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

Example 1 with Template

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

the class FilteredDatasetResource method createQuery.

@Override
protected Q createQuery(Context context, Request request, Response response) throws ResourceException {
    Template filter = null;
    Form form = getResourceRef(getRequest()).getQueryAsForm();
    try {
        includeMol = "true".equals(form.getFirstValue("mol"));
    } catch (Exception x) {
        includeMol = false;
    }
    Object dataset = form.getFirstValue(OpenTox.params.dataset_uri.toString());
    String[] filteruris = OpenTox.params.filter.getValuesArray(form);
    Object condition = form.getFirstValue(OpenTox.params.condition.toString());
    SetCondition.conditions sc = condition == null ? SetCondition.conditions.in : "no".equals(condition) ? SetCondition.conditions.not_in : SetCondition.conditions.in;
    // if (dataset==null) throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST,"Empty dataset");
    if (filteruris == null)
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No features to filter");
    setTemplate(createTemplate(context, request, response));
    try {
        filter = createTemplate(context, request, response, filteruris);
        if ((filter == null) || (filter.size() == 0))
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No features to filter");
        if (dataset == null) {
            QueryStructureByProperty q = new QueryStructureByProperty();
            q.setFieldname(filter);
            q.setCondition(new SetCondition(sc));
            setPaging(form, q);
            return (Q) q;
        }
        Object q = CallableQueryProcessor.getQueryObject(new Reference(dataset.toString()), getRequest().getRootRef(), getApplication().getContext(), getCookies(), getAgent(), getRequest().getResourceRef().toString());
        if (q == null) {
            throw new ResourceException(Status.SERVER_ERROR_NOT_IMPLEMENTED, "Processing foreign datasets not implemented!");
        } else if (q instanceof QueryDatasetByID) {
            QueryStructureByPropertyInDataset qz = new QueryStructureByPropertyInDataset();
            qz.setValue((QueryDatasetByID) q);
            qz.setFieldname(filter);
            qz.setCondition(new SetCondition(sc));
            setPaging(form, qz);
            return (Q) qz;
        } else if (q instanceof QueryStoredResults) {
            QueryStructuresByPropertyInResults qz = new QueryStructuresByPropertyInResults();
            qz.setValue((QueryStoredResults) q);
            qz.setFieldname(filter);
            qz.setCondition(new SetCondition(sc));
            setPaging(form, qz);
            return (Q) qz;
        } else if (q instanceof QueryStructureByID) {
            QueryStructureByPropertyInCompounds qz = new QueryStructureByPropertyInCompounds();
            qz.setValue((QueryStructureByID) q);
            qz.setFieldname(filter);
            qz.setCondition(new SetCondition(sc));
            setPaging(form, qz);
            return (Q) qz;
        } else
            throw new ResourceException(Status.SERVER_ERROR_NOT_IMPLEMENTED, dataset.toString() + " " + q.getClass().getName() + " not implemented!");
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    }
}

Example 2 with Template

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

the class StatisticsResource method createQuery.

@Override
protected Q createQuery(Context context, Request request, Response response) throws ResourceException {
    String[] datasetsURI = getParams().getValuesArray(OpenTox.params.dataset_uri.toString());
    Template t = new Template(String.format("%s%s/{%s}", getRequest().getRootRef(), DatasetStructuresResource.dataset, DatasetStructuresResource.datasetKey));
    setStatus(Status.SUCCESS_OK);
    mode = getSearchMode();
    switch(mode) {
        case dataset_intersection:
            {
                QueryCountDatasetIntersection q = null;
                for (int i = 0; i < datasetsURI.length; i++) {
                    if (q == null)
                        q = new QueryCountDatasetIntersection(null);
                    String datasetURI = datasetsURI[i];
                    Map<String, Object> vars = new HashMap<String, Object>();
                    t.parse(datasetURI, vars);
                    if (i == 0)
                        q.setFieldname(vars.get(DatasetStructuresResource.datasetKey).toString());
                    else
                        q.setValue(vars.get(DatasetStructuresResource.datasetKey).toString());
                }
                if (q == null)
                    throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Missing dataset_uri parameters!");
                return (Q) q;
            }
        case structures:
            {
                return (Q) new QueryCount<FACET>(mode.getURL());
            }
        case properties:
            {
                return (Q) new QueryCountProperties(mode.getURL());
            }
        case values:
            {
                return (Q) new QueryCountValues(mode.getURL());
            }
        case dataset:
            {
                return (Q) new QueryCountDataset(mode.getURL());
            }
        case models:
            {
                return (Q) new QueryCountModels(mode.getURL());
            }
        case substances:
            {
                return (Q) new QueryCountSubstances(mode.getURL());
            }
        case substancetypes:
            {
                return (Q) new QueryCountSubstanceTypes(mode.getURL());
            }
        case experiment_endpoints:
            {
                QueryCountEndpoints q = new QueryCountEndpoints(mode.getURL());
                q.setFieldname(getParams().getFirstValue("top"));
                q.setValue(getParams().getFirstValue("category"));
                q.setEndpoint(getParams().getFirstValue("search"));
                return (Q) q;
            }
        case protocol_applications:
            {
                QueryCountProtocolApplications q = new QueryCountProtocolApplications(mode.getURL());
                q.setPageSize(1000);
                // ?bundle_uri=
                // Object bundleURI =
                // OpenTox.params.bundle_uri.getFirstValue(getParams());
                Object bundleURI = getParams().getFirstValue("filterbybundle");
                if (bundleURI != null) {
                    Integer idbundle = getIdBundle(bundleURI, request);
                    q.setBundle(new SubstanceEndpointsBundle(idbundle));
                }
                q.setFieldname(getParams().getFirstValue("topcategory"));
                q.setValue(getParams().getFirstValue("category"));
                return (Q) q;
            }
        case data_availability:
            {
                QueryCountProtocolApplications q = new QueryCountProtocolApplications(mode.getURL(), QueryCountProtocolApplications._mode_related.data_availability);
                q.setPageSize(2000);
                q.setFieldname(getParams().getFirstValue("topcategory"));
                q.setValue(getParams().getFirstValue("category"));
                return (Q) q;
            }
        case study_summary:
            {
                QueryCountProtocolApplications q = new QueryCountProtocolApplications(mode.getURL(), QueryCountProtocolApplications._mode_related.detail);
                q.setPageSize(2000);
                // ?bundle_uri=
                // Object bundleURI =
                // OpenTox.params.bundle_uri.getFirstValue(getParams());
                /*
			 * Object bundleURI = getParams().getFirstValue("filterbybundle");
			 * if (bundleURI!=null) { Integer idbundle = getIdBundle(bundleURI,
			 * request); q.setBundle(new SubstanceEndpointsBundle(idbundle)); }
			 */
                q.setFieldname(getParams().getFirstValue("topcategory"));
                q.setValue(getParams().getFirstValue("category"));
                return (Q) q;
            }
        case interpretation_result:
            {
                QueryCountInterpretationResults q = new QueryCountInterpretationResults(mode.getURL());
                q.setFieldname(getParams().getFirstValue("top"));
                q.setValue(getParams().getFirstValue("category"));
                q.setInterpretation_result(getParams().getFirstValue("search"));
                return (Q) q;
            }
        case chemicals_in_dataset:
            {
                QueryCountChemicalInDataset q = null;
                for (int i = 0; i < datasetsURI.length; i++) {
                    if (q == null)
                        q = new QueryCountChemicalInDataset(mode.getURL());
                    String datasetURI = datasetsURI[i];
                    Map<String, Object> vars = new HashMap<String, Object>();
                    t.parse(datasetURI, vars);
                    q.setFieldname(vars.get(DatasetStructuresResource.datasetKey).toString());
                }
                if (q == null)
                    throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Missing dataset_uri parameters!");
                return (Q) q;
            }
        case bundles:
            {
                return (Q) new QueryCountBundles(mode.getURL());
            }
        default:
            {
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
            }
    }
}

Example 3 with Template

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

the class AmbitFacetResource method getProperty.

protected Template getProperty(String[] propertyURI, int max) throws ResourceException {
    if (propertyURI == null)
        return null;
    Template profile = new Template();
    Connection connection = null;
    try {
        DBConnection dbc = new DBConnection(getContext());
        connection = dbc.getConnection();
        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 (int i = 0; i < propertyURI.length; i++) {
            reader.process(new Reference(propertyURI[i]));
            if ((i + 1) >= max)
                break;
        }
        return profile;
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    } finally {
        try {
            connection.close();
        } catch (Exception x) {
        }
    }
}

Example 4 with Template

use of ambit2.base.data.Template 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 5 with Template

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

the class StructureQueryResource method createConvertor.

@Override
public RepresentationConvertor createConvertor(Variant variant) throws AmbitException, ResourceException {
    /* workaround for clients not being able to set accept headers */
    if ((queryObject == null) && !(variant.getMediaType().equals(MediaType.TEXT_HTML)))
        throw new NotFoundException();
    setTemplate(template);
    Form acceptform = getResourceRef(getRequest()).getQueryAsForm();
    String media = acceptform.getFirstValue("accept-header");
    if (media != null) {
        variant.setMediaType(new MediaType(media));
    }
    String filenamePrefix = getRequest().getResourceRef().getPath();
    if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLSDF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(template, getGroupProperties(), changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLSDF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLMOL)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(new Template(), getGroupProperties(), true, changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLMOL, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_CML)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CMLReporter<QueryStructureByID>(), ChemicalMediaType.CHEMICAL_CML, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_SMILES)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SmilesReporter<QueryStructureByID>(true, getTemplate()), ChemicalMediaType.CHEMICAL_SMILES, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_INCHI)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SmilesReporter<QueryStructureByID>(false, Mode.InChI, getTemplate()), ChemicalMediaType.CHEMICAL_INCHI, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_PDF)) {
        return new PDFConvertor<IStructureRecord, QueryStructureByID, PDFReporter<QueryStructureByID>>(new PDFReporter<QueryStructureByID>(getTemplate(), getGroupProperties()), filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.TEXT_PLAIN)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(createTXTReporter(), MediaType.TEXT_PLAIN);
    } else if (variant.getMediaType().equals(MediaType.TEXT_URI_LIST)) {
        ConformerURIReporter<QueryStructureByID> reporter = new ConformerURIReporter<QueryStructureByID>(getCompoundInDatasetPrefix(), getRequest(), queryObject.isPrescreen());
        return new StringConvertor(reporter, MediaType.TEXT_URI_LIST, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.IMAGE_PNG)) {
        return new ImageConvertor<IStructureRecord, QueryStructureByID>(new ImageReporter<QueryStructureByID>(MediaType.IMAGE_PNG.getMainType(), MediaType.IMAGE_PNG.getSubType()), MediaType.IMAGE_PNG);
    } else if (variant.getMediaType().equals(MediaType.IMAGE_GIF)) {
        return new ImageConvertor<IStructureRecord, QueryStructureByID>(new ImageReporter<QueryStructureByID>(MediaType.IMAGE_GIF.getMainType(), MediaType.IMAGE_GIF.getSubType()), MediaType.IMAGE_GIF);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JSON)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, bundles, getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix(), includeMol, null), MediaType.APPLICATION_JSON, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JAVASCRIPT)) {
        String jsonpcallback = getParams().getFirstValue("jsonp");
        if (jsonpcallback == null)
            jsonpcallback = getParams().getFirstValue("callback");
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, bundles, getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix(), includeMol, jsonpcallback), MediaType.APPLICATION_JAVASCRIPT, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.WEKA_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new ARFFResourceReporter(getTemplate(), getGroupProperties(), getRequest(), String.format("%s%s", getRequest().getRootRef(), getCompoundInDatasetPrefix())), ChemicalMediaType.WEKA_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.THREECOL_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new ARFF3ColResourceReporter(getTemplate(), getGroupProperties(), getRequest(), String.format("%s%s", getRequest().getRootRef(), getCompoundInDatasetPrefix())), ChemicalMediaType.THREECOL_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.TEXT_CSV)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(createCSVReporter(), MediaType.TEXT_CSV, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_XML)) {
        switch(rdfwriter) {
            case stax:
                {
                    return new RDFStaXConvertor<IStructureRecord, IQueryRetrieval<IStructureRecord>>(new DatasetRDFStaxReporter(getCompoundInDatasetPrefix(), getRequest(), getTemplate(), getGroupProperties()), filenamePrefix);
                }
            default:
                {
                    // jena
                    return new RDFJenaConvertor<IStructureRecord, IQueryRetrieval<IStructureRecord>>(new DatasetRDFReporter(getCompoundInDatasetPrefix(), getRequest(), variant.getMediaType(), getTemplate(), getGroupProperties()), variant.getMediaType(), filenamePrefix);
                }
        }
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_TURTLE) || variant.getMediaType().equals(MediaType.TEXT_RDF_N3) || variant.getMediaType().equals(MediaType.TEXT_RDF_NTRIPLES) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TRIG) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TRIX) || variant.getMediaType().equals(ChemicalMediaType.APPLICATION_JSONLD)) {
        return new RDFJenaConvertor<IStructureRecord, IQueryRetrieval<IStructureRecord>>(new DatasetRDFReporter(getCompoundInDatasetPrefix(), getRequest(), variant.getMediaType(), getTemplate(), getGroupProperties()), variant.getMediaType(), filenamePrefix);
    } else
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(template, getGroupProperties(), changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLSDF, filenamePrefix);
}