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

Example 1 with IStoredQuery

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

the class StructureRelationJSONReporter method header.

@Override
public void header(Writer output, Q query) {
    try {
        output.write("{\n");
        Reference datasetURI = baseReference.clone();
        datasetURI.addSegment(OpenTox.URI.dataset.name());
        Object dataset = (query instanceof AbstractQuery) ? ((AbstractQuery) query).getValue() : null;
        if (dataset instanceof IStoredQuery)
            datasetURI.addSegment(String.format("R%d", ((IStoredQuery) dataset).getID()));
        else if (dataset instanceof SourceDataset)
            datasetURI.addSegment(Integer.toString(((ISourceDataset) dataset).getID()));
        output.write(String.format("\"%s\":\"%s\",\n", jsonFeature.datasetURI.jsonname(), datasetURI));
        output.write("\"links\":[");
    } catch (Exception x) {
        x.printStackTrace();
    }
}

Example 2 with IStoredQuery

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

the class CallableQueryResultsCreator method createQueryResults.

protected TaskResult createQueryResults(IQueryObject<IStructureRecord> target) throws Exception {
    Connection connection = null;
    UpdateExecutor xx = new UpdateExecutor();
    try {
        DBConnection dbc = new DBConnection(context);
        connection = dbc.getConnection();
        SessionID session = new SessionID();
        session.setName(folder);
        CreateQueryFolder qfolder = new CreateQueryFolder();
        qfolder.setObject(session);
        xx.setConnection(connection);
        xx.process(qfolder);
        ProcessorCreateQuery p = new ProcessorCreateQuery();
        p.setQueryName(queryName == null ? UUID.randomUUID().toString() : queryName);
        p.setProfile(template);
        p.setDelete(clearPreviousContent);
        p.setCopy(true);
        p.setStoredQuery(storedQuery);
        p.setSession(session);
        p.setConnection(connection);
        IStoredQuery q = p.process((IQueryObject<IStructureRecord>) target);
        return new TaskResult(String.format("%s/dataset/%s%d", applicationRootReference, DatasetStructuresResource.QR_PREFIX, q.getId()));
    } catch (Exception x) {
        Context.getCurrentLogger().log(Level.SEVERE, x.getMessage(), x);
        throw x;
    } finally {
        Context.getCurrentLogger().fine("Done");
        try {
            xx.close();
        } catch (Exception x) {
        }
        try {
            connection.close();
        } catch (Exception x) {
            Context.getCurrentLogger().warning(x.getMessage());
        }
    }
}

Example 3 with IStoredQuery

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

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

the class QueryPairwiseTanimotoAndProperty method getSQL.

@Override
public String getSQL() throws AmbitException {
    if ((property == null) || (property.getId() <= 0))
        return super.getSQL();
    ISourceDataset q1 = (getFieldname() != null) ? getFieldname() : getValue();
    ISourceDataset q2 = (getValue() != null) ? getValue() : getFieldname();
    if (q1 instanceof IStoredQuery) {
        if (q2 instanceof IStoredQuery)
            return sql_rdataset;
        else
            return sql_dataset_rdataset;
    } else if (q2 instanceof IStoredQuery)
        return sql_dataset_rdataset;
    else
        return sql_dataset;
}

Example 5 with IStoredQuery

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

the class ProcessorCreateQueryTest method test.

@Test
public void test() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/descriptors-datasets.xml");
    IQueryObject q = new QueryStructureByID(100211, 100215);
    q.setPageSize(1000);
    IDatabaseConnection c = getConnection();
    ProcessorCreateSession ps = new ProcessorCreateSession();
    ps.setConnection(c.getConnection());
    SessionID s = new SessionID();
    s = ps.process(s);
    c = getConnection();
    ProcessorCreateQuery pq = new ProcessorCreateQuery();
    pq.setSession(s);
    pq.setConnection(c.getConnection());
    IStoredQuery storedQuery = pq.process(q);
    c = getConnection();
    ITable table = c.createQueryTable("EXPECTED", String.format("SELECT idsessions,title from sessions where title='%s'", s.getName()));
    Assert.assertEquals(1, table.getRowCount());
    Assert.assertEquals(s.getName(), table.getValue(0, "title").toString());
    Assert.assertEquals(3, storedQuery.getRows());
    c.close();
}