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WIP - refactoring LangevinPostProcessor, simulations results recovery
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132 changes: 33 additions & 99 deletions
132
vcell-core/src/main/java/cbit/vcell/simdata/LangevinPostProcessor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,142 +1,76 @@ | ||
| package cbit.vcell.simdata; | ||
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| import cbit.vcell.export.server.ExportSpecs; | ||
| import cbit.vcell.mapping.SimulationContext; | ||
| import cbit.vcell.solver.*; | ||
| import cbit.vcell.solver.ode.ODESimData; | ||
| import org.vcell.util.TokenMangler; | ||
| import org.vcell.util.document.SimulationVersion; | ||
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| import java.util.ArrayList; | ||
| import java.io.File; | ||
| import java.text.SimpleDateFormat; | ||
| import java.util.Hashtable; | ||
| import java.util.LinkedHashMap; | ||
| import java.util.Map; | ||
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| public class LangevinPostProcessor { | ||
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| public static final String FAILURE_KEY = "FAILURE_KEY"; | ||
| public static final String SIMULATION_KEY = "SIMULATION_KEY"; | ||
| public static final String SIMULATION_OWNER = "SIMULATION_OWNER"; | ||
| public static final String SIMULATION_OWNER_KEY = "SIMULATION_OWNER_KEY"; | ||
| public static final String ODE_SIM_DATA_MAP_KEY = "ODE_SIM_DATA_MAP_KEY"; | ||
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| boolean failure; | ||
| Simulation sim; | ||
| SimulationOwner simOwner; | ||
| Map<Integer, ODESimData> odeSimDataMap; | ||
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| public void postProcessLangevinResults(Hashtable<String, Object> hashTable) { | ||
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| failure = (boolean) hashTable.get(FAILURE_KEY); | ||
| sim = (Simulation)hashTable.get(SIMULATION_KEY); | ||
| simOwner = (SimulationOwner)hashTable.get(SIMULATION_OWNER);; | ||
| simOwner = (SimulationOwner)hashTable.get(SIMULATION_OWNER_KEY); | ||
| odeSimDataMap = (Map<Integer, ODESimData>)hashTable.get(ODE_SIM_DATA_MAP_KEY); | ||
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| if(sim.getVersion() == null) { | ||
| throw new RuntimeException("Missing Version."); | ||
| } | ||
| if(sim.getSimulationInfo() == null) { | ||
| throw new RuntimeException("Missing Simulation Info."); | ||
| if(failure) { | ||
| return; | ||
| } | ||
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| retrieveLangevinResultsTask(); | ||
| calculateLangevinAveragesTask(); | ||
| calculateLangevinAdvancedStatisticsTask(); | ||
| } | ||
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| private void retrieveLangevinResultsTask() { | ||
| private void calculateLangevinAveragesTask() { | ||
| SolverTaskDescription std = sim.getSolverTaskDescription(); | ||
| int numTrials = std.getNumTrials(); | ||
| VCSimulationIdentifier vcSimulationIdentifier = sim.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(); | ||
| MathOverrides mathOverrides = sim.getMathOverrides(); | ||
| int sizeOverrides = mathOverrides.getSize(); | ||
| int scanCount = mathOverrides.getScanCount(); | ||
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| System.out.println(" --- " + sim.getName() + ", numTrials = " + numTrials); | ||
| System.out.println(" --- " + sim.getName() + ", jobCount" + sim.getJobCount()); | ||
| System.out.println(" --- " + sim.getName() + ", sizeOverrides = " + sizeOverrides); | ||
| System.out.println(" --- " + sim.getName() + ", scanCount = " + scanCount); | ||
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| SimulationInfo simInfo = sim.getSimulationInfo(); | ||
| VCSimulationIdentifier asi = simInfo.getAuthoritativeVCSimulationIdentifier(); | ||
| VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(asi, 0); | ||
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| // ODEDataManager dm = (ODEDataManager)getDocumentWindowManager().getRequestManager().getDataManager(null, vcSimulationDataIdentifier, false); | ||
| // ODESimData osd = (ODESimData)dm.getODESolverResultSet(); | ||
| VCSimulationIdentifier vcSimulationIdentifier = simInfo.getAuthoritativeVCSimulationIdentifier(); | ||
| MathOverrides mathOverrides = sim.getMathOverrides(); | ||
| SimulationVersion simVersion = simInfo.getSimulationVersion(); | ||
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| // TODO: go through time series and compute averages, erc | ||
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| System.out.println(" ------------------------------------"); | ||
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| } | ||
| private void calculateLangevinAveragesTask() { | ||
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| } | ||
| private void calculateLangevinAdvancedStatisticsTask() { | ||
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| } | ||
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| // public void postProcessLangevinResults(Simulation sim) { | ||
| // | ||
| // final String FAILURE_KEY = "FAILURE_KEY"; | ||
| // final String SIMULATION_KEY = "SIMULATION_KEY"; | ||
| // Hashtable<String, Object> hashTable = new Hashtable<String, Object>(); | ||
| // hashTable.put(FAILURE_KEY, false); | ||
| // hashTable.put(SIMULATION_KEY, sim); | ||
| // | ||
| // ArrayList<AsynchClientTask> taskList = new ArrayList<AsynchClientTask>(); | ||
| // AsynchClientTask retrieveLangevinResultsTask = new AsynchClientTask("Retrieving results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) { | ||
| // public void run(Hashtable<String, Object> hashTable) throws Exception { | ||
| // boolean failure = (boolean) hashTable.get(FAILURE_KEY); | ||
| // SolverTaskDescription std = sim.getSolverTaskDescription(); | ||
| // int numTrials = std.getNumTrials(); | ||
| // System.out.println(sim.getName() + ", numTrials = " + numTrials); | ||
| //// LangevinSimulationOptions lso = std.getLangevinSimulationOptions(); | ||
| // final VCSimulationIdentifier vcSimulationIdentifier = sim.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(); | ||
| // SimulationOwner simOwner = getSimWorkspace().getSimulationOwner(); | ||
| // Simulation allSims[] = simOwner.getSimulations(); | ||
| // for (Simulation simCandidate : allSims) { | ||
| // if (simCandidate.getName().startsWith(sim.getName())) { | ||
| // System.out.println(" --- " + simCandidate.getName() + ", jobCount" + simCandidate.getJobCount()); | ||
| // MathOverrides mathOverrides = simCandidate.getMathOverrides(); | ||
| // int sizeOverrides = mathOverrides.getSize(); | ||
| // int scanCount = mathOverrides.getScanCount(); | ||
| // System.out.println(" --- " + sim.getName() + ", sizeOverrides = " + sizeOverrides); | ||
| // System.out.println(" --- " + sim.getName() + ", scanCount = " + scanCount); | ||
| // | ||
| // ExportSpecs.ExportParamScanInfo es = ExportSpecs.getParamScanInfo(simCandidate,0); | ||
| // ExportSpecs.ExportParamScanInfo es1 = ExportSpecs.getParamScanInfo(simCandidate,1); | ||
| // ExportSpecs.ExportParamScanInfo es2 = ExportSpecs.getParamScanInfo(simCandidate,2); | ||
| // | ||
| // if(sim.getVersion() == null) { | ||
| // throw new RuntimeException("Missing Version."); | ||
| // } | ||
| // SimulationInfo simInfo = sim.getSimulationInfo(); | ||
| // if(simInfo == null) { | ||
| // throw new RuntimeException("Missing Simulation Info."); | ||
| // } | ||
| // | ||
| // VCSimulationIdentifier asi = simInfo.getAuthoritativeVCSimulationIdentifier(); | ||
| // VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(asi, 0); | ||
| // | ||
| // ODEDataManager dm = (ODEDataManager)getDocumentWindowManager().getRequestManager().getDataManager(outputContext, vcSimulationDataIdentifier, false); | ||
| // ODESimData osd = (ODESimData)dm.getODESolverResultSet(); | ||
| // | ||
| // | ||
| // System.out.println(" ------------------------------------"); | ||
| // } | ||
| // } | ||
| // } | ||
| // }; | ||
| // AsynchClientTask calculateLangevinAveragesTask = new AsynchClientTask("Retrieving results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) { | ||
| // public void run(Hashtable<String, Object> hashTable) throws Exception { | ||
| // boolean failure = (boolean)hashTable.get(FAILURE_KEY); | ||
| // | ||
| // } | ||
| // }; | ||
| // AsynchClientTask calculateLangevinAdvancedStatisticsTask = new AsynchClientTask("Retrieving results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) { | ||
| // public void run(Hashtable<String, Object> hashTable) throws Exception { | ||
| // boolean failure = (boolean)hashTable.get(FAILURE_KEY); | ||
| // | ||
| // } | ||
| // }; | ||
| // taskList.add(retrieveLangevinResultsTask); | ||
| // taskList.add(calculateLangevinAveragesTask); | ||
| // taskList.add(calculateLangevinAdvancedStatisticsTask); | ||
| // AsynchClientTask[] taskArray = new AsynchClientTask[taskList.size()]; | ||
| // taskList.toArray(taskArray); | ||
| // ClientTaskDispatcher.dispatch(getDocumentWindowManager().getComponent(), hashTable, taskArray, false, true, null); | ||
| // | ||
| // private static final SimpleDateFormat simpleDateFormat = new SimpleDateFormat("yyyy_MM_dd_HHmmss"); | ||
| // private static File createDirFile(SimulationContext simulationContext){ | ||
| // String userid = simulationContext.getBioModel().getVersion().getOwner().getName(); | ||
| // String simContextDirName = | ||
| // TokenMangler.fixTokenStrict(userid)+"-"+ | ||
| // TokenMangler.fixTokenStrict(simulationContext.getBioModel().getName())+"-"+ | ||
| // TokenMangler.fixTokenStrict(simulationContext.getName())+"-"+ | ||
| // TokenMangler.fixTokenStrict(simpleDateFormat.format(simulationContext.getBioModel().getVersion().getDate())); | ||
| //// simContextDirName = TokenMangler.fixTokenStrict(simContextDirName); | ||
| // File dirFile = new File("C:\\temp\\ruleBasedTestDir\\"+simContextDirName); | ||
| // if(!dirFile.exists()){ | ||
| // dirFile.mkdirs(); | ||
| // } | ||
| // return dirFile; | ||
| // } | ||
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| } |