Examples with SubstanceEndpointsBundle ambit2.base.data.substance.SubstanceEndpointsBundle used on opensource projects

Example 1 with SubstanceEndpointsBundle

use of ambit2.base.data.substance.SubstanceEndpointsBundle 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 2 with SubstanceEndpointsBundle

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

the class StudySearchResource method createQuery.

@Override
protected QueryCountProtocolApplications createQuery(Context context, Request request, Response response) throws ResourceException {
    try {
        Form form = getRequest().getResourceRef().getQueryAsForm();
        mergeDatasets = Boolean.parseBoolean(form.getFirstValue("mergeDatasets"));
    } catch (Exception x) {
        mergeDatasets = false;
    }
    Object bundleURI = OpenTox.params.bundle_uri.getFirstValue(getParams());
    if (bundleURI != null) {
        Integer idbundle = getIdBundle(bundleURI, request);
        bundle = new SubstanceEndpointsBundle(idbundle);
    }
    QueryCountProtocolApplications q = super.createQuery(context, request, response);
    try {
        q.setMode(_mode_related.valueOf(getParams().getFirstValue("selected")));
    } catch (Exception x) {
        q.setMode(_mode_related.endpoints);
    }
    return q;
}

Example 3 with SubstanceEndpointsBundle

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

the class UserByURIResource method readBundle.

protected SubstanceEndpointsBundle readBundle(int idbundle) throws ResourceException {
    SubstanceEndpointsBundle dataset = new SubstanceEndpointsBundle();
    dataset.setID(idbundle);
    Connection c = null;
    ResultSet rs = null;
    QueryExecutor xx = null;
    try {
        DBConnection dbc = new DBConnection(getContext(), getAmbitConfigFile());
        c = dbc.getConnection();
        Set<_published_status> status = new TreeSet<_published_status>();
        status.add(_published_status.published);
        ReadBundle read = new ReadBundle(status);
        read.setValue(dataset);
        xx = new QueryExecutor();
        xx.setConnection(c);
        rs = xx.process(read);
        while (rs.next()) {
            dataset = read.getObject(rs);
        }
        return dataset;
    } catch (Exception x) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x.getMessage(), x);
    } finally {
        try {
            rs.close();
        } catch (Exception x) {
        }
        try {
            c.close();
        } catch (Exception x) {
        }
        try {
            xx.close();
        } catch (Exception x) {
        }
    }
}

Example 4 with SubstanceEndpointsBundle

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

the class UserByURIResource method createQuery.

@Override
protected ReadUser createQuery(Context context, Request request, Response response) throws ResourceException {
    if (!Method.GET.equals(request.getMethod()))
        return null;
    check(context, request, response);
    String usersdbname = getContext().getParameters().getFirstValue(AMBITConfig.users_dbname.name());
    Form form = request.getResourceRef().getQueryAsForm();
    Object search_value = null;
    try {
        search_value = form.getFirstValue(param_q);
        if (search_value == null)
            search_value = form.getFirstValue("search");
        if (search_value != null) {
            ReadUser query = new ReadUser();
            DBUser user = new DBUser();
            String s = String.format("^%s", search_value.toString());
            user.setLastname(s);
            user.setFirstname(s);
            query.setValue(user);
            addPublicGroup = true;
            return query;
        }
    } catch (Exception x) {
        search_value = null;
    }
    try {
        search_value = form.getFirstValue(param_bundle_uri);
        Integer idbundle = search_value == null ? null : getIdBundle(search_value, request);
        SubstanceEndpointsBundle bundle = readBundle(idbundle);
        ReadUserByBundleNumber query = new ReadUserByBundleNumber();
        query.setDatabaseName(usersdbname);
        query.setFieldname(bundle.getBundle_number().toString());
        search_value = form.getFirstValue(param_mode);
        if ("W".equals(search_value))
            query.setAllowWrite(true);
        else
            query.setAllowWrite(false);
        return query;
    } catch (Exception x) {
        search_value = null;
    }
    throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND);
}

Example 5 with SubstanceEndpointsBundle

use of ambit2.base.data.substance.SubstanceEndpointsBundle 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);
    }
}