📝 Adds rabbit ss1d example script for public-api [skip actions] (#3138)

tests/public-api/examples/.gitignore

@@ -2,3 +2,5 @@
 *.json
 *.txt
 *.ipynb
+# input files
+!data_rabbit_cardiac/

tests/public-api/examples/data_rabbit_cardiac/initial_WTstates.txt

@@ -0,0 +1 @@
+1.37502380000000e-03	9.87089040000000e-01	9.91792330000000e-01	7.01839599059895e-06	1.00067670000000e+00	2.71686070000000e-02	1.61672490000000e-02	4.30233143427199e-03	7.80717071021313e-01	4.30070614007387e-03	9.91776471924169e-01	1.92953960206578e-01	6.03487435980430e-02	7.83830949712806e-01	6.87394160908516e-07	1.89572432945224e-07	2.72749907930016e+00	5.94139243736699e-01	1.01817556868506e-02	1.07772490680837e-01	1.53675089037119e-02	2.53281010000000e-04	1.45194984664938e-03	1.38049879142935e-01	2.42453028953050e-03	7.94665117780574e-03	1.15032206558552e-02	7.72148958403062e-02	1.29512937945466e-01	1.22533949113428e+00	5.41856748595056e-01	5.66263070928663e+00	5.65803488782485e+00	5.65793960414529e+00	1.35000000000000e+02	1.87973841710593e-04	1.24175755576104e-04	9.80439326045149e-05	-8.46709654219819e+01	4.76724435751784e-01	0.00000000000000e+00	0.00000000000000e+00	2.54396524740325e+04	-1.61779918341570e+04	-1.89056393255094e+05	1.79868522042596e+05	2.63837800000000e-01	8.96327497908432e-02	8.42492982261963e-03	1.21975521245901e-03	3.26626538090676e-01	9.83564517952387e-03	1.12758648482790e-01	1.06074803099061e-02	1.54342185242217e-03	4.13351671573873e-01	1.23740090409898e-02	1.82464940000000e-08	2.17002140000000e-11	8.26062916474434e-01	2.24698596325533e-05	1.46097101414056e-02	1.08508307672484e-01	4.09476672435635e-05	5.07533657008860e-02	8.28518788627629e-01	2.34971524306373e-05	1.44586344628127e-02	1.07405533939698e-01	3.99761539610029e-05	4.95264603326507e-02	8.79587288126774e-01	2.27195074764805e-05	3.59555538012108e-03	2.67047140344325e-02	7.32547547699722e-05	9.00141866610291e-02	8.85784874410360e-01	2.31126063678609e-05	3.48258885399952e-03	2.58703452502185e-02	6.88339462452406e-05	8.47461860899517e-02	1.61197296381461e-06	2.08577373084540e-04	1.19065445556838e-01	7.58655435631373e-01	6.04551404486629e-02	9.48755677017729e-03	1.66090987262331e-05	0.00000000000000e+00	0.00000000000000e+00	2.39524978782952e-02	6.41644384969010e-11	1.19820407631612e-04	1.88032327044201e-05	3.28971137723882e-08	4.32110272330849e-16	4.14600638669982e-16	2.36953168780722e-13	1.50956358017391e-12	2.80183257033658e-02	8.58915687332272e-08	1.35149200867794e-08	2.45339571906417e-11	4.36074558006248e-08	0.00000000000000e+00	1.62668363490110e-24	6.41053442026113e-20	1.00686660060463e-20	1.79607163383628e-23	0.00000000000000e+00	0.00000000000000e+00	0.00000000000000e+00	0.00000000000000e+00	1.49843392018885e-304	0.00000000000000e+00	0.00000000000000e+00	0.00000000000000e+00	0.00000000000000e+00	0.00000000000000e+00	0.00000000000000e+00	4.64736956982462e-308	0.00000000000000e+00	0.00000000000000e+00	3.10083021551703e+02	1.52889432592164e+01	2.17165991156356e-02	0.00000000000000e+00	0.00000000000000e+00	0.00000000000000e+00	6.25423662824822e-01	1.70392706443729e-01	2.56713533507026e-04	1.42012427431816e-07	4.64851570532643e-08	3.24347125705691e-05	8.51926937302723e-04	6.95689012955649e-03	3.60966328077369e+00	5.43669998029717e-02	1.30758805639508e-04	1.35952373082443e-08	4.02034169944412e+00	2.54454801911598e+00	9.22860104152380e-05	2.66162821507126e-05	2.05179346147960e-05	1.87751969476251e-10	1.92476135791525e-15	3.85036350012499e-13	7.50785280086099e-04	3.49663333278284e-06	8.33961549884873e-06	7.89029758893487e-05	5.47294143136563e-02	1.04661405029684e-04	2.44123287931858e-09	5.01983277671203e+00	5.44221357647924e-01	1.22873074199756e-05	2.11059375521054e-05	2.00550698354832e-07	3.42362146247288e-15	3.53881975068991e-20	2.51868615353371e-17	7.87540959809223e-05	3.68753352895029e-07	1.75011101599083e-07	1.25079095005594e-07	1.64543925700837e+01	1.09157042751614e+01	2.97357231348733e+02	7.31005853939613e+01	2.83951986455465e-01	2.40580245812117e-07	0.00000000000000e+00	2.47551246368891e-02	3.82712905888321e+00	2.76260657536887e-02	1.29022777091755e-15	3.73934129310940e-04	5.74188223353930e-02	6.54316118275670e-04	5.80191388872594e-02	5.20107532057645e-02	0.00000000000000e+00	4.15919308703744e-02	3.60000000000000e-02	0.00000000000000e+00	4.86632231379200e-01	7.16671468785635e-02	8.27172793207883e-03	3.17804779433581e-03	2.78595406619341e-01	8.07506891729879e-03	9.14572121457175e-06	8.81934076803921e-01	6.95895393319336e-04	8.21087151601780e-04	3.29852404512875e-03	2.19146094413653e-01	1.53192920196010e-03	1.53192920195145e-03	1.83611114431063e-03	4.05926843054623e-03	0.00000000000000e+00

tests/public-api/examples/data_rabbit_cardiac/ss1d_meta.json

@@ -0,0 +1,128 @@
+{
+  "inputs": {
+    "Na": {
+      "displayOrder": 1,
+      "label": "Na blocker",
+      "description": "Na blocker drug concentration",
+      "type": "integer",
+      "defaultValue": "0"
+    },
+    "GKr": {
+      "displayOrder": 2,
+      "label": "GKr ratio",
+      "description": "GKr ratio",
+      "type": "integer",
+      "defaultValue": 1
+    },
+    "TotalSimulationTime": {
+      "displayOrder": 3,
+      "label": "Total simulation time",
+      "description": "Total simulation time",
+      "type": "integer",
+      "defaultValue": 300
+    },
+    "TargetHeartRatePhase1": {
+      "displayOrder": 4,
+      "label": "Target heart rate for phase 1",
+      "description": "Target heart rate for phase 1",
+      "type": "integer",
+      "defaultValue": 60
+    },
+    "TargetHeartRatePhase2": {
+      "displayOrder": 5,
+      "label": "Target heart rate for phase 2",
+      "description": "Target heart rate for phase 2",
+      "type": "integer",
+      "defaultValue": 150
+    },
+    "TargetHeartRatePhase3": {
+      "displayOrder": 6,
+      "label": "Target heart rate for phase 3",
+      "description": "Target heart rate for phase 3",
+      "type": "integer",
+      "defaultValue": 60
+    },
+    "cAMKII": {
+      "displayOrder": 7,
+      "label": "cAMKII activity levels",
+      "description": "cAMKII activity levels (expression = 'WT', 'OE', or 'KO'",
+      "type": "string",
+      "defaultValue": "WT"
+    },
+    "tissue_size_tw": {
+      "displayOrder": 8,
+      "label": "Tissue width (# of cells)",
+      "description": "Tissue width (# of cells)",
+      "type": "integer",
+      "defaultValue": "165"
+    },
+    "tissue_size_tl": {
+      "displayOrder": 9,
+      "label": "Tissue length (# of cells)",
+      "description": "Tissue length (# of cells)",
+      "type": "integer",
+      "defaultValue": "165"
+    },
+    "Homogeneity": {
+      "displayOrder": 10,
+      "label": "Homogeneity",
+      "description": "Homogeneity (expression = 'homogeneous', or 'heterogeneous'",
+      "type": "string",
+      "defaultValue": "homogeneous"
+    },
+    "initialWTStates": {
+      "displayOrder": 11,
+      "label": "Initial WT states",
+      "description": "Initial WT states",
+      "type": "data:text/plain",
+      "fileToKeyMap": {
+        "initial_WTstates.txt": "initialWTStates"
+      }
+    },
+    "num_threads": {
+      "displayOrder": 12,
+      "label": "# threads",
+      "description": "Desired number of threads",
+      "type": "integer",
+      "defaultValue": 2
+    }
+  },
+  "outputs": {
+    "output_1": {
+      "displayOrder": 1,
+      "label": "ECGs",
+      "description": "ECGs",
+      "type": "data:text/plain",
+      "fileToKeyMap": {
+        "ECGs.txt": "output_1"
+      }
+    },
+    "output_2": {
+      "displayOrder": 3,
+      "label": "APs",
+      "description": "APs",
+      "type": "data:text/plain",
+      "fileToKeyMap": {
+        "ap_1D.txt": "output_2"
+      }
+    },
+    "output_3": {
+      "displayOrder": 4,
+      "label": "CAIs",
+      "description": "CAIs",
+      "type": "data:text/plain",
+      "fileToKeyMap": {
+        "cai_1D.txt": "output_3"
+      }
+    },
+    "output_4": {
+      "displayOrder": 5,
+      "label": "Input from 1D",
+      "description": "Model input from 1D to 2D solver",
+      "type": "data:*/*",
+      "fileToKeyMap": {
+        "model_INPUT.from1D": "output_4"
+      }
+    }
+  }
+}

tests/public-api/examples/opencor.py

@@ -4,6 +4,8 @@
  $ make install-ci
  $ make .env
 
+
+Based on example https://github.com/nih-sparc/sparc-api/blob/v1.5.0/app/osparc.py
 """
 import json
 import os

tests/public-api/examples/rabbit_cardiac_ss1d.py

@@ -0,0 +1,138 @@
+"""
+Multi-scale rabbit cardiac electrophysiology models
+Rabbit Soltis-Saucerman model with full b-AR signalling (Rabbit SS 1D cardiac)
+
+ $ cd examples
+ $ make install-ci
+ $ make .env
+
+SEE https://sparc.science/datasets/4?type=dataset
+"""
+import os
+import sys
+import time
+from pathlib import Path
+from time import sleep
+from typing import Optional
+
+import osparc
+from dotenv import load_dotenv
+from osparc.models import File, JobStatus
+
+assert osparc.__version__ == "0.4.3"
+
+current_dir = Path(sys.argv[0] if __name__ == "__main__" else __file__).resolve().parent
+data_dir = current_dir / "data_rabbit_cardiac"
+
+load_dotenv()
+cfg = osparc.Configuration(
+    host=os.environ.get("OSPARC_API_URL", "http://127.0.0.1:8006"),
+    username=os.environ["OSPARC_API_KEY"],
+    password=os.environ["OSPARC_API_SECRET"],
+)
+print("Entrypoint", cfg.host)
+
+
+with osparc.ApiClient(cfg) as api_client:
+    # Upload init states file.
+
+    files_api = osparc.FilesApi(api_client)
+    initial_wtstates_file = files_api.upload_file(
+        str(data_dir / "initial_WTstates.txt")
+    )
+
+    # Create our simulation.
+
+    solvers_api = osparc.SolversApi(api_client)
+
+    solver = solvers_api.get_solver_release(
+        "simcore/services/comp/rabbit-ss-1d-cardiac-model", "1.0.0"
+    )
+
+    # SEE data_rabbit_cardiac/ss1d_meta.json::inputs
+    job = solvers_api.create_job(
+        solver.id,
+        solver.version,
+        osparc.JobInputs(
+            {
+                "Na": 0,
+                "GKr": 1,
+                "TotalSimulationTime": 50,
+                "TargetHeartRatePhase1": 60,
+                "TargetHeartRatePhase2": 150,
+                "TargetHeartRatePhase3": 60,
+                "cAMKII": "WT",
+                "tissue_size_tw": 165,
+                "tissue_size_tl": 165,
+                "Homogeneity": "homogeneous",
+                "num_threads": 4,
+                "initialWTStates": initial_wtstates_file,
+            }
+        ),
+    )
+    print("Job created", job)
+
+    # Start our simulation.
+    status = solvers_api.start_job(solver.id, solver.version, job.id)
+    start_t = time.perf_counter()
+
+    # Check the status of our simulation until it has completed.
+    while True:
+        status = solvers_api.inspect_job(solver.id, solver.version, job.id)
+
+        print(
+            f">>> Progress: {status.progress}% ",
+            f"[elapsed:{time.perf_counter() - start_t:4.2f}s]...",
+            flush=True,
+        )
+
+        if status.progress == 100:
+            break
+
+        sleep(1)
+
+    # Retrieve our simulation outputs.
+
+    print("---------------------------------------")
+    last_status: JobStatus = solvers_api.inspect_job(solver.id, solver.version, job.id)
+    print(">>> What is the status?", last_status)
+
+    outputs = solvers_api.get_job_outputs(solver.id, solver.version, job.id)
+
+    # SEE data_rabbit_cardiac/ss1d_meta.json::outputs
+    for output_name, result in outputs.results.items():
+        print(f">>> {output_name} = {result}")
+
+    # Retrieve our simulation results.
+
+    print("---------------------------------------")
+    result: Optional[File]
+
+    for output_name, result in outputs.results.items():
+        if result is None:
+            print(
+                "Can't retrieve our simulation results {output_name}...?!",
+                "Failed ?",
+                last_status.state,
+                "Finished ?",
+                last_status.progress == 100 or not last_status.stopped_at,
+            )
+        else:
+
+            # Print out the id of our simulation results file (?).
+
+            print("---------------------------------------")
+            print(">>> ", result.id)
+
+            # Download our simulation results file (?).
+
+            download_path: str = files_api.download_file(result.id)
+            print("Downloaded to", download_path)
+            print("Content-Type: ", result.content_type)
+            if result.content_type == "text/plain":
+                print("Result:", Path(download_path).read_text()[:100])
+            print("Status: ", Path(download_path).stat())
+
+    # List all the files that are available.
+    print("---------------------------------------")
+    print(files_api.list_files())