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📝 Adds rabbit ss1d example script for public-api [skip actions] (ITISFoundation#3138)
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‎tests/public-api/examples/.gitignore‎

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*.json
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*.txt
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*.ipynb
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# input files
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!data_rabbit_cardiac/

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

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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

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

‎tests/public-api/examples/opencor.py‎

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

‎tests/public-api/examples/rabbit_cardiac_ss1d.py‎

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

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