update to api script

bio_compose/api.py

@@ -0,0 +1,85 @@
+import os
+import time
+from functools import wraps
+
+from bio_compose.processing_tools import get_job_signature
+from bio_compose.runner import SimulationRunner, SimulationResult
+from bio_compose.verifier import Verifier, VerificationResult
+
+
+API_VERIFIER = Verifier()
+API_RUNNER = SimulationRunner()
+
+
+def get_compatible_simulators(entrypoint_file: str) -> list:
+    pass
+
+
+def verify(*args) -> VerificationResult:
+    """Verify and compare the outputs of simulators for a given entrypoint file of either sbml or omex.
+
+    :param args: Positional arguments
+
+    * 1 argument: submit omex verification with no time params. **OMEX verification only**.
+    * 2 arguments: omex filepath, simulators to include in the verification. **OMEX verification only**.
+    * 4 arguments: sbml filepath, start, stop, steps. **SBML verification only**.
+    * 5 arguments: sbml filepath, start, stop, steps, simulators. **SBML verification only**.
+
+    :return: instance of verification results.
+    :rtype: bio_compose.verifier.VerificationResult
+    """
+    verifier = Verifier()
+    if len(args) == 2:
+        simulators = args[1]
+    elif len(args) == 5:
+        simulators = args[4]
+    else:
+        simulators = ['amici', 'copasi', 'tellurium']
+
+    run_sbml = False
+    for arg in args:
+        if isinstance(arg, int):
+            run_sbml = True
+    submission = None
+
+    # parse executor and run
+    timeout = 50
+    buffer_time = 5
+    poll_time = 5
+    submission_generator = verifier.verify_sbml if run_sbml else verifier.verify_omex
+    print("Submitting verification...")
+    time.sleep(buffer_time)
+
+    # fetch params
+    submission = submission_generator(*args)
+    job_id = submission.get('job_id')
+
+    # poll gateway for results
+    n_attempts = 0
+    output = {}
+    if job_id is not None:
+        # polling loop
+        while True:
+            # quit after reaching timeout
+            n_attempts += 1
+            if n_attempts == timeout:
+                print('Timeout reached. Please try to call the function again.')
+                break
+
+            # get result after buffering (submission) or refresh if re-iteration
+            verification_result = verifier.get_output(job_id=job_id)
+
+            # report job status
+            current_status = verifier.get_output(job_id=job_id).get('content', {}).get('status', '')
+            print(f'> Status for job ending in {get_job_signature(job_id)}: {current_status} ', end='\r')
+
+            # finish if job failed or completed, otherwise re-poll
+            stop_conditions = ["COMPLETED", "FAILED"]
+            job_finished = any([current_status.endswith(condition) for condition in stop_conditions])
+            if not job_finished:
+                time.sleep(poll_time)
+            else:
+                output = verifier.get_output(job_id=job_id)
+                break
+
+    return VerificationResult(data=output)