Examples with QueryStructure ambit2.db.search.structure.QueryStructure used on opensource projects

Example 1 with QueryStructure

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

the class CompoundLookup method createQuery.

/*
	 */
@Override
protected IQueryRetrieval<IStructureRecord> createQuery(Context context, Request request, Response response) throws ResourceException {
    // parse params
    Object id = null;
    try {
        id = getRequest().getAttributes().get(resourceKey);
        if (id == null)
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No structure identifier");
        text = Reference.decode(id.toString().trim());
        if ("".equals(text))
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty query");
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, String.format("Invalid structure identifier", id));
    }
    id = null;
    try {
        id = getRequest().getAttributes().get(representationKey);
        if (id == null)
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No structure representation");
        rep_id = NCISearchProcessor.METHODS.valueOf(Reference.decode(id.toString()));
    } catch (Exception x) {
        rep_id = null;
    }
    Form form = getParams();
    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;
    }
    try {
        headless = Boolean.parseBoolean(form.getFirstValue("headless"));
    } catch (Exception x) {
        headless = false;
    }
    boolean casesens = "true".equals(form.getFirstValue(QueryResource.caseSensitive)) ? true : false;
    String scparam = form.getFirstValue(QueryResource.condition);
    setCondition(StringCondition.C_EQ);
    if (scparam != null)
        for (STRING_CONDITION sc : STRING_CONDITION.values()) {
            if (scparam.equals(sc.getSQL())) {
                setCondition(sc.getSQL());
                break;
            }
        }
    boolean retrieveProperties = "true".equals(form.getFirstValue(QueryResource.returnProperties)) ? true : false;
    String url = null;
    IQueryRetrieval<IStructureRecord> query = null;
    if (isInchiKey(text))
        try {
            String inchikey = getFirstParam(form);
            if ((inchikey == null) || (inchikey.trim().length() != 27))
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid InChI Key");
            QueryStructure q = new QueryStructure();
            q.setChemicalsOnly(true);
            q.setFieldname(ExactStructureSearchMode.inchikey);
            q.setValue(inchikey.trim());
            searchType = _searchtype.inchikey;
            query = q;
        } catch (ResourceException x) {
            throw x;
        } catch (Exception x) {
            throw new ResourceException(Status.SERVER_ERROR_BAD_GATEWAY, String.format("%s %s", url, x.getMessage()), x);
        }
    else if (isURL(text))
        try {
            url = getFirstParam(form);
            if (url == null)
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No search parameter!");
            Object q = CallableQueryProcessor.getQueryObject(new Reference(url), getRequest().getRootRef(), getApplication().getContext(), getCookies(), getAgent(), getRequest().getResourceRef().toString());
            if (q == null) {
                throw new ResourceException(Status.SERVER_ERROR_NOT_IMPLEMENTED, "TODO: retrieve compounds from foreign urls");
            } else if (q instanceof AbstractStructureQuery) {
                query = (IQueryRetrieval<IStructureRecord>) q;
            }
        } catch (ResourceException x) {
            throw x;
        } catch (Exception x) {
            throw new ResourceException(Status.SERVER_ERROR_BAD_GATEWAY, String.format("%s %s", url, x.getMessage()), x);
        }
    else {
        if (isSearchParam(text)) {
            text = getFirstParam(form);
            text_multi = getValuesArray(form);
        }
        Object idcompound = isAmbitID(text);
        // query
        if (idcompound != null) {
            switch(searchType) {
                case ambitid:
                    IStructureRecord record = new StructureRecord();
                    record.setIdchemical(((Integer) idcompound).intValue());
                    QueryStructureByID q = new QueryStructureByID();
                    q.setPageSize(1);
                    q.setChemicalsOnly(true);
                    q.setValue(record);
                    query = q;
                    break;
                case inchikey:
                    String inchikey = idcompound.toString();
                    if ((inchikey == null) || (inchikey.trim().length() != 27))
                        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid InChI Key");
                    QueryStructure q1 = new QueryStructure();
                    q1.setChemicalsOnly(true);
                    q1.setFieldname(ExactStructureSearchMode.inchikey);
                    q1.setValue(inchikey.trim());
                    searchType = _searchtype.inchikey;
                    query = q1;
                    break;
                default:
                    query = null;
                    break;
            }
        } else if ((text_multi != null) && (text_multi.length > 1)) {
            query = getMultiTextQuery(null, casesens, retrieveProperties, text_multi);
        } else if ((text == null) || "".equals(text)) {
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
        } else if (CASProcessor.isValidFormat(text)) {
            // number
            if (CASNumber.isValid(text.trim())) {
                searchType = _searchtype.cas;
                query = getTextQuery(Property.getCASInstance(), casesens, retrieveProperties, text);
            }
        } else if (EINECS.isValidFormat(text)) {
            // we'd better not search for invalid numbers
            if (EINECS.isValid(text.trim())) {
                searchType = _searchtype.einecs;
                query = getTextQuery(Property.getEINECSInstance(), casesens, retrieveProperties, text);
            }
        } else {
            if ("".equals(text)) {
            // if inchi
            } else if (isInChI(text)) {
                QueryStructure q = new QueryStructure();
                q.setChemicalsOnly(true);
                q.setFieldname(ExactStructureSearchMode.inchi);
                q.setValue(text);
                query = q;
            } else if (isMol(text)) {
                String[] inchi = mol2inchi(text);
                QueryStructure q = new QueryStructure();
                q.setChemicalsOnly(true);
                q.setFieldname(ExactStructureSearchMode.inchi);
                // eventually search by inchikey?
                q.setValue(inchi[0]);
                query = q;
            } else
                try {
                    // inchi, inchikey
                    String[] inchi = smiles2inchi(text.trim());
                    QueryStructure q = new QueryStructure();
                    q.setChemicalsOnly(true);
                    q.setFieldname(ExactStructureSearchMode.inchi);
                    // eventually search by inchikey?
                    q.setValue(inchi[0]);
                    query = q;
                } catch (InvalidSmilesException x) {
                    query = null;
                // otherwise this was valid smiles, but inchi failed!
                } catch (CDKException x) {
                    casesens = true;
                    query = null;
                } catch (Exception x) {
                    casesens = true;
                    query = null;
                }
        }
    }
    if (query == null)
        query = getTextQuery(null, casesens, retrieveProperties, text);
    setPaging(form, query);
    setTemplate(createTemplate(form));
    setGroupProperties(context, request, response);
    return query;
}

Example 2 with QueryStructure

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

the class CompoundResource method createQuery.

@Override
protected IQueryRetrieval<IStructureRecord> createQuery(Context context, Request request, Response response) throws ResourceException {
    media = getMediaParameter(request);
    Object key = null;
    try {
        Form form = request.getResourceRef().getQueryAsForm();
        try {
            includeMol = "true".equals(form.getFirstValue("mol"));
        } catch (Exception x) {
            includeMol = false;
        }
        DisplayMode defaultMode = null;
        try {
            defaultMode = DisplayMode.valueOf(form.getFirstValue("mode"));
        } catch (Exception x) {
        }
        _dmode = defaultMode == null ? DisplayMode.singleitem : defaultMode;
        try {
            headless = Boolean.parseBoolean(form.getFirstValue("headless"));
        } catch (Exception x) {
            headless = false;
        }
        key = request.getAttributes().get(OpenTox.URI.compound.getKey());
        if (key == null) {
            boolean byAlias = true;
            String condition = form.getFirstValue(QueryResource.condition);
            String casesens = form.getFirstValue(QueryResource.caseSensitive);
            String[] keys = form.getValuesArray(QueryResource.search_param);
            String[] properties = form.getValuesArray(OpenTox.params.sameas.toString());
            if ((properties == null) || (properties.length == 0)) {
                properties = form.getValuesArray(QueryResource.property);
                condition = (condition == null) ? "=" : condition;
                byAlias = false;
            } else
                condition = (condition == null) ? "=" : condition;
            if (keys != null) {
                _dmode = defaultMode == null ? DisplayMode.table : defaultMode;
                /*
					 * QueryCombinedStructure qcombined = new
					 * QueryCombinedStructure();
					 * qcombined.setCombine_as_and(true);
					 * qcombined.setChemicalsOnly(true);
					 * 
					 * IQueryRetrieval<IStructureRecord> query = qcombined;
					 */
                IQueryRetrieval<IStructureRecord> query = null;
                for (int i = 0; i < keys.length; i++) {
                    String theKey = Reference.decode(keys[i].trim());
                    String property = null;
                    try {
                        property = ((properties == null) || (i >= properties.length) || (properties[i] == null)) ? "" : Reference.decode(properties[i].trim());
                    } catch (Exception x) {
                        property = null;
                    }
                    casesens = CASProcessor.isValidFormat(theKey) ? "true" : casesens;
                    casesens = EINECS.isValidFormat(theKey) ? "true" : casesens;
                    casesens = theKey.startsWith(AmbitCONSTANTS.INCHI) ? "true" : casesens;
                    casesens = theKey.startsWith("AuxInfo=") ? "true" : casesens;
                    // check for smiles will be more time consuming, skip
                    // for now
                    IQueryRetrieval<IStructureRecord> q = createSingleQuery(property, condition, theKey, chemicalsOnly, byAlias, casesens == null ? false : "true".equals(casesens.toLowerCase()));
                    // keys.length==1);
                    query = q;
                    break;
                /*
						 * if (keys.length>1) qcombined.add(q); else query = q;
						 */
                }
                return query;
            } else
                return null;
        } else {
            try {
                IStructureRecord record = new StructureRecord();
                record.setIdchemical(Integer.parseInt(Reference.decode(key.toString())));
                return createQueryByID(record);
            } catch (NumberFormatException x) {
                String inchikey = key.toString().trim();
                if (inchikey.length() == 27) {
                    // assume InChIKey
                    QueryStructure q = new QueryStructure();
                    q.setChemicalsOnly(true);
                    q.setFieldname(ExactStructureSearchMode.inchikey);
                    q.setValue(inchikey.trim());
                    return q;
                }
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid resource id", x);
            }
        }
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x.getMessage(), x);
    }
}

Example 3 with QueryStructure

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

the class PropertyImporter method setPropertyKey.

public void setPropertyKey(IStructureKey propertyKey) {
    this.queryKey = propertyKey;
    if ((propertyKey instanceof SmilesKey) || (propertyKey instanceof InchiKey)) {
        query_property = new QueryStructure();
    } else if ((propertyKey.getType() == Number.class) || (propertyKey.getType() == Integer.class) || (propertyKey.getType() == Double.class))
        query_property = new QueryFieldNumeric();
    else
        query_property = new QueryField();
    query_property.setId(-1);
}

Example 4 with QueryStructure

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

the class QueryStructureTest method test.

@Test
public void test() throws Exception {
    QueryStructure qf = new QueryStructure();
    qf.setFieldname(ExactStructureSearchMode.smiles);
    qf.setValue("CC");
    qf.setCondition(StringCondition.getInstance("="));
    qf.setId(1);
    // Assert.assertEquals(String.format(QueryStructure.sqlSMILES, "", qf.getFieldname(),qf.getCondition(),qf.getFieldname(),qf.getCondition(),"")
    // ,qf.getSQL());
    List<QueryParam> params = qf.getParameters();
    Assert.assertNotNull(params);
    Assert.assertEquals(3, params.size());
    Assert.assertEquals(Integer.class, params.get(0).getType());
    Assert.assertEquals(String.class, params.get(1).getType());
    Assert.assertEquals(1, params.get(0).getValue());
    Assert.assertEquals("CC", params.get(1).getValue());
}

Example 5 with QueryStructure

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

the class Structure_crud_test method createVerify.

@Override
protected void createVerify(IQueryUpdate<Object, IStructureRecord> query) throws Exception {
    IDatabaseConnection c = getConnection();
    QueryStructure q = new QueryStructure();
    q.setFieldname(ExactStructureSearchMode.idchemical);
    q.setValue("10");
    RetrieveStructure r = new RetrieveStructure();
    // structure
    r.setFieldname(false);
    QueryExecutor execR = new QueryExecutor();
    execR.setConnection(c.getConnection());
    QueryExecutor exec = new QueryExecutor();
    exec.setConnection(c.getConnection());
    ResultSet rs = exec.process(q);
    int count = 0;
    while (rs.next()) {
        IStructureRecord record = q.getObject(rs);
        r.setValue(record);
        ResultSet rs1 = execR.process(r);
        while (rs1.next()) {
            record = r.getObject(rs1);
            if ("content".equals(record.getContent()))
                count++;
        }
        execR.closeResults(rs1);
    }
    exec.closeResults(rs);
    Assert.assertEquals(1, count);
    c.close();
}