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

Example 1 with QueryStoredResults

use of ambit2.db.search.structure.QueryStoredResults 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 QueryStoredResults

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

the class ProcessorCreateQuery method process.

public IStoredQuery process(IQueryObject<IStructureRecord> target) throws AmbitException {
    if (target == null)
        throw new AmbitException("Undefined query!");
    if (qexec == null) {
        qexec = new QueryExecutor();
        qexec.setCloseConnection(false);
    }
    qexec.setConnection(connection);
    try {
        if (result == null) {
            if (!copy & (target instanceof QueryStoredResults))
                return ((QueryStoredResults) target).getFieldname();
            result = new StoredQuery(-1);
            result.setName(queryName == null ? UUID.randomUUID().toString() : queryName);
        } else {
            if (target instanceof QueryStoredResults) {
                if ((((QueryStoredResults) target).getId() == result.getId()) && (result.getId() > 0))
                    // if we are copying to the same query , don't delete!
                    delete = false;
            }
        }
        result.setQuery(target);
        connection.setAutoCommit(false);
        // create entry in the query table
        if (result.getId() <= 0) {
            // read by name and folder title
            ReadStoredQuery findIfExists = new ReadStoredQuery();
            findIfExists.setValue(result);
            // <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
            findIfExists.setFieldname(getSession().getName());
            ResultSet found = null;
            try {
                found = qexec.process(findIfExists);
                while (found.next()) {
                    IStoredQuery q = findIfExists.getObject(found);
                    result.setID(q.getID());
                    break;
                }
            } catch (Exception x) {
                logger.warning(x.getMessage());
            } finally {
                try {
                    found.close();
                } catch (Exception x) {
                }
            }
            // if still not found, add it! TODO refactor it to use UpdateExecutor
            if (result.getId() <= 0) {
                PreparedStatement s = connection.prepareStatement(CreateStoredQuery.sql_byname, Statement.RETURN_GENERATED_KEYS);
                s.setNull(1, Types.INTEGER);
                if (result.getName().length() > 255)
                    s.setString(2, result.getName().substring(0, 255));
                else
                    s.setString(2, result.getName());
                try {
                    s.setString(3, result.getQuery().toString() == null ? "Results" : result.getQuery().toString());
                } catch (Exception x) {
                    s.setString(3, "Results");
                }
                s.setString(4, getSession().getName());
                // execute
                if (s.executeUpdate() > 0) {
                    ResultSet rss = s.getGeneratedKeys();
                    while (rss.next()) result.setId(new Integer(rss.getInt(1)));
                    rss.close();
                }
                s.close();
            }
        }
        // sometimes we want to remove the old content
        if (delete && (result.getId() > 0)) {
            PreparedStatement s = null;
            try {
                s = connection.prepareStatement("Delete from query_results where idquery=?");
                s.setInt(1, result.getId());
                s.executeUpdate();
            } catch (Exception x) {
            } finally {
                try {
                    if (s != null)
                        s.close();
                } catch (Exception x) {
                }
            }
        }
        if (result.getId() > 0) {
            int rows = 0;
            if ((result.getQuery() instanceof IQueryRetrieval) && ((IQueryRetrieval) result.getQuery()).isPrescreen()) {
                rows = insertScreenedResults(result, (IQueryRetrieval<IStructureRecord>) result.getQuery());
            } else {
                rows = insertResults(result);
                if (rows > 0)
                    connection.commit();
                else
                    connection.rollback();
            }
            insertProfile(result, profile);
        }
        return result;
    } catch (Exception x) {
        try {
            connection.rollback();
        } catch (SQLException xx) {
        }
        throw new ProcessorException(this, x);
    } finally {
        try {
            close();
        } catch (Exception e) {
        }
    }
}

Example 3 with QueryStoredResults

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

the class StoredQueryTableModel method selectRecords.

protected void selectRecords(SELECTION_MODE mode) throws Exception, SQLException {
    IStoredQuery query = null;
    if (storedResults == null)
        return;
    if (storedResults instanceof QueryStoredResults)
        query = ((QueryStoredResults) storedResults).getFieldname();
    else if (storedResults instanceof IStoredQuery)
        query = (IStoredQuery) storedResults;
    else
        return;
    UpdateSelectedRecords r = new UpdateSelectedRecords();
    r.setObject(mode);
    r.setGroup(query);
    int updated = updateExecutor.process(r);
    if (updated > 0)
        setQuery(getQuery());
}

Example 4 with QueryStoredResults

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

the class StoredQueryTableModelTest method createQuery.

/*
	public void test() throws Exception {
		final IStoredQuery query = new StoredQuery();
		query.setId(3);
		final StoredQueryTableModel queryModel = new StoredQueryTableModel();
		Profile profile = new Profile();
		Property prop = Property.getInstance("CAS","CAS");
		prop.setLabel("CAS RN");
		prop.setClazz(String.class);
		prop.setEnabled(true);
		profile.add(prop);
		queryModel.setProfile(profile);
	
	}
*/
@Override
protected QueryStoredResults createQuery() throws Exception {
    QueryStoredResults q = new QueryStoredResults();
    q.setFieldname(new StoredQuery(1));
    return q;
}

Example 5 with QueryStoredResults

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

the class DatasetStructuresResource method getQueryById.

protected Q getQueryById(String key) throws ResourceException {
    if (key.startsWith(QR_PREFIX)) {
        key = key.substring(QR_PREFIX.length());
        try {
            queryResultsID = Integer.parseInt(key.toString());
        } catch (NumberFormatException x) {
            throw new InvalidResourceIDException(key);
        }
    } else
        return getDatasetByName(key);
    if ((property > 0) && (search != null)) {
        Property p = new Property("");
        p.setId(property);
        DatasetQueryFieldGeneric q = getSearchQuery(search, p, cond);
        StoredQuery d = new StoredQuery(Integer.parseInt(key.toString()));
        q.setFieldname(d);
        Form form = getResourceRef(getRequest()).getQueryAsForm();
        setPaging(form, q);
        return (Q) q;
    } else {
        QueryStoredResults q = new QueryStoredResults();
        q.setChemicalsOnly(true);
        q.setFieldname(new StoredQuery(Integer.parseInt(key.toString())));
        q.setValue(null);
        return (Q) q;
    }
}