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

Example 1 with Property

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

the class SubstancePropertyresourceTest method testCreateEntry2.

@Test
public void testCreateEntry2() throws Exception {
    EffectRecord<String, IParams, String> effect = new EffectRecord<String, IParams, String>();
    effect.setConditions(new Params());
    effect.setEndpoint("EC10");
    effect.setUnit("mg/L");
    IParams conditions = new Params();
    effect.setConditions(conditions);
    /*
	Value v = new Value();
	v.setUnits("h");
	v.setLoValue(48.0);
	effect.getConditions().put("EC_DAPHNIATOX",v);
	*/
    // System.out.println(effect);
    SubstanceProperty prop = new SubstanceProperty(null, null, effect.getEndpoint(), effect.getUnit(), null);
    String key = prop.createHashedIdentifier(effect.getConditions());
    UUID protocol_uuid = UUID.nameUUIDFromBytes("http://localhost:8080/ambit2/dataset/Method%3A+other%3A+Am.+Soc.+Test.+Mater.+%281980%29+and+U.S.+EPA+%281975%29".getBytes());
    URL url = getClass().getClassLoader().getResource("feature.rdf");
    FileRepresentation rep = new FileRepresentation(url.getFile(), MediaType.APPLICATION_RDF_XML, 0);
    testAsyncPoll(new Reference(getTestURI()), MediaType.TEXT_URI_LIST, rep, Method.POST, new Reference(String.format("http://localhost:%d/property/ECOTOX/EC_DAPHNIATOX_SECTION/EC10/%s/NOTSPECIFIED/%s", port, key.toUpperCase(), protocol_uuid)));
}

Example 2 with Property

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

the class StaXRDFTest method testRDFXML.

@Test
public void testRDFXML() throws Exception {
    // testGet(getTestURI(),MediaType.APPLICATION_RDF_XML);
    RDFStructuresIterator i = new RDFStructuresIterator(new Reference(getTestURI()), "test");
    i.setBaseReference(new Reference(String.format("http://localhost:%d", port)));
    int count = 0;
    boolean propertyfound = false;
    while (i.hasNext()) {
        IStructureRecord record = i.next();
        Assert.assertTrue(record.getIdchemical() > 0);
        Assert.assertTrue(record.getIdstructure() > 0);
        int props = 0;
        for (Property p : record.getRecordProperties()) {
            System.out.println(p.getName());
            propertyfound = propertyfound || "Property 1".equals(p.getName());
            props++;
        }
        System.out.println(props);
        count++;
    }
    i.close();
    Assert.assertEquals(4, count);
    Assert.assertTrue(propertyfound);
}

Example 3 with Property

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

the class CallableSubstancePropertyCreatorTest method testCreateSubstanceProperty.

@Test
public void testCreateSubstanceProperty() throws Exception {
    Form form = new Form();
    form.add("endpointcategory", Protocol._categories.ZETA_POTENTIAL_SECTION.name());
    form.add("name", "ZETA POTENTIAL");
    form.add("unit", "mV");
    form.add("protocol", "Method: other: no data");
    Params p = new Params();
    Value v = new Value();
    v.setLoValue(4.26);
    p.put("pH", v);
    Assert.assertEquals("{\"pH\":{\"loValue\":4.26}}", p.toString());
    try {
        PropertyURIReporter reporter = new PropertyURIReporter(new Reference("http://localhost:8081/ambit2"));
        CallableSubstancePropertyCreator callable = new CallableSubstancePropertyCreator(reporter, Method.POST, form, null, null);
        TaskResult task = callable.call();
        Assert.assertTrue(task.getUri().startsWith("http://localhost:8081/ambit2/property/P-CHEM/ZETA_POTENTIAL_SECTION/ZETA+POTENTIAL/A597EBC063D7A5A605B9535656E09149A72F0C23"));
    // "http://localhost:8081/ambit2/property/P-CHEM/ZETA_POTENTIAL_SECTION/ZETA+POTENTIAL/945DEEC24F876DEE6116F92646EF729107F5B5FD"
    } catch (Exception x) {
        throw x;
    } finally {
    }
}

Example 4 with Property

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

the class CallableSubstancePropertyCreatorTest method testCreateSubstanceProperty_TO_BIODEG_WATER_SCREEN_SECTION.

/**
 * @throws Exception
 */
@Test
public void testCreateSubstanceProperty_TO_BIODEG_WATER_SCREEN_SECTION() throws Exception {
    Form form = new Form();
    form.add("endpointcategory", Protocol._categories.TO_BIODEG_WATER_SCREEN_SECTION.name());
    form.add("name", "% Degradation");
    form.add("unit", "%");
    form.add("protocol", "Method: other: no data");
    Params p = new Params();
    Value v = new Value();
    v.setUnits("d");
    v.setLoValue(7.0);
    p.put("Sampling time", v);
    form.add("conditions", p.toString());
    Assert.assertEquals("{\"Sampling time\":{\"loValue\":7,\"unit\":\"d\"}}", p.toString());
    try {
        PropertyURIReporter reporter = new PropertyURIReporter(new Reference("http://localhost:8081/ambit2"));
        CallableSubstancePropertyCreator callable = new CallableSubstancePropertyCreator(reporter, Method.POST, form, null, null);
        TaskResult task = callable.call();
        Assert.assertTrue(task.getUri().startsWith("http://localhost:8081/ambit2/property/ENV+FATE/TO_BIODEG_WATER_SCREEN_SECTION/%25+Degradation/3CF77D9EFE4E74744E691BF4880B4EF728B16FAE"));
    // /d4cd0dab-cf4c-3a22-ad92-fab40844c786
    /*
			 * "http://localhost:8080/ambit2/property/ENV+FATE/TO_BIODEG_WATER_SCREEN_SECTION/%25+Degradation/5FA6EFD4E83BEC47B626C6149DBBD3907084187F/1f255895-eb7d-37dc-8eb8-bc9580d8be25"
			 * :{
			 * 
			 * "type":"Feature", "title":"% Degradation", "units":"%",
			 * "isNominal":false, "isNumeric":false, "isMultiValue":true,
			 * "sameAs"
			 * :"http://www.opentox.org/echaEndpoints.owl#TO_BIODEG_WATER_SCREEN"
			 * , "isModelPredictionFeature":false,
			 * "creator":"Method: other: see below", "order":1087, "source":{
			 * "URI"
			 * :"http://localhost:8080/ambit2/dataset/Method%3A+other%3A+see+below"
			 * , "type":"Dataset" }, "annotation":[ { "p" : "Sampling time", "o"
			 * : "7.0 d"}]
			 * 
			 * },
			 */
    // http://localhost:8081/ambit2/property/P-CHEM/TO_BIODEG_WATER_SCREEN_SECTION/%25+Degradation/8C9DF1AF60CA3D8706C0156361E97E0DF4391C10/1f255895-eb7d-37dc-8eb8-bc9580d8be25
    } catch (Exception x) {
        throw x;
    } finally {
    }
}

Example 5 with Property

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

the class ChartResource method createImage.

protected BufferedImage createImage() throws ResourceException {
    BufferedImage image = null;
    Connection connection = null;
    try {
        DBConnection dbc = new DBConnection(getContext());
        connection = dbc.getConnection();
        ambit2.base.data.Template profile = new ambit2.base.data.Template();
        ProfileReader reader = new ProfileReader(getRequest().getRootRef(), profile, getApplication().getContext(), getToken(), getRequest().getCookies(), getRequest().getClientInfo() == null ? null : getRequest().getClientInfo().getAgent(), getRequest().getResourceRef().toString());
        reader.setCloseConnection(false);
        reader.setConnection(connection);
        for (String p : property) reader.process(new Reference(p));
        switch(mode) {
            case pie:
                {
                    Iterator<Property> i = profile.getProperties(true);
                    while (i.hasNext()) {
                        PieChartGenerator<ISourceDataset> chart = new PieChartGenerator<ISourceDataset>();
                        chart.setProperty(i.next());
                        chart.setConnection(connection);
                        chart.setLegend(legend);
                        chart.setThumbnail(thumbnail);
                        chart.setWidth(w);
                        chart.setHeight(h);
                        chart.setLogX(logX);
                        chart.setLogY(logY);
                        image = chart.process(dataset);
                        // ChartUtilities.writeImageMap(writer, name, info, useOverLibForToolTips)
                        break;
                    }
                    break;
                }
            case histogram:
                {
                    Iterator<Property> i = profile.getProperties(true);
                    while (i.hasNext()) {
                        HistogramChartGenerator chart = new HistogramChartGenerator();
                        chart.setLogX(logX);
                        chart.setLogY(logY);
                        chart.setMinX(minX);
                        chart.setMaxX(maxX);
                        chart.setPropertyX(i.next());
                        chart.setConnection(connection);
                        chart.setLegend(legend);
                        chart.setThumbnail(thumbnail);
                        chart.setWidth(w);
                        chart.setHeight(h);
                        image = chart.process(dataset);
                        // ChartUtilities.writeImageMap(writer, name, info, useOverLibForToolTips)
                        break;
                    }
                    break;
                }
            case xy:
                {
                    Property[] p = new Property[2];
                    int i = 0;
                    Iterator<Property> it = profile.getProperties(true);
                    while (it.hasNext()) {
                        p[i] = it.next();
                        i++;
                        if (i >= 2)
                            break;
                    }
                    PropertiesChartGenerator chart = new PropertiesChartGenerator();
                    chart.setLogX(logX);
                    chart.setLogY(logY);
                    chart.setThumbnail(thumbnail);
                    chart.setPropertyX(p[0]);
                    chart.setPropertyY(p.length < 2 ? p[0] : p[1]);
                    chart.setConnection(connection);
                    chart.setWidth(w);
                    chart.setHeight(h);
                    chart.setLegend(legend);
                    image = chart.process(dataset);
                    break;
                }
            case bar:
                {
                    Property[] p = new Property[2];
                    int i = 0;
                    Iterator<Property> it = profile.getProperties(true);
                    while (it.hasNext()) {
                        p[i] = it.next();
                        i++;
                        if (i >= 2)
                            break;
                    }
                    if (i == 0) {
                        FingerprintHistogramDataset chart = new FingerprintHistogramDataset();
                        chart.setLogX(logX);
                        chart.setLogY(logY);
                        chart.setConnection(connection);
                        chart.setLegend(legend);
                        chart.setParam(param);
                        chart.setThumbnail(thumbnail);
                        chart.setWidth(w);
                        chart.setHeight(h);
                        image = chart.process(dataset);
                    } else {
                        BarChartGeneratorDataset chart = new BarChartGeneratorDataset();
                        chart.setLogX(logX);
                        chart.setLogY(logY);
                        chart.setPropertyX(p[0]);
                        chart.setPropertyY(p.length < 2 ? p[0] : p[1]);
                        chart.setConnection(connection);
                        chart.setLegend(legend);
                        chart.setThumbnail(thumbnail);
                        chart.setWidth(w);
                        chart.setHeight(h);
                        image = chart.process(dataset);
                    }
                    break;
                }
            default:
                {
                    image = null;
                }
        }
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    } finally {
        try {
            connection.close();
        } catch (Exception x) {
        }
    }
    if (image == null)
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
    return image;
}