/*5/5/14, JTC, added persistent species data for players; system parameter masterSpeciesList,
  replaces mSpecies.
  Get previous timestep biomass for all species from web service*/
  public HashMap<Integer, SpeciesZoneType> getPrediction(
      String networkOrManipulationId,
      int startTimestep,
      int runTimestep,
      Map<Integer, Integer> addSpeciesNodeList,
      ZoneNodes zoneNodes)
      throws SimulationException {
    long milliseconds = System.currentTimeMillis();

    Log.printf("\nPrediction at %d\n", startTimestep);

    // Get previous timestep biomass for all species from web service
    // JTC, use new HashMap containing all current settings from zoneNodes, masterSpeciesList
    // HJR changing to make a deep copy here , I am getting a null while iterating
    HashMap<Integer, SpeciesZoneType> masterSpeciesList =
        new HashMap<Integer, SpeciesZoneType>(zoneNodes.getNodes());

    HashMap<Integer, SpeciesZoneType> mNewSpecies = new HashMap<Integer, SpeciesZoneType>();
    // JTC, mUpdateBiomass renamed from mUpdateSpecies
    HashMap<Integer, SpeciesZoneType> mUpdateBiomass = new HashMap<Integer, SpeciesZoneType>();
    // JTC, added new update type, mUpdateParams
    HashMap<Integer, SpeciesZoneType> mUpdateParams = new HashMap<Integer, SpeciesZoneType>();

    SpeciesZoneType szt;
    String nodeConfig = null;
    SimJob job = new SimJob();
    // {70=2494, 5=2000, 42=240, 14=1752, 31=1415}
    for (int node_id : addSpeciesNodeList.keySet()) {
      int addedBiomass = addSpeciesNodeList.get(node_id);

      if (!masterSpeciesList.containsKey(node_id)) {
        szt = createSpeciesZoneType(node_id, addedBiomass);
        mNewSpecies.put(node_id, szt);
        // jtc - 04/19/15
        masterSpeciesList.put(node_id, szt);
      } else {
        szt = masterSpeciesList.get(node_id);

        szt.setCurrentBiomass(Math.max(0, szt.getCurrentBiomass() + addedBiomass));
        szt.setBiomassUpdated(true);
      }
    }

    //      //JTC, separated this to capture biomass updates made to ZoneNodes that
    //      //are not received through addSpeciesNodeList (biomass and param updates)
    //      for (SpeciesZoneType species : masterSpeciesList.values()) {
    //          //param update also updates biomass, so insert into that list
    //          //preferentially; o/w use biomass update list
    //          if (species.paramUpdated) {
    //              mUpdateParams.put(species.getNodeIndex(), species);
    //              species.setParamUpdated(false);
    //          } else if (species.biomassUpdated) {
    //              mUpdateBiomass.put(species.getNodeIndex(), species);
    //              species.setBiomassUpdated(false);
    //          }
    //      }

    // Insert new species using web services
    if (!mNewSpecies.isEmpty()) {
      zoneNodes.addNodes(mNewSpecies);
    }
    try {
      nodeConfig =
          addMultipleSpeciesType(
              mNewSpecies, masterSpeciesList, startTimestep, false, networkOrManipulationId);
    } catch (Exception ex) {
      Log.println_e(ex.getMessage());
    }
    //      // Update biomass changes to existing species using web services
    //      if (!mUpdateBiomass.isEmpty()) {
    //          List<NodeBiomass> lNodeBiomass = new ArrayList<NodeBiomass>();
    //          for (SpeciesZoneType s : mUpdateBiomass.values()) {
    //              Log.printf("Updating Biomass: [%d] %s %f\n", s.getNodeIndex(), s.getName(),
    //                      s.getCurrentBiomass() / Constants.BIOMASS_SCALE);
    //              lNodeBiomass.add(new NodeBiomass(
    //                      s.getCurrentBiomass() / Constants.BIOMASS_SCALE, s.getNodeIndex()));
    //          }
    //          try {
    ////              updateBiomass(networkOrManipulationId, lNodeBiomass, startTimestep);
    //          } catch (Exception ex) {
    //              Log.println_e(ex.getMessage());
    //          }
    //      }

    //      // JTC Update changes to existing species parameters using web services (also
    //      // resubmits biomass, but couldn't find a way to do params w/o biomass
    //      if (!mUpdateParams.isEmpty()) {
    //          try {
    ////              increaseMultipleSpeciesType(
    ////                      mUpdateBiomass,
    ////                      masterSpeciesList,
    ////                      startTimestep,
    ////                      false,
    ////                      networkOrManipulationId
    ////              );
    //          } catch (Exception ex) {
    //              Log.println_e(ex.getMessage());
    //          }
    //      }

    //      run(startTimestep, runTimestep, networkOrManipulationId);

    // get new predicted biomass
    try {
      // JTC - changed variable from "mSpecies = " to "mUpdateBiomass = "
      // mUpdateBiomass = getBiomass(networkOrManipulationId, 0, startTimestep + runTimestep);
      if (!masterSpeciesList.isEmpty() || !mNewSpecies.isEmpty()) {
        mUpdateBiomass =
            submitManipRequest("ATN", nodeConfig, startTimestep + runTimestep, false, null);
      }
    } catch (Exception ex) {
      Log.println_e(ex.getMessage());
      return null;
    }
    //      getBiomassInfo(networkOrManipulationId);

    // JTC - add loop to update persistent player species biomass information
    SpeciesZoneType updS;
    for (SpeciesZoneType priorS : masterSpeciesList.values()) {
      System.out.println("priorS.nodeIndex " + priorS.nodeIndex);
      updS = mUpdateBiomass.get(priorS.nodeIndex);
      if (updS != null && updS.currentBiomass != 0) {
        masterSpeciesList
            .get(priorS.nodeIndex)
            .setCurrentBiomass(Math.ceil(updS.getCurrentBiomass()));
      }
      //          else {
      //              zoneNodes.removeNode(priorS.nodeIndex);
      //          }
    }

    Log.printf(
        "Total Time (Get Prediction): %.2f seconds",
        Math.round((System.currentTimeMillis() - milliseconds) / 10.0) / 100.0);

    return (HashMap) zoneNodes.getNodes();
  }
  // loop through current job/results, assembling dataset
  private HashMap<Integer, SpeciesZoneType> genSpeciesDataset(
      SimJob job,
      EcosystemTimesteps ecosysTimesteps,
      Map<Integer, NodeRelationships> ecosysRelationships) {
    // calc information relevant to entire ecosystem
    int speciesCnt = ecosysTimesteps.getNodeList().size(); // Number of species
    int timesteps = ecosysTimesteps.getTimesteps(); // Maximum number of timesteps to run simulation
    int timestepsToSave = 0; // Number of timesteps of data to save to output file
    int[] matchingTimesteps =
        null; // Array of matching timesteps returned by findMatchingTimesteps()

    // read in link parameters; this was explicitly configured to allow
    // manipulation of link parameter values, but no manipulation is
    // performed in this version
    LinkParams lPs = new LinkParams(propertiesConfig);

    // loop through node values and assemble summary data
    int[] speciesID = new int[speciesCnt];
    SimJobSZT[] sztArray = new SimJobSZT[speciesCnt];
    int spNum = 0;
    for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
      SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(nodeTimesteps.getNodeId());
      sztArray[spNum] = sjSzt;
      speciesID[spNum] = sjSzt.getNodeIndex();
      spNum++;
    }

    // define objects to track species' contributions
    double[][][] contribs = new double[timesteps][speciesCnt][speciesCnt];
    double[][] calcBiomass = new double[timesteps][speciesCnt];
    double[][] contribsT; // current timestep

    // note: WebServices ATN Model uses B0 with default = 0.5.  This presumes
    // that biomasses are small, i.e. < 1.0.  Division by biomassScale
    // here is consistent with usage in WoB_Server.SimulationEngine to
    // normalize biomasses.
    // need to store bm as it varies over time through integration;
    // start with initial bm for each species
    double[] currBiomass = new double[speciesCnt];
    for (int i = 0; i < speciesCnt; i++) {
      NodeTimesteps nodeTimeSteps = ecosysTimesteps.getTimestepMap().get(speciesID[i]);
      // manually set biomass vals for excluded initial timesteps; this
      // includes the first value to be used as input
      currBiomass[i] = nodeTimeSteps.getBiomass(initTimeIdx) / biomassScale;
      calcBiomass[0][i] = currBiomass[i];
    }

    if (Constants.useCommonsMathIntegrator) {

      // Use Apache Commons Math GraggBulirschStoerIntegrator

      FirstOrderIntegrator integrator =
          new GraggBulirschStoerIntegrator(
              1.0e-8, // minimal step
              100.0, // maximal step
              ATNEquations.EXTINCT, // allowed absolute error
              1.0e-10); // allowed relative error

      // Set up the ATN equations based on the current food web and parameters
      ATNEquations ode = new ATNEquations(sztArray, ecosysRelationships, lPs);

      ATNEventHandler eventHandler = new ATNEventHandler(ode);
      // FIXME: Choose best parameter values
      integrator.addEventHandler(
          new EventFilter(eventHandler, FilterType.TRIGGER_ONLY_DECREASING_EVENTS),
          1, // maximal time interval between switching function checks (this interval prevents
          // missing sign changes in case the integration steps becomes very large)
          0.0001, // convergence threshold in the event time search
          1000, // upper limit of the iteration count in the event time search
          new BisectionSolver());

      // Set up the StepHandler, which is triggered at each time step by the integrator,
      // and copies the current biomass of each species into calcBiomass[timestep].
      // See the "Continuous Output" section of
      // https://commons.apache.org/proper/commons-math/userguide/ode.html
      FixedStepHandler fixedStepHandler =
          new FixedStepHandler() {
            public void init(double t0, double[] y0, double t) {}

            private int timestep = 0;

            public void handleStep(double t, double[] y, double[] yDot, boolean isLast) {
              // Ensure we don't go past the last time step due to rounding error
              if (timestep < calcBiomass.length) {
                System.arraycopy(y, 0, calcBiomass[timestep], 0, speciesCnt);
              }
              timestep++;
            }
          };
      StepHandler stepHandler = new StepNormalizer(timeIntvl, fixedStepHandler);
      integrator.addStepHandler(stepHandler);

      // Run the integrator to compute the biomass time series
      integrator.integrate(ode, 0.0, currBiomass, timeIntvl * timesteps, currBiomass);
      if (eventHandler.integrationWasStopped()) {
        timestepsToSave = (int) (eventHandler.getTimeStopped() / timeIntvl);
      } else {
        // Check for an oscillating steady state,
        // and only save the data through the first period of the oscillation
        matchingTimesteps = findMatchingTimesteps(calcBiomass, timesteps - 1);
        System.err.println("\nmatchingTimesteps =  " + Arrays.toString(matchingTimesteps));

        // Save timesteps up through the second matching timestep,
        // or all timesteps if there was no second matching timestep.
        if (matchingTimesteps[1] != -1) {
          timestepsToSave = matchingTimesteps[1] + 1;
        } else {
          timestepsToSave = timesteps;
        }
      }

    } else {

      // Use BulirschStoerIntegration

      // create integration object
      boolean isTest = false;
      BulirschStoerIntegration bsi =
          new BulirschStoerIntegration(
              timeIntvl, speciesID, sztArray, ecosysRelationships, lPs, maxBSIErr, equationSet);

      // calculate delta-biomass and biomass "contributions" from each related
      // species
      for (int t = initTimeIdx + 1; t < timesteps; t++) {
        boolean success = bsi.performIntegration(time(initTime, t), currBiomass);
        if (!success) {
          System.out.printf("Integration failed to converge, t = %d\n", t);
          System.out.print(bsi.extrapArrayToString(biomassScale));
          break;
        }
        currBiomass = bsi.getYNew();
        System.arraycopy(currBiomass, 0, calcBiomass[t], 0, speciesCnt);

        contribsT = bsi.getContribs();
        for (int i = 0; i < speciesCnt; i++) {
          System.arraycopy(contribsT[i], 0, contribs[t - 1][i], 0, speciesCnt);
        }
      } // timestep loop
    }

    if (useHDF5) {
      saveHDF5OutputFile(
          calcBiomass, speciesID, matchingTimesteps, job.getNode_Config(), timestepsToSave);
      return null;
    }

    double[][] webServicesData = new double[speciesCnt][timesteps];
    if (Constants.useSimEngine) { // We need the webServicesData only for marginOfErrorCalculation
      // extract timestep data from CSV
      Functions.extractCSVDataRelns(job.getCsv(), ecosysTimesteps, ecosysRelationships);
      spNum = 0;
      for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
        // copy nodetimestep data to local array for easier access
        System.arraycopy(nodeTimesteps.getBiomassArray(), 0, webServicesData[spNum], 0, timesteps);

        spNum++;
      }
    }
    // output data
    // A. print header
    psATN.printf("timesteps");
    for (int i = 0; i < timesteps; i++) {
      psATN.printf(",%d", i);
    }
    psATN.println();

    /* Convert to CSV String */
    String biomassCSV = "";
    biomassCSV = "Manipulation_id: " + job.getATNManipulationId() + "\n\n";

    int maxTimestep = job.getTimesteps();
    // Create Timestep Labels
    for (int j = 1; j <= maxTimestep; j++) {
      biomassCSV += "," + j;
    }
    HashMap<Integer, SpeciesZoneType> mSpecies = new HashMap<Integer, SpeciesZoneType>();
    // loop through each species
    for (int i = 0; i < speciesCnt; i++) {
      if (Constants.useSimEngine) {
        psATN.printf("i.%d.sim", speciesID[i]);
        // B. print WebServices simulation data for species
        for (int t = 0; t < timesteps; t++) {
          psATN.printf(",%9.0f", webServicesData[i][t]);
        }
        psATN.println();
      }

      // B. print combined biomass contributions (i.e. locally calculated biomass)
      // for current species.
      psATN.printf("i.%d.calc", speciesID[i]);
      for (int t = 0; t < timesteps; t++) {
        psATN.printf(",%9.0f", calcBiomass[t][i] * biomassScale);
      }
      psATN.println();

      //           //C. print individual biomass contributions from other species
      //           for (int j = 0; j < speciesCnt; j++) {
      //               psATN.printf("i.%d.j.%d.", speciesID[i], speciesID[j]);
      //               for (int t = 0; t < timesteps; t++) {
      //                   psATN.printf(",%9.0f", contribs[t][i][j] * biomassScale);
      //               }
      //               psATN.println();
      //           }

      float extinction = 1.E-15f;
      SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(speciesID[i]);
      // add nodes to list in the order that they are received from infos
      String name = sjSzt.getName().replaceAll(",", " ") + " [" + sjSzt.getNodeIndex() + "]";
      String tempStr = name;
      for (int t = 0; t < maxTimestep; t++) {
        tempStr += ",";

        double biomass = calcBiomass[t][i] * biomassScale;

        if (biomass > 0) {
          tempStr += biomass > extinction ? Math.ceil(biomass) : 0;
        }

        if (t == maxTimestep - 1) {
          SpeciesZoneType szt = null;
          if (!mSpecies.containsKey(sjSzt.getNodeIndex())) {
            szt = new SpeciesZoneType(sjSzt.getName(), sjSzt.getNodeIndex(), 0, 0, biomass, null);
            mSpecies.put(sjSzt.getNodeIndex(), szt);

          } else { // update existing species current biomass
            szt = mSpecies.get(sjSzt.getNodeIndex());

            szt.setCurrentBiomass(biomass);
          }
        }
      }
      biomassCSV += "\n" + tempStr;
    }

    // Append node config to the ATN CSV
    psATN.println();
    psATN.println("\"node-config: " + job.getNode_Config() + "\"");

    biomassCSV += "\n\n";

    biomassCSV += job.getConsumeMap().toString() + "\n\n";

    biomassCSV += job.getPathTable().toString();

    job.setBiomassCsv(biomassCSV);

    // System.out.println(biomassCSV);
    return mSpecies;
  }