| import http
|
| import json
|
| import os
|
| from typing import BinaryIO, Union
|
|
|
| import requests
|
| from pydantic import BaseModel
|
|
|
| from vcutils.biosim_pipeline.data_manager import DataManager
|
| from vcutils.biosim_pipeline.datamodels import SourceOmex, Simulator, SimulationRun, BiosimulationsProject
|
|
|
|
|
| class _SimulationRunApiRequest(BaseModel):
|
| name: str
|
| simulator: str
|
| simulatorVersion: str
|
| maxTime: int
|
|
|
|
|
|
|
|
|
|
|
| def check_run_status(simulation_run: SimulationRun) -> str:
|
| api_base_url = os.environ.get('API_BASE_URL')
|
| assert(api_base_url is not None)
|
| getrun = requests.get(api_base_url + "/runs/" + simulation_run.simulation_id)
|
| if getrun.status_code == 404:
|
| return "not found"
|
| getrun_dict = getrun.json()
|
| result = getrun_dict['status']
|
| return result
|
|
|
|
|
| def run_project(
|
| source_omex: SourceOmex,
|
| simulator: Simulator,
|
| data_manager: DataManager) -> None:
|
| """
|
| This function runs the project on biosimulations.
|
| """
|
| runAPI = str(os.environ.get('API_BASE_URL')) + '/runs'
|
| runAppBaseUrl = str(os.environ.get('RUN_APP_BASE_URL'))
|
|
|
| simulation_run_request = _SimulationRunApiRequest(
|
| name=source_omex.project_id,
|
| simulator=simulator,
|
| simulatorVersion='latest',
|
| maxTime=600,
|
| )
|
|
|
| print(source_omex.omex_file)
|
| with open(source_omex.omex_file, 'rb') as omex_file_handle:
|
| multipart_form_data: dict[str, Union[tuple[str, BinaryIO], tuple[None, str]]] = {
|
| 'file': (source_omex.project_id + '.omex', omex_file_handle),
|
| 'simulationRun': (None, simulation_run_request.json()),
|
| }
|
| req = requests.post(runAPI, files=multipart_form_data)
|
| req.raise_for_status()
|
| res = req.json()
|
|
|
| simulation_id = res["id"]
|
| """
|
| simulator: Simulator
|
| simulator_version: str
|
| simulation_id: str
|
| project_id: str
|
| status: Optional[str] = "Unknown"
|
| """
|
| data_manager.write_run(SimulationRun(
|
| simulator=simulator,
|
| simulator_version=res['simulatorVersion'],
|
| simulation_id=simulation_id,
|
| project_id=source_omex.project_id,
|
| status=res['status']
|
| ))
|
|
|
| print("Ran " + source_omex.project_id + " on biosimulations with simulation id: " + simulation_id)
|
| print("View:", runAppBaseUrl + "/runs/" + simulation_id)
|
|
|
|
|
| def publish_project(data_manager: DataManager, run: SimulationRun, overwrite: bool = False) -> None:
|
| api_base_url = os.environ.get('API_BASE_URL')
|
| if run.status != "SUCCEEDED":
|
| print(run.project_id, "did not succeed - or status needs to be updated. status is", run.status)
|
| return
|
|
|
| for project in data_manager.read_projects():
|
| if project.project_id == run.project_id:
|
| print(run.project_id, "already published")
|
| return
|
|
|
| simulation_publish_data = {
|
| 'id': run.project_id,
|
| 'simulationRun': run.simulation_id,
|
| }
|
| token = get_token()
|
| headers = {
|
| "Authorization": f"{token}"
|
| }
|
| print(run.project_id, "publishing")
|
| getproj = requests.get(f"{api_base_url}/projects/" + run.project_id, headers=headers)
|
| if getproj.status_code == 404:
|
| req = requests.post(
|
| f"{api_base_url}/projects/" + run.project_id,
|
| json=simulation_publish_data, headers=headers)
|
| req.raise_for_status()
|
| data_manager.write_project(BiosimulationsProject(
|
| project_id=run.project_id,
|
| simulation_id=run.simulation_id
|
| ))
|
| elif overwrite:
|
| req = requests.put(
|
| f"{api_base_url}/projects/" + run.project_id,
|
| json=simulation_publish_data, headers=headers)
|
| req.raise_for_status()
|
| data_manager.write_project(BiosimulationsProject(
|
| project_id=run.project_id,
|
| simulation_id=run.simulation_id
|
| ))
|
|
|
|
|
| def get_token() -> str:
|
| client_id = os.environ.get('CLIENT_ID', "CLIENT_ID-not-set")
|
| client_secret = os.environ.get('CLIENT_SECRET', "CLIENT_SECRET-not-set")
|
| auth_host = os.environ.get('AUTH_HOST', "AUTH_HOST-not-set")
|
| auth_audience = os.environ.get('AUTH_AUDIENCE', "AUTH_AUDIENCE-not-set")
|
|
|
| conn = http.client.HTTPSConnection(auth_host)
|
| payload = f'{{"client_id":"{client_id}","client_secret":"{client_secret}",' \
|
| f'"audience":"{auth_audience}","grant_type":"client_credentials"}}'
|
| headers = {'content-type': "application/json"}
|
| conn.request("POST", "/oauth/token", payload, headers)
|
|
|
| res = conn.getresponse()
|
| data_bytes = res.read()
|
|
|
| data = data_bytes.decode("utf-8")
|
| data_dict = json.loads(data)
|
| token: str = data_dict['access_token']
|
| token = "Bearer " + token
|
| return token
|
|
|
|
|
|
|
