SiLeBAT/FSK-Lab

package de.bund.bfr.knime.pmm.common.writer;

import javax.xml.stream.XMLStreamException;

import de.bund.bfr.knime.pmm.common.AgentXml;
import de.bund.bfr.knime.pmm.common.LiteratureItem;
import de.bund.bfr.knime.pmm.common.MatrixXml;
import de.bund.bfr.knime.pmm.common.PmmXmlDoc;
import de.bund.bfr.knime.pmm.common.TimeSeriesXml;
import de.bund.bfr.knime.pmm.common.generictablemodel.KnimeTuple;
import de.bund.bfr.knime.pmm.extendedtable.pmmtablemodel.TimeSeriesSchema;
import de.bund.bfr.pmfml.ModelType;
import de.bund.bfr.pmfml.numl.AtomicDescription;
import de.bund.bfr.pmfml.numl.AtomicValue;
import de.bund.bfr.pmfml.numl.ConcentrationOntology;
import de.bund.bfr.pmfml.numl.NuMLDocument;
import de.bund.bfr.pmfml.numl.ResultComponent;
import de.bund.bfr.pmfml.numl.TimeOntology;
import de.bund.bfr.pmfml.numl.Tuple;
import de.bund.bfr.pmfml.numl.TupleDescription;
import de.bund.bfr.pmfml.sbml.Metadata;
import de.bund.bfr.pmfml.sbml.PMFCompartment;
import de.bund.bfr.pmfml.sbml.PMFSpecies;
import de.bund.bfr.pmfml.sbml.PMFUnitDefinition;
import de.bund.bfr.pmfml.sbml.Reference;
import de.bund.bfr.pmfml.sbml.ReferenceImpl;

public class DataParser {
    private NuMLDocument numlDocument;

    public DataParser(KnimeTuple tuple, Metadata metadata, String notes) {

        // Gets CondID and CombaseID
        int condId = tuple.getInt(TimeSeriesSchema.ATT_CONDID);
        String combaseId = tuple.getString(TimeSeriesSchema.ATT_COMBASEID);

        // Creates dim
        PmmXmlDoc mdData = tuple.getPmmXml(TimeSeriesSchema.ATT_TIMESERIES);
        double concValues[] = new double[mdData.size()];
        double timeValues[] = new double[mdData.size()];
        for (int i = 0; i < mdData.size(); i++) {
            TimeSeriesXml timeSeriesXml = (TimeSeriesXml) mdData.get(i);
            concValues[i] = timeSeriesXml.concentration;
            timeValues[i] = timeSeriesXml.time;
        }

        // Gets first point
        TimeSeriesXml aPoint = (TimeSeriesXml) tuple.getPmmXml(TimeSeriesSchema.ATT_TIMESERIES).get(0);
        String concUnit = aPoint.concentrationUnit;
        PMFUnitDefinition concUnitDef = null;
        try {
            concUnitDef = WriterUtils.createUnitFromDB(concUnit);
        } catch (XMLStreamException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }
        if (concUnitDef == null) {
            throw new IllegalArgumentException("Unit could not be found in DB: " + concUnit);
        }

        String timeUnit = aPoint.timeUnit;
        PMFUnitDefinition timeUnitDef = null;
        try {
            timeUnitDef = WriterUtils.createUnitFromDB(timeUnit);
        } catch (XMLStreamException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        if (timeUnitDef == null) {
            throw new IllegalArgumentException("Unit could not be found in DB: " + concUnit);
        }

        MatrixXml matrixXml = (MatrixXml) tuple.getPmmXml(TimeSeriesSchema.ATT_MATRIX).get(0);

        PmmXmlDoc miscDoc = tuple.getPmmXml(TimeSeriesSchema.ATT_MISC);
        PMFCompartment compartment = WriterUtils.matrixXml2Compartment(matrixXml, miscDoc);

        AgentXml agentXml = (AgentXml) tuple.getPmmXml(TimeSeriesSchema.ATT_AGENT).get(0);
        PMFSpecies species = WriterUtils.createSpecies(agentXml, concUnit, compartment.getId());

        // Gets microbial data literature
        PmmXmlDoc mdLitDoc = tuple.getPmmXml(TimeSeriesSchema.ATT_LITMD);
        Reference[] refs = new ReferenceImpl[mdLitDoc.size()];
        for (int i = 0; i < mdLitDoc.size(); i++) {
            refs[i] = WriterUtils.literatureItem2Reference((LiteratureItem) mdLitDoc.get(i));
        }

        // Creates time ontology
        TimeOntology timeOntology = new TimeOntology(timeUnitDef);

        // Creates concentration ontology
        ConcentrationOntology concOntology = new ConcentrationOntology(concUnitDef, compartment, species);

        AtomicDescription concDesc = new AtomicDescription("concentration", ConcentrationOntology.TERM);
        AtomicDescription timeDesc = new AtomicDescription("time", TimeOntology.TERM);
        TupleDescription tupleDesc = new TupleDescription(concDesc, timeDesc);

        Tuple[] values = new Tuple[timeValues.length];
        for (int i = 0; i < timeValues.length; i++) {
            AtomicValue concValue = new AtomicValue(concValues[i]);
            AtomicValue timeValue = new AtomicValue(timeValues[i]);
            values[i] = new Tuple(concValue, timeValue);
        }

        String creatorGivenName = metadata.getGivenName();
        String creatorFamilyName = metadata.getFamilyName();
        String creatorContact = metadata.getContact();
        String createdDate = metadata.getCreatedDate();
        String modifiedDate = metadata.getModifiedDate();
        String rights = metadata.getRights();
        ModelType modelType = metadata.getType();

        ResultComponent resultComponent = new ResultComponent("exp1", condId, combaseId, creatorGivenName,
                creatorFamilyName, creatorContact, createdDate, modifiedDate, modelType, rights, notes, refs, tupleDesc,
                values);

        numlDocument = new NuMLDocument(concOntology, timeOntology, resultComponent);
    }

    public NuMLDocument getDocument() {
        return numlDocument;
    }
}