 +4,11 @@ from typing import Annotated from fastapi import Body, Depends, HTTPException -from pydantic import BaseModel +from pydantic import BaseModel, model_validator from diracx.core.models.job import InsertedJob from diracx.db.sql import JobDB, JobLoggingDB +from diracx.logic.jobs.cwl_submission import submit_cwl_jobs as submit_cwl_jobs_bl from diracx.logic.jobs.submission import submit_jdl_jobs as submit_jdl_jobs_bl from diracx.routers.dependencies import Config @@ -73,3 +74,95 @@ async def submit_jdl_jobs( detail=str(e), ) from e return inserted_jobs + + +class CWLJobSubmission(BaseModel): + """Request body for CWL job submission.""" + + workflow: str # CWL workflow definition as YAML string + inputs: list[dict] = [] # Per-job input parameters; each dict produces one job + range_param: str | None = None + range_start: int | None = None + range_end: int | None = None + range_step: int | None = None + base_inputs: dict | None = None + + @model_validator(mode="after") + def validate_mutual_exclusion(self): + has_inputs = bool(self.inputs) + has_range = self.range_param is not None + if has_inputs and has_range: + raise ValueError("'inputs' and 'range_param' are mutually exclusive") + if has_range and self.range_end is None: + raise ValueError("'range_end' is required when 'range_param' is set") + return self + + +@router.post("/") +async def submit_cwl_jobs( + body: CWLJobSubmission, + job_db: JobDB, + job_logging_db: JobLoggingDB, + user_info: Annotated[AuthorizedUserInfo, Depends(verify_dirac_access_token)], + check_permissions: CheckWMSPolicyCallable, + config: Config, +) -> list[InsertedJob]: + """Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + """ + await check_permissions(action=ActionType.CREATE, job_db=job_db) + + # Handle range expansion + if body.range_param: + from diracx.logic.jobs.cwl_submission import expand_range_inputs + + # range_end is guaranteed non-None here by the model validator + assert body.range_end is not None + body.inputs = expand_range_inputs( + range_param=body.range_param, + range_start=body.range_start or 0, + range_end=body.range_end, + range_step=body.range_step or 1, + base_inputs=body.base_inputs, + ) + + input_params_list: list[dict | None] = list(body.inputs) if body.inputs else [None] + + try: + inserted_jobs = await submit_cwl_jobs_bl( + body.workflow, + input_params_list, + job_db=job_db, + job_logging_db=job_logging_db, + user_info=user_info, + config=config, + ) + except (ValueError, NotImplementedError) as e: + raise HTTPException( + status_code=HTTPStatus.BAD_REQUEST, + detail=str(e), + ) from e + return inserted_jobs + + +@router.get("/workflows/{workflow_id}") +async def get_workflow( + workflow_id: str, + job_db: JobDB, + user_info: Annotated[AuthorizedUserInfo, Depends(verify_dirac_access_token)], + check_permissions: CheckWMSPolicyCallable, +) -> dict[str, str]: + """Retrieve a CWL workflow definition by its content-addressed ID.""" + await check_permissions(action=ActionType.QUERY, job_db=job_db) + + try: + cwl = await job_db.get_workflow(workflow_id) + except Exception as e: + raise HTTPException( + status_code=HTTPStatus.NOT_FOUND, + detail=str(e), + ) from e + return {"workflow_id": workflow_id, "cwl": cwl} diff --git a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/aio/operations/_operations.py b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/aio/operations/_operations.py index a2e0565c5..110bf10ec 100644 --- a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/aio/operations/_operations.py +++ b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/aio/operations/_operations.py @@ -42,11 +42,13 @@ build_jobs_get_job_sandbox_request, build_jobs_get_job_sandboxes_request, build_jobs_get_sandbox_file_request, + build_jobs_get_workflow_request, build_jobs_initiate_sandbox_upload_request, build_jobs_patch_metadata_request, build_jobs_reschedule_jobs_request, build_jobs_search_request, build_jobs_set_job_statuses_request, + build_jobs_submit_cwl_jobs_request, build_jobs_submit_jdl_jobs_request, build_jobs_summary_request, build_jobs_unassign_bulk_jobs_sandboxes_request, @@ -2325,6 +2327,167 @@ async def submit_jdl_jobs(self, body: Union[list[str], IO[bytes]], **kwargs: Any return deserialized # type: ignore + @overload + async def submit_cwl_jobs( + self, body: _models.CWLJobSubmission, *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: ~_generated.models.CWLJobSubmission + :keyword content_type: Body Parameter content-type. Content type parameter for JSON body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @overload + async def submit_cwl_jobs( + self, body: IO[bytes], *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: IO[bytes] + :keyword content_type: Body Parameter content-type. Content type parameter for binary body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @distributed_trace_async + async def submit_cwl_jobs( + self, body: Union[_models.CWLJobSubmission, IO[bytes]], **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Is either a CWLJobSubmission type or a IO[bytes] type. Required. + :type body: ~_generated.models.CWLJobSubmission or IO[bytes] + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + _params = kwargs.pop("params", {}) or {} + + content_type: Optional[str] = kwargs.pop("content_type", _headers.pop("Content-Type", None)) + cls: ClsType[list[_models.InsertedJob]] = kwargs.pop("cls", None) + + content_type = content_type or "application/json" + _json = None + _content = None + if isinstance(body, (IOBase, bytes)): + _content = body + else: + _json = self._serialize.body(body, "CWLJobSubmission") + + _request = build_jobs_submit_cwl_jobs_request( + content_type=content_type, + json=_json, + content=_content, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = await self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("[InsertedJob]", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore + + @distributed_trace_async + async def get_workflow(self, workflow_id: str, **kwargs: Any) -> dict[str, str]: + """Get Workflow. + + Retrieve a CWL workflow definition by its content-addressed ID. + + :param workflow_id: Required. + :type workflow_id: str + :return: dict mapping str to str + :rtype: dict[str, str] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = kwargs.pop("headers", {}) or {} + _params = kwargs.pop("params", {}) or {} + + cls: ClsType[dict[str, str]] = kwargs.pop("cls", None) + + _request = build_jobs_get_workflow_request( + workflow_id=workflow_id, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = await self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("{str}", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore + class LollygagOperations: """ diff --git a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/__init__.py b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/__init__.py index b97d2e439..f898cc08f 100644 --- a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/__init__.py +++ b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/__init__.py @@ -16,6 +16,7 @@ BodyAuthRevokeRefreshTokenByRefreshToken, BodyJobsRescheduleJobs, BodyJobsUnassignBulkJobsSandboxes, + CWLJobSubmission, ExtendedMetadata, GroupInfo, HTTPValidationError, @@ -63,6 +64,7 @@ "BodyAuthRevokeRefreshTokenByRefreshToken", "BodyJobsRescheduleJobs", "BodyJobsUnassignBulkJobsSandboxes", + "CWLJobSubmission", "ExtendedMetadata", "GroupInfo", "HTTPValidationError", diff --git a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/_models.py b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/_models.py index 69b8ffcf1..c4814a822 100644 --- a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/_models.py +++ b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/models/_models.py @@ -184,6 +184,79 @@ def __init__(self, *, job_ids: list[int], **kwargs: Any) -> None: self.job_ids = job_ids +class CWLJobSubmission(_serialization.Model): + """Request body for CWL job submission. + + All required parameters must be populated in order to send to server. + + :ivar workflow: Workflow. Required. + :vartype workflow: str + :ivar inputs: Inputs. + :vartype inputs: list[dict[str, any]] + :ivar range_param: Range Param. + :vartype range_param: str + :ivar range_start: Range Start. + :vartype range_start: int + :ivar range_end: Range End. + :vartype range_end: int + :ivar range_step: Range Step. + :vartype range_step: int + :ivar base_inputs: Base Inputs. + :vartype base_inputs: dict[str, any] + """ + + _validation = { + "workflow": {"required": True}, + } + + _attribute_map = { + "workflow": {"key": "workflow", "type": "str"}, + "inputs": {"key": "inputs", "type": "[{object}]"}, + "range_param": {"key": "range_param", "type": "str"}, + "range_start": {"key": "range_start", "type": "int"}, + "range_end": {"key": "range_end", "type": "int"}, + "range_step": {"key": "range_step", "type": "int"}, + "base_inputs": {"key": "base_inputs", "type": "{object}"}, + } + + def __init__( + self, + *, + workflow: str, + inputs: list[dict[str, Any]] = [], + range_param: Optional[str] = None, + range_start: Optional[int] = None, + range_end: Optional[int] = None, + range_step: Optional[int] = None, + base_inputs: Optional[dict[str, Any]] = None, + **kwargs: Any + ) -> None: + """ + :keyword workflow: Workflow. Required. + :paramtype workflow: str + :keyword inputs: Inputs. + :paramtype inputs: list[dict[str, any]] + :keyword range_param: Range Param. + :paramtype range_param: str + :keyword range_start: Range Start. + :paramtype range_start: int + :keyword range_end: Range End. + :paramtype range_end: int + :keyword range_step: Range Step. + :paramtype range_step: int + :keyword base_inputs: Base Inputs. + :paramtype base_inputs: dict[str, any] + """ + super().__init__(**kwargs) + self.workflow = workflow + self.inputs = inputs + self.range_param = range_param + self.range_start = range_start + self.range_end = range_end + self.range_step = range_step + self.base_inputs = base_inputs + + class ExtendedMetadata(_serialization.Model): """ExtendedMetadata. diff --git a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/operations/_operations.py b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/operations/_operations.py index 7dcaa92ee..68ee447a3 100644 --- a/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/operations/_operations.py +++ b/extensions/gubbins/gubbins-client/src/gubbins/client/_generated/operations/_operations.py @@ -565,6 +565,42 @@ def build_jobs_submit_jdl_jobs_request(**kwargs: Any) -> HttpRequest: return HttpRequest(method="POST", url=_url, headers=_headers, **kwargs) +def build_jobs_submit_cwl_jobs_request(**kwargs: Any) -> HttpRequest: + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + + content_type: Optional[str] = kwargs.pop("content_type", _headers.pop("Content-Type", None)) + accept = _headers.pop("Accept", "application/json") + + # Construct URL + _url = "/api/jobs/" + + # Construct headers + if content_type is not None: + _headers["Content-Type"] = _SERIALIZER.header("content_type", content_type, "str") + _headers["Accept"] = _SERIALIZER.header("accept", accept, "str") + + return HttpRequest(method="POST", url=_url, headers=_headers, **kwargs) + + +def build_jobs_get_workflow_request(workflow_id: str, **kwargs: Any) -> HttpRequest: + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + + accept = _headers.pop("Accept", "application/json") + + # Construct URL + _url = "/api/jobs/workflows/{workflow_id}" + path_format_arguments = { + "workflow_id": _SERIALIZER.url("workflow_id", workflow_id, "str"), + } + + _url: str = _url.format(**path_format_arguments) # type: ignore + + # Construct headers + _headers["Accept"] = _SERIALIZER.header("accept", accept, "str") + + return HttpRequest(method="GET", url=_url, headers=_headers, **kwargs) + + def build_lollygag_insert_owner_object_request( # pylint: disable=name-too-long owner_name: str, **kwargs: Any ) -> HttpRequest: @@ -2901,6 +2937,167 @@ def submit_jdl_jobs(self, body: Union[list[str], IO[bytes]], **kwargs: Any) -> l return deserialized # type: ignore + @overload + def submit_cwl_jobs( + self, body: _models.CWLJobSubmission, *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: ~_generated.models.CWLJobSubmission + :keyword content_type: Body Parameter content-type. Content type parameter for JSON body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @overload + def submit_cwl_jobs( + self, body: IO[bytes], *, content_type: str = "application/json", **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Required. + :type body: IO[bytes] + :keyword content_type: Body Parameter content-type. Content type parameter for binary body. + Default value is "application/json". + :paramtype content_type: str + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + + @distributed_trace + def submit_cwl_jobs( + self, body: Union[_models.CWLJobSubmission, IO[bytes]], **kwargs: Any + ) -> list[_models.InsertedJob]: + """Submit Cwl Jobs. + + Submit CWL workflow jobs. + + Accepts a CWL workflow definition (YAML string) and zero or more + input parameter dicts. Each input dict produces a separate job. + If no inputs are provided, a single job is created with no input parameters. + + :param body: Is either a CWLJobSubmission type or a IO[bytes] type. Required. + :type body: ~_generated.models.CWLJobSubmission or IO[bytes] + :return: list of InsertedJob + :rtype: list[~_generated.models.InsertedJob] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = case_insensitive_dict(kwargs.pop("headers", {}) or {}) + _params = kwargs.pop("params", {}) or {} + + content_type: Optional[str] = kwargs.pop("content_type", _headers.pop("Content-Type", None)) + cls: ClsType[list[_models.InsertedJob]] = kwargs.pop("cls", None) + + content_type = content_type or "application/json" + _json = None + _content = None + if isinstance(body, (IOBase, bytes)): + _content = body + else: + _json = self._serialize.body(body, "CWLJobSubmission") + + _request = build_jobs_submit_cwl_jobs_request( + content_type=content_type, + json=_json, + content=_content, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("[InsertedJob]", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore + + @distributed_trace + def get_workflow(self, workflow_id: str, **kwargs: Any) -> dict[str, str]: + """Get Workflow. + + Retrieve a CWL workflow definition by its content-addressed ID. + + :param workflow_id: Required. + :type workflow_id: str + :return: dict mapping str to str + :rtype: dict[str, str] + :raises ~azure.core.exceptions.HttpResponseError: + """ + error_map: MutableMapping = { + 401: ClientAuthenticationError, + 404: ResourceNotFoundError, + 409: ResourceExistsError, + 304: ResourceNotModifiedError, + } + error_map.update(kwargs.pop("error_map", {}) or {}) + + _headers = kwargs.pop("headers", {}) or {} + _params = kwargs.pop("params", {}) or {} + + cls: ClsType[dict[str, str]] = kwargs.pop("cls", None) + + _request = build_jobs_get_workflow_request( + workflow_id=workflow_id, + headers=_headers, + params=_params, + ) + _request.url = self._client.format_url(_request.url) + + _stream = False + pipeline_response: PipelineResponse = self._client._pipeline.run( # pylint: disable=protected-access + _request, stream=_stream, **kwargs + ) + + response = pipeline_response.http_response + + if response.status_code not in [200]: + map_error(status_code=response.status_code, response=response, error_map=error_map) + raise HttpResponseError(response=response) + + deserialized = self._deserialize("{str}", pipeline_response.http_response) + + if cls: + return cls(pipeline_response, deserialized, {}) # type: ignore + + return deserialized # type: ignore + class LollygagOperations: """ diff --git a/pixi.lock b/pixi.lock index a0fee9acf..b8094d68e 100644 --- a/pixi.lock +++ b/pixi.lock @@ -23,6 +23,7 @@ environments: - 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