Package org.openbel.framework.common.model

Examples of org.openbel.framework.common.model.Parameter

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            // unmapped namespace values
            SkinnyUUID[] uuids = new SkinnyUUID[params.size()];
            Parameter[] parray = params.toArray(new Parameter[params.size()]);
            boolean missing = false;
            for (int i = 0; i < parray.length; i++) {
                Parameter param = parray[i];
                Namespace ns = param.getNamespace();
                if (ns == null) {
                    missing = true;
                    break;
                }

                String value = clean(param.getValue());

                SkinnyUUID uuid = null;
                try {
                    uuid = equivalencer.getUUID(ns, value);
                } catch (EquivalencerException e) {
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        }

        loadEquivalencingEngine();

        // convert namespace and value to parameter (common model).
        final Parameter sp = new Parameter(sourceNamespace, sourceValue);

        try {
            Parameter parameter = this.paramEquivalencer.findEquivalence(sp,
                    targetNamespace);
            return parameter == null ? null : parameter.getValue();
        } catch (InvalidArgument e) {
            //TODO change exception when paramEquivalencer is changed
            return null;
        } catch (Exception e) {
            final String fmt = "Unable to find equivalences for '%s'";
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            throw new InvalidArgument("sourceValue", sourceValue);
        }

        loadEquivalencingEngine();

        final Parameter sp = new Parameter(sourceNamespace, sourceValue);

        try {
            final List<Parameter> equivalences = this.paramEquivalencer
                    .findEquivalences(sp);
            Map<Namespace, String> equivalenceMap = sizedHashMap(equivalences
                    .size());

            for (final Parameter equivalence : equivalences) {
                equivalenceMap.put(equivalence.getNamespace(),
                        equivalence.getValue());
            }

            return equivalenceMap;
        } catch (InvalidArgument e) {
            //TODO change exception when paramEquivalencer is changed
            return null;
        } catch (Exception e) {
            final String fmt = "Unable to find equivalences for '%s'";
            final String msg = format(fmt, sp.toBELShortForm());
            throw new EquivalencerException(msg, e);
        }
    }
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        }

        loadEquivalencingEngine();

        try {
            Parameter parameter = this.paramEquivalencer.findEquivalence(
                    sourceUUID, targetNamespace);
            return parameter == null ? null : parameter.getValue();
        } catch (InvalidArgument e) {
            //TODO change exception when paramEquivalencer is changed
            return null;
        } catch (Exception e) {
            final String fmt = "Unable to find equivalences for '%s'";
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     *             equivalences
     */
    public SkinnyUUID getUUID(Namespace namespace, String value)
            throws EquivalencerException {
        loadEquivalencingEngine();
        final Parameter p = new Parameter(namespace, value);

        try {
            return paramEquivalencer.getUUID(p);
        } catch (InvalidArgument e) {
            //TODO change when paramEquivalencer exception is changed
            return null;
        } catch (Exception e) {
            final String fmt = "Unable to find UUID for '%s'";
            final String msg = format(fmt, p.toBELShortForm());
            throw new EquivalencerException(msg, e);
        }
    }
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        String cached = labelCache.get(nodeLabel);
        if (cached != null) {
            return cached;
        }

        final Parameter param = convert(speciesParam);

        try {
            // find first term and convert to species namespaces
            final List<BelTerm> terms = kAMStore
                    .getSupportingTerms(kamNode);
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    private Parameter convert(KAMStoreDaoImpl.TermParameter tp) {
        final KAMStoreDaoImpl.Namespace kns = tp.getNamespace();
        final Namespace ns =
                new Namespace(kns.getPrefix(), kns.getResourceLocation());
        return new Parameter(ns, tp.getParameterValue());
    }
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                    .getNamespace().getResourceLocation(),
                    equivalenceEntry.getKey(),
                    sourceParameter.getValue());

            if (equivalentValue != null) {
                equivalentParameters.add(new Parameter(new Namespace("",
                        equivalenceEntry.getKey()), equivalentValue));
            }
        }
        return equivalentParameters;
    }
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        if (equivalentValue == null) {
            return null;
        }

        return new Parameter(destinationNamespace, equivalentValue);
    }
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            final String equivalentValue = doFindEquivalence(
                    equivalenceEntry.getKey(),
                    sourceUUID);

            if (equivalentValue != null) {
                equivalentParameters.add(new Parameter(new Namespace("",
                        equivalenceEntry.getKey()), equivalentValue));
            }
        }
        return equivalentParameters;
    }
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Related Classes of org.openbel.framework.common.model.Parameter

  • org.openbel.framework.api.DefaultSpeciesDialect
  • org.openbel.framework.api.Equivalencer
  • org.openbel.framework.api.Resolver
  • org.openbel.framework.common.bel.parser.BELStatementParser
  • org.openbel.framework.common.protonetwork.model.StatementTable
  • org.openbel.framework.common.xbel.converters.ParameterConverter
  • org.openbel.framework.compiler.PhaseThreeImpl
  • org.openbel.framework.core.compiler.expansion.ModificationExpansionRule
  • org.openbel.framework.core.compiler.SemanticServiceImpl
  • org.openbel.framework.core.compiler.SemanticServiceImplTest
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