| import json | |
| import os | |
| from pathlib import Path | |
| from typing import Optional | |
| from vcutils.biosim_pipeline.datamodels import ( | |
| BiosimulationsProject, | |
| SourceOmex, | |
| SimulationRun, | |
| SimulatorComparison | |
| ) | |
| def _get_project_name(omex_file: Path) -> str: | |
| return str(omex_file.name).split(".")[0] | |
| class DataManager(object): | |
| omex_src_dir: Path | |
| out_dir: Path | |
| projects_ndjson_file: Path | |
| runs_ndjson_file: Path | |
| def __init__(self, omex_src_dir: Optional[Path] = None, out_dir: Optional[Path] = None): | |
| self.omex_src_dir = Path(os.environ.get("OMEX_SOURCE_DIR", "OMEX_SOURCE_DIR-not-specified")) | |
| if omex_src_dir is not None: | |
| self.omex_src_dir = omex_src_dir | |
| if not os.path.exists(self.omex_src_dir): | |
| raise ValueError(f"Base source directory {self.omex_src_dir} does not exist") | |
| self.out_dir = Path(os.environ.get("OMEX_OUTPUT_DIR", "OMEX_OUTPUT_DIR-not-specified")) | |
| if out_dir is not None: | |
| self.out_dir = out_dir | |
| if not os.path.exists(self.out_dir): | |
| os.makedirs(self.out_dir) | |
| self.projects_ndjson_file = self.out_dir / 'biosimulations_projects.ndjson' | |
| self.runs_ndjson_file = self.out_dir / 'biosimulations_runs.ndjson' | |
| self.compare_ndjson_file = self.out_dir / 'biosimulations_comparisons.ndjson' | |
| def read_run_requests(self) -> list[SimulationRun]: | |
| projects: list[SimulationRun] | |
| if os.path.exists(self.runs_ndjson_file): | |
| with open(self.runs_ndjson_file) as f: | |
| projects = [SimulationRun(**json.loads(line)) for line in f.readlines()] | |
| else: | |
| projects = [] | |
| return projects | |
| def read_projects(self) -> list[BiosimulationsProject]: | |
| projects: list[BiosimulationsProject] | |
| if os.path.exists(self.projects_ndjson_file): | |
| with open(self.projects_ndjson_file) as f: | |
| projects = [BiosimulationsProject(**json.loads(line)) for line in f.readlines()] | |
| else: | |
| projects = [] | |
| return projects | |
| def write_project(self, project: BiosimulationsProject) -> None: | |
| with open(self.projects_ndjson_file, 'a') as f: | |
| f.write(json.dumps(project.dict()) + "\n") | |
| def get_spec_omex_list(self) -> list[Path]: | |
| omex_files: list[Path] = [] | |
| for omex_file in os.listdir(self.omex_src_dir): | |
| if not str(omex_file).endswith(".omex"): | |
| continue | |
| omex_files.append(self.omex_src_dir / str(omex_file)) | |
| return omex_files | |
| def get_source_omex_archives(self) -> list[SourceOmex]: | |
| source_omex_archives: list[SourceOmex] = [] | |
| for omex_file_name in os.listdir(self.omex_src_dir): | |
| if not str(omex_file_name).endswith(".omex"): | |
| continue | |
| omex_file = self.omex_src_dir / str(omex_file_name) | |
| project_id = _get_project_name(omex_file) | |
| source_omex_archives.append(SourceOmex(omex_file=omex_file, project_id=project_id)) | |
| return source_omex_archives | |
| def write_run(self, simulation_run: SimulationRun) -> None: | |
| with open(self.runs_ndjson_file, 'a') as f: | |
| f.write(json.dumps(simulation_run.dict()) + "\n") | |
| def write_runs(self, runs: list[SimulationRun]): | |
| with open(self.runs_ndjson_file, 'wt') as f: | |
| for run in runs: | |
| f.write(json.dumps(run.dict()) + "\n") | |
| def write_comparison(self, simulation_comparison: SimulatorComparison) -> None: | |
| with open(self.compare_ndjson_file, 'a') as f: | |
| f.write(json.dumps(simulation_comparison.dict()) + "\n") | |
| def read_comparisons(self) -> list[SimulatorComparison]: | |
| comparisons: list[SimulatorComparison] | |
| if os.path.exists(self.compare_ndjson_file): | |
| with open(self.compare_ndjson_file) as f: | |
| comparisons = [SimulatorComparison(**json.loads(line)) for line in f.readlines()] | |
| else: | |
| comparisons = [] | |
| return comparisons | |
| def get_run_output_dir(self, simulation_run: SimulationRun) -> Path: | |
| run_out_dir = self.out_dir / simulation_run.project_id / simulation_run.simulator.value / simulation_run.simulator_version | |
| if not os.path.exists(run_out_dir): | |
| os.makedirs(run_out_dir) | |
| return run_out_dir | |