org.opendatakit.aggregate.odktables.api.perf.AggregateSynchronizer.java Source code

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/*
 * Copyright (C) 2012 University of Washington
 *
 * Licensed under the Apache License, Version 2.0 (the "License"); you may not
 * use this file except in compliance with the License. You may obtain a copy of
 * the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
 * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
 * License for the specific language governing permissions and limitations under
 * the License.
 */
package org.opendatakit.aggregate.odktables.api.perf;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileFilter;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.net.CookieHandler;
import java.net.CookieManager;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLEncoder;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Set;
import java.util.TimeZone;

import javax.ws.rs.core.HttpHeaders;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.ext.RuntimeDelegate;

import org.apache.commons.lang3.CharEncoding;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.http.HttpStatus;
import org.apache.wink.client.ClientConfig;
import org.apache.wink.client.ClientResponse;
import org.apache.wink.client.ClientWebException;
import org.apache.wink.client.EntityType;
import org.apache.wink.client.Resource;
import org.apache.wink.client.RestClient;
import org.apache.wink.client.internal.handlers.GzipHandler;
import org.opendatakit.aggregate.odktables.rest.ApiConstants;
import org.opendatakit.aggregate.odktables.rest.entity.ChangeSetList;
import org.opendatakit.aggregate.odktables.rest.entity.Column;
import org.opendatakit.aggregate.odktables.rest.entity.OdkTablesFileManifest;
import org.opendatakit.aggregate.odktables.rest.entity.OdkTablesFileManifestEntry;
import org.opendatakit.aggregate.odktables.rest.entity.Row;
import org.opendatakit.aggregate.odktables.rest.entity.RowList;
import org.opendatakit.aggregate.odktables.rest.entity.RowOutcomeList;
import org.opendatakit.aggregate.odktables.rest.entity.RowResourceList;
import org.opendatakit.aggregate.odktables.rest.entity.TableDefinition;
import org.opendatakit.aggregate.odktables.rest.entity.TableDefinitionResource;
import org.opendatakit.aggregate.odktables.rest.entity.TableResource;
import org.opendatakit.aggregate.odktables.rest.entity.TableResourceList;
import org.opendatakit.aggregate.odktables.api.SyncETagsUtils;
import org.opendatakit.aggregate.odktables.api.SyncProgressState;
import org.opendatakit.aggregate.odktables.api.SyncRow;
import org.opendatakit.aggregate.odktables.api.SyncRowPending;
import org.opendatakit.aggregate.odktables.api.Synchronizer;
import org.opendatakit.aggregate.odktables.api.exceptions.InvalidAuthTokenException;

/**
 * Implementation of {@link Synchronizer} for ODK Aggregate.
 *
 * @author the.dylan.price@gmail.com
 * @author sudar.sam@gmail.com
 *
 */
public class AggregateSynchronizer implements Synchronizer {
    private static final Log logger = LogFactory.getLog(AggregateSynchronizer.class);

    private static final String LOGTAG = AggregateSynchronizer.class.getSimpleName();
    private static final String TOKEN_INFO = "https://www.googleapis.com/oauth2/v1/tokeninfo?access_token=";

    // parameters for queries that could return a lot of data...
    public static final String CURSOR_PARAMETER = "cursor";
    public static final String FETCH_LIMIT = "fetchLimit";

    // parameter for file downloads -- if we want to have it come down as an attachment.
    public static final String PARAM_AS_ATTACHMENT = "as_attachment";

    int CONNECTION_TIMEOUT = 30000;

    // parameters for data/diff/query APIs.
    public static final String QUERY_DATA_ETAG = "data_etag";
    public static final String QUERY_SEQUENCE_VALUE = "sequence_value";
    public static final String QUERY_ACTIVE_ONLY = "active_only";
    // parameters for query API
    public static final String QUERY_START_TIME = "startTime";
    public static final String QUERY_END_TIME = "endTime";

    /** Timeout (in ms) we specify for each http request */
    public static final int HTTP_REQUEST_TIMEOUT_MS = 30 * 1000;
    /** Path to the file servlet on the Aggregate server. */

    private static final String FORWARD_SLASH = "/";

    static Map<String, String> mimeMapping;
    static {

        Map<String, String> m = new HashMap<String, String>();
        m.put("jpeg", "image/jpeg");
        m.put("jpg", "image/jpeg");
        m.put("png", "image/png");
        m.put("gif", "image/gif");
        m.put("pbm", "image/x-portable-bitmap");
        m.put("ico", "image/x-icon");
        m.put("bmp", "image/bmp");
        m.put("tiff", "image/tiff");

        m.put("mp2", "audio/mpeg");
        m.put("mp3", "audio/mpeg");
        m.put("wav", "audio/x-wav");

        m.put("asf", "video/x-ms-asf");
        m.put("avi", "video/x-msvideo");
        m.put("mov", "video/quicktime");
        m.put("mpa", "video/mpeg");
        m.put("mpeg", "video/mpeg");
        m.put("mpg", "video/mpeg");
        m.put("mp4", "video/mp4");
        m.put("qt", "video/quicktime");

        m.put("css", "text/css");
        m.put("htm", "text/html");
        m.put("html", "text/html");
        m.put("csv", "text/csv");
        m.put("txt", "text/plain");
        m.put("log", "text/plain");
        m.put("rtf", "application/rtf");
        m.put("pdf", "application/pdf");
        m.put("zip", "application/zip");
        m.put("xlsx", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
        m.put("docx", "application/vnd.openxmlformats-officedocument.wordprocessingml.document");
        m.put("pptx", "application/vnd.openxmlformats-officedocument.presentationml.presentation");
        m.put("xml", "application/xml");
        m.put("js", "application/x-javascript");
        m.put("json", "application/x-javascript");
        mimeMapping = m;

        // Android does not support Runtime delegation. Set it up manually...
        // force this once...
        org.apache.wink.common.internal.runtime.RuntimeDelegateImpl rd = new org.apache.wink.common.internal.runtime.RuntimeDelegateImpl();
        RuntimeDelegate.setInstance(rd);
    }

    private final String context;
    private final String appName;
    private final String odkClientApiVersion;
    private final String aggregateUri;
    private String accessToken;
    private final RestClient tokenRt;
    private final RestClient rt;
    private final Map<String, TableResource> resources;
    /** normalized aggregateUri */
    private final URI baseUri;
    // cookie manager 
    private final CookieManager cm;

    private final URI normalizeUri(String aggregateUri, String additionalPathPortion) {
        URI uriBase = URI.create(aggregateUri).normalize();
        String term = uriBase.getPath();
        if (term.endsWith(FORWARD_SLASH)) {
            if (additionalPathPortion.startsWith(FORWARD_SLASH)) {
                term = term.substring(0, term.length() - 1);
            }
        } else if (!additionalPathPortion.startsWith(FORWARD_SLASH)) {
            term = term + FORWARD_SLASH;
        }
        term = term + additionalPathPortion;
        URI uri = uriBase.resolve(term).normalize();
        logger.debug("normalizeUri: " + uri.toString());
        return uri;
    }

    private static final String escapeSegment(String segment) {
        return segment;
        // String encoding = CharEncoding.UTF_8;
        // String encodedSegment;
        // try {
        // encodedSegment = URLEncoder.encode(segment, encoding)
        // .replaceAll("\\+", "%20")
        // .replaceAll("\\%21", "!")
        // .replaceAll("\\%27", "'")
        // .replaceAll("\\%28", "(")
        // .replaceAll("\\%29", ")")
        // .replaceAll("\\%7E", "~");
        //
        // } catch (UnsupportedEncodingException e) {
        // e.printStackTrace();;
        // throw new IllegalStateException("Should be able to encode with " +
        // encoding);
        // }
        // return encodedSegment;
    }

    /**
     * Format a file path to be pushed up to aggregate. Essentially escapes the
     * string as for an html url, but leaves forward slashes. The path must begin
     * with a forward slash, as if starting at the root directory.
     * 
     * @return a properly escaped url, with forward slashes remaining.
     */
    private String uriEncodeSegments(String path) {
        String[] parts = path.split("/");
        StringBuilder b = new StringBuilder();
        for (int i = 0; i < parts.length; ++i) {
            if (i != 0) {
                b.append("/");
            }
            b.append(escapeSegment(parts[i]));
        }
        String escaped = b.toString();
        return escaped;
    }

    private String getTablesUriFragment() {
        /**
         * Path to the tables servlet (the one that manages table definitions) on
         * the Aggregate server.
         */
        return "/odktables/" + escapeSegment(appName) + "/tables/";
    }

    private String getManifestUriFragment() {
        /**
         * Path to the tables servlet (the one that manages table definitions) on
         * the Aggregate server.
         */
        return "/odktables/" + escapeSegment(appName) + "/manifest/" + escapeSegment(odkClientApiVersion) + "/";
    }

    /**
     * Get the URI for the file servlet on the Aggregate server located at
     * aggregateUri.
     *
     * @param aggregateUri
     * @return
     */
    private String getFilePathURI() {
        return "/odktables/" + escapeSegment(appName) + "/files/" + escapeSegment(odkClientApiVersion) + "/";
    }

    /**
     * Simple Resource for all server interactions.
     * 
     * @param uri
     * @return
     * @throws InvalidAuthTokenException 
     */
    private Resource buildBasicResource(URI uri) throws InvalidAuthTokenException {

        Resource rsc = rt.resource(uri);

        // report our locale... (not currently used by server)
        rsc.acceptLanguage(Locale.getDefault());

        // set the access token...
        rsc.header(ApiConstants.ACCEPT_CONTENT_ENCODING_HEADER, ApiConstants.GZIP_CONTENT_ENCODING);
        rsc.header(ApiConstants.OPEN_DATA_KIT_VERSION_HEADER, ApiConstants.OPEN_DATA_KIT_VERSION);
        rsc.header(HttpHeaders.USER_AGENT, "Sync it (gzip)");
        GregorianCalendar g = new GregorianCalendar(TimeZone.getTimeZone("GMT"));
        Date now = new Date();
        g.setTime(now);
        SimpleDateFormat formatter = new SimpleDateFormat("E, dd MMM yyyy HH:mm:ss zz", Locale.US);
        formatter.setCalendar(g);
        rsc.header(ApiConstants.DATE_HEADER, formatter.format(now));

        if (accessToken != null && baseUri != null) {
            if (uri.getHost().equals(baseUri.getHost()) && uri.getPort() == baseUri.getPort()) {
                rsc.header("Authorization", "Bearer " + accessToken);
            }
        }

        return rsc;
    }

    private Resource buildResource(URI uri, MediaType contentType) throws InvalidAuthTokenException {

        Resource rsc = buildBasicResource(uri);

        rsc.contentType(contentType);

        // set our preferred response media type to json using quality parameters
        Map<String, String> mediaTypeParams;
        // we really like JSON
        mediaTypeParams = new HashMap<String, String>();
        mediaTypeParams.put("q", "1.0");
        MediaType json = new MediaType(MediaType.APPLICATION_JSON_TYPE.getType(),
                MediaType.APPLICATION_JSON_TYPE.getSubtype(), mediaTypeParams);
        // don't really want plaintext...
        mediaTypeParams = new HashMap<String, String>();
        mediaTypeParams.put("charset", CharEncoding.UTF_8.toLowerCase(Locale.ENGLISH));
        mediaTypeParams.put("q", "0.4");
        MediaType tplainUtf8 = new MediaType(MediaType.TEXT_PLAIN_TYPE.getType(),
                MediaType.TEXT_PLAIN_TYPE.getSubtype(), mediaTypeParams);

        // accept either json or plain text (no XML to device)
        rsc.accept(json, tplainUtf8);

        // set the response entity character set to CharEncoding.UTF_8
        rsc.header("Accept-Charset", CharEncoding.UTF_8);

        return rsc;
    }

    /**
     * Simple Resource for file download.
     * 
     * @param uri
     * @return
     * @throws InvalidAuthTokenException 
     */
    private Resource buildFileDownloadResource(URI uri) throws InvalidAuthTokenException {

        Resource rsc = buildBasicResource(uri);

        return rsc;
    }

    private Resource buildResource(URI uri) throws InvalidAuthTokenException {

        // select our preferred protocol...
        MediaType protocolType = MediaType.APPLICATION_JSON_TYPE;

        Resource rsc = buildResource(uri, protocolType);

        return rsc;
    }

    public AggregateSynchronizer(String ctxt, String appName, String odkApiVersion, String aggregateUri,
            String accessToken) throws InvalidAuthTokenException {
        this.context = ctxt;
        this.appName = appName;
        this.odkClientApiVersion = odkApiVersion;
        this.aggregateUri = aggregateUri;
        logger.debug("AggregateUri:" + aggregateUri);
        this.baseUri = normalizeUri(aggregateUri, "/");
        logger.error("baseUri:" + baseUri);

        // This is technically not correct, as we should really have a global
        // that we manage for this... If there are two or more service threads
        // running, we could forget other session cookies. But, by creating a 
        // new cookie manager here, we ensure that we don't have any stale 
        // session cookies at the start of each sync.

        cm = new CookieManager();
        CookieHandler.setDefault(cm);

        // now everything should work...
        ClientConfig cc;

        cc = new ClientConfig();
        cc.setLoadWinkApplications(false);
        cc.applications(new ODKClientApplication());
        cc.handlers(new GzipHandler(), new ReAuthSecurityHandler(this));
        cc.connectTimeout(CONNECTION_TIMEOUT);
        cc.readTimeout(2 * CONNECTION_TIMEOUT);
        cc.followRedirects(true);

        this.rt = new RestClient(cc);

        cc = new ClientConfig();
        cc.setLoadWinkApplications(false);
        cc.applications(new ODKClientApplication());
        cc.connectTimeout(CONNECTION_TIMEOUT);
        cc.readTimeout(2 * CONNECTION_TIMEOUT);
        cc.followRedirects(true);

        this.tokenRt = new RestClient(cc);

        this.resources = new HashMap<String, TableResource>();

        checkAccessToken(accessToken);
        this.accessToken = accessToken;

    }

    private static final String ACCOUNT_TYPE_G = "com.google";
    private final static String authString = "oauth2:https://www.googleapis.com/auth/userinfo.email";

    public String updateAccessToken() throws InvalidAuthTokenException {
        // no-op
        return accessToken;
    }

    private void checkAccessToken(String accessToken) throws InvalidAuthTokenException {
        try {
            @SuppressWarnings("unused")
            Object responseEntity = tokenRt
                    .resource(TOKEN_INFO + URLEncoder.encode(accessToken, ApiConstants.UTF8_ENCODE))
                    .get(Object.class);
        } catch (ClientWebException e) {
            logger.error("HttpClientErrorException in checkAccessToken");
            Object o = null;
            try {
                String entityBody = e.getResponse().getEntity(String.class);
                o = ODKFileUtils.mapper.readValue(entityBody, Object.class);
            } catch (Exception e1) {
                e1.printStackTrace();
                throw new InvalidAuthTokenException(
                        "Unable to parse response from auth token verification (" + e.toString() + ")", e);
            }
            if (o != null && o instanceof Map) {
                @SuppressWarnings("rawtypes")
                Map m = (Map) o;
                if (m.containsKey("error")) {
                    throw new InvalidAuthTokenException(
                            "Invalid auth token (" + m.get("error").toString() + "): " + accessToken, e);
                } else {
                    throw new InvalidAuthTokenException(
                            "Unknown response from auth token verification (" + e.toString() + ")", e);
                }
            }
        } catch (Exception e) {
            logger.error("HttpClientErrorException in checkAccessToken");
            e.printStackTrace();
            ;
            throw new InvalidAuthTokenException("Invalid auth token (): " + accessToken, e);
        }
    }

    @Override
    public TableResourceList getTables(String webSafeResumeCursor)
            throws ClientWebException, InvalidAuthTokenException {

        TableResourceList tableResources;
        try {
            String tableFrag = getTablesUriFragment();
            tableFrag = tableFrag.substring(0, tableFrag.length() - 1);
            URI uri = normalizeUri(aggregateUri, tableFrag);
            if (webSafeResumeCursor == null) {
                tableResources = buildResource(uri).get(TableResourceList.class);
            } else {
                tableResources = buildResource(uri).queryParam(CURSOR_PARAMETER, webSafeResumeCursor)
                        .get(TableResourceList.class);
            }
        } catch (ClientWebException e) {
            logger.error("Exception while requesting list of tables from server: " + e.toString());
            throw e;
        }

        return tableResources;
    }

    @Override
    public TableDefinitionResource getTableDefinition(String tableDefinitionUri)
            throws ClientWebException, InvalidAuthTokenException {
        URI uri = URI.create(tableDefinitionUri).normalize();
        TableDefinitionResource definitionRes = buildResource(uri).get(TableDefinitionResource.class);
        return definitionRes;
    }

    @Override
    public URI constructTableInstanceFileUri(String tableId, String schemaETag) {
        // e.g., https://msundt-test.appspot.com:443/odktables/tables/tables/Milk_bank/ref/uuid:bb26cdaf-9ccf-4a4f-8e28-c114fe30358a/attachments
        URI instanceFileUri = normalizeUri(aggregateUri,
                getTablesUriFragment() + tableId + "/ref/" + schemaETag + "/attachments");
        return instanceFileUri;
    }

    @Override
    public TableResource createTable(String tableId, String schemaETag, ArrayList<Column> columns)
            throws ClientWebException, InvalidAuthTokenException {

        // build request
        URI uri = normalizeUri(aggregateUri, getTablesUriFragment() + tableId);
        TableDefinition definition = new TableDefinition(tableId, schemaETag, columns);
        // create table
        TableResource resource;
        try {
            // TODO: we also need to put up the key value store/properties.
            resource = buildResource(uri).put(new EntityType<TableResource>() {
            }, definition);
        } catch (ClientWebException e) {
            logger.error("ResourceAccessException in createTable: " + tableId + " exception: " + e.toString());
            throw e;
        }

        // save resource
        this.resources.put(resource.getTableId(), resource);
        return resource;
    }

    @Override
    public void deleteTable(TableResource table) throws ClientWebException, InvalidAuthTokenException {
        URI uri = URI.create(table.getDefinitionUri()).normalize();
        buildResource(uri).delete();
        this.resources.remove(table.getTableId());
    }

    @Override
    public ChangeSetList getChangeSets(TableResource table, String dataETag)
            throws ClientWebException, InvalidAuthTokenException {

        String tableId = table.getTableId();
        URI uri;
        Resource resource;
        uri = normalizeUri(table.getDiffUri(), "/changeSets");
        resource = buildResource(uri);
        if ((table.getDataETag() != null) && dataETag != null) {
            resource = buildResource(uri).queryParam(QUERY_DATA_ETAG, dataETag);
        }

        ChangeSetList changeSets;
        try {
            changeSets = resource.get(ChangeSetList.class);
            return changeSets;
        } catch (ClientWebException e) {
            logger.error("Exception while requesting list of changeSets from server: " + tableId + " exception: "
                    + e.toString());
            throw e;
        }
    }

    @Override
    public RowResourceList getChangeSet(TableResource table, String dataETag, boolean activeOnly,
            String websafeResumeCursor) throws ClientWebException, InvalidAuthTokenException {

        String tableId = table.getTableId();
        URI uri;
        Resource resource;
        if ((table.getDataETag() == null) || dataETag == null) {
            throw new IllegalArgumentException("dataETag cannot be null!");
        }

        uri = normalizeUri(table.getDiffUri(), "/changeSets/" + dataETag);
        resource = buildResource(uri);

        if (activeOnly) {
            resource = resource.queryParam(QUERY_ACTIVE_ONLY, "true");
        }

        // and apply the cursor...
        if (websafeResumeCursor != null) {
            resource = resource.queryParam(CURSOR_PARAMETER, websafeResumeCursor);
        }

        RowResourceList rows;
        try {
            rows = resource.get(RowResourceList.class);
            return rows;
        } catch (ClientWebException e) {
            logger.error("Exception while requesting changeSet rows from server: " + tableId + " exception: "
                    + e.toString());
            throw e;
        }
    }

    @Override
    public RowResourceList getUpdates(TableResource table, String dataETag, String websafeResumeCursor)
            throws ClientWebException, InvalidAuthTokenException {

        String tableId = table.getTableId();
        URI uri;
        Resource resource;
        if ((table.getDataETag() == null) || dataETag == null) {
            uri = URI.create(table.getDataUri());
            resource = buildResource(uri);
        } else {
            uri = URI.create(table.getDiffUri());
            resource = buildResource(uri).queryParam(QUERY_DATA_ETAG, dataETag);
        }
        // and apply the cursor...
        if (websafeResumeCursor != null) {
            resource = resource.queryParam(CURSOR_PARAMETER, websafeResumeCursor);
        }
        RowResourceList rows;
        try {
            rows = resource.get(RowResourceList.class);
            return rows;
        } catch (ClientWebException e) {
            logger.error("Exception while requesting list of rows from server: " + tableId + " exception: "
                    + e.toString());
            throw e;
        }
    }

    @Override
    public RowOutcomeList alterRows(TableResource resource, List<SyncRow> rowsToInsertUpdateOrDelete)
            throws ClientWebException, InvalidAuthTokenException {

        ArrayList<Row> rows = new ArrayList<Row>();
        for (SyncRow rowToAlter : rowsToInsertUpdateOrDelete) {
            Row row = Row.forUpdate(rowToAlter.getRowId(), rowToAlter.getRowETag(), rowToAlter.getFormId(),
                    rowToAlter.getLocale(), rowToAlter.getSavepointType(), rowToAlter.getSavepointTimestamp(),
                    rowToAlter.getSavepointCreator(), rowToAlter.getFilterScope(), rowToAlter.getValues());
            row.setDeleted(rowToAlter.isDeleted());
            rows.add(row);
        }
        RowList rlist = new RowList(rows, resource.getDataETag());

        URI uri = URI.create(resource.getDataUri());
        RowOutcomeList outcomes;
        try {
            outcomes = buildResource(uri).put(new EntityType<RowOutcomeList>() {
            }, rlist);
        } catch (ClientWebException e) {
            logger.error("Exception while updating rows on server: " + resource.getTableId() + " exception: "
                    + e.toString());
            throw e;
        }
        return outcomes;
    }

    private static List<String> filterOutTableIdAssetFiles(List<String> relativePaths) {
        List<String> newList = new ArrayList<String>();
        for (String relativePath : relativePaths) {
            if (relativePath.startsWith("assets/csv/")) {
                // by convention, the files here begin with their identifying tableId
                continue;
            } else {
                newList.add(relativePath);
            }
        }
        return newList;
    }

    /**
     * Remove all assets/*.init files (e.g., tables.init) that only alter the data
     * tables of the application. These are not needed on the server because their
     * actions have already caused changes in the data tables that will be shared
     * across all devices. I.e., they only need to be executed on the one starter
     * device, and then everything gets replicated everywhere else.
     * 
     * @param relativePaths
     * @return
     */
    private static List<String> filterOutAssetInitFiles(List<String> relativePaths) {
        List<String> newList = new ArrayList<String>();
        for (String relativePath : relativePaths) {
            if (relativePath.equals("assets/tables.init")) {
                continue;
            } else {
                newList.add(relativePath);
            }
        }
        return newList;
    }

    private static List<String> filterInTableIdFiles(List<String> relativePaths, String tableId) {
        List<String> newList = new ArrayList<String>();
        for (String relativePath : relativePaths) {
            if (relativePath.startsWith("assets/csv/")) {
                // by convention, the files here begin with their identifying tableId
                String[] parts = relativePath.split("/");
                if (parts.length >= 3) {
                    String[] nameElements = parts[2].split("\\.");
                    if (nameElements[0].equals(tableId)) {
                        newList.add(relativePath);
                    }
                }
            }
        }
        return newList;
    }

    /**
     * Get all the files under the given folder, excluding those directories that
     * are the concatenation of folder and a member of excluding. If the member of
     * excluding is a directory, none of its children will be synched either.
     * <p>
     * If the folder doesn't exist it returns an empty list.
     * <p>
     * If the file exists but is not a directory, logs an error and returns an
     * empty list.
     * 
     * @param folder
     * @param excluding
     *          can be null--nothing will be excluded. Should be relative to the
     *          given folder.
     * @param relativeTo
     *          the path to which the returned paths will be relative. A null
     *          value makes them relative to the folder parameter. If it is non
     *          null, folder must start with relativeTo, or else the files in
     *          folder could not possibly be relative to relativeTo. In this case
     *          will throw an IllegalArgumentException.
     * @return the relative paths of the files under the folder--i.e. the paths
     *         after the folder parameter, not including the first separator
     * @throws IllegalArgumentException
     *           if relativeTo is not a substring of folder.
     */
    private List<String> getAllFilesUnderFolder(File baseFolder, final Set<String> excludingNamedItemsUnderFolder) {
        String appName = ODKFileUtils.extractAppNameFromPath(baseFolder);

        // Return an empty list of the folder doesn't exist or is not a directory
        if (!baseFolder.exists()) {
            return new ArrayList<String>();
        } else if (!baseFolder.isDirectory()) {
            logger.error("[getAllFilesUnderFolder] folder is not a directory: " + baseFolder.getAbsolutePath());
            return new ArrayList<String>();
        }

        // construct the set of starting directories and files to process
        File[] partials = baseFolder.listFiles(new FileFilter() {
            @Override
            public boolean accept(File pathname) {
                if (excludingNamedItemsUnderFolder == null) {
                    return true;
                } else {
                    return !excludingNamedItemsUnderFolder.contains(pathname.getName());
                }
            }
        });

        if (partials == null) {
            return Collections.emptyList();
        }

        LinkedList<File> unexploredDirs = new LinkedList<File>();
        List<File> nondirFiles = new ArrayList<File>();

        // copy the starting set into a queue of unexploredDirs
        // and a list of files to be sync'd
        for (int i = 0; i < partials.length; ++i) {
            if (partials[i].isDirectory()) {
                unexploredDirs.add(partials[i]);
            } else {
                nondirFiles.add(partials[i]);
            }
        }

        while (!unexploredDirs.isEmpty()) {
            File exploring = unexploredDirs.removeFirst();
            File[] files = exploring.listFiles();
            for (File f : files) {
                if (f.isDirectory()) {
                    // we'll need to explore it
                    unexploredDirs.add(f);
                } else {
                    // we'll add it to our list of files.
                    nondirFiles.add(f);
                }
            }
        }

        List<String> relativePaths = new ArrayList<String>();
        // we want the relative path, so drop the necessary bets.
        for (File f : nondirFiles) {
            // +1 to exclude the separator.
            relativePaths.add(ODKFileUtils.asRelativePath(appName, f));
        }
        return relativePaths;
    }

    @Override
    public boolean syncAppLevelFiles(boolean pushLocalFiles, String serverReportedAppLevelETag,
            SynchronizerStatus syncStatus) throws ClientWebException, InvalidAuthTokenException {
        // Get the app-level files on the server.
        syncStatus.updateNotification(SyncProgressState.APP_FILES, RString.getting_app_level_manifest, null, 1.0,
                false);
        List<OdkTablesFileManifestEntry> manifest = getAppLevelFileManifest(pushLocalFiles,
                serverReportedAppLevelETag);

        if (manifest == null) {
            logger.info("no change in app-leve manifest -- skipping!");
            // short-circuited -- no change in manifest
            syncStatus.updateNotification(SyncProgressState.APP_FILES, RString.getting_app_level_manifest, null,
                    100.0, false);
            return true;
        }

        // Get the app-level files on our device.
        Set<String> dirsToExclude = ODKFileUtils.getDirectoriesToExcludeFromSync(true);
        File appFolder = new File(ODKFileUtils.getAppFolder(appName));
        List<String> relativePathsOnDevice = getAllFilesUnderFolder(appFolder, dirsToExclude);
        relativePathsOnDevice = filterOutTableIdAssetFiles(relativePathsOnDevice);
        relativePathsOnDevice = filterOutAssetInitFiles(relativePathsOnDevice);

        boolean success = true;
        double stepSize = 100.0 / (1 + relativePathsOnDevice.size() + manifest.size());
        int stepCount = 1;

        if (pushLocalFiles) {
            // if we are pushing, we want to push the local files that are different
            // up to the server, then remove the files on the server that are not
            // in the local set.
            List<String> serverFilesToDelete = new ArrayList<String>();

            for (OdkTablesFileManifestEntry entry : manifest) {
                File localFile = ODKFileUtils.asAppFile(appName, entry.filename);
                if (!localFile.exists() || !localFile.isFile()) {
                    // we need to delete this file from the server.
                    serverFilesToDelete.add(entry.filename);
                } else if (ODKFileUtils.getMd5Hash(appName, localFile).equals(entry.md5hash)) {
                    // we are ok -- no need to upload or delete
                    relativePathsOnDevice.remove(entry.filename);
                }
            }

            // this is the actual step size when we are pushing...
            stepSize = 100.0 / (1 + relativePathsOnDevice.size() + serverFilesToDelete.size());

            for (String relativePath : relativePathsOnDevice) {

                syncStatus.updateNotification(SyncProgressState.APP_FILES, RString.uploading_local_file,
                        new Object[] { relativePath }, stepCount * stepSize, false);

                File localFile = ODKFileUtils.asAppFile(appName, relativePath);
                String wholePathToFile = localFile.getAbsolutePath();
                if (!uploadFile(wholePathToFile, relativePath)) {
                    success = false;
                    logger.error("Unable to upload file to server: " + relativePath);
                }

                ++stepCount;
            }

            for (String relativePath : serverFilesToDelete) {

                syncStatus.updateNotification(SyncProgressState.APP_FILES, RString.deleting_file_on_server,
                        new Object[] { relativePath }, stepCount * stepSize, false);

                if (!deleteFile(relativePath)) {
                    success = false;
                    logger.error("Unable to delete file on server: " + relativePath);
                }

                ++stepCount;
            }
        } else {
            // if we are pulling, we want to pull the server files that are different
            // down from the server, then remove the local files that are not present
            // on the server.

            for (OdkTablesFileManifestEntry entry : manifest) {
                syncStatus.updateNotification(SyncProgressState.APP_FILES, RString.verifying_local_file,
                        new Object[] { entry.filename }, stepCount * stepSize, false);

                // make sure our copy is current
                compareAndDownloadFile(null, entry);
                // remove it from the set of app-level files we found before the sync
                relativePathsOnDevice.remove(entry.filename);

                // this is the corrected step size based upon matching files
                stepSize = 100.0 / (1 + relativePathsOnDevice.size() + manifest.size());

                ++stepCount;
            }

            for (String relativePath : relativePathsOnDevice) {

                syncStatus.updateNotification(SyncProgressState.APP_FILES, RString.deleting_local_file,
                        new Object[] { relativePath }, stepCount * stepSize, false);

                // and remove any remaining files, as these do not match anything on
                // the server.
                File f = ODKFileUtils.asAppFile(appName, relativePath);
                if (!f.delete()) {
                    success = false;
                    logger.error("Unable to delete " + f.getAbsolutePath());
                }

                ++stepCount;
            }
        }

        return success;
    }

    private String determineContentType(String fileName) {
        int ext = fileName.lastIndexOf('.');
        if (ext == -1) {
            return "application/octet-stream";
        }
        String type = fileName.substring(ext + 1);
        String mimeType = mimeMapping.get(type);
        if (mimeType == null) {
            return "application/octet-stream";
        }
        return mimeType;
    }

    @Override
    public void syncTableLevelFiles(String tableId, String serverReportedTableLevelETag,
            OnTablePropertiesChanged onChange, boolean pushLocalFiles, SynchronizerStatus syncStatus)
            throws ClientWebException, InvalidAuthTokenException {

        syncStatus.updateNotification(SyncProgressState.TABLE_FILES, RString.getting_table_manifest,
                new Object[] { tableId }, 1.0, false);

        // get the table files on the server
        List<OdkTablesFileManifestEntry> manifest = getTableLevelFileManifest(tableId, serverReportedTableLevelETag,
                pushLocalFiles);

        if (manifest == null) {
            logger.info("no change in table manifest -- skipping!");
            // short-circuit because our files should match those on the server
            syncStatus.updateNotification(SyncProgressState.TABLE_FILES, RString.getting_table_manifest,
                    new Object[] { tableId }, 100.0, false);

            return;
        }

        String tableIdPropertiesFile = "tables" + File.separator + tableId + File.separator + "properties.csv";

        boolean tablePropertiesChanged = false;

        // Get any assets/csv files that begin with tableId
        Set<String> dirsToExclude = new HashSet<String>();
        File assetsCsvFolder = new File(ODKFileUtils.getAssetsFolder(appName) + "/csv");
        List<String> relativePathsToTableIdAssetsCsvOnDevice = getAllFilesUnderFolder(assetsCsvFolder,
                dirsToExclude);
        relativePathsToTableIdAssetsCsvOnDevice = filterInTableIdFiles(relativePathsToTableIdAssetsCsvOnDevice,
                tableId);

        // We don't want to sync anything in the instances directory, because this
        // contains things like media attachments.
        File tableFolder = new File(ODKFileUtils.getTablesFolder(appName, tableId));
        dirsToExclude.add(ODKFileUtils.INSTANCES_FOLDER_NAME);
        List<String> relativePathsOnDevice = getAllFilesUnderFolder(tableFolder, dirsToExclude);

        // mix in the assets files for this tableId, if any...
        relativePathsOnDevice.addAll(relativePathsToTableIdAssetsCsvOnDevice);

        double stepSize = 100.0 / (1 + relativePathsOnDevice.size() + manifest.size());
        int stepCount = 1;

        if (pushLocalFiles) {
            // if we are pushing, we want to push the local files that are different
            // up to the server, then remove the files on the server that are not
            // in the local set.
            List<String> serverFilesToDelete = new ArrayList<String>();

            for (OdkTablesFileManifestEntry entry : manifest) {
                File localFile = ODKFileUtils.asAppFile(appName, entry.filename);
                if (!localFile.exists() || !localFile.isFile()) {
                    // we need to delete this file from the server.
                    serverFilesToDelete.add(entry.filename);
                } else if (ODKFileUtils.getMd5Hash(appName, localFile).equals(entry.md5hash)) {
                    // we are ok -- no need to upload or delete
                    relativePathsOnDevice.remove(entry.filename);
                }
            }

            // this is the actual step size when we are pushing...
            stepSize = 100.0 / (1 + relativePathsOnDevice.size() + serverFilesToDelete.size());

            boolean success = true;
            for (String relativePath : relativePathsOnDevice) {

                syncStatus.updateNotification(SyncProgressState.TABLE_FILES, RString.uploading_local_file,
                        new Object[] { relativePath }, stepCount * stepSize, false);

                File localFile = ODKFileUtils.asAppFile(appName, relativePath);
                String wholePathToFile = localFile.getAbsolutePath();
                if (!uploadFile(wholePathToFile, relativePath)) {
                    success = false;
                    logger.error("Unable to upload file to server: " + relativePath);
                }

                ++stepCount;
            }

            for (String relativePath : serverFilesToDelete) {

                syncStatus.updateNotification(SyncProgressState.TABLE_FILES, RString.deleting_file_on_server,
                        new Object[] { relativePath }, stepCount * stepSize, false);

                if (!deleteFile(relativePath)) {
                    success = false;
                    logger.error("Unable to delete file on server: " + relativePath);
                }

                ++stepCount;
            }

            if (!success) {
                logger.info("unable to delete one or more files!");
            }

        } else {
            // if we are pulling, we want to pull the server files that are different
            // down from the server, then remove the local files that are not present
            // on the server.

            for (OdkTablesFileManifestEntry entry : manifest) {

                syncStatus.updateNotification(SyncProgressState.TABLE_FILES, RString.verifying_local_file,
                        new Object[] { entry.filename }, stepCount * stepSize, false);

                // make sure our copy is current
                boolean outcome = compareAndDownloadFile(tableId, entry);
                // and if it was the table properties file, remember whether it changed.
                if (entry.filename.equals(tableIdPropertiesFile)) {
                    tablePropertiesChanged = outcome;
                }
                // remove it from the set of app-level files we found before the sync
                relativePathsOnDevice.remove(entry.filename);

                // this is the corrected step size based upon matching files
                stepSize = 100.0 / (1 + relativePathsOnDevice.size() + manifest.size());

                ++stepCount;
            }

            boolean success = true;
            for (String relativePath : relativePathsOnDevice) {

                syncStatus.updateNotification(SyncProgressState.TABLE_FILES, RString.deleting_local_file,
                        new Object[] { relativePath }, stepCount * stepSize, false);

                // and remove any remaining files, as these do not match anything on
                // the server.
                File f = ODKFileUtils.asAppFile(appName, relativePath);
                if (!f.delete()) {
                    success = false;
                    logger.error("Unable to delete " + f.getAbsolutePath());
                }

                ++stepCount;
            }

            if (tablePropertiesChanged && (onChange != null)) {
                // update this table's KVS values...
                onChange.onTablePropertiesChanged(tableId);
            }

            if (!success) {
                logger.info("unable to delete one or more files!");
            }

            // should we return our status?
        }
    }

    public List<OdkTablesFileManifestEntry> getAppLevelFileManifest(boolean pushLocalFiles,
            String serverReportedAppLevelETag) throws ClientWebException, InvalidAuthTokenException {
        SyncETagsUtils seu = new SyncETagsUtils();
        URI fileManifestUri = normalizeUri(aggregateUri, getManifestUriFragment());
        String eTag = seu.getManifestSyncETag(context, appName, fileManifestUri, null);
        Resource rsc = buildResource(fileManifestUri);
        // don't short-circuit manifest if we are pushing local files,
        // as we need to know exactly what is on the server to minimize
        // transmissions of files being pushed up to the server.
        if (!pushLocalFiles && eTag != null) {
            rsc.header(HttpHeaders.IF_NONE_MATCH, eTag);
            if (serverReportedAppLevelETag != null && serverReportedAppLevelETag.equals(eTag)) {
                // no change -- we can skip the request to the server
                return null;
            }
        }
        ClientResponse rsp = rsc.get();
        if (rsp.getStatusCode() == HttpStatus.SC_NOT_MODIFIED) {
            // signal this by returning null;
            return null;
        }
        if (rsp.getStatusCode() < 200 || rsp.getStatusCode() >= 300) {
            throw new ClientWebException(null, rsp);
        }
        if (!rsp.getHeaders().containsKey(ApiConstants.OPEN_DATA_KIT_VERSION_HEADER)) {
            throw new ClientWebException(null, rsp);
        }

        // retrieve the manifest...
        OdkTablesFileManifest manifest;
        manifest = rsp.getEntity(OdkTablesFileManifest.class);
        List<OdkTablesFileManifestEntry> theList = null;
        if (manifest != null) {
            theList = manifest.getFiles();
        }
        if (theList == null) {
            theList = Collections.emptyList();
        }
        // update the manifest ETag record...
        eTag = rsp.getHeaders().getFirst(HttpHeaders.ETAG);
        seu.updateManifestSyncETag(context, appName, fileManifestUri, null, eTag);
        // and return the list of values...
        return theList;
    }

    public List<OdkTablesFileManifestEntry> getTableLevelFileManifest(String tableId,
            String serverReportedTableLevelETag, boolean pushLocalFiles)
            throws ClientWebException, InvalidAuthTokenException {
        SyncETagsUtils seu = new SyncETagsUtils();
        URI fileManifestUri = normalizeUri(aggregateUri, getManifestUriFragment() + tableId);
        String eTag = seu.getManifestSyncETag(context, appName, fileManifestUri, tableId);
        Resource rsc = buildResource(fileManifestUri);
        // don't short-circuit manifest if we are pushing local files,
        // as we need to know exactly what is on the server to minimize
        // transmissions of files being pushed up to the server.
        if (!pushLocalFiles && eTag != null) {
            rsc.header(HttpHeaders.IF_NONE_MATCH, eTag);
            if (serverReportedTableLevelETag != null && serverReportedTableLevelETag.equals(eTag)) {
                // no change -- we can skip the request to the server
                return null;
            }
        }
        ClientResponse rsp = rsc.get();
        if (rsp.getStatusCode() == HttpStatus.SC_NOT_MODIFIED) {
            // signal this by returning null;
            return null;
        }
        if (rsp.getStatusCode() < 200 || rsp.getStatusCode() >= 300) {
            throw new ClientWebException(null, rsp);
        }
        if (!rsp.getHeaders().containsKey(ApiConstants.OPEN_DATA_KIT_VERSION_HEADER)) {
            throw new ClientWebException(null, rsp);
        }

        // retrieve the manifest...
        OdkTablesFileManifest manifest;
        manifest = rsp.getEntity(OdkTablesFileManifest.class);
        List<OdkTablesFileManifestEntry> theList = null;
        if (manifest != null) {
            theList = manifest.getFiles();
        }
        if (theList == null) {
            theList = Collections.emptyList();
        }
        // update the manifest ETag record...
        eTag = rsp.getHeaders().getFirst(HttpHeaders.ETAG);
        seu.updateManifestSyncETag(context, appName, fileManifestUri, tableId, eTag);
        // and return the list of values...
        return theList;
    }

    private boolean deleteFile(String pathRelativeToAppFolder)
            throws ClientWebException, InvalidAuthTokenException {
        String escapedPath = uriEncodeSegments(pathRelativeToAppFolder);
        URI filesUri = normalizeUri(aggregateUri, getFilePathURI() + escapedPath);
        logger.info("[deleteFile] fileDeleteUri: " + filesUri.toString());
        buildResource(filesUri).delete();
        // TODO: verify whether or not this worked.
        return true;
    }

    private boolean uploadFile(String wholePathToFile, String pathRelativeToAppFolder)
            throws InvalidAuthTokenException {
        File file = new File(wholePathToFile);
        String escapedPath = uriEncodeSegments(pathRelativeToAppFolder);
        URI filesUri = normalizeUri(aggregateUri, getFilePathURI() + escapedPath);
        logger.info("[uploadFile] filePostUri: " + filesUri.toString());
        String ct = determineContentType(file.getName());
        MediaType contentType = MediaType.valueOf(ct);
        ClientResponse response = buildResource(filesUri, contentType).post(file);
        if (response.getStatusCode() < 200 || response.getStatusCode() >= 300) {
            return false;
        }
        if (!response.getHeaders().containsKey(ApiConstants.OPEN_DATA_KIT_VERSION_HEADER)) {
            return false;
        }
        return true;
    }

    private boolean uploadInstanceFile(File file, URI instanceFileUri) throws InvalidAuthTokenException {
        logger.info("[uploadFile] filePostUri: " + instanceFileUri.toString());
        String ct = determineContentType(file.getName());
        MediaType contentType = MediaType.valueOf(ct);
        ClientResponse response = buildResource(instanceFileUri, contentType).post(file);
        if (response.getStatusCode() < 200 || response.getStatusCode() >= 300) {
            return false;
        }
        if (!response.getHeaders().containsKey(ApiConstants.OPEN_DATA_KIT_VERSION_HEADER)) {
            return false;
        }
        return true;
    }

    /**
     * Get the URI to which to post in order to upload the file.
     *
     * @param pathRelativeToAppFolder
     * @return
     */
    public URI getFilePostUri(String appName, String pathRelativeToAppFolder) {
        String escapedPath = uriEncodeSegments(pathRelativeToAppFolder);
        URI filesUri = normalizeUri(aggregateUri, getFilePathURI() + escapedPath);
        return filesUri;
    }

    /**
     *
     * @param entry
     * @return
     */
    private boolean compareAndDownloadFile(String tableId, OdkTablesFileManifestEntry entry) {
        String basePath = ODKFileUtils.getAppFolder(appName);

        SyncETagsUtils seu = new SyncETagsUtils();

        // if the file is a placeholder on the server, then don't do anything...
        if (entry.contentLength == 0) {
            return false;
        }
        // now we need to look through the manifest and see where the files are
        // supposed to be stored. Make sure you don't return a bad string.
        if (entry.filename == null || entry.filename.equals("")) {
            logger.info("returned a null or empty filename");
            return false;
        } else {

            URI uri = null;
            URL urlFile = null;
            try {
                logger.info("[downloadFile] downloading at url: " + entry.downloadUrl);
                urlFile = new URL(entry.downloadUrl);
                uri = urlFile.toURI();
            } catch (MalformedURLException e) {
                logger.error(e.toString());
                e.printStackTrace();
                ;
                return false;
            } catch (URISyntaxException e) {
                logger.error(e.toString());
                e.printStackTrace();
                ;
                return false;
            }

            // filename is the unrooted path of the file, so prepend the basepath.
            String path = basePath + File.separator + entry.filename;
            // Before we try dl'ing the file, we have to make the folder,
            // b/c otherwise if the folders down to the path have too many non-
            // existent folders, we'll get a FileNotFoundException when we open
            // the FileOutputStream.
            File newFile = new File(path);
            String folderPath = newFile.getParent();
            ODKFileUtils.createFolder(folderPath);
            if (!newFile.exists()) {
                // the file doesn't exist on the system
                // filesToDL.add(newFile);
                try {
                    int statusCode = downloadFile(newFile, uri);
                    if (statusCode == HttpStatus.SC_OK) {
                        seu.updateFileSyncETag(context, appName, uri, tableId, newFile.lastModified(),
                                entry.md5hash);
                        return true;
                    } else {
                        return false;
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                    ;
                    logger.error("trouble downloading file for first time");
                    return false;
                }
            } else {
                boolean hasUpToDateEntry = true;
                String md5hash = seu.getFileSyncETag(context, appName, uri, tableId, newFile.lastModified());
                if (md5hash == null) {
                    // file exists, but no record of what is on the server
                    // compute local value
                    hasUpToDateEntry = false;
                    md5hash = ODKFileUtils.getMd5Hash(appName, newFile);
                }
                // so as it comes down from the manifest, the md5 hash includes a
                // "md5:" prefix. Add that and then check.
                if (!md5hash.equals(entry.md5hash)) {
                    hasUpToDateEntry = false;
                    // it's not up to date, we need to download it.
                    try {
                        int statusCode = downloadFile(newFile, uri);
                        if (statusCode == HttpStatus.SC_OK || statusCode == HttpStatus.SC_NOT_MODIFIED) {
                            seu.updateFileSyncETag(context, appName, uri, tableId, newFile.lastModified(), md5hash);
                            return true;
                        } else {
                            return false;
                        }
                    } catch (Exception e) {
                        e.printStackTrace();
                        ;
                        // TODO throw correct exception
                        logger.error("trouble downloading new version of existing file");
                        return false;
                    }
                } else {
                    if (!hasUpToDateEntry) {
                        seu.updateFileSyncETag(context, appName, uri, tableId, newFile.lastModified(), md5hash);
                    }
                    // no change
                    return false;
                }
            }
        }
    }

    /**
     *
     * @param destFile
     * @param downloadUrl
     * @return true if the download was successful
     * @throws Exception
     */
    private int downloadFile(File destFile, URI downloadUrl) throws Exception {

        // WiFi network connections can be renegotiated during a large form download
        // sequence.
        // This will cause intermittent download failures. Silently retry once after
        // each
        // failure. Only if there are two consecutive failures, do we abort.
        boolean success = false;
        int attemptCount = 0;
        while (!success && attemptCount++ <= 2) {

            Resource resource = buildFileDownloadResource(downloadUrl);
            if (destFile.exists()) {
                String md5Hash = ODKFileUtils.getMd5Hash(appName, destFile);
                resource.header(HttpHeaders.IF_NONE_MATCH, md5Hash);
            }

            ClientResponse response = null;
            try {
                response = resource.get();
                int statusCode = response.getStatusCode();

                if (statusCode != HttpStatus.SC_OK) {
                    response.consumeContent();
                    if (statusCode == HttpStatus.SC_UNAUTHORIZED) {
                        // clear the cookies -- should not be necessary?
                        // ss: might just be a collect thing?
                    }
                    logger.warn("downloading " + downloadUrl.toString() + " returns " + statusCode);
                    return statusCode;
                }

                if (!response.getHeaders().containsKey(ApiConstants.OPEN_DATA_KIT_VERSION_HEADER)) {
                    response.consumeContent();
                    logger.warn("downloading " + downloadUrl.toString() + " appears to have been redirected.");
                    return 302;
                }

                File tmp = new File(destFile.getParentFile(), destFile.getName() + ".tmp");
                int totalLen = 0;
                InputStream is = null;
                BufferedOutputStream os = null;
                try {
                    // open the InputStream of the (uncompressed) entity body...
                    is = response.getEntity(InputStream.class);
                    os = new BufferedOutputStream(new FileOutputStream(tmp));

                    // write connection to temporary file
                    byte buf[] = new byte[8192];
                    int len;
                    while ((len = is.read(buf, 0, buf.length)) >= 0) {
                        if (len != 0) {
                            totalLen += len;
                            os.write(buf, 0, len);
                        }
                    }
                    is.close();
                    is = null;

                    os.flush();
                    os.close();
                    os = null;

                    success = tmp.renameTo(destFile);
                } catch (Exception e) {
                    // most likely a socket timeout
                    e.printStackTrace();
                    logger.error("downloading " + downloadUrl.toString() + " failed after " + totalLen + " bytes: "
                            + e.toString());
                    try {
                        // signal to the framework that this socket is hosed.
                        // with the various nested streams, this may not work...
                        is.reset();
                    } catch (Exception ex) {
                        // ignore
                    }
                    throw e;
                } finally {
                    if (os != null) {
                        try {
                            os.close();
                        } catch (Exception e) {
                            // no-op
                        }
                    }
                    if (is != null) {
                        try {
                            // ensure stream is consumed...
                            byte buf[] = new byte[8192];
                            while (is.read(buf) >= 0)
                                ;
                        } catch (Exception e) {
                            // no-op
                        }
                        try {
                            is.close();
                        } catch (Exception e) {
                            // no-op
                        }
                    }
                    if (tmp.exists()) {
                        tmp.delete();
                    }
                    response.consumeContent();
                }
            } catch (ClientWebException e) {
                e.printStackTrace();
                ;
                if (response != null) {
                    response.consumeContent();
                }
                if (attemptCount != 1) {
                    throw e;
                }
            }
        }
        return HttpStatus.SC_OK;
    }

    private static final class CommonFileAttachmentTerms {
        File localFile;
        URI instanceFileDownloadUri;
    }

    private CommonFileAttachmentTerms computeCommonFileAttachmentTerms(String instanceFileUri, String instanceId,
            File instanceFolder, String relativePath) {
        // clean up the value...
        if (relativePath.startsWith("/")) {
            relativePath = relativePath.substring(1);
        }

        File localFile = ODKFileUtils.getAsFile(appName, relativePath);
        String baseInstanceFolder = instanceFolder.getAbsolutePath();
        String baseLocalAttachment = localFile.getAbsolutePath();
        if (!baseLocalAttachment.startsWith(baseInstanceFolder)) {
            throw new IllegalStateException("instance data file is not within the instances tree!");
        }
        String partialValue = baseLocalAttachment.substring(baseInstanceFolder.length());
        if (partialValue.startsWith("/")) {
            partialValue = partialValue.substring(1);
        }

        URI instanceFileDownloadUri = normalizeUri(instanceFileUri, instanceId + "/file/" + partialValue);

        CommonFileAttachmentTerms cat = new CommonFileAttachmentTerms();
        cat.localFile = localFile;
        cat.instanceFileDownloadUri = instanceFileDownloadUri;

        return cat;
    }

    @Override
    public boolean getFileAttachments(String instanceFileUri, String tableId, SyncRowPending serverRow,
            boolean deferInstanceAttachments) throws ClientWebException {

        if (serverRow.getUriFragments().isEmpty()) {
            throw new IllegalStateException("should never get here!");
        }

        SyncETagsUtils seu = new SyncETagsUtils();

        /**********************************************
         * 
         * 
         * 
         * 
         * With the new mechanism, we can directly fetch any file from the server
         * in the fileAttachmentColumns. And we can include any md5Hash we might
         * have of the local file. This would enable the server to say
         * "yes, it is identical".
         */
        boolean success = true;
        try {
            // 1) Get this row's instanceId (rowId)
            String instanceId = serverRow.getRowId();

            // 2) Get the folder holding the instance attachments
            File instanceFolder = new File(ODKFileUtils.getInstanceFolder(appName, tableId, instanceId));

            // 3) get all the files in that folder...
            List<String> relativePathsToAppFolderOnDevice = getAllFilesUnderFolder(instanceFolder, null);

            // 4) Iterate over all non-null file attachments in the data row
            for (String relativePath : serverRow.getUriFragments()) {
                // clean up the value...
                if (relativePath.startsWith("/")) {
                    relativePath = relativePath.substring(1);
                }

                // remove it from the local files list
                relativePathsToAppFolderOnDevice.remove(relativePath);

                CommonFileAttachmentTerms cat = computeCommonFileAttachmentTerms(instanceFileUri, instanceId,
                        instanceFolder, relativePath);

                if (!cat.localFile.exists()) {

                    if (deferInstanceAttachments) {
                        return false;
                    }

                    int statusCode = downloadFile(cat.localFile, cat.instanceFileDownloadUri);
                    if (statusCode == HttpStatus.SC_OK || statusCode == HttpStatus.SC_NOT_MODIFIED) {
                        String md5Hash = ODKFileUtils.getMd5Hash(appName, cat.localFile);
                        seu.updateFileSyncETag(context, appName, cat.instanceFileDownloadUri, tableId,
                                cat.localFile.lastModified(), md5Hash);
                    } else {
                        success = false;
                    }
                } else {
                    // assume that if the local file exists, it matches exactly the
                    // content on the server.
                    // this could be inaccurate if there are buggy programs on the
                    // device!
                    String md5hash = seu.getFileSyncETag(context, appName, cat.instanceFileDownloadUri, tableId,
                            cat.localFile.lastModified());
                    if (md5hash == null) {
                        md5hash = ODKFileUtils.getMd5Hash(appName, cat.localFile);
                        seu.updateFileSyncETag(context, appName, cat.instanceFileDownloadUri, tableId,
                                cat.localFile.lastModified(), md5hash);
                    }
                }
            }

            // we usually do this, but, when we have a conflict row, we pull the
            // server files down, and leave the local files. Upon the next sync,
            // we will resolve what to do and clean up.
            if (serverRow.shouldDeleteExtraneousLocalFiles()) {
                for (String relativePath : relativePathsToAppFolderOnDevice) {
                    // remove local files that are not on server...
                    File localFile = ODKFileUtils.asAppFile(appName, relativePath);
                    if (!localFile.delete()) {
                        success = false;
                    }
                }
            }
            return success;
        } catch (ClientWebException e) {
            logger.error("Exception while getting attachment: " + e.toString());
            throw e;
        } catch (Exception e) {
            e.printStackTrace();
            ;
            return false;
        }
        /******************************************************
         * End of the new file attachment mechanism...
         *
         * 
         * 
         * 
         * 
         */
    }

    @Override
    public boolean putFileAttachments(String instanceFileUri, String tableId, SyncRowPending localRow,
            boolean deferInstanceAttachments) throws ClientWebException {

        if (localRow.getUriFragments().isEmpty()) {
            throw new IllegalStateException("should never get here!");
        }

        /**********************************************
         * 
         * 
         * 
         * 
         * With the new mechanism, we can directly fetch any file from the server
         * in the fileAttachmentColumns. For PUT, we don't know if the local file
         * exists on the server, so we need to PUT every attachment. This can be 
         * done by retrieving the manifest, and comparing that against the local 
         * directory, or we can issue an if-none-match GET request for each file 
         * we need. If we do not get a NOT_MODIFIED return, then we upload it. 
         */
        boolean success = true;
        try {
            // 1) Get this row's instanceId (rowId)
            String instanceId = localRow.getRowId();

            // 2) Get the folder holding the instance attachments
            File instanceFolder = new File(ODKFileUtils.getInstanceFolder(appName, tableId, instanceId));

            // 3) Iterate over all non-null file attachments in the data row
            for (String relativePath : localRow.getUriFragments()) {
                // clean up the value...
                if (relativePath.startsWith("/")) {
                    relativePath = relativePath.substring(1);
                }

                CommonFileAttachmentTerms cat = computeCommonFileAttachmentTerms(instanceFileUri, instanceId,
                        instanceFolder, relativePath);

                if (cat.localFile.exists()) {

                    // issue a GET. If the return is NOT_MODIFIED, then we don't need to
                    // POST it.
                    int statusCode = downloadFile(cat.localFile, cat.instanceFileDownloadUri);
                    if (statusCode == HttpStatus.SC_NOT_MODIFIED) {
                        // no-op... what is on server matches local.
                    } else if (statusCode == HttpStatus.SC_OK) {
                        // The test for ODK header ensures we detect wifi login overlays
                        // this should not happen -- indicates something is corrupted.
                        logger.error(
                                "Unexpectedly overwriting attachment: " + cat.instanceFileDownloadUri.toString());
                    } else if (statusCode == HttpStatus.SC_NOT_FOUND || statusCode == HttpStatus.SC_NO_CONTENT) {

                        if (deferInstanceAttachments) {
                            return false;
                        }

                        // upload it...
                        boolean outcome = uploadInstanceFile(cat.localFile, cat.instanceFileDownloadUri);
                        if (!outcome) {
                            success = false;
                        }
                    } else {
                        success = false;
                    }
                } else {
                    // we will pull these files later during a getFileAttachments() call,
                    // if needed...
                }
            }
            return success;
        } catch (ClientWebException e) {
            logger.error("Exception while putting attachment: " + e.toString());
            throw e;
        } catch (Exception e) {
            logger.error("Exception during sync: " + e.toString());
            return false;
        }
        /******************************************************
         * End of the new file attachment mechanism...
         *
         * 
         * 
         * 
         * 
         */
    }
}