Examples with ProcessorException ambit2.base.processors.ProcessorException used on opensource projects

Example 1 with ProcessorException

use of ambit2.base.processors.ProcessorException 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 2 with ProcessorException

use of ambit2.base.processors.ProcessorException in project ambit-mirror by ideaconsult.

the class QueryExecutor method process.

public synchronized ResultSet process(Q target) throws AmbitException {
    long now = System.currentTimeMillis();
    Connection c = getConnection();
    if (c == null)
        throw new AmbitException("no connection");
    ResultSet rs = null;
    try {
        List<QueryParam> params = target.getParameters();
        if (params == null) {
            statement = c.createStatement(getResultType(), getResultTypeConcurency());
            String sql = getSQL(target);
            rs = statement.executeQuery(sql);
        } else {
            String sql = getSQL(target);
            sresults = getCachedStatement(sql);
            if (sresults == null) {
                if (target instanceof IStoredProcStatement) {
                    sresults = c.prepareCall(sql);
                } else {
                    sresults = c.prepareStatement(sql, getResultType(), getResultTypeConcurency());
                    sresults.setFetchDirection(ResultSet.FETCH_FORWARD);
                    sresults.setFetchSize(Integer.MIN_VALUE);
                }
                if (isUseCache())
                    addStatementToCache(sql, sresults);
            } else {
                sresults.clearParameters();
            }
            QueryExecutor.setParameters(sresults, params);
            // logger.log(Level.FINEST,sql);
            rs = sresults.executeQuery();
        }
    } catch (Exception x) {
        try {
            logger.log(Level.SEVERE, x.getMessage() + " " + sresults);
        } catch (Exception xx) {
        }
        throw new ProcessorException(this, x);
    } catch (Throwable x) {
        throw new ProcessorException(this, x.getMessage());
    } finally {
    }
    return rs;
}

Example 3 with ProcessorException

use of ambit2.base.processors.ProcessorException in project ambit-mirror by ideaconsult.

the class HTTPRequest method process.

public Result process(Target target) throws AmbitException {
    int retry = 0;
    int status = 200;
    setCancelled(false);
    while (!isCancelled()) {
        try {
            URL url = new URL(getUrl());
            URLConnection connection = url.openConnection();
            if (connection instanceof HttpURLConnection) {
                HttpURLConnection hc = ((HttpURLConnection) connection);
                hc.setReadTimeout(timeout);
                hc.setConnectTimeout(timeout);
                hc.setRequestMethod(httpMethod);
                hc.setDoOutput(true);
                prepareOutput(target, hc.getOutputStream());
                InputStream in = hc.getInputStream();
                Result result = parseInput(target, hc.getInputStream());
                in.close();
                status = hc.getResponseCode();
                switch(status) {
                    case 200:
                        return result;
                    case 404:
                        return null;
                    case 500:
                        {
                            retry++;
                            setCancelled(retry >= 10);
                        }
                    default:
                        {
                            throw new ProcessorException(this, String.format("STATUS: %d", status));
                        }
                }
            } else
                return null;
        } catch (SocketTimeoutException x) {
            retry++;
            setCancelled(retry >= maxretry);
            if (isCancelled())
                if (maxretry > 1)
                    throw new ProcessorException(this, "Maximum retry count reached " + maxretry);
                else
                    throw new ProcessorException(this, x);
        } catch (FileNotFoundException x) {
            throw new ambit2.pubchem.FileNotFoundException(this, x);
        } catch (IOException x) {
            if (x.getMessage().indexOf("Server returned HTTP response code: 4") >= 0)
                setCancelled(true);
            throw new ProcessorException(this, x);
        } catch (Exception x) {
            throw new ProcessorException(this, x);
        } finally {
        }
    }
    if (isCancelled())
        throw new ProcessorException(this, "Maximum retry count reached " + maxretry);
    else
        throw new ProcessorException(this, "STATUS: " + status);
}

Example 4 with ProcessorException

use of ambit2.base.processors.ProcessorException in project ambit-mirror by ideaconsult.

the class NCISearchProcessor method parseInput.

@Override
protected String parseInput(String target, InputStream in) throws ProcessorException {
    StringBuilder builder = new StringBuilder();
    try {
        BufferedReader reader = new BufferedReader(new InputStreamReader(in));
        String line = null;
        while ((line = reader.readLine()) != null) {
            builder.append(line);
            builder.append((getOption().equals(METHODS.sdf)) ? '\n' : '\t');
        }
        return builder.toString();
    } catch (Exception x) {
        throw new ProcessorException(this, x);
    }
}

Example 5 with ProcessorException

use of ambit2.base.processors.ProcessorException in project ambit-mirror by ideaconsult.

the class PUGProcessor method createDownloadHTTPRequest.

protected HTTPRequest<List<IStructureRecord>, List<IStructureRecord>> createDownloadHTTPRequest(List<IStructureRecord> record) {
    HTTPRequest<List<IStructureRecord>, List<IStructureRecord>> request = new HTTPRequest<List<IStructureRecord>, List<IStructureRecord>>() {

        @Override
        protected List<IStructureRecord> parseInput(List<IStructureRecord> target, InputStream in) throws ProcessorException {
            try {
                DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
                DocumentBuilder builder = factory.newDocumentBuilder();
                Document doc = builder.parse(new InputSource(new InputStreamReader(in)));
                doc.normalize();
                return parseOutput(doc);
            } catch (IOException x) {
                throw new ProcessorException(this, x);
            } catch (SAXException x) {
                throw new ProcessorException(this, x);
            } catch (ParserConfigurationException x) {
                throw new ProcessorException(this, x);
            }
        }

        @Override
        protected void prepareOutput(List<IStructureRecord> target, OutputStream out) throws ProcessorException {
            try {
                Writer w = new OutputStreamWriter(out);
                createDownloadRequest(target, w);
                w.flush();
                w.close();
            } catch (ParserConfigurationException x) {
                throw new ProcessorException(this, x);
            } catch (TransformerException x) {
                throw new ProcessorException(this, x);
            } catch (IOException x) {
                throw new ProcessorException(this, x);
            }
        }
    };
    request.setUrl(pugURL);
    return request;
}