Examples with StoredQuery ambit2.db.search.StoredQuery used on opensource projects

Example 1 with StoredQuery

use of ambit2.db.search.StoredQuery in project ambit-mirror by ideaconsult.

the class ConsensusLabelQueryResource method createQuery.

@Override
protected IQueryRetrieval<IStructureRecord> createQuery(Context context, Request request, Response response) throws ResourceException {
    // collapsed = true;
    setGroupProperties(context, request, response);
    setTemplate(createTemplate(context, request, response));
    QueryStructureByQualityPairLabel q = new QueryStructureByQualityPairLabel();
    Form form = request.getResourceRef().getQueryAsForm();
    Object key = form.getFirstValue(QueryResource.search_param);
    ConsensusLabel label = new ConsensusLabel();
    if (key != null) {
        try {
            label.setLabel(CONSENSUS_LABELS.valueOf(Reference.decode(key.toString())));
        } catch (Exception x) {
            StringBuilder b = new StringBuilder();
            b.append("Valid values are ");
            for (CONSENSUS_LABELS v : CONSENSUS_LABELS.values()) {
                b.append(v);
                b.append('\t');
            }
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, b.toString(), x);
        }
    } else {
        label.setLabel(CONSENSUS_LABELS.Consensus);
    }
    q.setValue(label);
    key = form.getFirstValue("text");
    if (key != null)
        label.setText(key.toString());
    Object id = request.getAttributes().get(OpenTox.URI.dataset.getKey());
    if (id != null)
        try {
            datasetID = Integer.parseInt(id.toString());
            SourceDataset dataset = new SourceDataset();
            dataset.setId(datasetID);
            q.setFieldname(dataset);
            return q;
        } catch (Exception x) {
            if (id.toString().startsWith("R")) {
                queryResultsID = Integer.parseInt(id.toString().substring(1));
                StoredQuery dataset = new StoredQuery();
                dataset.setId(queryResultsID);
                q.setFieldname(dataset);
            } else
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid dataset id");
        }
    return q;
// throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST,"No dataset !");
}

Example 2 with StoredQuery

use of ambit2.db.search.StoredQuery in project ambit-mirror by ideaconsult.

the class QLabelQueryResource method createQuery.

@Override
protected IQueryRetrieval<IStructureRecord> createQuery(Context context, Request request, Response response) throws ResourceException {
    QueryStructureByQuality q = new QueryStructureByQuality();
    Form form = request.getResourceRef().getQueryAsForm();
    try {
        includeMol = "true".equals(form.getFirstValue("mol"));
    } catch (Exception x) {
        includeMol = false;
    }
    Object key = form.getFirstValue(QueryResource.search_param);
    if (key != null) {
        try {
            q.setValue(new QLabel(QUALITY.valueOf(Reference.decode(key.toString()))));
        } catch (Exception x) {
            StringBuilder b = new StringBuilder();
            b.append("Valid values are ");
            for (QUALITY v : QUALITY.values()) {
                b.append(v);
                b.append('\t');
            }
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, b.toString(), x);
        }
    } else {
        q.setValue(new QLabel(QUALITY.OK));
    }
    Object id = request.getAttributes().get(OpenTox.URI.dataset.getKey());
    if (id != null)
        try {
            datasetID = Integer.parseInt(id.toString());
            SourceDataset dataset = new SourceDataset();
            dataset.setId(datasetID);
            q.setFieldname(dataset);
            return q;
        } catch (Exception x) {
            if (id.toString().startsWith("R")) {
                queryResultsID = Integer.parseInt(id.toString().substring(1));
                StoredQuery dataset = new StoredQuery();
                dataset.setId(queryResultsID);
                q.setFieldname(dataset);
                return q;
            } else
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid dataset id");
        }
    throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No dataset !");
}

Example 3 with StoredQuery

use of ambit2.db.search.StoredQuery 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 4 with StoredQuery

use of ambit2.db.search.StoredQuery in project ambit-mirror by ideaconsult.

the class DatasetChemicalsQualityStatsResource method createQuery.

@Override
protected DatasetChemicalsQualityStats createQuery(Context context, Request request, Response response) throws ResourceException {
    Form form = getRequest().getResourceRef().getQueryAsForm();
    DatasetChemicalsQualityStats q = new DatasetChemicalsQualityStats(getResourceRef(getRequest()).toString());
    try {
        q.setSummary(Boolean.parseBoolean(form.getFirstValue("summary").toString()));
    } catch (Exception x) {
        q.setSummary(true);
    }
    Object id = request.getAttributes().get(OpenTox.URI.dataset.getKey());
    if (id != null)
        try {
            datasetID = Integer.parseInt(id.toString());
            SourceDataset dataset = new SourceDataset();
            dataset.setId(datasetID);
            q.setValue(dataset);
        } catch (Exception x) {
            /*
			if (id.toString().startsWith("R")) {
				queryResultsID = Integer.parseInt(id.toString().substring(1));
				StoredQuery dataset = new StoredQuery();
				dataset.setId(queryResultsID);
				q.setFieldname(dataset);
				return q;
			} else 
			*/
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid dataset id");
        }
    return q;
}

Example 5 with StoredQuery

use of ambit2.db.search.StoredQuery in project ambit-mirror by ideaconsult.

the class DatasetStructureQualityStatsResource method createQuery.

@Override
protected DatasetStructureQualityStats createQuery(Context context, Request request, Response response) throws ResourceException {
    DatasetStructureQualityStats q = new DatasetStructureQualityStats(getResourceRef(getRequest()).toString());
    Object id = request.getAttributes().get(OpenTox.URI.dataset.getKey());
    if (id != null)
        try {
            datasetID = Integer.parseInt(id.toString());
            SourceDataset dataset = new SourceDataset();
            dataset.setId(datasetID);
            q.setValue(dataset);
        } catch (Exception x) {
            /*
			if (id.toString().startsWith("R")) {
				queryResultsID = Integer.parseInt(id.toString().substring(1));
				StoredQuery dataset = new StoredQuery();
				dataset.setId(queryResultsID);
				q.setFieldname(dataset);
				return q;
			} else 
			*/
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid dataset id");
        }
    return q;
}