Merge pull request #212 from indralab/fix-test-file

Fix test file path

docker/Dockerfile

@@ -30,5 +30,8 @@ RUN python -m pip install git+https://github.com/indralab/mira.git@main#egg=mira
  python -m pip uninstall -y bootstrap_flask && \
  python -m pip install bootstrap_flask
 
+# Copy the example json for reconstructing the ode semantics
+RUN wget -O /sw/sir_flux_span.json https://raw.githubusercontent.com/indralab/mira/main/tests/sir_flux_span.json
+
 COPY startup.sh startup.sh
 ENTRYPOINT ["/bin/bash", "/sw/startup.sh"]

mira/dkg/model.py

@@ -34,7 +34,7 @@
 from mira.modeling.petri import PetriNetModel, PetriNetResponse
 from mira.modeling.viz import GraphicalModel
 from mira.sources.askenet.flux_span import reproduce_ode_semantics, \
- test_file_path
+ test_file_path, docker_test_file_path
 from mira.sources.askenet.petrinet import template_model_from_askenet_json
 from mira.sources.bilayer import template_model_from_bilayer
 from mira.sources.biomodels import get_sbml_model
@@ -700,15 +700,19 @@ def askepetrinet_model_comparison(
  return resp
 
 
+flux_span_path = docker_test_file_path if docker_test_file_path.exists() else \
+ test_file_path
+
+
 class FluxSpanQuery(BaseModel):
  model: Dict[str, Any] = Field(
  ...,
- example=json.load(test_file_path.open()),
+ example=json.load(flux_span_path.open()),
  description="The model to recover the ODE-semantics from.",
  )
 
 
-@model_blueprint.post("/reconstruct_ode_semnatics",
+@model_blueprint.post("/reconstruct_ode_semantics",
  response_model=TemplateModel,
  tags=["modeling"])
 def reproduce_ode_semantics_endpoint(

mira/sources/askenet/flux_span.py

@@ -158,10 +158,13 @@ def set_semantics(tm, model_index):
 test_file_path = Path(
  __file__
 ).resolve().parent.parent.parent.parent.joinpath('tests/sir_flux_span.json')
+docker_test_file_path = Path("/sw/sir_flux_span.json")
 
 
 if __name__ == "__main__":
- with open(test_file_path.as_posix()) as fh:
+ path = docker_test_file_path if docker_test_file_path.exists() else \
+ test_file_path
+ with open(path.as_posix()) as fh:
  flux_span = json.load(fh)
  tm = reproduce_ode_semantics(flux_span)
  tm.annotations.name = 'SIR-Two-City-Flux Stratified Model with ODE Semantics'

tests/test_model_api.py

@@ -675,10 +675,14 @@ def test_counts_to_dimensionless_amr(self):
 
  def test_reconstruct_ode_semantics_endpoint(self):
  # Load test file
- from mira.sources.askenet.flux_span import test_file_path
- strat_model = json.load(test_file_path.open())
+ from mira.sources.askenet.flux_span import test_file_path, \
+ docker_test_file_path
+ path = test_file_path if test_file_path.exists() else \
+ docker_test_file_path
+
+ strat_model = json.load(path.open())
  response = self.client.post(
- "/api/reconstruct_ode_semnatics",
+ "/api/reconstruct_ode_semantics",
  json={"model": strat_model}
  )
  self.assertEqual(200, response.status_code)