Examples with UpdateExecutor ambit2.db.UpdateExecutor used on opensource projects

Example 1 with UpdateExecutor

use of ambit2.db.UpdateExecutor 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 2 with UpdateExecutor

use of ambit2.db.UpdateExecutor 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 UpdateExecutor

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

the class SubstanceWriterTest method delete.

public int delete(SubstanceEndpointsBundle bundle, IRawReader<IStructureRecord> reader, Connection connection) throws Exception {
    /*
		 * DBSubstanceWriter writer; if (bundle != null) writer = new
		 * DBBundleStudyWriter(bundle, DBSubstanceWriter.datasetMeta(), new
		 * SubstanceRecord()); else writer = new
		 * DBSubstanceWriter(DBSubstanceWriter.datasetMeta(), new
		 * SubstanceRecord(), clearMeasurements, clearComposition);
		 * writer.setSplitRecord(splitRecord); writer.setConnection(connection);
		 * writer.open();
		 */
    UpdateExecutor<IQueryUpdate> writer = new UpdateExecutor<IQueryUpdate>();
    writer.setConnection(connection);
    DeleteMatrixValue q = new DeleteMatrixValue();
    q.setGroup(bundle);
    int records = 0;
    while (reader.hasNext()) {
        Object record = reader.next();
        if (record == null)
            continue;
        Assert.assertTrue(record instanceof SubstanceRecord);
        Assert.assertEquals("IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734", ((SubstanceRecord) record).getSubstanceUUID());
        for (ProtocolApplication pa : ((SubstanceRecord) record).getMeasurements()) {
            Assert.assertTrue(pa instanceof ProtocolApplicationAnnotated);
            // System.out.println(((ProtocolApplicationAnnotated) pa)getRecords_to_delete());
            ProtocolApplicationAnnotated paa = (ProtocolApplicationAnnotated) pa;
            List<ValueAnnotated> vaa = paa.getRecords_to_delete();
            for (ValueAnnotated va : vaa) {
                q.setObject(va);
                writer.process(q);
            }
        }
        // writer.setImportedRecord((SubstanceRecord) record);
        // writer.process((IStructureRecord) record);
        records++;
    }
    writer.close();
    return records;
}

Example 4 with UpdateExecutor

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

the class CallableWekaModelCreator method createReference.

@Override
protected TaskResult createReference(Connection connection) throws Exception {
    builder.setTrainingData(((RDFInstancesParser) batch).getInstances());
    UpdateExecutor<CreateModel> x = new UpdateExecutor<CreateModel>();
    try {
        model = createModel();
        CreateModel update = new CreateModel(model);
        x.setConnection(connection);
        x.process(update);
        writeAnnotations(model.getPredicted(), x);
        return new TaskResult(builder.getModelReporter().getURI(model));
    } catch (WekaException e) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage(), e);
    } catch (AmbitException e) {
        Context.getCurrentLogger().severe(e.getMessage());
        if ((e.getCause() != null) && (e.getCause() instanceof WekaException))
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getCause().getMessage(), e.getCause());
        else
            throw e;
    } catch (Exception e) {
        Context.getCurrentLogger().severe(e.getMessage());
        throw e;
    } finally {
        try {
            x.close();
        } catch (Exception xx) {
        }
    }
}

Example 5 with UpdateExecutor

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

the class CallableWafflesModelCreator method createReference.

/**
 *	TODO download ARFF directly, instead of reading Weka instances in memory
 *	protected AbstractBatchProcessor createBatch(Object target) throws Exception{
 *		if (target == null) throw new Exception("No dataset URI");
 *
 *		File.createTempFile(prefix, suffix);
 *		DownloadTool.download(url, file);
 *		builder.setTrainingData(trainingData);
 *		return null;
 *	}
 */
@Override
protected TaskResult createReference(Connection connection) throws Exception {
    File trainingData = File.createTempFile("wfltrain_", ".arff");
    trainingData.deleteOnExit();
    Instances instances = ((RDFInstancesParser) batch).getInstances();
    instances.deleteAttributeAt(0);
    // sort attributes by name (i.e. attribute URI).
    List<Attribute> sorted = new ArrayList<Attribute>();
    for (int i = 0; i < instances.numAttributes(); i++) sorted.add(instances.attribute(i));
    Collections.sort(sorted, new Comparator<Attribute>() {

        @Override
        public int compare(Attribute o1, Attribute o2) {
            return o1.name().compareTo(o2.toString());
        }
    });
    StringBuilder order = null;
    for (int i = 0; i < sorted.size(); i++) {
        if (order == null)
            order = new StringBuilder();
        else
            order.append(",");
        order.append(sorted.get(i).index() + 1);
    }
    Reorder reorder = new Reorder();
    String[] options = new String[2];
    options[0] = "-R";
    options[1] = order.toString();
    reorder.setOptions(options);
    reorder.setInputFormat(instances);
    instances = Filter.useFilter(instances, reorder);
    SparseToNonSparse sp = new SparseToNonSparse();
    sp.setInputFormat(instances);
    Instances newInstances = Filter.useFilter(instances, sp);
    ArffSaver saver = new ArffSaver();
    saver.setInstances(newInstances);
    saver.setFile(trainingData);
    saver.writeBatch();
    // Leave the header only
    newInstances.delete();
    builder.setHeader(newInstances);
    builder.setTrainingData(trainingData);
    UpdateExecutor<CreateModel> x = new UpdateExecutor<CreateModel>();
    try {
        model = createModel();
        // trainingData.delete();
        CreateModel update = new CreateModel(model);
        x.setConnection(connection);
        x.process(update);
        writeAnnotations(model.getPredicted(), x);
        return new TaskResult(builder.getModelReporter().getURI(model));
    } catch (WekaException e) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage(), e);
    } catch (Exception e) {
        Context.getCurrentLogger().severe(e.getMessage());
        throw e;
    } finally {
        try {
            x.close();
        } catch (Exception xx) {
        }
    }
}