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@@ -61,7 +61,23 @@
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" #copy last for settings\n",
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" for v in ['lut','lutSE','setup','model','parameters','qt','sOut']:\n",
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" out[v]=seq[-1][v]\n",
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- " return out "
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+ " return out \n",
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+ "\n",
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+ "def updateSetup(job):\n",
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+ " setupFileSrc=job['setupFile']\n",
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+ " setupFile=os.path.join(job['jobDir'],'setupInput.json')\n",
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+ "\n",
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+ " with open(setupFileSrc,'r') as f:\n",
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+ " setup=json.load(f)\n",
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+ " try:\n",
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+ " setup.update(job['setupUpdates'])\n",
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+ " except KeyError:\n",
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+ " pass\n",
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+ " \n",
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+ " with open(setupFile,'w+') as f:\n",
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+ " f.write(json.dumps(setup))\n",
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+ " return setupFile\n",
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+ " "
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]
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},
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{
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@@ -191,6 +207,7 @@
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"d['modelFile']=os.path.join(fh,'software','src','PBPK','models','cDiazepam.json')\n",
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"d['parameterFile']=os.path.join(fh,'software','src','PBPK','models','cDiazepam_parameters3.json')\n",
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"d['setupFile']=os.path.join(fh,'software','src','PBPK','setup','setupHours.json')\n",
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+ "#d['setupUpdates']={'mode':'solveMatrix','method':'separately'}\n",
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"d['srcDir']='NONE'\n",
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"d['doCalculate']=True\n",
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"#data['cDiazepamB']=[d]\n",
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@@ -204,7 +221,11 @@
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" \n",
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" if not os.path.isdir(job['jobDir']):\n",
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" os.mkdir(job['jobDir'])\n",
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- " runSolver.main([job['setupFile'],job['modelFile'],job['parameterFile']],job['jobDir'],job['srcDir'])\n",
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+ " \n",
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+ " #adjust local setup file with ad-hoc modifications\n",
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+ " setupFile=updateSetup(job)\n",
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+ " \n",
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+ " runSolver.main([setupFile,job['modelFile'],job['parameterFile']],job['jobDir'],job['srcDir'])\n",
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" \n",
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"\n",
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"#t0,y0,S1,lut,lutSE=runSolver.getStartPoint(setup)\n"
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