Examples with PropertyAnnotations ambit2.base.data.PropertyAnnotations used on opensource projects

Example 11 with PropertyAnnotations

use of ambit2.base.data.PropertyAnnotations in project ambit-mirror by ideaconsult.

the class RDFPropertyIterator method parseRecord.

public Property parseRecord(RDFNode propertyEntry, Property property, int level) {
    if (property == null)
        property = createRecord();
    if (propertyEntry.isLiteral()) {
        property.setName(((Literal) propertyEntry).getString());
        return property;
    }
    Resource newEntry = (Resource) propertyEntry;
    Reference thisurl = null;
    try {
        String uri = getURI(newEntry);
        thisurl = uri != null ? new Reference(uri) : null;
    } catch (Exception x) {
    }
    parseObjectURI(newEntry, property);
    if ((property.getId() > 0) && !thisurl.equals(reference)) {
        // ours,
        // let's
        // retrieve
        // what we
        // have
        RDFPropertyIterator iterator = null;
        try {
            iterator = new RDFPropertyIterator(thisurl, referer);
            iterator.setCloseModel(true);
            iterator.setBaseReference(getBaseReference());
            while (iterator.hasNext()) {
                property = iterator.next();
                break;
            }
            if (!forceReadRDFLocalObjects)
                return property;
        // otherwise read what's in rdf as well
        } catch (Exception x) {
        } finally {
            try {
                iterator.close();
            } catch (Exception x) {
            }
        }
    }
    // foreign, will live with what's available in RDF
    String name = thisurl == null ? null : thisurl.toString();
    String label = name;
    try {
        name = getTitle(newEntry);
    } catch (Exception x) {
    }
    try {
        Statement t = newEntry.getProperty(OWL.sameAs);
        if (t != null) {
            RDFNode resource = t.getObject();
            if (resource.isLiteral())
                label = ((Literal) resource).getString();
            else
                label = resource.isURIResource() ? ((Resource) resource).getURI() : resource.toString();
        }
    } catch (Exception x) {
        label = Property.guessLabel(name);
    }
    Statement t = ((Resource) propertyEntry).getProperty(OTProperty.smarts.createProperty(jenaModel));
    RDFNode smarts = t == null ? null : t.getObject();
    String fragment = null;
    if ((smarts != null) && smarts.isLiteral()) {
        fragment = smarts.asLiteral().getString();
        property.setUnits(fragment);
        // TODO set ot:smarts property
        property.setNominal(true);
        property.setName(String.format("%s#%s", name, Reference.encode(fragment)));
    } else
        property.setName(name == null ? thisurl == null ? label : thisurl.toString() : name);
    property.setLabel(label);
    try {
        property.setUnits(((Literal) newEntry.getProperty(OT.DataProperty.units.createProperty(jenaModel)).getObject()).getString());
    } catch (Exception x) {
        property.setUnits("");
    }
    Statement stmt = newEntry.getProperty(DC.creator);
    String creator = (stmt == null) ? "Default" : (stmt.getObject() == null) ? "Default" : stmt.getObject().isLiteral() ? ((Literal) stmt.getObject()).getString() : stmt.getObject().toString();
    String hasSource = creator;
    property.setReference(processSource(newEntry, hasSource, creator));
    // predicate =
    // jenaModel.createProperty(String.format("http://www.opentox.org/api/1.1#%s",
    property.setClazz(String.class);
    StmtIterator it = null;
    property.setNominal(false);
    try {
        it = jenaModel.listStatements(new SimpleSelector(newEntry, RDF.type, (RDFNode) null));
        while (it.hasNext()) {
            Statement st = it.next();
            if (!st.getObject().isResource())
                continue;
            Resource resource = st.getResource();
            if (resource.hasURI(OT.OTClass.Feature.getNS()))
                continue;
            if (resource.hasURI(OT.OTClass.NumericFeature.getNS()))
                property.setClazz(Number.class);
            else if (resource.hasURI(OT.OTClass.TupleFeature.getNS()))
                property.setClazz(Dictionary.class);
            else if (resource.hasURI(OT.OTClass.NominalFeature.getNS()))
                property.setNominal(true);
            else if (resource.hasURI(OT.OTClass.ModelConfidenceFeature.getNS())) {
            // TODO
            } else if (resource.hasURI(OT.OTClass.ModelPredictionFeature.getNS())) {
            // TODO
            }
        }
    } catch (Exception x) {
    } finally {
        try {
            it.close();
        } catch (Exception x) {
        }
    }
    // confidence
    try {
        t = newEntry.getProperty(OTProperty.confidenceOf.createProperty(jenaModel));
        if (t != null) {
            PropertyAnnotation pa = null;
            Property theFeature = null;
            RDFNode resource = t.getObject();
            if (resource == newEntry) {
            // link to itself, ignore
            } else if (resource.isAnon()) {
                try {
                    PropertyAnnotation<Property> ppa = new PropertyAnnotation<Property>();
                    if (confidenceLinks != null)
                        theFeature = confidenceLinks.get(resource);
                    if (theFeature == null) {
                        theFeature = parseRecord(resource, null, level + 1);
                        if (theFeature != null) {
                            if (confidenceLinks == null)
                                confidenceLinks = new Hashtable<RDFNode, Property>();
                            confidenceLinks.put(resource, theFeature);
                        }
                    }
                    if (theFeature != null) {
                        ppa.setObject(theFeature);
                        pa = ppa;
                    }
                } catch (Exception x) {
                    pa = null;
                }
            } else {
                PropertyAnnotation<String> psa = new PropertyAnnotation<String>();
                if (resource.isLiteral())
                    psa.setObject(((Literal) resource).getString());
                else
                    psa.setObject(resource.isURIResource() ? ((Resource) resource).getURI() : resource.toString());
                pa = psa;
            }
            pa.setPredicate(OTProperty.confidenceOf.getURI());
            pa.setType(OTClass.ModelConfidenceFeature.name());
            if (property.getAnnotations() == null)
                property.setAnnotations(new PropertyAnnotations());
            property.getAnnotations().add(pa);
        }
    } catch (Exception x) {
        x.printStackTrace();
    } finally {
        t = null;
    }
    if (property.getName() == null)
        property.setName("Unnamed");
    return property;
}

Example 12 with PropertyAnnotations

use of ambit2.base.data.PropertyAnnotations in project ambit-mirror by ideaconsult.

the class WafflesModelBuilder method process.

@Override
public ModelQueryResults process(Algorithm algorithm) throws AmbitException {
    ModelQueryResults model = new ModelQueryResults();
    File dataset = trainingData;
    if ((dataset == null) || !dataset.exists())
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty dataset!");
    ShellWafflesLearn waffles = null;
    try {
        Class clazz = this.getClass().getClassLoader().loadClass(algorithm.getContent().toString());
        waffles = (ShellWafflesLearn) clazz.newInstance();
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, algorithm.getContent().toString(), x);
    }
    // return the model representation as string, not file, so we store it
    // into the DB
    waffles.setOutputFile(null);
    waffles.setOutProperty(WafflesLearnOption.model.name());
    Properties in = new Properties();
    in.put(WafflesLearnOption.command.name(), WafflesLearnCommand.train.name());
    if ((parameters != null) && (parameters.length > 0))
        in.put(WafflesLearnOption.alg_opts.name(), parameters[0]);
    in.put(WafflesLearnOption.dataset.name(), dataset.getAbsolutePath());
    in.put(WafflesLearnOption.algorithm.name(), waffles.getAlgorithm().name());
    if (dataOptions != null)
        in.put(WafflesLearnOption.data_opts.name(), dataOptions);
    try {
        Properties out = waffles.runShell(in);
        if ((out == null) || (out.getProperty(waffles.getOutProperty()) == null))
            throw new AmbitException(String.format("Model not generated", waffles.getOutProperty()));
        if (!"0".equals(out.getProperty(ShellWafflesLearn.getExitcodeProperty())))
            throw new AmbitException(String.format("Model not generated [exit code = %s] %s", out.getProperty(ShellWafflesLearn.getExitcodeProperty()), out.getProperty(waffles.getOutProperty())));
        String name = String.format("%s.%s.%s", waffles.getAlgorithm().name(), UUID.randomUUID().toString(), waffles.getClass().getName());
        model.setContentMediaType(algorithm.getFormat().getMediaType());
        model.setParameters(parameters);
        model.setId(null);
        model.setName(name);
        model.setAlgorithm(alg_reporter.getURI(algorithm));
        /**
         * Variables
         */
        AlgorithmURIReporter r = new AlgorithmURIReporter();
        LiteratureEntry entry = new LiteratureEntry(name, algorithm == null ? waffles.getClass().getName() : r.getURI(applicationRootReference.toString(), algorithm));
        LiteratureEntry prediction = new LiteratureEntry(model.getName(), model_reporter.getURI(applicationRootReference.toString(), model));
        prediction.setType(_type.Model);
        Template predictors = null;
        Template dependent = null;
        PredictedVarsTemplate predicted = null;
        dependent = new Template(name + "#Dependent");
        predicted = new PredictedVarsTemplate(name + "#Predicted");
        predictors = new Template(name + "#Independent");
        StringBuilder labels = null;
        for (int i = 0; i < header.numAttributes(); i++) {
            boolean isTarget = false;
            for (String t : getTargetURI()) if (header.attribute(i).name().equals(t)) {
                header.setClassIndex(header.attribute(i).index());
                // but could be multiple targets
                if (labels == null)
                    labels = new StringBuilder();
                else
                    labels.append(",");
                labels.append(i);
                // dependent property
                Property property = createPropertyFromReference(new Reference(header.attribute(i).name()), entry, referer);
                property.setOrder(i + 1);
                dependent.add(property);
                // predicted property
                Property predictedProperty = new Property(property.getName(), prediction);
                predictedProperty.setOrder(i + 1);
                predictedProperty.setLabel(property.getLabel());
                predictedProperty.setUnits(property.getUnits());
                predictedProperty.setClazz(property.getClazz());
                predictedProperty.setNominal(property.isNominal());
                predictedProperty.setEnabled(true);
                predicted.add(predictedProperty);
                // link to dependent - necessary for multilabel
                PropertyAnnotations annotations = new PropertyAnnotations();
                PropertyAnnotation annotation = new PropertyAnnotation();
                annotation.setObject(header.attribute(i).name());
                annotation.setPredicate("predictionOf");
                annotation.setType("Feature");
                annotations.add(annotation);
                predictedProperty.setAnnotations(annotations);
                if (header.attribute(i).isNominal()) {
                    Enumeration e = header.attribute(i).enumerateValues();
                    while (e.hasMoreElements()) {
                        String value = e.nextElement().toString();
                        predictedProperty.addAllowedValue(value);
                        annotation = new PropertyAnnotation();
                        annotation.setObject(value);
                        annotation.setPredicate("acceptValue");
                        annotation.setType("Feature");
                        annotations.add(annotation);
                    }
                    predictedProperty.setAnnotations(annotations);
                }
                isTarget = true;
                break;
            }
            if (!isTarget) {
                Property property = createPropertyFromReference(new Reference(header.attribute(i).name()), entry, referer);
                property.setOrder(i + 1);
                predictors.add(property);
            }
        }
        model.setContent(serializeModel(out.getProperty(waffles.getOutProperty()), header));
        // if (supportsDistribution(classifier)) {}
        if (labels != null)
            setDataOptions(String.format("-labels %s", labels));
        model.setPredictors(predictors);
        model.setDependent(dependent);
        model.setPredicted(predicted);
        // model.setParameters(new String[] {"-labels",labels.toString()});
        return model;
    } catch (AmbitException x) {
        throw x;
    } catch (Exception x) {
        throw new AmbitException(x);
    }
}

Example 13 with PropertyAnnotations

use of ambit2.base.data.PropertyAnnotations in project ambit-mirror by ideaconsult.

the class PropertyAnnotationTest method testMany.

@Test
public void testMany() throws Exception {
    PropertyAnnotations as = new PropertyAnnotations();
    PropertyAnnotation a1 = new PropertyAnnotation();
    a1.setObject("o");
    a1.setPredicate("p");
    a1.setType("t");
    as.add(a1);
    PropertyAnnotation a2 = new PropertyAnnotation();
    a2.setObject("o1");
    a2.setPredicate("p1");
    a2.setType("t1");
    as.add(a2);
    Assert.assertEquals("\n\t{\t\"type\" : \"t\",\t\"p\" : \"p\",\t\"o\" : \"o\"},\n\t{\t\"type\" : \"t1\",\t\"p\" : \"p1\",\t\"o\" : \"o1\"}", as.toJSON());
}

Example 14 with PropertyAnnotations

use of ambit2.base.data.PropertyAnnotations in project ambit-mirror by ideaconsult.

the class CoverageModelBuilder method process.

public ModelQueryResults process(Algorithm algorithm) throws AmbitException {
    Instances instances = trainingData;
    if ((instances == null) || (instances.numInstances() == 0) || (instances.numAttributes() == 0))
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty dataset!");
    try {
        RemoveWithValues removeMissingValues = new RemoveWithValues();
        String[] options = new String[1];
        options[0] = "-M";
        removeMissingValues.setOptions(options);
        removeMissingValues.setInputFormat(instances);
        Instances newInstances = Filter.useFilter(instances, removeMissingValues);
        instances = newInstances;
    } catch (Exception x) {
    // use unfiltered
    }
    // int numAttr = 0;
    // for (int j=0; j < instances.numAttributes();j++)
    // if (instances.attribute(j).isNumeric()) numAttr++;
    // if (numAttr==0) throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST,"No numeric attributes!");
    Matrix matrix = new Matrix(instances.numInstances(), instances.numAttributes() - 1);
    for (int i = 0; i < instances.numInstances(); i++) for (int j = 1; j < instances.numAttributes(); j++) try {
        double value = instances.instance(i).value(j);
        if (Double.isNaN(value))
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, String.format("Missing value %s in record %s", instances.attribute(j), instances.instance(i)));
        matrix.set(i, j - 1, value);
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    }
    DataCoverage coverage = null;
    try {
        Class clazz = this.getClass().getClassLoader().loadClass(algorithm.getContent().toString());
        coverage = (DataCoverage) clazz.newInstance();
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    }
    String name = String.format("%s.%s", UUID.randomUUID().toString(), coverage.getName());
    ModelQueryResults m = new ModelQueryResults();
    m.setParameters(parameters);
    m.setId(null);
    m.setContentMediaType(AlgorithmFormat.WEKA.getMediaType());
    m.setName(name);
    m.setAlgorithm(alg_reporter.getURI(algorithm));
    AlgorithmURIReporter r = new AlgorithmURIReporter();
    LiteratureEntry entry = new LiteratureEntry(name, algorithm == null ? coverage.getClass().getName() : r.getURI(applicationRootReference.toString(), algorithm));
    LiteratureEntry prediction = new LiteratureEntry(m.getName(), model_reporter.getURI(applicationRootReference.toString(), m));
    prediction.setType(_type.Model);
    Template predictors = null;
    Template dependent = null;
    PredictedVarsTemplate predicted = null;
    if (coverage != null) {
        coverage.build(matrix);
        predicted = new PredictedVarsTemplate(name + "#ApplicabilityDomain");
        Property property = new Property(coverage.getMetricName(), prediction);
        property.setEnabled(true);
        property.setLabel(String.format("http://www.opentox.org/api/1.1#%s", coverage.getMetricName()));
        predicted.add(property);
        property = new Property(coverage.getDomainName(), prediction);
        property.setLabel(Property.opentox_ConfidenceFeature);
        property.setClazz(Number.class);
        property.setEnabled(true);
        // this is a confidence feature
        if (predictedFeatureURI != null) {
            PropertyAnnotation<String> a = new PropertyAnnotation<String>();
            a.setType(OT.OTClass.ModelConfidenceFeature.name());
            a.setPredicate(OT.OTProperty.confidenceOf.name());
            a.setObject(predictedFeatureURI);
            PropertyAnnotations aa = new PropertyAnnotations();
            aa.add(a);
            property.setAnnotations(aa);
        }
        predicted.add(property);
        dependent = new Template("Empty");
        predictors = new Template(name + "#Independent");
        for (int i = 1; i < instances.numAttributes(); i++) {
            property = createPropertyFromReference(new Reference(instances.attribute(i).name()), entry, referer);
            property.setOrder(i + 1);
            predictors.add(property);
        }
    }
    m.setPredictors(predictors);
    m.setDependent(dependent);
    m.setPredicted(predicted);
    try {
        serializeModel(coverage, instances, m);
    } catch (IOException x) {
        throw new AmbitException(x);
    }
    m.setContentMediaType(AlgorithmFormat.COVERAGE_SERIALIZED.getMediaType());
    return m;
}

Example 15 with PropertyAnnotations

use of ambit2.base.data.PropertyAnnotations in project ambit-mirror by ideaconsult.

the class DXParser method process.

@Override
public IStructureRecord process(IStructureRecord record) throws AmbitException {
    cleanPropertyRefs();
    ILiteratureEntry reference = null;
    Map<Property, Object> properties = new Hashtable<Property, Object>();
    PropertyAnnotations pa = new PropertyAnnotations();
    for (Property p : record.getRecordProperties()) {
        Object value = record.getRecordProperty(p);
        JsonNode strucProperty = dxRoot.get(json_fields.StructureProperties.name()).get(p.getName());
        if (strucProperty != null) {
            JsonNode propertyRef = strucProperty.get(json_fields.referenceFor.name());
            if (propertyRef != null) {
                JsonNode prop = dxRoot.get(json_fields.StructureProperties.name()).get(propertyRef.textValue());
                if (prop != null && (prop instanceof ObjectNode))
                    ((ObjectNode) prop).put(json_fields.reference.name(), value.toString());
            }
            continue;
        }
        JsonNode reportProperty = dxRoot.get(json_fields.Report.name()).get(p.getName());
        if (reportProperty == null)
            continue;
        if (reportProperty.get("import").asBoolean())
            try {
                importas ias = importas.valueOf(reportProperty.get("importas").textValue());
                switch(ias) {
                    case reference:
                        {
                            reference = LiteratureEntry.getDXReference(value.toString());
                            break;
                        }
                    case annotation:
                        {
                            PropertyAnnotation a = new PropertyAnnotation();
                            a.setPredicate(p.getName());
                            a.setObject(value.toString());
                            pa.add(a);
                            break;
                        }
                    default:
                        {
                        }
                }
            } catch (Exception x) {
            }
    }
    if (reference == null)
        reference = LiteratureEntry.getDXReference();
    for (Property p : record.getRecordProperties()) {
        Object value = record.getRecordProperty(p);
        JsonNode reportProperty = dxRoot.get(json_fields.Report.name()).get(p.getName());
        JsonNode strucProperty = dxRoot.get(json_fields.StructureProperties.name()).get(p.getName());
        if (reportProperty != null)
            continue;
        if (strucProperty != null) {
            ILiteratureEntry propReference = reference;
            if (strucProperty.get(json_fields.referenceFor.name()) != null)
                continue;
            if (strucProperty.get(json_fields.reference.name()) != null) {
                try {
                    propReference = LiteratureEntry.getDXReference(strucProperty.get(json_fields.reference.name()).textValue());
                } catch (Exception x) {
                }
            }
            if (strucProperty.get(json_fields.ot.name()) != null)
                try {
                    p.setLabel(strucProperty.get(json_fields.ot.name()).textValue());
                } catch (Exception x) {
                }
            p.setReference(propReference);
            properties.put(p, value);
        } else if ("Superendpoints".equals(p.getName())) {
            verifySuperEndpoints(record, p);
        } else if (p.getName().startsWith(DXPrefix)) {
            Property dx = verifyDXProperty(p, value, reference);
            if (dx != null) {
                properties.put(dx, value);
                for (PropertyAnnotation a : pa) {
                    dx.getAnnotations().add(a);
                }
            }
        } else
            properties.put(p, value);
    }
    record.clearProperties();
    record.addRecordProperties(properties);
    return record;
}