Package org.openbel.framework.api.internal.KAMStoreDaoImpl

Examples of org.openbel.framework.api.internal.KAMStoreDaoImpl.BelTerm

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            final TermParameter eg116590 = createTermParameter(3, eg, "116590");
            final TermParameter rgdMapk1 = createTermParameter(4, rgd, "Mapk1");

            Collection<KamNode> kn = kam.getNodes();
            final KamNode[] nodes = kn.toArray(new KamNode[kn.size()]);
            BelTerm belTerm = createBelTerm(0,
                    "kinaseActivity(proteinAbundance(MGI:Mapk1))");
            when(kamstore.getSupportingTerms(nodes[0])).thenReturn(
                    Arrays.asList(belTerm));
            when(kamstore.getTermParameters(info, belTerm)).thenReturn(
                    Arrays.asList(mgiMapk1));
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            final TermParameter pfr1433 = createTermParameter(2, pfr,
                    "14-3-3 Family");

            final Collection<KamNode> kn = kam.getNodes();
            final KamNode[] nodes = kn.toArray(new KamNode[kn.size()]);
            BelTerm belTerm = createBelTerm(0,
                    "phosphataseActivity(proteinAbundance(PFH:\"14-3-3 Family\"))");
            when(kamstore.getSupportingTerms(nodes[0])).thenReturn(
                    Arrays.asList(belTerm));
            when(kamstore.getTermParameters(info, belTerm)).thenReturn(
                    Arrays.asList(pfh1433));
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            final TermParameter ncrAP1 = createTermParameter(2, ncr,
                    "AP-1 Complex");

            final Collection<KamNode> kn = kam.getNodes();
            final KamNode[] nodes = kn.toArray(new KamNode[kn.size()]);
            BelTerm belTerm = createBelTerm(0,
                    "kinaseActivity(complexAbundance(NCH:\"AP-1 Complex\"))");
            when(kamstore.getSupportingTerms(nodes[0])).thenReturn(
                    Arrays.asList(belTerm));
            when(kamstore.getTermParameters(info, belTerm)).thenReturn(
                    Arrays.asList(nchAP1));
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        if (label == null) {
            label = kamNode.getLabel();
            try {
                List<BelTerm> terms = kAMStore.getSupportingTerms(kamNode);
                if (!terms.isEmpty()) {
                    BelTerm bt = terms.get(0);
                    Term t = BELParser.parseTerm(bt.getLabel());
                    label = displayLongForm ? t.toBELLongForm() : t
                            .toBELShortForm();
                }
            } catch (Exception e) {
                // TODO exception
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        try {
            // find first term and convert to species namespaces
            final List<BelTerm> terms = kAMStore
                    .getSupportingTerms(kamNode);
            if (hasItems(terms)) {
                final BelTerm term = terms.get(0);
                final Term ts = BELParser.parseTerm(term.getLabel());
                final Term converted = convert(ts, param);

                cached = displayLongForm ? converted.toBELLongForm()
                        : converted.toBELShortForm();
                labelCache.put(nodeLabel, cached);
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        if (label == null) {
            label = kamNode.getLabel();
            try {
                List<BelTerm> terms = kAMStore.getSupportingTerms(kamNode);
                if (!terms.isEmpty()) {
                    BelTerm bt = terms.get(0);
                    Term t = BELParser.parseTerm(bt.getLabel());
                    label = t.toBELShortForm();
                }
            } catch (Exception e) {
                // TODO exception
            }
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     * @throws KAMStoreException
     */
    protected String labelNode(KamNode node) throws KAMStoreException {
        List<BelTerm> terms = kAMStore.getSupportingTerms(node);
        if (!terms.isEmpty()) {
            BelTerm bt = terms.get(0);
            Term parsed;
            try {
                parsed = BELParser.parseTerm(bt.getLabel());
            } catch (Exception e) {
                return null;
            }
            Term converted = convert(parsed);

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import org.openbel.framework.api.internal.KAMStoreDaoImpl.TermParameter;

public class KamStoreUtil {

    public static BelTerm createBelTerm(final Integer id, final String lbl) {
        return new BelTerm(id, lbl);
    }
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Related Classes of org.openbel.framework.api.internal.KAMStoreDaoImpl.BelTerm

  • org.openbel.framework.api.DefaultDialect
  • org.openbel.framework.api.DefaultSpeciesDialect
  • org.openbel.framework.api.internal.KamStoreUtil
  • org.openbel.framework.api.SpeciesKamTest
  • org.openbel.framework.ws.dialect.CustomDialect
  • org.openbel.framework.ws.dialect.DefaultDialect
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