Example usage for org.dom4j Element getTextTrim

List of usage examples for org.dom4j Element getTextTrim

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In this page you can find the example usage for org.dom4j Element getTextTrim.

Prototype

String getTextTrim();

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Usage

From source file:edu.ku.brc.specify.plugins.ipadexporter.VerifyCollectionDlg.java

License:Open Source License

/**
 * /*w w  w  . j a  va  2s  .  co  m*/
 */
private void processResults() {
    //loadAndPushResourceBundle("stats");

    RelationshipType paleoRelType = isCollectionPaleo ? ExportPaleo.discoverPaleRelationshipType()
            : RelationshipType.eTypeError;

    boolean hasCritical = false;

    UIRegistry.setDoShowAllResStrErors(false);
    //logMsg("Verifying the Collection...");

    File tmpFile = ipadExporter.getConfigFile(VERIFY_XML);
    if (tmpFile != null && tmpFile.exists()) {
        Statement stmt0 = null;
        try {
            Element root = XMLHelper.readFileToDOM4J(tmpFile);
            if (root != null) {
                ArrayList<String> okMsgs = new ArrayList<String>();
                ArrayList<String> warnMsgs = new ArrayList<String>();
                ArrayList<String> criticalMsgs = new ArrayList<String>();
                int issueCnt = 0;

                String mainFont = "<font face='verdana' color='black'>";
                String headHTML = "<htmL><head></head><body bgcolor='#EEEEEE'>" + mainFont;
                StringBuilder sb = new StringBuilder(headHTML);
                htmlPane.setText(sb.toString() + "<BR><BR>Verifying collection...</font></body></html>");

                List<?> items = root.selectNodes("eval"); //$NON-NLS-1$

                stmt0 = DBConnection.getInstance().getConnection()
                        .createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_READ_ONLY);
                stmt0.setFetchSize(Integer.MIN_VALUE);

                for (Iterator<?> capIter = items.iterator(); capIter.hasNext();) {
                    Element fieldNode = (Element) capIter.next();
                    //String  name      = fieldNode.attributeValue("name"); //$NON-NLS-1$
                    String desc = fieldNode.attributeValue("desc"); //$NON-NLS-1$
                    String sql = fieldNode.getTextTrim();
                    String cond = fieldNode.attributeValue("cond");
                    String vStr = fieldNode.attributeValue("val");
                    String isFmt = fieldNode.attributeValue("fmt");
                    String stop = fieldNode.attributeValue("stop");
                    boolean doStop = stop != null && stop.equals("true");

                    String display = fieldNode.attributeValue("display");
                    boolean doDsp = display == null || display.equals("true");

                    String paleo = fieldNode.attributeValue("isPaleo");
                    boolean isPaleo = paleo != null && paleo.equals("true");
                    if (isPaleo && !isCollectionPaleo)
                        continue;

                    String paleoTypeStr = fieldNode.attributeValue("paleotype"); //$NON-NLS-1$
                    if (isCollectionPaleo && StringUtils.isNotEmpty(paleoTypeStr)) {
                        if (paleoRelType != paleoLookupHash.get(paleoTypeStr)) {
                            continue;
                        }
                    }

                    sql = ipadExporter.adjustSQL(sql);

                    Object rv = BasicSQLUtils.querySingleObj(sql);
                    Integer retVal = cnvToInt(rv);

                    boolean isError = false;
                    if (retVal != null && StringUtils.isNotEmpty(cond) && StringUtils.isNotEmpty(vStr)) {
                        Integer value = cnvToInt(vStr);
                        if (value != null) {
                            if (cond.equals(">")) {
                                isError = retVal.intValue() > value.intValue();
                            } else if (cond.equals("=")) {
                                isError = retVal.intValue() == value.intValue();
                            } else if (cond.equals("<")) {
                                isError = retVal.intValue() < value.intValue();
                            }
                        }
                    }
                    /*
                                            String fontSt = isError ? "<font color='"+(doStop ? "red" : "orange")+"'>" : "";
                                            String fontEn = isError ? "</font>" : "";
                                            if (StringUtils.isNotEmpty(isFmt) && isFmt.equalsIgnoreCase("true"))
                                            {
                                              sb.append(String.format("<LI>%s%s%s</LI>", fontSt, String.format(desc,  retVal), fontEn));
                                              issueCnt++;
                                            } else
                                            {
                                               sb.append(String.format("<LI>%s%s%s</LI>", fontSt, desc, fontEn));
                                               issueCnt++;
                                            }                        
                     */
                    String fullMsg;
                    if (StringUtils.isNotEmpty(isFmt) && isFmt.equalsIgnoreCase("true")) {
                        fullMsg = String.format(desc, retVal);
                    } else {
                        fullMsg = desc;
                    }

                    if (isError) {
                        if (doStop) {
                            criticalMsgs.add(fullMsg);
                            hasCritical = true;
                        } else {
                            warnMsgs.add(fullMsg);
                        }

                    } else if (doDsp) {
                        okMsgs.add(fullMsg);
                    }

                    issueCnt++;
                    //worker.firePropertyChange(PROGRESS, 0, cnt);
                }
                stmt0.close();

                sb = new StringBuilder(headHTML);
                if (issueCnt == 0) {
                    sb.append("<BR><BR>There were no issues to report.");
                } else {
                    listMsgs(sb, "Passed", okMsgs, "green", true);
                    listMsgs(sb, "Warnings", warnMsgs, "yellow", true);
                    listMsgs(sb, "Critical Errors - Cannot proceed.", criticalMsgs, "red", true);
                }
                sb.append(mainFont + "<BR>Verification Complete.<BR><BR></font></body></html>");

                htmlPane.setText(sb.toString());

                // For external report
                sb = new StringBuilder("<htmL><head><title>Collection Verification</title></head><body>");
                listMsgs(sb, "Passed", okMsgs, "green", false);
                listMsgs(sb, "Warnings", warnMsgs, "yellow", false);
                listMsgs(sb, "Critical Errors - Cannot proceed.", criticalMsgs, "red", false);
                sb.append("</body></html>");
                try {
                    TableWriter tblWriter = new TableWriter(reportPath, "Collection Verification Report", true);
                    tblWriter.println(sb.toString());
                    tblWriter.close();

                } catch (FileNotFoundException e) {
                    e.printStackTrace();
                } catch (UnsupportedEncodingException e) {
                    e.printStackTrace();
                }
            }

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

        } finally {
            try {
                if (stmt0 != null)
                    stmt0.close();
            } catch (Exception ex) {
            }
        }
    }
    okBtn.setEnabled(!hasCritical);
}

From source file:edu.ku.brc.specify.tools.datamodelgenerator.DatamodelGenerator.java

License:Open Source License

/**
 * Reads in file that provides listing of tables with their respective Id's and default views.
 * @return boolean true if reading of tableId file was successful.
 *///from  ww  w. j a va 2 s .c om
private boolean readTableMetadataFromFile(final String tableIdListingFilePath) {
    Hashtable<String, Boolean> abbrvHashLocal = new Hashtable<String, Boolean>();

    log.info("Preparing to read in Table and TableID listing from file: " + tableIdListingFilePath);
    try {
        File tableIdFile = new File(tableIdListingFilePath);
        FileInputStream fileInputStream = new FileInputStream(tableIdFile);
        SAXReader reader = new SAXReader();
        reader.setValidation(false);
        org.dom4j.Document doc = reader.read(fileInputStream);
        Element root = doc.getRootElement();
        Element dbNode = (Element) root.selectSingleNode("database");
        if (dbNode != null) {
            for (Iterator<?> i = dbNode.elementIterator("table"); i.hasNext();) {
                Element element = (Element) i.next();
                String tablename = element.attributeValue("name");
                String defaultView = element.attributeValue("view");
                String id = element.attributeValue("id");
                String abbrv = XMLHelper.getAttr(element, "abbrev", null);
                boolean isSearchable = XMLHelper.getAttr(element, "searchable", false);

                if (StringUtils.isNotEmpty(abbrv)) {
                    if (abbrvHashLocal.get(abbrv) == null) {
                        abbrvHashLocal.put(abbrv, true);
                    } else {
                        throw new RuntimeException(
                                "`abbrev` [" + abbrv + "]  or table[" + tablename + "] ids already in use.");
                    }

                } else {
                    throw new RuntimeException("`abbrev` is missing or empty for table[" + tablename + "]");
                }

                String busRule = "";
                Element brElement = (Element) element.selectSingleNode("businessrule");
                if (brElement != null) {
                    busRule = brElement.getTextTrim();
                }
                //log.debug("Creating TableMetaData and putting in tblMetaDataHashtable for name: " + tablename + " id: " + id + " defaultview: " + defaultView);

                TableMetaData tblMetaData = new TableMetaData(id, defaultView, createDisplay(element),
                        createFieldAliases(element), isSearchable, busRule, abbrv);
                tblMetaDataHash.put(tablename, tblMetaData);

                for (Iterator<?> ir = element.elementIterator("relationship"); ir.hasNext();) {
                    Element relElement = (Element) ir.next();
                    String relName = relElement.attributeValue("relationshipname");
                    boolean isLike = XMLHelper.getAttr(relElement, "likemanytoone", false);
                    tblMetaData.setIsLikeManyToOne(relName, isLike);
                }

            }

        } else {
            log.debug("Ill-formatted file for reading in Table and TableID listing.  Filename:"
                    + tableIdFile.getAbsolutePath());
        }
        fileInputStream.close();
        return true;

    } catch (Exception ex) {
        edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount();
        edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(DatamodelGenerator.class, ex);
        ex.printStackTrace();
        log.fatal(ex);
    }
    return false;

}

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

License:Open Source License

/**
 * //from   w w  w  .  ja  v a  2s . c  o  m
 */
protected void loadFieldsToSkip() {
    ClassDisplayInfo.setPackageName(packageName);

    try {
        Element root = XMLHelper.readFileToDOM4J(
                new File(UIRegistry.getDefaultWorkingPath() + File.separator + "config/ClassDisplayInfo.xml"));
        for (Object cls : root.selectNodes("/classes/class")) {
            Element clsElement = (Element) cls;
            String clsName = XMLHelper.getAttr(clsElement, "name", null);
            if (StringUtils.isNotEmpty(clsName)) {

                ClassDisplayInfo cdi = null;

                String linkField = XMLHelper.getAttr(clsElement, "linkfield", "");
                String indexField = XMLHelper.getAttr(clsElement, "indexfield", "");
                boolean useIdent = XMLHelper.getAttr(clsElement, "useindentity", false);

                try {
                    String fullName = packageName + clsName;
                    Class<?> clsObj = Class.forName(fullName);
                    Class<?> indexClass = getClassForField(clsObj, indexField);

                    cdi = new ClassDisplayInfo(clsName, clsObj, indexField, indexClass, linkField, useIdent);
                    classHash.put(clsName, cdi);

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

                Element titleEl = (Element) clsElement.selectSingleNode("title");
                if (titleEl != null) {
                    String getterStr = XMLHelper.getAttr(titleEl, "getter", null);
                    if (getterStr != null) {
                        try {
                            Class<?> getterCls = Class.forName(getterStr);
                            TitleGetterIFace titleGetter = (TitleGetterIFace) getterCls.newInstance();
                            cdi.setTitleGetter(titleGetter);

                        } catch (Exception ex) {

                        }
                    } else {
                        cdi.setTitleField(XMLHelper.getAttr(titleEl, "field", null));
                    }
                }

                for (Object fld : clsElement.selectNodes("skip/field")) {
                    Element fldElement = (Element) fld;
                    boolean isAvailForSearch = XMLHelper.getAttr(fldElement, "search", false);

                    cdi.addSkipped(new FieldDisplayInfo(fldElement.getTextTrim(), false, isAvailForSearch));
                }

                int inx = 0;
                for (Object fld : clsElement.selectNodes("order/field")) {
                    Element fldElement = (Element) fld;
                    String pickList = XMLHelper.getAttr(clsElement, "pl", "");
                    //boolean isAvailForSearch = XMLHelper.getAttr(fldElement, "skip", false);
                    boolean isForDisplay = XMLHelper.getAttr(fldElement, "display", true);

                    cdi.addOrdered(
                            new FieldDisplayInfo(inx, fldElement.getTextTrim(), pickList, isForDisplay, true));
                    inx++;
                }

                for (Object fld : clsElement.selectNodes("additional/field")) {
                    Element fldElement = (Element) fld;
                    String name = fldElement.getTextTrim();
                    String type = XMLHelper.getAttr(fldElement, "type", "");
                    String label = XMLHelper.getAttr(fldElement, "label", "");
                    String level = XMLHelper.getAttr(fldElement, "labellevel", "");

                    AdditionalDisplayField adf = new AdditionalDisplayField(inx, type, label, level, name);
                    cdi.addAdditional(adf);
                    inx++;
                }

                for (Object st : clsElement.selectNodes("stats/stat")) {
                    Element statElement = (Element) st;
                    String url = XMLHelper.getAttr(statElement, "url", null);
                    if (StringUtils.isNotEmpty(url)) {
                        cdi.addStat(new StatsDisplayInfo(url, statElement.getTextTrim()));
                    }
                }
            }
        }
        sortedClassList = new Vector<ClassDisplayInfo>(classHash.values());
        Collections.sort(sortedClassList);

    } catch (Exception ex) {
        log.error(ex);
        System.out.println(ex.toString());
    }
}

From source file:edu.ku.brc.stats.StatsMgr.java

License:Open Source License

/**
 * // ww w  . j av a2  s  .co  m
 */
@SuppressWarnings("unchecked")
private static void loadStatTooltips() {
    nameToToolTipHash.clear();

    boolean hasResBundle = false;
    if (StringUtils.isNotEmpty(StatsMgr.getResourceName())) {
        hasResBundle = UIRegistry.loadAndPushResourceBundle(StatsMgr.getResourceName()) != null;
    }

    try {
        Element dom = getDOM();
        if (dom != null) {
            for (Element element : (List<Element>) (dom.selectNodes("/statistics/stat"))) {
                String name = XMLHelper.getAttr(element, "name", null);
                if (name != null) {
                    String tooltipName = null;
                    Element el = (Element) element.selectSingleNode("chartinfo/tooltip");
                    if (el != null) {
                        tooltipName = el.getTextTrim();
                    } else {
                        el = (Element) element.selectSingleNode("tooltip");
                        if (el != null) {
                            tooltipName = el.getTextTrim();
                        }
                    }

                    if (tooltipName != null) {
                        nameToToolTipHash.put(name, UIRegistry.getResourceString(tooltipName));
                    }
                }
            }
        }

    } finally {
        if (hasResBundle) {
            UIRegistry.popResourceBundle();
        }
    }
}

From source file:edu.ku.brc.stats.StatsMgr.java

License:Open Source License

/**
 * Looks up statName and creates the appropriate SubPane.
 * @param statName the name of the stat to be displayed
 *///from www  .  j a  v a 2  s. co m
private JPanel createStatPaneInternal(final String statName) {
    if (StringUtils.isNotEmpty(resourceName)) {
        resBundle = UIRegistry.loadAndPushResourceBundle(resourceName);
    }

    try {
        String nameStr;
        String idStr = null;
        int inx = statName.indexOf(',');
        if (inx == -1) {
            nameStr = statName;
        } else {
            nameStr = statName.substring(0, inx);
            idStr = statName.substring(inx + 4, statName.length());
        }

        Element dom = getDOM();
        if (dom != null) {
            Element element = (Element) dom.selectSingleNode("/statistics/stat[@name='" + nameStr + "']");
            if (element != null) {
                String displayType = element.attributeValue(DISPLAY).toLowerCase();

                if (displayType.equalsIgnoreCase(BAR_CHART)) {
                    BarChartPanel barChart = new BarChartPanel();
                    createChart(nameStr, element, barChart, barChart, barChart);
                    return barChart;

                } else if (displayType.equalsIgnoreCase(PIE_CHART)) {
                    PieChartPanel pieChart = new PieChartPanel();
                    createChart(nameStr, element, pieChart, pieChart, pieChart);
                    return pieChart;

                } else if (displayType.equalsIgnoreCase(FORM)) {
                    createView(element, idStr);

                } else if (displayType.equals(TABLE)) {
                    Element sqlElement = (Element) element.selectSingleNode("sql");
                    if (sqlElement == null) {
                        throw new RuntimeException("sql element is null!");
                    }

                    Element titleElement = (Element) element.selectSingleNode("title");
                    if (titleElement == null) {
                        throw new RuntimeException("sql element is null!");
                    }

                    String tooltip = XMLHelper.getAttr((Element) element.selectSingleNode("tooltip"), "tooltip",
                            null);
                    if (tooltip != null) {
                        nameToToolTipHash.put(statName, tooltip);
                    }

                    StatsTask statTask = (StatsTask) ContextMgr.getTaskByName(StatsTask.STATISTICS);
                    SQLQueryPane queryPane = new SQLQueryPane(titleElement.getTextTrim(), statTask, true, true);
                    String sqlStr = sqlElement.getTextTrim();
                    if (idStr != null) {
                        int substInx = sqlStr.lastIndexOf("%s");
                        if (substInx > -1) {
                            sqlStr = sqlStr.substring(0, substInx - 1) + idStr
                                    + sqlStr.substring(substInx + 2, sqlStr.length());
                        } else {
                            log.error("Couldn't find the substitue string \"%s\" in [" + sqlStr + "]");
                        }

                        //sqlStr = String.format(sqlStr, new Object[] {idStr});
                    }
                    //System.out.println(sqlStr);
                    queryPane.setSQLStr(sqlStr);
                    queryPane.doQuery();
                    SubPaneMgr.getInstance().addPane(queryPane);

                } else {
                    // error
                    log.error("Wrong type of display [" + displayType + "] this type is not supported!");
                }
            }
        } else {
            log.error("DOM is NULL!!");
        }

    } finally {
        if (resBundle != null) {
            UIRegistry.popResourceBundle();
        }
    }

    return null;
}

From source file:edu.ku.brc.util.WebStoreAttachmentMgr.java

License:Open Source License

/**
 * @param webAssetFile/*w  ww .  j  a  v a  2s.com*/
 * @return
 */
private boolean getURLSFromStr(final String data) {
    try {
        Element root = XMLHelper.readStrToDOM4J(data);
        if (root != null) {
            for (Iterator<?> i = root.elementIterator("url"); i.hasNext();) //$NON-NLS-1$
            {
                Element urlNode = (Element) i.next();
                String type = urlNode.attributeValue("type"); //$NON-NLS-1$
                String urlStr = urlNode.getTextTrim();

                if (type.equals("read")) {
                    readURLStr = urlStr;

                } else if (type.equals("write")) {
                    writeURLStr = urlStr;

                } else if (type.equals("delete")) {
                    delURLStr = urlStr;

                } else if (type.equals("fileget")) {
                    fileGetURLStr = urlStr;

                } else if (type.equals("getmetadata")) {
                    fileGetMetaDataURLStr = urlStr;
                } else if (type.equals("testkey")) {
                    testKeyURLStr = urlStr;
                }
            }
        }
        return StringUtils.isNotEmpty(readURLStr) && StringUtils.isNotEmpty(writeURLStr)
                && StringUtils.isNotEmpty(delURLStr);

    } catch (Exception e) {
        e.printStackTrace();
    }
    return false;
}

From source file:edu.umd.cs.findbugs.PluginLoader.java

License:Open Source License

private void loadPluginComponents() throws PluginException {
    Document pluginDescriptor = getPluginDescriptor();
    List<Document> messageCollectionList = getMessageDocuments();
    List<Node> cloudNodeList = XMLUtil.selectNodes(pluginDescriptor, "/FindbugsPlugin/Cloud");
    for (Node cloudNode : cloudNodeList) {

        String cloudClassname = cloudNode.valueOf("@cloudClass");
        String cloudId = cloudNode.valueOf("@id");
        String usernameClassname = cloudNode.valueOf("@usernameClass");
        boolean onlineStorage = Boolean.valueOf(cloudNode.valueOf("@onlineStorage"));
        String propertiesLocation = cloudNode.valueOf("@properties");
        boolean disabled = Boolean.valueOf(cloudNode.valueOf("@disabled"))
                && !cloudId.equals(CloudFactory.DEFAULT_CLOUD);
        if (disabled) {
            continue;
        }//from w w  w  .  ja  v  a  2 s.  c  o m
        boolean hidden = Boolean.valueOf(cloudNode.valueOf("@hidden"))
                && !cloudId.equals(CloudFactory.DEFAULT_CLOUD);

        Class<? extends Cloud> cloudClass = getClass(classLoader, cloudClassname, Cloud.class);

        Class<? extends NameLookup> usernameClass = getClass(classLoader, usernameClassname, NameLookup.class);
        Node cloudMessageNode = findMessageNode(messageCollectionList,
                "/MessageCollection/Cloud[@id='" + cloudId + "']",
                "Missing Cloud description for cloud " + cloudId);
        String description = getChildText(cloudMessageNode, "Description").trim();
        String details = getChildText(cloudMessageNode, "Details").trim();
        PropertyBundle properties = new PropertyBundle();
        if (propertiesLocation != null && propertiesLocation.length() > 0) {
            URL properiesURL = classLoader.getResource(propertiesLocation);
            if (properiesURL == null) {
                continue;
            }
            properties.loadPropertiesFromURL(properiesURL);
        }
        List<Node> propertyNodes = XMLUtil.selectNodes(cloudNode, "Property");
        for (Node node : propertyNodes) {
            String key = node.valueOf("@key");
            String value = node.getText().trim();
            properties.setProperty(key, value);
        }

        CloudPlugin cloudPlugin = new CloudPluginBuilder().setFindbugsPluginId(plugin.getPluginId())
                .setCloudid(cloudId).setClassLoader(classLoader).setCloudClass(cloudClass)
                .setUsernameClass(usernameClass).setHidden(hidden).setProperties(properties)
                .setDescription(description).setDetails(details).setOnlineStorage(onlineStorage)
                .createCloudPlugin();
        plugin.addCloudPlugin(cloudPlugin);
    }

    // Create PluginComponents
    try {
        List<Node> componentNodeList = XMLUtil.selectNodes(pluginDescriptor, "/FindbugsPlugin/PluginComponent");
        for (Node componentNode : componentNodeList) {
            @DottedClassName
            String componentKindname = componentNode.valueOf("@componentKind");
            if (componentKindname == null) {
                throw new PluginException(
                        "Missing @componentKind for " + plugin.getPluginId() + " loaded from " + loadedFrom);
            }
            @DottedClassName
            String componentClassname = componentNode.valueOf("@componentClass");
            if (componentClassname == null) {
                throw new PluginException("Missing @componentClassname for " + plugin.getPluginId()
                        + " loaded from " + loadedFrom);
            }
            String componentId = componentNode.valueOf("@id");
            if (componentId == null) {
                throw new PluginException(
                        "Missing @id for " + plugin.getPluginId() + " loaded from " + loadedFrom);
            }

            try {
                String propertiesLocation = componentNode.valueOf("@properties");
                boolean disabled = Boolean.valueOf(componentNode.valueOf("@disabled"));

                Node filterMessageNode = findMessageNode(messageCollectionList,
                        "/MessageCollection/PluginComponent[@id='" + componentId + "']",
                        "Missing Cloud description for PluginComponent " + componentId);
                String description = getChildText(filterMessageNode, "Description").trim();
                String details = getChildText(filterMessageNode, "Details").trim();
                PropertyBundle properties = new PropertyBundle();
                if (propertiesLocation != null && propertiesLocation.length() > 0) {
                    URL properiesURL = classLoaderForResources.getResource(propertiesLocation);
                    if (properiesURL == null) {
                        AnalysisContext.logError("Could not load properties for " + plugin.getPluginId()
                                + " component " + componentId + " from " + propertiesLocation);
                        continue;
                    }
                    properties.loadPropertiesFromURL(properiesURL);
                }
                List<Node> propertyNodes = XMLUtil.selectNodes(componentNode, "Property");
                for (Node node : propertyNodes) {
                    String key = node.valueOf("@key");
                    String value = node.getText();
                    properties.setProperty(key, value);
                }

                Class<?> componentKind = classLoader.loadClass(componentKindname);
                loadComponentPlugin(plugin, componentKind, componentClassname, componentId, disabled,
                        description, details, properties);
            } catch (RuntimeException e) {
                AnalysisContext.logError("Unable to load ComponentPlugin " + componentId + " : "
                        + componentClassname + " implementing " + componentKindname, e);
            }
        }

        // Create FindBugsMains

        if (!FindBugs.isNoMains()) {
            List<Node> findBugsMainList = XMLUtil.selectNodes(pluginDescriptor, "/FindbugsPlugin/FindBugsMain");
            for (Node main : findBugsMainList) {
                String className = main.valueOf("@class");
                if (className == null) {
                    throw new PluginException("Missing @class for FindBugsMain in plugin" + plugin.getPluginId()
                            + " loaded from " + loadedFrom);
                }
                String cmd = main.valueOf("@cmd");
                if (cmd == null) {
                    throw new PluginException("Missing @cmd for for FindBugsMain in plugin "
                            + plugin.getPluginId() + " loaded from " + loadedFrom);
                }
                String kind = main.valueOf("@kind");
                boolean analysis = Boolean.valueOf(main.valueOf("@analysis"));
                Element mainMessageNode = (Element) findMessageNode(messageCollectionList,
                        "/MessageCollection/FindBugsMain[@cmd='" + cmd
                        // + " and @class='" + className
                                + "']/Description",
                        "Missing FindBugsMain description for cmd " + cmd);
                String description = mainMessageNode.getTextTrim();
                try {
                    Class<?> mainClass = classLoader.loadClass(className);
                    plugin.addFindBugsMain(mainClass, cmd, description, kind, analysis);
                } catch (Exception e) {
                    String msg = "Unable to load FindBugsMain " + cmd + " : " + className + " in plugin "
                            + plugin.getPluginId() + " loaded from " + loadedFrom;
                    PluginException e2 = new PluginException(msg, e);
                    AnalysisContext.logError(msg, e2);
                }
            }
        }

        List<Node> detectorNodeList = XMLUtil.selectNodes(pluginDescriptor, "/FindbugsPlugin/Detector");
        int detectorCount = 0;
        for (Node detectorNode : detectorNodeList) {
            String className = detectorNode.valueOf("@class");
            String speed = detectorNode.valueOf("@speed");
            String disabled = detectorNode.valueOf("@disabled");
            String reports = detectorNode.valueOf("@reports");
            String requireJRE = detectorNode.valueOf("@requirejre");
            String hidden = detectorNode.valueOf("@hidden");
            if (speed == null || speed.length() == 0) {
                speed = "fast";
            }
            // System.out.println("Found detector: class="+className+", disabled="+disabled);

            // Create DetectorFactory for the detector
            Class<?> detectorClass = null;
            if (!FindBugs.isNoAnalysis()) {
                detectorClass = classLoader.loadClass(className);

                if (!Detector.class.isAssignableFrom(detectorClass)
                        && !Detector2.class.isAssignableFrom(detectorClass)) {
                    throw new PluginException(
                            "Class " + className + " does not implement Detector or Detector2");
                }
            }
            DetectorFactory factory = new DetectorFactory(plugin, className, detectorClass,
                    !"true".equals(disabled), speed, reports, requireJRE);
            if (Boolean.valueOf(hidden).booleanValue()) {
                factory.setHidden(true);
            }
            factory.setPositionSpecifiedInPluginDescriptor(detectorCount++);
            plugin.addDetectorFactory(factory);

            // Find Detector node in one of the messages files,
            // to get the detail HTML.
            Node node = findMessageNode(messageCollectionList,
                    "/MessageCollection/Detector[@class='" + className + "']/Details",
                    "Missing Detector description for detector " + className);

            Element details = (Element) node;
            String detailHTML = details.getText();
            StringBuilder buf = new StringBuilder();
            buf.append("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\">\n");
            buf.append("<HTML><HEAD><TITLE>Detector Description</TITLE></HEAD><BODY>\n");
            buf.append(detailHTML);
            buf.append("</BODY></HTML>\n");
            factory.setDetailHTML(buf.toString());
        }
    } catch (ClassNotFoundException e) {
        throw new PluginException("Could not instantiate detector class: " + e, e);
    }

    // Create ordering constraints
    Node orderingConstraintsNode = pluginDescriptor.selectSingleNode("/FindbugsPlugin/OrderingConstraints");
    if (orderingConstraintsNode != null) {
        // Get inter-pass and intra-pass constraints
        List<Element> elements = XMLUtil.selectNodes(orderingConstraintsNode, "./SplitPass|./WithinPass");
        for (Element constraintElement : elements) {
            // Create the selectors which determine which detectors are
            // involved in the constraint
            DetectorFactorySelector earlierSelector = getConstraintSelector(constraintElement, plugin,
                    "Earlier");
            DetectorFactorySelector laterSelector = getConstraintSelector(constraintElement, plugin, "Later");

            // Create the constraint
            DetectorOrderingConstraint constraint = new DetectorOrderingConstraint(earlierSelector,
                    laterSelector);

            // Keep track of which constraints are single-source
            constraint.setSingleSource(earlierSelector instanceof SingleDetectorFactorySelector);

            // Add the constraint to the plugin
            if ("SplitPass".equals(constraintElement.getName())) {
                plugin.addInterPassOrderingConstraint(constraint);
            } else {
                plugin.addIntraPassOrderingConstraint(constraint);
            }
        }
    }

    // register global Category descriptions

    List<Node> categoryNodeListGlobal = XMLUtil.selectNodes(pluginDescriptor, "/FindbugsPlugin/BugCategory");
    for (Node categoryNode : categoryNodeListGlobal) {
        String key = categoryNode.valueOf("@category");
        if ("".equals(key)) {
            throw new PluginException("BugCategory element with missing category attribute");
        }
        BugCategory bc = plugin.addOrCreateBugCategory(key);

        boolean hidden = Boolean.valueOf(categoryNode.valueOf("@hidden"));
        if (hidden) {
            bc.setHidden(hidden);
        }
    }

    for (Document messageCollection : messageCollectionList) {
        List<Node> categoryNodeList = XMLUtil.selectNodes(messageCollection, "/MessageCollection/BugCategory");
        if (DEBUG) {
            System.out.println("found " + categoryNodeList.size() + " categories in " + plugin.getPluginId());
        }
        for (Node categoryNode : categoryNodeList) {
            String key = categoryNode.valueOf("@category");
            if ("".equals(key)) {
                throw new PluginException("BugCategory element with missing category attribute");
            }
            BugCategory bc = plugin.addOrCreateBugCategory(key);
            String shortDesc = getChildText(categoryNode, "Description");
            bc.setShortDescription(shortDesc);
            try {
                String abbrev = getChildText(categoryNode, "Abbreviation");
                if (bc.getAbbrev() == null) {
                    bc.setAbbrev(abbrev);
                    if (DEBUG) {
                        System.out.println("category " + key + " abbrev -> " + abbrev);
                    }
                } else if (DEBUG) {
                    System.out.println(
                            "rejected abbrev '" + abbrev + "' for category " + key + ": " + bc.getAbbrev());
                }
            } catch (PluginException pe) {
                if (DEBUG) {
                    System.out.println("missing Abbreviation for category " + key + "/" + shortDesc);
                    // do nothing else -- Abbreviation is required, but handle
                    // its omission gracefully
                }
            }
            try {
                String details = getChildText(categoryNode, "Details");
                if (bc.getDetailText() == null) {
                    bc.setDetailText(details);
                    if (DEBUG) {
                        System.out.println("category " + key + " details -> " + details);
                    }
                } else if (DEBUG) {
                    System.out.println("rejected details [" + details + "] for category " + key + ": ["
                            + bc.getDetailText() + ']');
                }
            } catch (PluginException pe) {
                // do nothing -- LongDescription is optional
            }

        }
    }

    // Create BugPatterns
    List<Node> bugPatternNodeList = XMLUtil.selectNodes(pluginDescriptor, "/FindbugsPlugin/BugPattern");
    for (Node bugPatternNode : bugPatternNodeList) {
        String type = bugPatternNode.valueOf("@type");
        String abbrev = bugPatternNode.valueOf("@abbrev");
        String category = bugPatternNode.valueOf("@category");
        boolean experimental = Boolean.parseBoolean(bugPatternNode.valueOf("@experimental"));

        // Find the matching element in messages.xml (or translations)
        String query = "/MessageCollection/BugPattern[@type='" + type + "']";
        Node messageNode = findMessageNode(messageCollectionList, query,
                "messages.xml missing BugPattern element for type " + type);
        Node bugsUrlNode = messageNode.getDocument()
                .selectSingleNode("/MessageCollection/Plugin/" + (experimental ? "AllBugsUrl" : "BugsUrl"));

        String bugsUrl = bugsUrlNode == null ? null : bugsUrlNode.getText();

        String shortDesc = getChildText(messageNode, "ShortDescription");
        String longDesc = getChildText(messageNode, "LongDescription");
        String detailText = getChildText(messageNode, "Details");
        int cweid = 0;
        try {
            String cweString = bugPatternNode.valueOf("@cweid");
            if (cweString.length() > 0) {
                cweid = Integer.parseInt(cweString);
            }
        } catch (RuntimeException e) {
            assert true; // ignore
        }

        BugPattern bugPattern = new BugPattern(type, abbrev, category, experimental, shortDesc, longDesc,
                detailText, bugsUrl, cweid);

        try {
            String deprecatedStr = bugPatternNode.valueOf("@deprecated");
            boolean deprecated = deprecatedStr.length() > 0 && Boolean.valueOf(deprecatedStr).booleanValue();
            if (deprecated) {
                bugPattern.setDeprecated(deprecated);
            }
        } catch (RuntimeException e) {
            assert true; // ignore
        }

        plugin.addBugPattern(bugPattern);

    }

    // Create BugCodes
    Set<String> definedBugCodes = new HashSet<String>();
    for (Document messageCollection : messageCollectionList) {
        List<Node> bugCodeNodeList = XMLUtil.selectNodes(messageCollection, "/MessageCollection/BugCode");
        for (Node bugCodeNode : bugCodeNodeList) {
            String abbrev = bugCodeNode.valueOf("@abbrev");
            if ("".equals(abbrev)) {
                throw new PluginException("BugCode element with missing abbrev attribute");
            }
            if (definedBugCodes.contains(abbrev)) {
                continue;
            }
            String description = bugCodeNode.getText();

            String query = "/FindbugsPlugin/BugCode[@abbrev='" + abbrev + "']";
            Node fbNode = pluginDescriptor.selectSingleNode(query);
            int cweid = 0;
            if (fbNode != null) {
                try {
                    cweid = Integer.parseInt(fbNode.valueOf("@cweid"));
                } catch (RuntimeException e) {
                    assert true; // ignore
                }
            }
            BugCode bugCode = new BugCode(abbrev, description, cweid);
            plugin.addBugCode(bugCode);
            definedBugCodes.add(abbrev);
        }

    }

    // If an engine registrar is specified, make a note of its classname
    Node node = pluginDescriptor.selectSingleNode("/FindbugsPlugin/EngineRegistrar");
    if (node != null) {
        String engineClassName = node.valueOf("@class");
        if (engineClassName == null) {
            throw new PluginException("EngineRegistrar element with missing class attribute");
        }

        try {
            Class<?> engineRegistrarClass = classLoader.loadClass(engineClassName);
            if (!IAnalysisEngineRegistrar.class.isAssignableFrom(engineRegistrarClass)) {
                throw new PluginException(
                        engineRegistrarClass + " does not implement IAnalysisEngineRegistrar");
            }

            plugin.setEngineRegistrarClass(
                    engineRegistrarClass.<IAnalysisEngineRegistrar>asSubclass(IAnalysisEngineRegistrar.class));
        } catch (ClassNotFoundException e) {
            throw new PluginException("Could not instantiate analysis engine registrar class: " + e, e);
        }

    }
    try {
        URL bugRankURL = getResource(BugRanker.FILENAME);

        if (bugRankURL == null) {
            // see
            // https://sourceforge.net/tracker/?func=detail&aid=2816102&group_id=96405&atid=614693
            // plugin can not have bugrank.txt. In this case, an empty
            // bugranker will be created
            if (DEBUG) {
                System.out.println("No " + BugRanker.FILENAME + " for plugin " + plugin.getPluginId());
            }
        }
        BugRanker ranker = new BugRanker(bugRankURL);
        plugin.setBugRanker(ranker);
    } catch (IOException e) {
        throw new PluginException("Couldn't parse \"" + BugRanker.FILENAME + "\"", e);
    }
}

From source file:edu.wustl.cab2b.common.util.ResultConfigurationParser.java

License:BSD License

/**
 * Method to parse Attribute values under entity tag and store them in map
 *///from ww  w  .j av  a 2s . co m

private void setElementData(List<Element> elementList, String parentMapKey) {
    for (Element entityElement : elementList) {
        String mapKey = parentMapKey;
        if (entityElement.attributeValue(NAME) != null) {
            mapKey = mapKey + KEY_DELIM + entityElement.attributeValue(NAME);
        }

        Element resultTransformer = entityElement.element(RESULT_TRANSFORMER);
        Element resultRenderer = entityElement.element(RESULT_RENDERER);
        Element dataListTransformer = entityElement.element(DATALIST_TRANSFORMERS);

        String resultTransformerValue = null;
        String resultRendererValue = null;

        if (resultTransformer != null) {
            resultTransformerValue = resultTransformer.getTextTrim();
        }

        if (resultRenderer != null) {
            resultRendererValue = resultRenderer.getTextTrim();
        }

        DataListTransformer dataListTransformerValue = null;
        if (dataListTransformer != null) {
            Element saverElem = dataListTransformer.element(DATALIST_SAVER);
            Element retrieverElem = dataListTransformer.element(DATALIST_RETRIEVER);

            dataListTransformerValue = new DataListTransformer(saverElem.getTextTrim(),
                    retrieverElem.getTextTrim());
        }

        EntityTransformerInfo entityAttributes = new EntityTransformerInfo(resultTransformerValue,
                resultRendererValue, dataListTransformerValue);

        applicationEntityNameMap.put(mapKey, entityAttributes);

    }
}

From source file:edu.wustl.cab2b.server.multimodelcategory.MmcValidator.java

License:BSD License

/**
 * Gets paths/*from   w  w w.ja  v a 2  s . co  m*/
 */
public void getPathsForPair(String pairsFileName, String consoleFile) {
    List<ClassPair> pairs = new ArrayList<ClassPair>();

    try {
        FileInputStream fileInputStream = new FileInputStream(pairsFileName);
        Document document = new SAXReader().read(fileInputStream);

        Element pairsElement = document.getRootElement();
        List<Element> pairElements = (List<Element>) pairsElement.elements("pair");
        for (Element pairElement : pairElements) {
            Element source = pairElement.element("source");
            Element target = pairElement.element("target");

            pairs.add(new ClassPair(source.getTextTrim(), target.getTextTrim()));
        }
    } catch (FileNotFoundException e) {
        throw new RuntimeException("Given Pairs XML file not found: " + pairsFileName, e);
    } catch (DocumentException e) {
        throw new RuntimeException("Unable to parse pairs XML file: " + pairsFileName, e);
    }

    /*
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.Participant", "edu.wustl.catissuecore.domain.Race"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.Participant", "edu.wustl.catissuecore.domain.SpecimenCollectionGroup"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.TissueSpecimen","edu.wustl.catissuecore.domain.EmbeddedEventParameters"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.TissueSpecimen","edu.wustl.catissuecore.domain.FixedEventParameters"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.TissueSpecimen","edu.wustl.catissuecore.domain.FrozenEventParameters"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.MolecularSpecimen","edu.wustl.catissuecore.domain.FrozenEventParameters"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.CellSpecimen","edu.wustl.catissuecore.domain.FrozenEventParameters"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.CellSpecimen","edu.wustl.catissuecore.domain.FixedEventParameters"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.FluidSpecimen","edu.wustl.catissuecore.domain.FrozenEventParameters"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.SpecimenCollectionGroup","edu.wustl.catissuecore.domain.TissueSpecimen"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.SpecimenCollectionGroup","edu.wustl.catissuecore.domain.MolecularSpecimen"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.SpecimenCollectionGroup","edu.wustl.catissuecore.domain.CellSpecimen"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.SpecimenCollectionGroup", "edu.wustl.catissuecore.domain.FluidSpecimen"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.CollectionProtocolRegistration", "edu.wustl.catissuecore.domain.User"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.CollectionProtocolRegistration", "edu.wustl.catissuecore.domain.CollectionProtocol"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.CollectionProtocol", "edu.wustl.catissuecore.domain.User"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.TissueSpecimen", "edu.wustl.catissuecore.domain.QuantityInMicrogram"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.Participant", "edu.wustl.catissuecore.domain.CollectionProtocolRegistration"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.TissueSpecimen", "edu.wustl.catissuecore.domain.SpecimenCharacteristics"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.MolecularSpecimen", "edu.wustl.catissuecore.domain.SpecimenCharacteristics"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.CellSpecimen", "edu.wustl.catissuecore.domain.SpecimenCharacteristics"));
    pairs.add(new ClassPair("edu.wustl.catissuecore.domain.FluidSpecimen", "edu.wustl.catissuecore.domain.SpecimenCharacteristics"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.sample.Sample", "gov.nih.nci.caarray.domain.hybridization.Hybridization"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.hybridization.Hybridization", "gov.nih.nci.caarray.domain.data.RawArrayData"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.data.RawArrayData", "gov.nih.nci.caarray.domain.project.Experiment"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.project.Experimen", "gov.nih.nci.caarray.domain.sample.Source"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.sample.Source", "gov.nih.nci.caarray.domain.vocabulary.Term"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.project.Experiment", "edu.georgetown.pir.Organism"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.project.Experimen", "gov.nih.nci.caarray.domain.array.ArrayDesign"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.array.ArrayDesign", "gov.nih.nci.caarray.domain.contact.Organization"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.project.Experiment", "gov.nih.nci.caarray.domain.sample.Source"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.sample.Source", "gov.nih.nci.caarray.domain.vocabulary.Term"));
    pairs.add(new ClassPair("gov.nih.nci.caarray.domain.project.Experiment", "gov.nih.nci.caarray.domain.array.ArrayDesign"));
    */

    try {
        redirectConsoleToFile(consoleFile);
    } catch (FileNotFoundException e) {
        throw new RuntimeException("Given path for console file in incorrect." + pairsFileName, e);
    }

    Collection<EntityGroupInterface> groups = cache.getEntityGroups();
    for (EntityGroupInterface eg : groups) {
        for (ClassPair pair : pairs) {
            getPaths(eg, pair);
        }
    }
}

From source file:eu.delving.metadata.RecordValidator.java

License:EUPL

private boolean validateElement(Element element, Path path, List<String> problems, Set<String> entries,
        Map<Path, Counter> counters) {
    path.push(Tag.create(element.getNamespacePrefix(), element.getName()));
    boolean hasElements = false;
    Iterator walk = element.elementIterator();
    while (walk.hasNext()) {
        Element subelement = (Element) walk.next();
        boolean remove = validateElement(subelement, path, problems, entries, counters);
        if (remove) {
            walk.remove();/*ww  w. java  2 s.co  m*/
        }
        hasElements = true;
    }
    if (!hasElements) {
        boolean fieldRemove = validatePath(element.getTextTrim(), path, problems, entries, counters);
        path.pop();
        return fieldRemove;
    }
    path.pop();
    return false;
}