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

Example 1 with ISourceDataset

use of ambit2.base.data.ISourceDataset 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;
}

Example 2 with ISourceDataset

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

the class ChartResource method getDataset.

protected ISourceDataset getDataset(String uri) throws InvalidResourceIDException {
    Map<String, Object> vars = new HashMap<String, Object>();
    Template template = OpenTox.URI.dataset.getTemplate(getRequest().getRootRef());
    String id = null;
    try {
        template.parse(uri, vars);
        id = vars.get(OpenTox.URI.dataset.getKey()).toString();
    } catch (Exception x) {
        return null;
    }
    if (id != null)
        try {
            Integer idnum = new Integer(Reference.decode(id.toString()));
            SourceDataset dataset = new SourceDataset();
            dataset.setID(idnum);
            return dataset;
        } catch (NumberFormatException x) {
            if (id.toString().startsWith(DatasetStructuresResource.QR_PREFIX)) {
                String key = id.toString().substring(DatasetStructuresResource.QR_PREFIX.length());
                try {
                    ISourceDataset dataset = new StoredQuery();
                    dataset.setID(Integer.parseInt(key.toString()));
                    return dataset;
                } catch (NumberFormatException xx) {
                    throw new InvalidResourceIDException(id);
                }
            }
        } catch (Exception x) {
            throw new InvalidResourceIDException(id);
        }
    return null;
}

Example 3 with ISourceDataset

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

the class MetadatasetResource method createObjectIterator.

@Override
protected RDFObjectIterator<M> createObjectIterator(Representation entity) throws ResourceException {
    RDFMetaDatasetIterator iterator = new RDFMetaDatasetIterator(entity, entity.getMediaType()) {

        @Override
        protected ISourceDataset createRecord() {
            return new SourceDataset();
        }
    };
    iterator.setForceReadRDFLocalObjects(true);
    iterator.setBaseReference(getRequest().getRootRef());
    return iterator;
}

Example 4 with ISourceDataset

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

the class SimilarityResource method createQuery.

@Override
protected Q createQuery(Context context, Request request, Response response) throws ResourceException {
    Form form = getResourceRef(getRequest()).getQueryAsForm();
    try {
        Object bundleURI = OpenTox.params.bundle_uri.getFirstValue(form);
        Integer idbundle = bundleURI == null ? null : getIdBundle(bundleURI, request);
        SubstanceEndpointsBundle bundle = new SubstanceEndpointsBundle(idbundle);
        bundles = new SubstanceEndpointsBundle[1];
        bundles[0] = bundle;
    } catch (Exception x) {
        bundles = null;
    }
    try {
        includeMol = "true".equals(form.getFirstValue("mol"));
    } catch (Exception x) {
        includeMol = false;
    }
    folders = form.getValuesArray("folder");
    filterBySubstance = false;
    try {
        String filter = form.getFirstValue("filterBySubstance");
        if (filter != null) {
            filter = filter.toLowerCase();
            filterBySubstance = "yes".equals(filter) || "on".equals(filter) || "true".equals(filter);
        }
    } catch (Exception x) {
        filterBySubstance = false;
    }
    QueryAtomEnvironment.q_modifier ae = null;
    try {
        String filter = form.getFirstValue("mode");
        if (filter != null) {
            filter = filter.toLowerCase();
            ae = QueryAtomEnvironment.q_modifier.valueOf(filter.replace("ae", ""));
        }
    } catch (Exception x) {
        ae = null;
    }
    mol = getMolecule(form);
    if ((mol == null) || (mol.getAtomCount() == 0))
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "Empty molecule");
    threshold = 0.0;
    try {
        threshold = new Double(Reference.decode(form.getFirstValue("threshold")));
    } catch (Exception x) {
        threshold = 0.9;
    }
    QuerySimilarity q = null;
    if (ae != null) {
        q = new QueryAtomEnvironment(ae);
        try {
            q.setValue(getAE(mol));
        } catch (Exception x) {
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x);
        }
    } else
        try {
            q = new QuerySimilarityBitset();
            q.setValue(getBitset(mol));
        } catch (Exception x) {
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x);
        }
    q.setChemicalsOnly(true);
    q.setThreshold(threshold);
    q.setCondition(NumberCondition.getInstance(">"));
    q.setName("Similarity");
    try {
        q.setForceOrdering(((AmbitApplication) getApplication()).isSimilarityOrder());
    } catch (Exception x) {
        q.setForceOrdering(true);
    }
    try {
        if (filterBySubstance) {
            ChemicalBySubstanceRelation qa = new ChemicalBySubstanceRelation();
            QueryCombinedStructure qc = new QueryCombinedStructure();
            qc.add(q);
            qc.setChemicalsOnly(true);
            qc.setScope(qa);
            setTemplate(createTemplate(context, request, response));
            setGroupProperties(context, request, response);
            return (Q) qc;
        } else if ((folders != null) && (folders.length > 0)) {
            ChemicalByQueryFolder qa = new ChemicalByQueryFolder(folders);
            QueryCombinedStructure qc = new QueryCombinedStructure();
            qc.add(q);
            qc.setChemicalsOnly(true);
            qc.setScope(qa);
            setTemplate(createTemplate(context, request, response));
            setGroupProperties(context, request, response);
            return (Q) qc;
        } else {
            Object datasetURI = OpenTox.params.dataset_uri.getFirstValue(form);
            ISourceDataset srcdataset = null;
            if (datasetURI != null)
                try {
                    srcdataset = getDataset(datasetURI.toString());
                    QueryCombinedStructure qc = new QueryCombinedStructure();
                    qc.add(q);
                    qc.setChemicalsOnly(true);
                    if (srcdataset instanceof SourceDataset) {
                        ChemicalByDataset cd = new ChemicalByDataset(new Integer(srcdataset.getID()));
                        qc.setScope(cd);
                        setTemplate(createTemplate(context, request, response));
                        setGroupProperties(context, request, response);
                        return (Q) qc;
                    } else {
                    // TODO, resort to all db
                    }
                } catch (Exception x) {
                    srcdataset = null;
                }
            QueryCombinedStructure qc = null;
            try {
                this.dataset_id = Reference.decode(getRequest().getAttributes().get(DatasetResource.datasetKey).toString());
                qc = new QueryCombinedStructure();
                qc.add(q);
                qc.setChemicalsOnly(true);
                ChemicalByDataset cd = new ChemicalByDataset(new Integer(dataset_id));
                qc.setScope(cd);
                setTemplate(createTemplate(context, request, response));
                setGroupProperties(context, request, response);
                return (Q) qc;
            } catch (Exception x) {
                setTemplate(createTemplate(context, request, response));
                setGroupProperties(context, request, response);
                return (Q) q;
            }
        }
    } catch (Exception x) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x);
    }
}

Example 5 with ISourceDataset

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

the class StructureRelationJSONReporter method header.

@Override
public void header(Writer output, Q query) {
    try {
        output.write("{\n");
        Reference datasetURI = baseReference.clone();
        datasetURI.addSegment(OpenTox.URI.dataset.name());
        Object dataset = (query instanceof AbstractQuery) ? ((AbstractQuery) query).getValue() : null;
        if (dataset instanceof IStoredQuery)
            datasetURI.addSegment(String.format("R%d", ((IStoredQuery) dataset).getID()));
        else if (dataset instanceof SourceDataset)
            datasetURI.addSegment(Integer.toString(((ISourceDataset) dataset).getID()));
        output.write(String.format("\"%s\":\"%s\",\n", jsonFeature.datasetURI.jsonname(), datasetURI));
        output.write("\"links\":[");
    } catch (Exception x) {
        x.printStackTrace();
    }
}