Example usage for java.util Hashtable clear

List of usage examples for java.util Hashtable clear

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Introduction

In this page you can find the example usage for java.util Hashtable clear.

Prototype

public synchronized void clear()

Source Link

Document

Clears this hashtable so that it contains no keys.

Usage

From source file:com.instantme.api.InstagramAPI.java

public boolean login(String user, String password, IAnimation anim) {

    IHTTPResponseHandler step1 = new IHTTPResponseHandler() {
        public boolean Response30X(HttpConnection connection, Hashtable cookies) {
            return false;
        }//from  www  .j a va  2  s .c  om

        public boolean Response20X(HttpConnection connection, Hashtable cookies) {
            return cookies.get("csrftoken") != null;
        }

        public boolean ResponseOthers(HttpConnection connection, Hashtable cookies) {
            return false;
        }
    };
    IHTTPResponseHandler step2 = new IHTTPResponseHandler() {
        public boolean Response30X(HttpConnection connection, Hashtable cookies) {
            if (cookies.get("sessionid") == null) {
                return false;
            } else {
                parseUserID();
                return true;
            }
        }

        public boolean Response20X(HttpConnection connection, Hashtable cookies) {
            return false;
        }

        public boolean ResponseOthers(HttpConnection connection, Hashtable cookies) {
            return false;
        }
    };
    IHTTPResponseHandler step3 = new IHTTPResponseHandler() {
        public boolean Response30X(HttpConnection connection, Hashtable cookies) {
            return cookies.get("accessToken") != null;
        }

        public boolean Response20X(HttpConnection connection, Hashtable cookies) {
            return true;
        }

        public boolean ResponseOthers(HttpConnection connection, Hashtable cookies) {
            return false;
        }
    };
    IHTTPResponseHandler step4 = new IHTTPResponseHandler() {
        public boolean Response30X(HttpConnection connection, Hashtable cookies) {
            return cookies.get("accessToken") != null;
        }

        public boolean Response20X(HttpConnection connection, Hashtable cookies) {
            return false;
        }

        public boolean ResponseOthers(HttpConnection connection, Hashtable cookies) {
            return false;
        }
    };

    this.user = user;
    this.password = password;
    // clear all cookies and session information
    cookies.clear();
    lastUrl = "";
    logged = false;

    Hashtable getParams = new Hashtable();
    getParams.put("client_id", CLIENT_ID);
    getParams.put("redirect_uri", REDIRECT_URI);
    getParams.put("response_type", "token");
    getParams.put("scope", "basic+likes+comments+relationships");

    println("Step 1");
    setAnimation(anim);
    updateProgress(Locale.getInst().getStr(Locale.LOGIN_1_4));
    logged = HttpLoginRequest(HttpConnection.GET, LOGIN_URL, getParams, null, step1);

    if (logged == false) {
        println("Failed at step 1");
        return false;
    }

    Hashtable postParams = new Hashtable();
    postParams.put("csrfmiddlewaretoken", cookies.get("csrftoken"));
    postParams.put("username", user);
    postParams.put("password", password);
    postParams.put("scope", "basic+likes+comments+relationships");

    println("Step 2");
    updateProgress(Locale.getInst().getStr(Locale.LOGIN_2_4));
    logged = HttpLoginRequest(HttpConnection.POST, LOGIN_URL, getParams, postParams, step2);

    if (logged == false) {
        println("Failed at step 2");
        return logged;
    }

    println("Step 3");
    updateProgress(Locale.getInst().getStr(Locale.LOGIN_3_4));
    logged = HttpLoginRequest(HttpConnection.GET, AUTH_URL, getParams, null, step3);

    if (logged == false) {
        println("Failed at step 3");
        return logged;
    }

    step1 = step2 = step3 = null;

    updateProgress(Locale.getInst().getStr(Locale.LOGIN_4_4));
    if (cookies.get("accessToken") == null) {
        postParams.clear();
        postParams.put("csrfmiddlewaretoken", cookies.get("csrftoken"));
        postParams.put("allow", "Authorize");
        postParams.put("scope", "basic+likes+comments+relationships");

        println("Step 4");
        logged = HttpLoginRequest(HttpConnection.POST, AUTH_URL, getParams, postParams, step4);

        if (logged == false) {
            println("Failed at step 4");
            return logged;
        }
    }

    step4 = null;

    // update user info
    getFullUserInfo(userInfo, getAuthUserID(), anim);

    return logged;
}

From source file:com.fiorano.openesb.application.aps.OutPortInst.java

protected void populate(FioranoStaxParser parser) throws XMLStreamException, FioranoException {
    if (parser.markCursor(APSConstants.OUTPORT_INST)) {
        // Get Attributes if needs to accessed later. This MUST be done before accessing any data of element.
        Hashtable attributes = parser.getAttributes();
        m_bIsSyncRequestType = XMLUtils//w w w . jav a2 s.com
                .getStringAsBoolean((String) attributes.get(APSConstants.IS_SYNC_REQUEST_TYPE));//XMLDmiUtil.getAttributeAsBoolean(port, "isSyncRequestType");
        m_bisDisabled = XMLUtils.getStringAsBoolean((String) attributes.get(APSConstants.IS_DISABLED));//XMLDmiUtil.getAttributeAsBoolean(port, "isSyncRequestType");
        while (parser.nextElement()) {
            String nodeName = parser.getLocalName();
            if (nodeName.equalsIgnoreCase("Name")) {
                m_strPortName = parser.getText();//XMLUtils.getNodeValueAsString(child).toUpperCase();

            }

            else if (nodeName.equalsIgnoreCase("Description")) {
                m_strDscription = parser.getText();//XMLUtils.getNodeValueAsString(child);

            }

            else if (nodeName.equalsIgnoreCase("StandardXSD")) {
                if ("ON_EXCEPTION".equals(m_strPortName))
                    m_strXSD = CommonSchemas.ERROR_XSD;
            }

            else if (nodeName.equalsIgnoreCase(PortInstConstants.PORT_XSD)) {
                m_strXSD = parser.getCData();//XMLUtils.getNodeValueAsString(child);

            }

            else if (nodeName.equalsIgnoreCase(PortInstConstants.PORT_XSDREF)) {
                m_strXSDRef = parser.getText();//XMLUtils.getNodeValueAsString(child);

            }

            else if (nodeName.equalsIgnoreCase("SetContextXSL")) {
                m_strContextXSL = parser.getCData();//XMLUtils.getNodeValueAsString(child);

            }

            else if (nodeName.equalsIgnoreCase("SetContextInfo")) {
                m_strContextInfo = parser.getCData();//XMLUtils.getNodeValueAsString(child);

            } else if (nodeName.equalsIgnoreCase("SetTransformationType")) {
                m_transformerType = parser.getText();//XMLUtils.getNodeValueAsString(child);

            } else if (nodeName.equalsIgnoreCase("JavaClass")) {
                m_strJavaClass = parser.getText();//XMLUtils.getNodeValueAsString(child);

            }

            else if (nodeName.equalsIgnoreCase("Param")) {
                Param paramDmi = new Param();

                paramDmi.setFieldValues(parser);
                addParam(paramDmi);
            }
        }
        if (attributes != null) {
            attributes.clear();
            attributes = null;
        }

    }
    validate();
}

From source file:edu.ku.brc.specify.web.SpecifyExplorer.java

/**
 * @param dataObj//from ww w.j a  va 2s.  c o m
 * @param labelHashMap
 */
protected void fillLabelMap(final FormDataObjIFace dataObj, final Hashtable<String, String> labelHashMap) {
    labelHashMap.clear();

    if (dataObj instanceof Treeable<?, ?, ?>) {
        Treeable<?, ?, ?> node = (Treeable<?, ?, ?>) dataObj;

        TreeDefItemIface<?, ?, ?> def = node.getDefinitionItem();
        //String defName = def.getName();

        Treeable<?, ?, ?> parentNode = node.getParent();
        if (parentNode != null) {
            TreeDefItemIface<?, ?, ?> parentDef = parentNode.getDefinitionItem();
            if (parentDef != null) {
                String parentDefName = parentDef.getName();
                labelHashMap.put("parent", parentDefName);
            }
        }

        TreeDefItemIface<?, ?, ?> childDef = def.getChild();
        if (childDef != null) {
            String childDefName = childDef.getName();
            labelHashMap.put("children", childDefName);
        }
        if (dataObj.getClass() == Taxon.class) {
            labelHashMap.put("definitionItem", "Taxonomy");
        }
    }
}

From source file:org.treasurehunter.bcaching.ImportBcachingTask.java

protected void doInBackground(Handler handler) {
    try {/*from ww w  .  j av  a 2s .  com*/
        Log.d("TreasureHunter", "Doing bcaching login");
        mComm.validateCredentials();
    } catch (Exception ex) {
        Log.e("TreasureHunter", "Bcaching.com login failed", ex);
        mProcessStatus.abortedBeforeStart();
        if (!isAborted())
            mErrorDisplayer.displayError(R.string.bcaching_login_failed);
        return;
    }

    if (isAborted()) {
        mProcessStatus.abortedBeforeStart();
        return;
    }

    Hashtable<String, String> params = new Hashtable<String, String>();
    params.put("a", "find");
    if (mUsesCenterCoord) {
        params.put("lat", String.valueOf(mCenterLat));
        params.put("lon", String.valueOf(mCenterLon));
    } else {
        // bbox=lat1,lon1,lat2,lon2
        params.put("bbox", String.valueOf(mLatLow) + "," + String.valueOf(mLonLow) + ","
                + String.valueOf(mLatHigh) + "," + String.valueOf(mLonHigh));
        params.put("lon", String.valueOf(mCenterLon));
    }
    params.put("wpts", "0");
    params.put("maxcount", Integer.toString(mMaxCount));
    params.put("fmt", "json");
    params.put("timeAsLong", "1"); // Don't return "new Date(xxxx)"
    params.put("idsonly", "1"); // Don't get name or other additional
                                // properties
    if (mBcachingConfig.shouldDownloadMyFinds()) {
        params.put("found", "b");
    } else {
        params.put("found", "0");
    }
    if (mBcachingConfig.shouldDownloadMyHides()) {
        params.put("own", "b");
    } else {
        params.put("own", "0");
    }
    params.put("app", "TreasureHunter");

    String response;
    try {
        Log.d("TreasureHunter", "Sending query");
        response = readResponse(mComm.SendRequest(params));
    } catch (Exception ex) {
        Log.e("TreasureHunter", "SendRequest failed", ex);
        mProcessStatus.abortedBeforeStart();
        if (!isAborted())
            mErrorDisplayer.displayError(R.string.bcaching_sendrequest_failed);
        return;
    }

    if (isAborted()) {
        mProcessStatus.abortedBeforeStart();
        return;
    }

    StringBuilder csvIds = new StringBuilder();
    int detailsCount = 0;

    try {
        JSONObject obj = new JSONObject(response);
        JSONArray summary = obj.getJSONArray("data");
        int count = summary.length();
        Log.v("TreasureHunter", "Number of caches: " + count);
        mProcessStatusListener.onProcessNewMaxProgress(count);

        if (count == 0) {
            mProcessStatus.abortedBeforeStart();
            if (!isAborted())
                mErrorDisplayer.displayError(R.string.bcaching_no_nearby_caches);
            return;
        }

        if (isAborted()) {
            mProcessStatus.abortedBeforeStart();
            return;
        }

        for (int i = 0; i < count; i++) {
            JSONObject cacheObject = summary.getJSONObject(i);
            String cacheId = cacheObject.getString("wpt");
            long localLastMod = mDbFrontend.getLastUpdatedTime(cacheId);
            long serverLastMod = 1;
            if (localLastMod != 0) {
                // String serverLastModStr =
                // cacheObject.getString("lastMod");
                // serverLastMod =
                // Long.parseLong(serverLastModStr.replace("new Date(",
                // "").replace(")", ""));
                serverLastMod = cacheObject.getLong("lastMod");
            }

            if (serverLastMod >= localLastMod) {
                detailsCount += 1;
                if (csvIds.length() > 0) {
                    csvIds.append(',');
                }
                int id = cacheObject.getInt("id");
                csvIds.append(String.valueOf(id));
            }
        }
    } catch (Exception ex) {
        Log.e("TreasureHunter", "Processing SendRequest result failed", ex);
        mProcessStatus.abortedBeforeStart();
        if (!isAborted())
            mErrorDisplayer.displayError(R.string.bcaching_processing_result_failed);
        return;
    }

    mProcessStatus.setMaxProgress(detailsCount);

    params.clear();
    params.put("a", "detail");
    params.put("desc", "html");
    params.put("ids", csvIds.toString());
    params.put("tbs", "1");
    params.put("wpts", "1");
    params.put("logs", "20");
    params.put("fmt", "gpx");
    params.put("app", "TreasureHunter");

    if (isAborted()) {
        mProcessStatus.abortedBeforeStart();
        return;
    }

    InputStream is;
    try {
        Log.d("TreasureHunter", "Downloading cache details");
        is = mComm.SendRequest(params);
    } catch (Exception ex) {
        Log.e("TreasureHunter", "Detail Request failed", ex);
        mProcessStatus.abortedBeforeStart();
        if (!isAborted())
            mErrorDisplayer.displayError(R.string.bcaching_detail_request_failed);
        return;
    }

    if (isAborted()) {
        mProcessStatus.abortedBeforeStart();
        return;
    }

    InputStreamReader isr = new InputStreamReader(is);

    mProcessStatus.willStartLoading();
    boolean success = false;
    try {
        XmlFiniteStateMachine.importFromReader(Source.BCACHING, isr, mProcessStatus, this, mUsername);
        success = true; // No assertion thrown
    } catch (XmlPullParserException e) {
        if (!isAborted())
            mErrorDisplayer.displayError(R.string.error_parsing_file, e.getMessage());
    } catch (IOException e) {
        if (!isAborted())
            mErrorDisplayer.displayError(R.string.error_reading_file, e.getMessage());
    }
    mProcessStatus.stoppedAllLoading(success);
}

From source file:edu.ku.brc.specify.web.SpecifyExplorer.java

/**
 * @param dataObj/* w  w w. j  a v a2  s  .co m*/
 */
protected void processDataList(final PrintWriter out, final List<?> list, final String sql)

{
    if (StringUtils.isEmpty(template)) {
        out.println("The template file is empty!");
    }

    FormDataObjIFace dataObj = (FormDataObjIFace) list.get(0);

    String linkField = "";
    ClassDisplayInfo cdi = classHash.get(dataObj.getClass().getSimpleName());
    if (cdi != null) {
        linkField = cdi.getLinkField();
    }

    int contentInx = template.indexOf(contentTag);
    String subContent = template.substring(0, contentInx);
    out.println(StringUtils.replace(subContent, "<!-- Title -->", dataObj.getIdentityTitle()));

    //fillLabelMap(dataObj, labelMap);

    Hashtable<Integer, String> ordered = new Hashtable<Integer, String>();
    Vector<String> unOrdered = new Vector<String>();

    Hashtable<String, Boolean> hasData = new Hashtable<String, Boolean>();

    out.println("<table border=\"0\" width=\"100%\"<tr><td nowrap=\"nowrap\">select * "
            + StringUtils.replace(sql, packageName, "") + "</td></tr>");
    out.println("<tr><td nowrap=\"nowrap\">Records Returned: " + list.size() + "</td></tr></table><br/>");
    out.println("<table width=\"100%\" cellspacing=\"0\" class=\"brdr\">\n");
    try {
        for (Object dobj : list) {
            dataObj = (FormDataObjIFace) dobj;
            for (Field field : dataObj.getClass().getDeclaredFields()) {
                String fieldName = field.getName();
                FieldDisplayInfo fdi = cdi.getField(fieldName);

                if (fdi != null && (fdi.isSkipped() || !fdi.isForDisplay())) {
                    continue;
                }

                String fldNameLower = fieldName.toLowerCase();
                if (fldNameLower.startsWith(dataObj.getClass().getSimpleName().toLowerCase())
                        && fldNameLower.endsWith("id")) {
                    continue;
                }

                try {
                    Object data = getData(field, dataObj);
                    if (data != null && !(data instanceof Set<?>)) {
                        hasData.put(fieldName, true);
                    }
                } catch (Exception ex) {
                    ex.printStackTrace();
                }
            }
        }

        out.println("<tr><th class=\"brdr\">Row</th>");
        for (Field field : dataObj.getClass().getDeclaredFields()) {
            String fieldName = field.getName();

            if (hasData.get(fieldName) == null) {
                continue;
            }

            FieldDisplayInfo fdi = cdi.getField(fieldName); // should never be null

            String labelStr = labelMap.get(fieldName);
            if (StringUtils.isEmpty(labelStr)) {
                labelStr = UIHelper.makeNamePretty(fieldName);
            }

            String row = "<th class=\"brdr\">" + labelStr + "</th>";
            Integer inx = fdi != null ? fdi.getOrder() : null;
            if (inx == null) {
                unOrdered.add(row);
            } else {
                ordered.put(inx, row);
            }

        }
        fillRows(out, ordered, unOrdered);

        out.println("</tr>");

        int cnt = 1;
        for (Object dobj : list) {
            ordered.clear();
            unOrdered.clear();

            out.println("<tr><th class=\"brdr\" align=\"center\">" + cnt + "</th>");

            dataObj = (FormDataObjIFace) dobj;

            for (Field field : dataObj.getClass().getDeclaredFields()) {
                String fieldName = field.getName();

                if (hasData.get(fieldName) == null) {
                    continue;
                }

                FieldDisplayInfo fdi = cdi.getField(fieldName);

                String row = null;
                try {
                    Object data = getData(field, dataObj);
                    if (data != null && !(data instanceof Set<?>)) {
                        String val;
                        if (fieldName.equals(linkField)) {
                            val = formatFDI(dataObj, formatValue(data));
                        } else {
                            val = formatValue(data);
                        }
                        row = "<td align=\"center\" class=\"brdr" + ((cnt % 2 == 0) ? "even" : "odd") + "\">"
                                + (StringUtils.isNotEmpty(val) ? val : "&nbsp;") + "</td>";
                    } else {
                        row = "<td align=\"center\" class=\"brdr" + ((cnt % 2 == 0) ? "even" : "odd")
                                + "\">&nbsp;</td>";
                    }
                } catch (Exception ex) {
                    ex.printStackTrace();
                }

                if (row != null) {
                    Integer inx = fdi != null ? fdi.getOrder() : null;
                    if (inx == null) {
                        unOrdered.add(row);
                    } else {
                        ordered.put(inx, row);
                    }
                }
            }
            fillRows(out, ordered, unOrdered);
            out.println("</tr>\n");
            cnt++;
        }
        out.println("</table>\n");

        // This should be externalized
        if (dataObj.getClass() == Locality.class || dataObj.getClass() == CollectingEvent.class
                || dataObj.getClass() == CollectionObject.class || dataObj.getClass() == Taxon.class
                || dataObj.getClass() == Accession.class) {
            createMapLink(out, list, dataObj.getClass());
        }

        out.println(template.substring(contentInx + contentTag.length() + 1, template.length()));

    } catch (Exception ex) {
        ex.printStackTrace();
        System.out.println(ex.toString());
        out.println("Sorry");
    }
}

From source file:org.sakaiproject.dav.DavServlet.java

/**
 * Copy or name a resource or collection.
 * //from   ww w.j a  v  a2s. co m
 * @param resources
 *        Resources implementation to be used
 * @param errorList
 *        Hashtable containing the list of errors which occurred during the copy operation
 * @param source
 *        Path of the resource to be copied
 * @param dest
 *        Destination path
 */
private boolean copyResource(DirContextSAKAI resources, Hashtable<String, Integer> errorList, String source,
        String dest, boolean move) {

    if (M_log.isDebugEnabled())
        M_log.debug("Copy: " + source + " To: " + dest);

    source = fixDirPathSAKAI(source);
    dest = fixDirPathSAKAI(dest);

    if (prohibited(source) || prohibited(dest)) {
        errorList.put(source, new Integer(SakaidavStatus.SC_FORBIDDEN));
        return false;
    }

    source = adjustId(source);
    dest = adjustId(dest);

    // Copy

    try {
        boolean isCollection = contentHostingService.getProperties(source)
                .getBooleanProperty(ResourceProperties.PROP_IS_COLLECTION);

        /* https://jira.sakaiproject.org/browse/SAK-23639
        if (move) {
           contentHostingService.rename(source, dest);
        }
        else */
        // NOTE: moves cause a copy as below and a delete around line 2960, if rename() is fixed the remove that code also
        if (isCollection) {
            copyCollection(source, dest);
        } else {
            contentHostingService.copy(source, dest);
        }
    } catch (EntityPropertyNotDefinedException e) {
        // System.out.println("propnotdef " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_INTERNAL_SERVER_ERROR));
        return false;
    } catch (EntityPropertyTypeException e) {
        // System.out.println("propntype " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_INTERNAL_SERVER_ERROR));
        return false;
    } catch (IdUsedException e)
    // internal error because caller checked for this
    {
        // System.out.println("idunused " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_INTERNAL_SERVER_ERROR));
        return false;
    } catch (IdUniquenessException e) {
        // System.out.println("iduniqu " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_INTERNAL_SERVER_ERROR));
        return false;
    } catch (IdLengthException e) {
        // System.out.println("idlen " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_FORBIDDEN));
        return false;
    } catch (InconsistentException e) {
        // System.out.println("inconsis " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_CONFLICT));
        return false;
    } catch (PermissionException e) {
        // System.out.println("perm " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_FORBIDDEN));
        return false;
    } catch (InUseException e) {
        // System.out.println("in use " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_CONFLICT));
        return false;
    } catch (IdUnusedException e) {
        // System.out.println("unused " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_NOT_FOUND));
        return false;
    } catch (OverQuotaException e) {
        // System.out.println("quota " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_FORBIDDEN));
        return false;
    } catch (IdInvalidException e) {
        // System.out.println("quota " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_FORBIDDEN));
        return false;
    } catch (TypeException e) {
        // System.out.println("type " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_FORBIDDEN));
        return false;
    } catch (ServerOverloadException e) {
        // System.out.println("overload " + e);
        errorList.put(source, new Integer(SakaidavStatus.SC_INTERNAL_SERVER_ERROR));
        return false;
    }

    // We did not have an error
    errorList.clear();
    return true;

}

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

/**
 * @param treeDef//  ww w .ja  va2  s. c o m
 * @return
 */
public LithoStrat convertLithoStratFromCSV(final LithoStratTreeDef treeDef) {
    Hashtable<String, LithoStrat> lithoStratHash = new Hashtable<String, LithoStrat>();

    lithoStratHash.clear();

    File file = new File("demo_files/Stratigraphy.csv");
    if (!file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir");
        file = XMLHelper.getConfigDir("Stratigraphy.csv");
        if (!file.exists()) {
            file = new File("Specify/demo_files/Stratigraphy.csv");
        }
    }

    if (file == null || !file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "]");
        return null;
    }

    List<String> lines = null;
    try {
        lines = FileUtils.readLines(file);

    } catch (Exception ex) {
        ex.printStackTrace();
        return null;
    }

    startTx();

    // setup the root Geography record (planet Earth)
    LithoStrat earth = new LithoStrat();
    earth.initialize();
    earth.setName(getResourceString("Earth"));
    earth.setFullName(earth.getName());
    earth.setNodeNumber(1);
    earth.setHighestChildNodeNumber(1);
    earth.setRankId(0);
    earth.setDefinition(treeDef);
    LithoStratTreeDefItem defItem = treeDef.getDefItemByRank(0);
    earth.setDefinitionItem(defItem);

    persist(earth);

    frame.setDesc("Adding Stratigraphy Objects");
    frame.setProcess(0, lines.size());

    int counter = 0;
    // for each old record, convert the record
    for (String line : lines) {
        if (counter == 0) {
            counter = 1;
            continue; // skip header line
        }

        if (counter % 100 == 0) {
            frame.setProcess(counter);
            log.info("Converted " + counter + " Stratigraphy records");
        }

        String[] columns = StringUtils.splitPreserveAllTokens(line, ',');
        if (columns.length < 7) {
            log.error("Skipping[" + line + "]");
            continue;
        }

        // grab the important data fields from the old record
        String superGroup = columns[2];
        String lithoGroup = columns[3];
        String formation = columns[4];
        String member = columns[5];
        String bed = columns[6];

        // create a new Litho Stratigraphy object from the old data
        @SuppressWarnings("unused")
        LithoStrat newStrat = convertOldStratRecord(superGroup, lithoGroup, formation, member, bed, earth);

        counter++;
    }

    frame.setProcess(counter);

    log.info("Converted " + counter + " Stratigraphy records");

    TreeHelper.fixFullnameForNodeAndDescendants(earth);
    earth.setNodeNumber(1);
    fixNodeNumbersFromRoot(earth);

    commitTx();

    /*startTx();
    TreeHelper.fixFullnameForNodeAndDescendants(earth);
    earth.setNodeNumber(1);
    fixNodeNumbersFromRoot(earth);
            
    printTree(earth, 0);
    saveTree(earth);
            
    commitTx();*/

    log.info("Converted " + counter + " Stratigraphy records");

    // set up Geography foreign key mapping for locality
    lithoStratHash.clear();

    return earth;
}

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

/**
 * @param treeDef//from  w  w  w.j  a va2 s  . c  o  m
 * @return
 */
public Geography convertGeographyFromXLS(final GeographyTreeDef treeDef) {
    frame.setDesc("Building Geography Tree...");

    Hashtable<String, Geography> geoHash = new Hashtable<String, Geography>();

    geoHash.clear();

    String fileName = "Geography.xls";
    File file = XMLHelper.getConfigDir("../demo_files/" + fileName);
    if (!file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir");
        file = XMLHelper.getConfigDir(fileName);
        if (!file.exists()) {
            file = new File("Specify/demo_files/" + fileName);
        }
    }

    if (file == null || !file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "]");
        return null;
    }

    // setup the root Geography record (planet Earth)
    Geography earth = new Geography();
    earth.initialize();
    earth.setName(getResourceString("Earth"));
    earth.setFullName(earth.getName());
    earth.setNodeNumber(1);
    earth.setHighestChildNodeNumber(1);
    earth.setRankId(0);
    earth.setDefinition(treeDef);
    GeographyTreeDefItem defItem = treeDef.getDefItemByRank(0);
    earth.setDefinitionItem(defItem);

    int counter = 0;

    try {
        startTx();

        persist(earth);

        String[] cells = new String[4];
        InputStream input = new FileInputStream(file);
        POIFSFileSystem fs = new POIFSFileSystem(input);
        HSSFWorkbook workBook = new HSSFWorkbook(fs);
        HSSFSheet sheet = workBook.getSheetAt(0);
        Iterator<?> rows = sheet.rowIterator();

        int lastRowNum = sheet.getLastRowNum();
        if (frame != null) {
            final int mx = lastRowNum;
            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    frame.setProcess(0, mx);
                }
            });
        }

        while (rows.hasNext()) {
            if (counter == 0) {
                counter = 1;
                rows.next();
                continue;
            }
            if (counter % 100 == 0) {
                if (frame != null)
                    frame.setProcess(counter);
                log.info("Converted " + counter + " Geography records");
            }

            HSSFRow row = (HSSFRow) rows.next();
            Iterator<?> cellsIter = row.cellIterator();
            int i = 0;
            while (cellsIter.hasNext() && i < 4) {
                HSSFCell cell = (HSSFCell) cellsIter.next();
                if (cell != null) {
                    cells[i] = StringUtils.trim(cell.getRichStringCellValue().getString());
                    i++;
                }
            }
            // Sets nulls to unused cells
            for (int j = i; j < 4; j++) {
                cells[j] = null;
            }
            //System.out.println();
            @SuppressWarnings("unused")
            Geography newGeo = convertGeographyRecord(cells[0], cells[1], cells[2], cells[3], earth);

            counter++;
        }

    } catch (Exception ex) {
        ex.printStackTrace();
    }

    if (frame != null)
        frame.setProcess(counter);

    log.info("Converted " + counter + " Geography records");

    frame.setDesc("Saving Geography Tree...");
    frame.getProcessProgress().setIndeterminate(true);

    TreeHelper.fixFullnameForNodeAndDescendants(earth);
    earth.setNodeNumber(1);
    fixNodeNumbersFromRoot(earth);

    commitTx();

    /*startTx();
    TreeHelper.fixFullnameForNodeAndDescendants(earth);
    earth.setNodeNumber(1);
    fixNodeNumbersFromRoot(earth);
            
    printTree(earth, 0);
    saveTree(earth);
            
    commitTx();*/

    log.info("Converted " + counter + " Stratigraphy records");

    // set up Geography foreign key mapping for locality
    geoHash.clear();

    return earth;
}

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

/**
 * @param treeDef//  ww w  .  ja  va  2  s.  c  o m
 * @return
 */
public GeologicTimePeriod convertChronoStratFromXLS(final GeologicTimePeriodTreeDef treeDef,
        final Agent userAgent) {
    startTx();

    GeologicTimePeriodTreeDefItem root = createGeologicTimePeriodTreeDefItem(null, treeDef, "Root", 0);
    GeologicTimePeriodTreeDefItem era = createGeologicTimePeriodTreeDefItem(root, treeDef, "Erathem/Era", 100);
    GeologicTimePeriodTreeDefItem period = createGeologicTimePeriodTreeDefItem(era, treeDef, "System/Period",
            200);
    GeologicTimePeriodTreeDefItem series = createGeologicTimePeriodTreeDefItem(period, treeDef, "Series/Epoch",
            300);
    @SuppressWarnings("unused")
    GeologicTimePeriodTreeDefItem member = createGeologicTimePeriodTreeDefItem(series, treeDef, "Stage/Age",
            400);
    persist(root);
    commitTx();

    series.setIsInFullName(true);

    frame.setDesc("Building ChronoStratigraphy Tree...");

    Hashtable<String, GeologicTimePeriod> chronoHash = new Hashtable<String, GeologicTimePeriod>();

    chronoHash.clear();

    String fileName = "chronostrat_tree.xls";
    File file = XMLHelper.getConfigDir("../demo_files/" + fileName);
    if (!file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir");
        file = XMLHelper.getConfigDir(fileName);
        if (!file.exists()) {
            file = new File("Specify/demo_files/" + fileName);
        }
    }

    if (file == null || !file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "]");
        return null;
    }

    // setup the root ChronoStrat record (planet Earth)
    GeologicTimePeriod rootNode = new GeologicTimePeriod();
    rootNode.initialize();
    rootNode.setName(getResourceString("Root"));
    rootNode.setFullName(rootNode.getName());
    rootNode.setRankId(0);
    rootNode.setDefinition(treeDef);
    rootNode.setDefinitionItem(root);
    rootNode.setCreatedByAgent(userAgent);

    int counter = 0;

    try {
        startTx();

        persist(rootNode);

        String[] cells = new String[4];
        InputStream input = new FileInputStream(file);
        POIFSFileSystem fs = new POIFSFileSystem(input);
        HSSFWorkbook workBook = new HSSFWorkbook(fs);
        HSSFSheet sheet = workBook.getSheetAt(0);
        Iterator<?> rows = sheet.rowIterator();

        int lastRowNum = sheet.getLastRowNum();
        if (frame != null) {
            final int mx = lastRowNum;
            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    frame.setProcess(0, mx);
                }
            });
        }

        while (rows.hasNext()) {
            if (counter == 0) {
                counter = 1;
                continue;
            }
            if (counter % 100 == 0) {
                if (frame != null)
                    frame.setProcess(counter);
                log.info("Converted " + counter + " ChronoStrat records");
            }

            HSSFRow row = (HSSFRow) rows.next();
            Iterator<?> cellsIter = row.cellIterator();
            int i = 0;
            while (cellsIter.hasNext() && i < 4) {
                HSSFCell cell = (HSSFCell) cellsIter.next();
                if (cell != null) {
                    cells[i] = StringUtils.trim(cell.getRichStringCellValue().getString());
                    i++;
                }
            }
            for (int j = i; j < 4; j++) {
                cells[j] = null;
            }
            //System.out.println();
            @SuppressWarnings("unused")
            GeologicTimePeriod newGeo = convertChronoStratRecord(cells[0], cells[1], cells[2], cells[3],
                    rootNode, userAgent);

            counter++;
        }

        input.close();

    } catch (Exception ex) {
        ex.printStackTrace();
    }

    if (frame != null)
        frame.setProcess(counter);

    log.info("Converted " + counter + " ChronoStrat records");

    TreeHelper.fixFullnameForNodeAndDescendants(rootNode);
    rootNode.setNodeNumber(1);
    fixNodeNumbersFromRoot(rootNode);

    commitTx();

    log.info("Converted " + counter + " Stratigraphy records");

    // set up ChronoStrat foreign key mapping for locality
    chronoHash.clear();

    return rootNode;
}

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

/**
 * @param treeDef/*from ww  w. j  a va 2  s  .c  o m*/
 * @param fileName
 * @param doUserProvidedFile
 * @return
 */
public Taxon convertTaxonFromXLS(final TaxonTreeDef treeDef, final String fileName,
        final boolean doUserProvidedFile) {
    Hashtable<String, Taxon> taxonHash = new Hashtable<String, Taxon>();

    taxonHash.clear();

    File file = TaxonLoadSetupPanel.getFileForTaxon(fileName, doUserProvidedFile);
    if (file == null) {
        return null;
    }

    Vector<TaxonTreeDefItem> rankedItems = new Vector<TaxonTreeDefItem>();
    Hashtable<String, Boolean> colNames = new Hashtable<String, Boolean>();
    for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) {
        colNames.put(item.getName().toLowerCase(), true);
        rankedItems.add(item);
    }

    Collections.sort(rankedItems, new Comparator<TaxonTreeDefItem>() {
        @Override
        public int compare(TaxonTreeDefItem o1, TaxonTreeDefItem o2) {
            return o1.getRankId().compareTo(o2.getRankId());
        }
    });

    Connection conn = null;
    Statement stmt = null;

    TaxonTreeDefItem rootTreeDefItem = rankedItems.get(0);
    Set<Taxon> rootKids = rootTreeDefItem.getTreeEntries();
    Taxon root = rootKids.iterator().next();

    Vector<Pair<String, Integer>> nodeList = new Vector<Pair<String, Integer>>();
    Pair<String, Integer> rootNode = new Pair<String, Integer>(root.getName(), root.getId());
    nodeList.add(rootNode);

    int counter = 0;
    int numDataCols = 0;
    try {
        startTx();

        for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) {
            persist(item);
        }

        persist(root);

        commitTx();

        String[] cells = new String[35];
        String[] header = new String[35];
        InputStream input = new FileInputStream(file);
        POIFSFileSystem fs = new POIFSFileSystem(input);
        HSSFWorkbook workBook = new HSSFWorkbook(fs);
        HSSFSheet sheet = workBook.getSheetAt(0);
        Iterator<?> rows = sheet.rowIterator();

        int lastRowNum = sheet.getLastRowNum();
        if (frame != null) {
            final int mx = lastRowNum;
            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    frame.setProcess(0, mx);
                }
            });
        }

        conn = DBConnection.getInstance().createConnection();
        //conn.setAutoCommit(false);
        stmt = conn.createStatement();

        rows = sheet.rowIterator();
        while (rows.hasNext()) {
            for (int i = 0; i < cells.length; i++) {
                cells[i] = null;
            }

            if (counter == 0) {
                HSSFRow row = (HSSFRow) rows.next();
                Iterator<?> cellsIter = row.cellIterator();
                int i = 0;
                while (cellsIter.hasNext()) {
                    HSSFCell cell = (HSSFCell) cellsIter.next();
                    if (cell != null) {
                        cells[i] = getXLSCellValueAsStr(cell);
                        header[i] = cells[i];
                        i++;
                    }
                }
                for (i = 0; i < cells.length; i++) {
                    if (cells[i] == null)
                        break;

                    if (colNames.get(cells[i].toLowerCase()) != null) {
                        numDataCols = i + 1;
                    } else {
                        for (String key : colNames.keySet()) {
                            System.err.println("key[" + key + "]");
                        }
                        System.err.println("Not Found: [" + cells[i].toLowerCase() + "]");
                        break;
                    }
                }
                loadIndexes(cells);
                counter = 1;

                for (String hdr : header) {
                    if (hdr == null)
                        break;

                    int inx = 0;
                    for (TaxonTreeDefItem item : rankedItems) {
                        if (hdr.equalsIgnoreCase(item.getName())) {
                            log.debug("Header: " + hdr + " -> " + inx);
                            taxonIndexes.put(hdr, inx);
                            item.setIsInFullName(item.getRankId() >= TaxonTreeDef.GENUS);

                        } else {
                            log.debug("Header: " + hdr + " -> skipped.");
                        }
                        inx++;
                    }
                }
                continue;
            }

            if (counter % 100 == 0) {
                if (frame != null)
                    frame.setProcess(counter);
                //log.info("Converted " + counter + " of "+lastRowNum+" Taxon records");
            }

            HSSFRow row = (HSSFRow) rows.next();
            Iterator<?> cellsIter = row.cellIterator();
            int i = 0;
            while (cellsIter.hasNext() && i < cells.length) {
                HSSFCell cell = (HSSFCell) cellsIter.next();
                if (cell != null) {
                    cells[i] = getXLSCellValueAsStr(cell);
                    i++;
                }
            }

            convertTaxonNodes(conn, stmt, header, cells, numDataCols, rootNode, nodeList, rankedItems,
                    root.getDefinition().getId());

            counter++;
        }

        stmt.executeUpdate(
                "UPDATE taxon SET IsAccepted = true WHERE IsAccepted IS NULL and AcceptedID IS NULL AND TaxonTReeDefID = "
                        + treeDef.getId());

        // Clear all GUIDs in Taxon.
        stmt.executeUpdate("UPDATE taxon SET GUID = NULL WHERE TaxonTreeDefID = " + treeDef.getId());

        conn.close();

        input.close();

        if (frame != null)
            frame.setProcess(lastRowNum);

        root = (Taxon) session.createQuery("FROM Taxon WHERE id = " + root.getId()).list().get(0);

    } catch (Exception ex) {
        ex.printStackTrace();
        edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount();
        edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BackupServiceFactory.class, ex);

    } finally {
        try {
            if (stmt != null) {
                stmt.close();
            }
            if (conn != null) {
                conn.close();
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }

    if (frame != null) {
        frame.setDesc("Saving Taxon Tree...");
        frame.getProcessProgress().setIndeterminate(true);
    }

    NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem> nodeNumberer = new NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem>(
            root.getDefinition());
    nodeNumberer.doInBackground();

    //startTx();
    //TreeHelper.fixFullnameForNodeAndDescendants(root);
    //root.setNodeNumber(1);
    //fixNodeNumbersFromRoot(root);
    //commitTx();

    log.info("Converted " + counter + " Taxon records");

    // set up Taxon foreign key mapping for locality
    taxonHash.clear();

    return root;
}