File size: 4,347 Bytes
9d54b72 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 | 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
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