enforce predetermined BiosimulatorVersion use throughout and fix tests

biosim_server/api/main.py

@@ -142,19 +142,32 @@ async def start_verify_omex(
     omex_file: OmexFile = await get_cached_omex_file_from_upload(uploaded_file=uploaded_file)
 
     # ---- create workflow input ---- #
-    simulator_specs: list[BiosimSimulatorSpec] = []
+    simulator_versions: list[BiosimulatorVersion] = []
+    biosim_service = get_biosim_service()
+    assert biosim_service is not None
+    all_simulator_versions = await biosim_service.get_simulator_versions()
     for simulator in simulators:
+        simulator_version: Optional[BiosimulatorVersion] = None
         if ":" in simulator:
             name, version = simulator.split(":")
-            simulator_specs.append(BiosimSimulatorSpec(simulator=name, version=version))
+            for sv in all_simulator_versions:
+                if sv.id == name and sv.version == version:
+                    simulator_version = sv
+                    break
         else:
-            simulator_specs.append(BiosimSimulatorSpec(simulator=simulator, version=None))
-    omex_file = OmexFile(omex_gcs_path=omex_file.omex_gcs_path, uploaded_filename="BIOMD0000000010_tellurium_Negative_feedback_and_ultrasen.omex", file_hash_md5="hash", file_size=100, bucket_name="bucket")
+            for sv in all_simulator_versions:
+                if sv.id == simulator:
+                    simulator_version = sv  # don't break, we want the last one in the list
+        if simulator_version is not None:
+            simulator_versions.append(simulator_version)
+        else:
+            raise HTTPException(status_code=400, detail=f"Simulator {simulator} not found.")
+
     workflow_id = f"{workflow_id_prefix}{uuid.uuid4()}"
     omex_verify_workflow_input = OmexVerifyWorkflowInput(
         omex_file=omex_file,
         user_description=user_description,
-        requested_simulators=simulator_specs,
+        requested_simulators=simulator_versions,
         include_outputs=include_outputs,
         rel_tol=rel_tol,
         abs_tol_min=abs_tol_min,

biosim_server/common/biosim1_client/biosim_service.py

@@ -13,7 +13,7 @@ async def get_sim_run(self, simulation_run_id: str) -> BiosimSimulationRun:
         pass
 
     @abstractmethod
-    async def run_biosim_sim(self, local_omex_path: str, omex_name: str, simulator_spec: BiosimSimulatorSpec) -> BiosimSimulationRun:
+    async def run_biosim_sim(self, local_omex_path: str, omex_name: str, simulator_version: BiosimulatorVersion) -> BiosimSimulationRun:
         pass
 
     @abstractmethod

biosim_server/common/biosim1_client/biosim_service_rest.py

@@ -34,48 +34,61 @@ async def get_sim_run(self, simulation_run_id: str) -> BiosimSimulationRun:
                 resp.raise_for_status()
                 res = await resp.json()
 
-        sim_run = BiosimSimulationRun(id=res["id"], name=res["name"], simulator=res['simulator'],
-                                      simulatorVersion=res['simulatorVersion'], simulatorDigest=res['simulatorDigest'],
-                                      status=BiosimSimulationRunStatus(res['status']))
-
+        assert res["id"] == simulation_run_id
+
+        sim_id: str = res['simulator']
+        sim_ver: str = res['simulatorVersion']
+        sim_digest: str = res['simulatorDigest']
+        sim_status = BiosimSimulationRunStatus(res['status'])
+        simulator_version = await self._get_simulator_version(sim_id=sim_id, sim_ver=sim_ver, sim_digest=sim_digest)
+        sim_run = BiosimSimulationRun(id=res["id"], name=res["name"], simulator_version=simulator_version, status=sim_status)
         return sim_run
 
 
     @override
     async def run_biosim_sim(self, local_omex_path: str, omex_name: str,
-                             simulator_spec: BiosimSimulatorSpec) -> BiosimSimulationRun:
+                             simulator_version: BiosimulatorVersion) -> BiosimSimulationRun:
         logger.info(f"Submitting simulation for {omex_name} with local path {local_omex_path} with simulator {simulator_version.id}")
-        This function runs the project on biosimulations.
-        """
-        api_base_url = get_settings().biosimulations_api_base_url
 
-        simulation_run_request = BiosimSimulationRunApiRequest(name=omex_name, simulator=simulator_spec.simulator,
-                                                               simulatorVersion=simulator_spec.version or "latest",
-                                                               maxTime=600, )
+        simulation_run_request = BiosimSimulationRunApiRequest(name=omex_name, simulator=simulator_version.id,
+                                                               simulatorVersion=simulator_version.version, maxTime=600)
 
-        print(local_omex_path)
         async with aiohttp.ClientSession() as session:
             with Path(local_omex_path).open('rb') as f:
                 data = FormData()
                 data.add_field(name='file', value=f, filename='omex.omex', content_type='multipart/form-data')
                 data.add_field(name='simulationRun', value=simulation_run_request.model_dump_json(),
                                content_type='multipart/form-data')
 
+                api_base_url = get_settings().biosimulations_api_base_url
                 async with session.post(url=api_base_url + '/runs', data=data) as resp:
                     resp.raise_for_status()
                     res = await resp.json()
 
-        if simulator_spec.version is None:
-            simulator_spec.version = res['simulatorVersion']
+        sim_id: str = res['simulator']
+        sim_ver: str = res['simulatorVersion']
+        sim_digest: str = res['simulatorDigest']
+        assert simulator_version.version == sim_ver
+        assert simulator_version.id == sim_id
+        assert simulator_version.image.digest == sim_digest
 
-        sim_run = BiosimSimulationRun(id=res["id"], name=res["name"], simulator=res['simulator'],
-                                      simulatorVersion=res['simulatorVersion'], simulatorDigest=res['simulatorDigest'],
-                                      status=BiosimSimulationRunStatus(res['status']))
+        sim_status = BiosimSimulationRunStatus(res['status'])
+        simulator_version = await self._get_simulator_version(sim_id=sim_id, sim_ver=sim_ver, sim_digest=sim_digest)
+        sim_run = BiosimSimulationRun(id=res["id"], name=res["name"], simulator_version=simulator_version, status=sim_status)
 
         # logger.info("Submitted " + omex_name + " on biosimulations with simulation id: " + sim_run.id)
         # logger.info("View:", api_base_url + "/runs/" + sim_run.id)
         return sim_run
 
+
+    async def _get_simulator_version(self, sim_id: str, sim_ver: str, sim_digest: str) -> BiosimulatorVersion:
+        simulator_version: BiosimulatorVersion
+        for simulator_version in await self.get_simulator_versions():
+            if simulator_version.id == sim_id and simulator_version.version == sim_ver and simulator_version.image.digest == sim_digest:
+                return simulator_version
+        raise Exception(f"Simulator version not found for simulator id: {sim_id}, version: {sim_ver}, digest: {sim_digest}")
+
+
     @override
     async def get_hdf5_metadata(self, simulation_run_id: str) -> HDF5File:
         api_base_url = get_settings().simdata_api_base_url

biosim_server/workflows/simulate/biosim_activities.py

@@ -33,16 +33,15 @@ async def get_sim_run(get_sim_run_input: GetSimRunInput) -> BiosimSimulationRun:
                 return BiosimSimulationRun(
                     id=get_sim_run_input.biosim_run_id,
                     name="",
-                    simulator="",
-                    simulatorVersion="",
-                    status=BiosimSimulationRunStatus.RUN_ID_NOT_FOUND
+                    simulator_version=BiosimulatorVersion(id="", name="", version="", image=DockerContainerInfo(url="", digest="")),
+                    status=BiosimSimulationRunStatus.RUN_ID_NOT_FOUND,
                 )
         raise e
 
 
 class SubmitBiosimSimInput(BaseModel):
     omex_file: OmexFile
-    simulator_spec: BiosimSimulatorSpec
+    simulator_version: BiosimulatorVersion
 
 
 @activity.defn
@@ -57,7 +56,7 @@ async def submit_biosim_sim(input: SubmitBiosimSimInput) -> BiosimSimulationRun:
     (_, local_omex_path) = await file_service.download_file(gcs_path=input.omex_file.omex_gcs_path)
     activity.logger.info(f"Downloaded OMEX file from gcs_path {input.omex_file.omex_gcs_path} to local path {local_omex_path}")
     simulation_run = await biosim_service.run_biosim_sim(local_omex_path=local_omex_path, omex_name=input.omex_file.uploaded_filename,
-                                                         simulator_spec=input.simulator_spec)
+                                                         simulator_version=input.simulator_version)
     os.remove(local_omex_path)
     activity.logger.info(f"Deleted local OMEX file at {local_omex_path}")
     return simulation_run

biosim_server/workflows/simulate/omex_sim_workflow.py

@@ -15,7 +15,7 @@
 
 class OmexSimWorkflowInput(BaseModel):
     omex_file: OmexFile
-    simulator_spec: BiosimSimulatorSpec
+    simulator_version: BiosimulatorVersion
 
 
 class OmexSimWorkflowStatus(StrEnum):
@@ -54,11 +54,11 @@ def get_omex_sim_workflow_run(self) -> OmexSimWorkflowOutput:
     async def run(self, sim_input: OmexSimWorkflowInput) -> OmexSimWorkflowOutput:
         self.sim_output.workflow_id = workflow.info().workflow_id
         workflow.logger.setLevel(level=logging.DEBUG)
-        workflow.logger.info(f"Child workflow started for {sim_input.simulator_spec.simulator}.")
+        workflow.logger.info(f"Child workflow started for {sim_input.simulator_version.id}.")
 
-        workflow.logger.info(f"submitting job for simulator {sim_input.simulator_spec.simulator}.")
+        workflow.logger.info(f"submitting job for simulator {sim_input.simulator_version.id}.")
         submit_biosim_input = SubmitBiosimSimInput(omex_file=sim_input.omex_file,
-                                                   simulator_spec=sim_input.simulator_spec)
+                                                   simulator_version=sim_input.simulator_version)
         self.sim_output.biosim_run = await workflow.execute_activity(
             submit_biosim_sim,
             args=[submit_biosim_input],
@@ -67,7 +67,7 @@ async def run(self, sim_input: OmexSimWorkflowInput) -> OmexSimWorkflowOutput:
         )
 
         workflow.logger.info(
-            f"Job {self.sim_output.biosim_run.id} for {sim_input.simulator_spec.simulator}, "
+            f"Job {self.sim_output.biosim_run.id} for {sim_input.simulator_version.id}, "
             f"status is {self.sim_output.biosim_run.status}.")
 
         while self.sim_output.biosim_run is not None and self.sim_output.biosim_run.status not in [
@@ -82,7 +82,7 @@ async def run(self, sim_input: OmexSimWorkflowInput) -> OmexSimWorkflowOutput:
             )
 
             workflow.logger.info(
-                f"Job {self.sim_output.biosim_run.id} for {sim_input.simulator_spec.simulator}, "
+                f"Job {self.sim_output.biosim_run.id} for {sim_input.simulator_version.id}, "
                 f"status is {self.sim_output.biosim_run.status}.")
 
             if self.sim_output.biosim_run.status == BiosimSimulationRunStatus.FAILED:

biosim_server/workflows/simulate/trigger_sim_workflow.py

@@ -6,17 +6,23 @@
 from biosim_server.common.biosim1_client import BiosimService
 from biosim_server.common.database.data_models import OmexFile
 from biosim_server.common.temporal import pydantic_data_converter
+from biosim_server.dependencies import get_biosim_service, init_standalone, shutdown_standalone
 from biosim_server.workflows.simulate import OmexSimWorkflow, OmexSimWorkflowInput, OmexSimWorkflowOutput
 
 
 async def start_workflow() -> None:
+    await init_standalone()
+
     client = await Client.connect("localhost:7233", data_converter=pydantic_data_converter)
     omex_file = OmexFile(file_hash_md5="hash", uploaded_filename="BIOMD0000000010_tellurium_Negative_feedback_and_ultrasen.omex", file_size=100, omex_gcs_path="path/to/hash.omex", bucket_name="bucket")
-    omex_sim_workflow_input = OmexSimWorkflowInput(omex_file=omex_file, simulator_spec=BiosimSimulatorSpec(simulator="vcell"))
+    biosim_service: BiosimService | None = get_biosim_service()
+    assert biosim_service is not None
+    simulator_version = (await biosim_service.get_simulator_versions())[0]
+    omex_sim_workflow_input = OmexSimWorkflowInput(omex_file=omex_file, simulator_version=simulator_version)
     handle = await client.start_workflow(
         OmexSimWorkflow.run,
         args=[OmexSimWorkflowInput(omex_file=omex_sim_workflow_input.omex_file,
-                                   simulator_spec=omex_sim_workflow_input.simulator_spec)],
+                                   simulator_version=omex_sim_workflow_input.simulator_version)],
         task_queue="verification_tasks",
         id=uuid.uuid4().hex,
     )
@@ -25,6 +31,8 @@ async def start_workflow() -> None:
     query_result: OmexSimWorkflowOutput = await handle.query(OmexSimWorkflow.get_omex_sim_workflow_run, args=[])
     print(f"Workflow status: {query_result.workflow_status}")
 
+    await shutdown_standalone()
+
 
 
 if __name__ == "__main__":

biosim_server/workflows/verify/activities.py

@@ -84,7 +84,7 @@ async def generate_statistics(gen_stats_input: GenerateStatisticsInput) -> Gener
             labels_i = sim_run_info_i.hdf5_file.datasets[dataset_name].sedml_labels
             data_i: Hdf5DataValues = results_i[dataset_name]
             array_i: NDArray[np.float64] = np.array(data_i.values, dtype=np.float64).reshape(data_i.shape)
-            simulation_version_i = f"{sim_run_info_i.biosim_sim_run.simulator}:{sim_run_info_i.biosim_sim_run.simulatorVersion}"
+            simulation_version_i = f"{sim_run_info_i.biosim_sim_run.simulator_version.id}:{sim_run_info_i.biosim_sim_run.simulator_version.version}"
 
             ds_comparison_i: list[ComparisonStatistics] = []  # holds comparisons [i,:] for this dataset
 
@@ -93,7 +93,7 @@ async def generate_statistics(gen_stats_input: GenerateStatisticsInput) -> Gener
                 run_id_j = sim_run_info_j.biosim_sim_run.id
                 results_j: dict[str, Hdf5DataValues] = datasets[run_id_j]
                 labels_j = sim_run_info_j.hdf5_file.datasets[dataset_name].sedml_labels
-                simulation_version_j = f"{sim_run_info_j.biosim_sim_run.simulator}:{sim_run_info_j.biosim_sim_run.simulatorVersion}"
+                simulation_version_j = f"{sim_run_info_j.biosim_sim_run.simulator_version.id}:{sim_run_info_j.biosim_sim_run.simulator_version.version}"
 
                 # create a comparison statistics object with default values, add data or error message if needed
                 stats_i_j = ComparisonStatistics(simulator_version_i=simulation_version_i,

biosim_server/workflows/verify/omex_verify_workflow.py

@@ -28,7 +28,7 @@ def __str__(self) -> str:
 class OmexVerifyWorkflowInput(BaseModel):
     omex_file: OmexFile
     user_description: str
-    requested_simulators: list[BiosimSimulatorSpec]
+    requested_simulators: list[BiosimulatorVersion]
     include_outputs: bool
     rel_tol: float
     abs_tol_min: float
@@ -41,7 +41,7 @@ class OmexVerifyWorkflowOutput(BaseModel):
     workflow_input: OmexVerifyWorkflowInput
     workflow_status: OmexVerifyWorkflowStatus
     timestamp: str
-    actual_simulators: Optional[list[BiosimSimulatorSpec]] = None
+    actual_simulators: Optional[list[BiosimulatorVersion]] = None
     workflow_run_id: Optional[str] = None
     workflow_results: Optional[GenerateStatisticsOutput] = None
 
@@ -77,9 +77,9 @@ async def run(self, verify_input: OmexVerifyWorkflowInput) -> OmexVerifyWorkflow
         for simulator_spec in verify_input.requested_simulators:
             child_workflows.append(
                 workflow.start_child_workflow(OmexSimWorkflow.run,  # type: ignore
-                    args=[OmexSimWorkflowInput(omex_file=verify_input.omex_file, simulator_spec=simulator_spec)],
-                    result_type=OmexSimWorkflowOutput,
-                    task_queue="verification_tasks", execution_timeout=timedelta(minutes=10), ))
+                                              args=[OmexSimWorkflowInput(omex_file=verify_input.omex_file, simulator_version=simulator_spec)],
+                                              result_type=OmexSimWorkflowOutput,
+                                              task_queue="verification_tasks", execution_timeout=timedelta(minutes=10), ))
 
         workflow.logger.info(f"waiting for {len(child_workflows)} child simulation workflows.")
         # Wait for all child workflows to complete

biosim_server/workflows/verify/runs_verify_workflow.py

@@ -44,7 +44,7 @@ class RunsVerifyWorkflowOutput(BaseModel):
     workflow_status: RunsVerifyWorkflowStatus
     timestamp: str
     workflow_error: Optional[str] = None
-    actual_simulators: Optional[list[BiosimSimulatorSpec]] = None
+    actual_simulators: Optional[list[BiosimulatorVersion]] = None
     workflow_run_id: Optional[str] = None
     workflow_results: Optional[GenerateStatisticsOutput] = None
 

biosim_server/workflows/verify/trigger_verify_workflow.py

@@ -7,16 +7,22 @@
 
 
 async def start_workflow() -> None:
-    client = await Client.connect("localhost:7233", data_converter=pydantic_data_converter)
+    await init_standalone()
+
+    client = get_temporal_client()
+    assert client is not None
     omex_file = OmexFile(omex_gcs_path="path/to/model.omex", uploaded_filename="BIOMD0000000010_tellurium_Negative_feedback_and_ultrasen.omex", file_hash_md5="hash", file_size=100, bucket_name="bucket")
+
+    biosim_service = get_biosim_service()
+    assert biosim_service is not None
+    simulator_versions: list[BiosimulatorVersion] = await biosim_service.get_simulator_versions()
     workflow_id = uuid.uuid4().hex
     handle = await client.start_workflow(
         OmexVerifyWorkflow.run,
         args=[OmexVerifyWorkflowInput(
             omex_file=omex_file,
             user_description="description",
-            requested_simulators=[BiosimSimulatorSpec(simulator="vcell", version="latest"),
-                                  BiosimSimulatorSpec(simulator="copasi", version="latest")],
+            requested_simulators=[simulator_versions[0], simulator_versions[1]],
             include_outputs=True,
             rel_tol=1e-4,
             abs_tol_min=1e-3,
@@ -28,6 +34,8 @@ async def start_workflow() -> None:
     )
     print(f"Started workflow with ID: {handle.id}")
 
+    await shutdown_standalone()
+
 
 if __name__ == "__main__":
     asyncio.run(start_workflow())

tests/api/test_main.py

@@ -48,7 +48,7 @@ async def test_omex_verify_and_get_output_mockGCS(omex_verify_workflow_input: Om
     assert omex_verify_workflow_input.observables is not None
     query_params: dict[str, float | str | list[str]] = {
         "workflow_id_prefix": "verification-",
-        "simulators": [sim.simulator for sim in omex_verify_workflow_input.requested_simulators],
+        "simulators": [f"{sim.id}:{sim.version}" for sim in omex_verify_workflow_input.requested_simulators],
         "include_outputs": omex_verify_workflow_input.include_outputs,
         "user_description": omex_verify_workflow_input.user_description,
         "observables": omex_verify_workflow_input.observables,
@@ -91,7 +91,7 @@ async def test_omex_verify_and_get_output_GCS(omex_verify_workflow_input: OmexVe
     assert omex_verify_workflow_input.observables is not None
     query_params: dict[str, float | str | list[str]] = {
         "workflow_id_prefix": "verification-",
-        "simulators": [sim.simulator for sim in omex_verify_workflow_input.requested_simulators],
+        "simulators": [f"{sim.id}:{sim.version}" for sim in omex_verify_workflow_input.requested_simulators],
         "include_outputs": omex_verify_workflow_input.include_outputs,
         "user_description": omex_verify_workflow_input.user_description,
         "observables": omex_verify_workflow_input.observables,