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Allow multiple simulators to run, and picking up where you left off. #7

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Allow multiple simulators to run, and picking up where you left off. #7

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41 changes: 38 additions & 3 deletions biosimulations_runutils/biosim_pipeline/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,16 +25,32 @@ def list_commands(self, ctx):

@app.command("upload_omex", help="(1) upload and run OMEX files at BioSimulations")
def upload_omex(
simulator: Annotated[Simulator, typer.Option(help="simulator to run")] = Simulator.vcell,
simulator: Annotated[Simulator, typer.Option(help="simulator to run")] = None,
simulator_version: Annotated[str, typer.Option(help="simulator version to run - defaults to 'latest'")] = "latest",
project_id: Annotated[Union[str, None], typer.Option(help="filter by project_id")] = None,
omex_src_dir: Annotated[Union[Path, None], typer.Option(help="defaults env.OMEX_SOURCE_DIR")] = None,
out_dir: Annotated[Union[Path, None], typer.Option(help="defaults to env.OMEX_OUTPUT_DIR")] = None
out_dir: Annotated[Union[Path, None], typer.Option(help="defaults to env.OMEX_OUTPUT_DIR")] = None,
redo: Annotated[Union[str, None], typer.Option(help="Whether to re-run all files in directory ('all'), nothing that was already run before ('none'), or only new and previously-failed runs ('failed')")] = "all"
) -> None:
load_dotenv()
data_manager = DataManager(omex_src_dir=omex_src_dir, out_dir=out_dir)

if simulator_version is not None and simulator is None:
raise ValueError("Unable to set simulator_version without specifying a single simulator.")

projects = data_manager.read_projects()
runs: list[SimulationRun] = data_manager.read_run_requests()
previous = set()
if redo == "none":
for run in runs:
previous.add((run.simulator, run.project_id))
elif redo == "failed":
for run in runs:
if run.status.lower()!="failed":
previous.add((run.simulator, run.project_id))
elif redo != "all":
raise ValueError(f"Unknown 'redo' option {redo}: valid options are 'all', 'new', and 'failed'")


for source_omex in data_manager.get_source_omex_archives():
if source_omex.project_id in projects:
Expand All @@ -43,7 +59,19 @@ def upload_omex(
if project_id is not None and source_omex.project_id != project_id:
continue
print(source_omex.project_id)
run_project(source_omex=source_omex, simulator=simulator, simulator_version=simulator_version, data_manager=data_manager)
if simulator is not None:
if (simulator, source_omex.project_id) in previous:
print(f"project {source_omex.project_id} has been run before using {simulator}.")
continue
print("Running", source_omex.project_id, "on", simulator)
run_project(source_omex=source_omex, simulator=simulator, simulator_version=simulator_version, data_manager=data_manager)
else:
for sim in [Simulator.tellurium, Simulator.vcell, Simulator.amici, Simulator.pysces, Simulator.libsbmlsim, Simulator.copasi]:
if (sim, source_omex.project_id) in previous:
print(f"project {source_omex.project_id} has been run before using {simulator}.")
continue
print("Running", source_omex.project_id, "on", sim)
run_project(source_omex=source_omex, simulator=simulator, simulator_version=simulator_version, data_manager=data_manager)


@app.command("refresh_status", help="(2) fetch status of runs and update biosimulations_runs.ndjson")
Expand All @@ -54,10 +82,17 @@ def refresh_status(
data_manager = DataManager(out_dir=out_dir)

runs: list[SimulationRun] = data_manager.read_run_requests()
alldone = True
for run in runs:
if run.status is not None and (run.status.lower() == "succeeded" or run.status.lower() == "failed"):
continue
print("Checking", run)
run.status = check_run_status(run)
print("New status:", run.status)
if not (run.status is not None and (run.status.lower() == "succeeded" or run.status.lower() == "failed")):
alldone = False
if alldone:
print("All runs have now either succeeded or failed.")
data_manager.write_runs(runs)


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