Example usage for java.util.regex Matcher groupCount

List of usage examples for java.util.regex Matcher groupCount

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Introduction

In this page you can find the example usage for java.util.regex Matcher groupCount.

Prototype

public int groupCount()

Source Link

Document

Returns the number of capturing groups in this matcher's pattern.

Usage

From source file:com.bluexml.side.portal.alfresco.reverse.reverser.LayoutReverser.java

public void readAttributes(Map<String, String> properties, String string, int groupId, int groupValue) {
    Pattern regexpDiv = Pattern.compile(string);
    Matcher matcher = regexpDiv.matcher(currentLine);

    while (matcher.find()) {
        // System.out.println("MATCHS");
        String group = matcher.group();
        // System.out.println("\tgroup:" + group);
        int groupCount = matcher.groupCount();
        for (int i = 0; i <= groupCount; i++) {
            String group2 = matcher.group(i);
            // System.out.println("\tgroup (" + i + "):" + group2);
        }/*from  w  w  w.  j  av a 2s.  c  o m*/

        String attId = matcher.group(groupId);
        String attvalue = matcher.group(groupValue);

        properties.put(attId, attvalue);

    }
}

From source file:br.com.blackhubos.eventozero.util.Framework.java

/**
 * Converte a String feita do fromLocation(Location) devolta para uma localizao.
 *
 * @param serial O serial obtido no mtodo que transformou anteriormente a localizao em String.
 * @return retorna a Localizao convertida.
 *///from  ww  w. ja  v  a2 s. c o  m
public static Location toLocation(final String serial) {
    final Pattern pattern = Pattern.compile(
            "^World\\s*\\[([a-zA-Z0-9_-]+)\\]\\s*X\\s*\\[([0-9]+)\\]\\s*Y\\s*\\[([0-9]+)\\]\\s*Z\\s*\\[([0-9]+)\\](\\s*Yaw\\s*\\[([0-9\\.]+)\\]\\s*Pitch\\s*\\[([0-9\\.]+)\\])?");
    final Matcher m = pattern.matcher(serial);
    if (m.matches()) {
        if ((m.groupCount() >= 5) && (m.group(5) != null) && (m.group(6) != null) && (m.group(7) != null)) {
            return new Location(Framework.getWorld(m.group(1)), Framework.getInt(m.group(2)),
                    Framework.getInt(m.group(3)), Framework.getInt(m.group(4)), Framework.getFloat(m.group(6)),
                    Framework.getFloat(m.group(7)));
        } else {
            return new Location(Framework.getWorld(m.group(1)), Framework.getInt(m.group(2)),
                    Framework.getInt(m.group(3)), Framework.getInt(m.group(4)));
        }
    } else {
        return null;
    }
}

From source file:com.isecpartners.gizmo.FourthIdea.java

private String apply_macros(String command_string) {
    if (command_translation == null)
        return command_string;

    for (Object obj : command_translation.keySet()) {
        String key = (String) obj;
        String value = (String) command_translation.get(key);
        String regex = "^([\\s]*\\" + key + ").*";
        // so the goal here is to substitute the pattern *only* if it shows up first
        // and ignore trailing spaces.  i want to take the first group, remove that
        // and then prepend the replacement string to what's left.
        Matcher match = Pattern.compile(regex).matcher(command_string);
        if (match.matches()) {
            if (match.groupCount() != 1)
                break;

            String found_str = match.group(1);
            int end_of_match = command_string.indexOf(found_str) + found_str.length();
            command_string = value + " " + command_string.substring(end_of_match + 1);
        }//w ww.  java  2s .co  m
        command_string = Pattern.compile(key).matcher(command_string).replaceAll(value);
    }

    return command_string;
}

From source file:br.com.blackhubos.eventozero.util.Framework.java

public static void printGroups(final Pattern pattern, final String literal) {
    final Matcher matcher = pattern.matcher(literal);
    if (matcher.find()) {
        for (int i = 1; i <= matcher.groupCount(); i++) {
            System.out.println("Group " + i + ":  \""
                    + (matcher.group(i) != null ? matcher.group(i) : "(no encontrado)") + "\"");
        }//from   ww  w.ja  v a  2s .c  o  m
    }
}

From source file:fr.smile.liferay.LiferayUrlRewriter.java

/**
 * Fix all resources urls and return the result.
 *
 * @param input        The original charSequence to be processed.
 * @param requestUrl   The request URL.// ww  w.j  a v  a2 s  .c o m
 * @param baseUrlParam The base URL selected for this request.
 * @return the result of this renderer.
 */
public CharSequence rewriteHtml(CharSequence input, String requestUrl, Pattern pattern, String baseUrlParam,
        String visibleBaseUrl) {
    if (LOG.isDebugEnabled()) {
        LOG.debug("input=" + input);
        LOG.debug("rewriteHtml (requestUrl=" + requestUrl + ", pattern=" + pattern + ",baseUrlParam)"
                + baseUrlParam + ",strVisibleBaseUrl=" + visibleBaseUrl + ")");
    }

    StringBuffer result = new StringBuffer(input.length());
    Matcher m = pattern.matcher(input);
    while (m.find()) {
        if (LOG.isTraceEnabled()) {
            LOG.trace("found match: " + m);
        }
        String url = input.subSequence(m.start(3) + 1, m.end(3) - 1).toString();
        url = rewriteUrl(url, requestUrl, baseUrlParam, visibleBaseUrl);
        url = url.replaceAll("\\$", "\\\\\\$"); // replace '$' -> '\$' as it
        // denotes group
        StringBuffer tagReplacement = new StringBuffer("<$1$2=\"").append(url).append("\"");
        if (m.groupCount() > 3) {
            tagReplacement.append("$4");
        }
        tagReplacement.append('>');
        if (LOG.isTraceEnabled()) {
            LOG.trace("replacement: " + tagReplacement);
        }
        m.appendReplacement(result, tagReplacement.toString());
    }
    m.appendTail(result);

    return result;
}

From source file:guru.qas.martini.jmeter.sampler.MartiniSampler.java

protected SampleResult getSubResult(Step step, Method method, Pattern pattern) {
    String label = getLabel(step);
    SampleResult result = new SampleResult();
    result.setSuccessful(true);/*from www  . ja v a2  s  .com*/
    result.sampleStart();

    SamplerContext samplerContext = new SamplerContext(super.getThreadContext());

    try {
        ApplicationContext applicationContext = this.getApplicationContext();
        Parameter[] parameters = method.getParameters();
        Object[] arguments = new Object[parameters.length];

        if (parameters.length > 0) {
            String text = step.getText();
            Matcher matcher = pattern.matcher(text);
            checkState(matcher.find(), "unable to locate substitution parameters for pattern %s with input %s",
                    pattern.pattern(), text);

            ConversionService conversionService = applicationContext.getBean(ConversionService.class);

            int groupCount = matcher.groupCount();
            for (int i = 0; i < groupCount; i++) {
                String parameterAsString = matcher.group(i + 1);
                Parameter parameter = parameters[i];
                Class<?> parameterType = parameter.getType();
                Object converted = conversionService.convert(parameterAsString, parameterType);
                arguments[i] = converted;
            }
        }

        samplerContext.setStatus(Status.PASSED);
        Class<?> declaringClass = method.getDeclaringClass();
        Object bean = applicationContext.getBean(declaringClass);
        Object returnValue = method.invoke(bean, arguments);
        if (HttpEntity.class.isInstance(returnValue)) {
            HttpEntity entity = HttpEntity.class.cast(returnValue);
            samplerContext.setHttpEntities(Collections.singleton(entity));
        }
    } catch (Exception e) {
        samplerContext.setStatus(Status.FAILED);
        samplerContext.setException(e);
        result.setSuccessful(false);
        label = "FAIL: " + label;
    } finally {
        result.sampleEnd();
        result.setSampleLabel(label);
    }
    return result;
}

From source file:gtu._work.ui.RegexCatchReplacer_Ebao.java

/**
 * @param fromPattern//ww  w .  j a va  2  s  . c  o m
 *            ???pattern
 * @param toFormat
 *            ??pattern
 * @param replaceText
 *            ??
 */
void replacer(String fromPattern, String toFormat, String replaceText) {
    try {
        Pattern pattern = Pattern.compile(fromPattern);
        Matcher matcher = pattern.matcher(replaceText);
        Map<String, Integer> tmap = new LinkedHashMap<String, Integer>();
        String tempStr = null;
        for (; matcher.find();) {
            tempStr = toFormat.toString();
            for (int ii = 0; ii <= matcher.groupCount(); ii++) {
                System.out.println(ii + " -- " + matcher.group(ii));
                tempStr = tempStr.replaceAll("#" + ii + "#", Matcher.quoteReplacement(matcher.group(ii)));
                if (!tmap.containsKey(tempStr)) {
                    tmap.put(tempStr, 0);
                }
                tmap.put(tempStr, tmap.get(tempStr) + 1);
            }
        }
        DefaultTableModel model = JTableUtil.createModel(true, "match", "count");
        for (String str : tmap.keySet()) {
            model.addRow(new Object[] { str, tmap.get(str) });
        }
        setTitle("total : " + model.getRowCount());
        resultArea.setModel(model);

        // ebao?
        JTableUtil resultAreaUtil = JTableUtil.newInstance(resultArea);
        DefaultTableModel model2 = JTableUtil.createModel(true, "msgId", "Label");
        boolean isExactSearch = exactEbaoSearchChk.isSelected();
        ebaoTable.setModel(model2);
        for (int ii = 0; ii < model.getRowCount(); ii++) {
            String msgId = (String) resultAreaUtil.getRealValueAt(ii, 0);
            callEbaoMsgId(msgId, isExactSearch);
        }
    } catch (Exception ex) {
        JOptionPaneUtil.newInstance().iconErrorMessage().showMessageDialog(ex.getMessage(), getTitle());
        ex.printStackTrace();
    }
}

From source file:org.commoncrawl.mapred.pipelineV3.domainmeta.blogs.postfrequency.ScanDatabaseStep.java

@Override
public void map(TextBytes key, TextBytes jsonMetadata, OutputCollector<TextBytes, HitsByMonth> collector,
        Reporter reporter) throws IOException {

    String url = key.toString();//w  w  w . j a  va2s  .  c  om

    Matcher topLevelMatcher = topLevelBlogPattern.matcher(url);
    Matcher nestedBlogMatcher = nestedBlogPattern.matcher(url);
    Matcher indexHTMLBlogMatcher = indexHTMLBlogPattern.matcher(url);
    Matcher indexBlogMatcher = indexBlogPattern.matcher(url);
    Matcher nestedIndexHTMLBlogMatcher = nestedIndexHTMLBlogPattern.matcher(url);
    Matcher nestedIndexBlogMatcher = nestedIndexBlogPattern.matcher(url);
    Matcher tumblrPostMatcher = tumblrStyleBlogPattern.matcher(url);

    if (indexHTMLBlogMatcher.matches() && indexHTMLBlogMatcher.groupCount() >= 1) {
        reporter.incrCounter(Counters.MATCHED_INDEX_HTML_PATTERN, 1);
        HitsByMonth hits = new HitsByMonth();
        hits.setFlags(PostFrequencyInfo.Flags.HAS_INDEX_HTML_AFTER_DATE);
        collector.collect(new TextBytes("http://" + indexHTMLBlogMatcher.group(1) + "/"), hits);
    } else if (indexBlogMatcher.matches() && indexBlogMatcher.groupCount() >= 1) {
        reporter.incrCounter(Counters.MATCHED_INDEX_PATTERN, 1);
        HitsByMonth hits = new HitsByMonth();
        hits.setFlags(PostFrequencyInfo.Flags.HAS_YEAR_MONTH_SLASH_INDEX);
        collector.collect(new TextBytes("http://" + indexBlogMatcher.group(1) + "/"), hits);
    } else if (nestedIndexHTMLBlogMatcher.matches() && nestedIndexHTMLBlogMatcher.groupCount() >= 2) {
        reporter.incrCounter(Counters.MATCHED_NESTED_INDEX_HTML_PATTERN, 1);
        HitsByMonth hits = new HitsByMonth();
        hits.setFlags(PostFrequencyInfo.Flags.HAS_INDEX_HTML_AFTER_DATE);
        collector.collect(new TextBytes("http://" + nestedIndexHTMLBlogMatcher.group(1) + "/"
                + nestedIndexHTMLBlogMatcher.group(2) + "/"), hits);
    } else if (nestedIndexBlogMatcher.matches() && nestedIndexBlogMatcher.groupCount() >= 2) {
        reporter.incrCounter(Counters.MATCHED_NESTED_INDEX_PATTERN, 1);
        HitsByMonth hits = new HitsByMonth();
        hits.setFlags(PostFrequencyInfo.Flags.HAS_YEAR_MONTH_SLASH_INDEX);
        collector.collect(new TextBytes(
                "http://" + nestedIndexBlogMatcher.group(1) + "/" + nestedIndexBlogMatcher.group(2) + "/"),
                hits);
    } else if (tumblrPostMatcher.matches() && tumblrPostMatcher.groupCount() >= 2) {
        reporter.incrCounter(Counters.MATCHED_TUMBLR_BLOG_POST_PATTERN, 1);

        String uniqueURL = new String("http://" + tumblrPostMatcher.group(1) + "/");

        try {
            // HACK
            long postId = Long.parseLong(tumblrPostMatcher.group(2));
            long relativeMonth = postId / 1000000000L;
            Date dateStart = new Date(110, 6, 1);
            Date dateOfPost = new Date(dateStart.getTime() + (relativeMonth * 30 * 24 * 60 * 60 * 1000));

            HitsByMonth hits = new HitsByMonth();
            hits.setHitCount(1);
            hits.setYear(dateOfPost.getYear() + 1900);
            hits.setMonth(dateOfPost.getMonth() + 1);

            collector.collect(new TextBytes(uniqueURL), hits);
        } catch (Exception e) {
            reporter.incrCounter(Counters.CAUGHT_EXCEPTION_DURING_TUMBLR_POST_PARSE, 1);
            LOG.error("Exception parsing url:" + url + " Exception:" + StringUtils.stringifyException(e));
        }

    } else if (topLevelMatcher.matches() && topLevelMatcher.groupCount() >= 3) {

        reporter.incrCounter(Counters.MATCHED_TOP_LEVEL_POST_PATTERN, 1);

        String uniqueURL = new String("http://" + topLevelMatcher.group(1) + "/");
        int year = Integer.parseInt(topLevelMatcher.group(2));
        int month = Integer.parseInt(topLevelMatcher.group(3));

        HitsByMonth hits = new HitsByMonth();
        hits.setHitCount(1);
        hits.setYear(year);
        hits.setMonth(month);

        hits.setFlags(scanForGenerator(key, jsonMetadata, reporter));

        collector.collect(new TextBytes(uniqueURL), hits);
    } else if (nestedBlogMatcher.matches() && nestedBlogMatcher.groupCount() >= 4) {

        reporter.incrCounter(Counters.MATCHED_NESTED_POST_PATTERN, 1);

        if (!nestedBlogMatcher.group(1).endsWith("tumblr.com")) {
            String uniqueURL = new String(
                    "http://" + nestedBlogMatcher.group(1) + "/" + nestedBlogMatcher.group(2) + "/");

            int year = Integer.parseInt(nestedBlogMatcher.group(3));
            int month = Integer.parseInt(nestedBlogMatcher.group(4));

            HitsByMonth hits = new HitsByMonth();
            hits.setHitCount(1);
            hits.setYear(year);
            hits.setMonth(month);

            hits.setFlags(scanForGenerator(key, jsonMetadata, reporter));

            collector.collect(new TextBytes(uniqueURL), hits);
        }
    }

}

From source file:net.sf.logsaw.dialect.websphere.WebsphereDialect.java

@Override
public void parse(ILogResource log, InputStream input, ILogEntryCollector collector) throws CoreException {
    Assert.isNotNull(log, "log"); //$NON-NLS-1$
    Assert.isNotNull(input, "input"); //$NON-NLS-1$
    Assert.isNotNull(collector, "collector"); //$NON-NLS-1$
    Assert.isTrue(isConfigured(), "Dialect should be configured by now"); //$NON-NLS-1$
    try {/*from  w ww  .java  2s  .  co  m*/
        LogEntry currentEntry = null;
        IHasEncoding enc = (IHasEncoding) log.getAdapter(IHasEncoding.class);
        IHasLocale loc = (IHasLocale) log.getAdapter(IHasLocale.class);
        // WebSphere Dialect doesn't need to care about the timezone, because it is encoded in the log messages
        DateFormat df = getDateFormat(loc.getLocale());
        LineIterator iter = IOUtils.lineIterator(input, enc.getEncoding());
        int lineNo = 0;
        try {
            while (iter.hasNext()) {
                // Error handling
                lineNo++;
                List<IStatus> statuses = null;
                boolean fatal = false; // determines whether to interrupt parsing

                String line = iter.nextLine();
                Matcher m = getInternalPattern().matcher(line);
                if (m.find()) {
                    // The next line matches, so flush the previous entry and continue
                    if (currentEntry != null) {
                        collector.collect(currentEntry);
                        currentEntry = null;
                    }
                    currentEntry = new LogEntry();
                    for (int i = 0; i < m.groupCount(); i++) {
                        try {
                            extractField(currentEntry, i + 1, m.group(i + 1), df);
                        } catch (CoreException e) {
                            // Mark for interruption
                            fatal = fatal || e.getStatus().matches(IStatus.ERROR);

                            // Messages will be displayed later
                            if (statuses == null) {
                                statuses = new ArrayList<IStatus>();
                            }
                            if (e.getStatus().isMultiStatus()) {
                                Collections.addAll(statuses, e.getStatus().getChildren());
                            } else {
                                statuses.add(e.getStatus());
                            }
                        }
                    }

                    // We encountered errors or warnings
                    if (statuses != null && !statuses.isEmpty()) {
                        currentEntry = null; // Stop propagation
                        IStatus status = new MultiStatus(WebsphereDialectPlugin.PLUGIN_ID, 0,
                                statuses.toArray(new IStatus[statuses.size()]),
                                NLS.bind(Messages.WebsphereDialect_error_failedToParseLine, lineNo), null);
                        if (fatal) {
                            // Interrupt parsing in case of error
                            throw new CoreException(status);
                        } else {
                            collector.addMessage(status);
                        }
                    }
                } else if (currentEntry != null) {
                    // Append to message
                    String msg = currentEntry.get(getFieldProvider().getMessageField());
                    StringWriter strWriter = new StringWriter();
                    PrintWriter printWriter = new PrintWriter(strWriter);
                    printWriter.print(msg);
                    printWriter.println();
                    printWriter.print(line);
                    currentEntry.put(getFieldProvider().getMessageField(), strWriter.toString());
                }

                if (collector.isCanceled()) {
                    // Cancel parsing
                    break;
                }
            }

            if (currentEntry != null) {
                // Collect left over entry
                collector.collect(currentEntry);
            }
        } finally {
            LineIterator.closeQuietly(iter);
        }
    } catch (Exception e) {
        throw new CoreException(new Status(IStatus.ERROR, WebsphereDialectPlugin.PLUGIN_ID,
                NLS.bind(Messages.WebsphereDialect_error_failedToParseFile,
                        new Object[] { log.getName(), e.getLocalizedMessage() }),
                e));
    }
}

From source file:com.cdd.bao.importer.KeywordMapping.java

public JSONObject createAssay(JSONObject keydata, Schema schema, Map<Schema.Assignment, SchemaTree> treeCache)
        throws JSONException, IOException {
    String uniqueID = null;//  w  w  w . j a v  a2  s  .  c o  m
    List<String> linesTitle = new ArrayList<>(), linesBlock = new ArrayList<>();
    List<String> linesSkipped = new ArrayList<>(), linesProcessed = new ArrayList<>();
    Set<String> gotAnnot = new HashSet<>(), gotLiteral = new HashSet<>();
    JSONArray jsonAnnot = new JSONArray();
    final String SEP = "::";

    // assertions: these always supply a term
    for (Assertion asrt : assertions) {
        JSONObject obj = new JSONObject();
        obj.put("propURI", ModelSchema.expandPrefix(asrt.propURI));
        obj.put("groupNest", new JSONArray(expandPrefixes(asrt.groupNest)));
        obj.put("valueURI", ModelSchema.expandPrefix(asrt.valueURI));
        jsonAnnot.put(obj);

        String hash = asrt.propURI + SEP + asrt.valueURI + SEP
                + (asrt.groupNest == null ? "" : String.join(SEP, asrt.groupNest));
        gotAnnot.add(hash);
    }

    // go through the columns one at a time
    for (String key : keydata.keySet()) {
        String data = keydata.getString(key);

        Identifier id = findIdentifier(key);
        if (id != null) {
            if (uniqueID == null)
                uniqueID = id.prefix + data;
            continue;
        }

        TextBlock tblk = findTextBlock(key);
        if (tblk != null) {
            if (Util.isBlank(tblk.title))
                linesTitle.add(data);
            else
                linesBlock.add(tblk.title + ": " + data);
        }

        Value val = findValue(key, data);
        if (val != null) {
            if (Util.isBlank(val.valueURI)) {
                linesSkipped.add(key + ": " + data);
            } else {
                String hash = val.propURI + SEP + val.valueURI + SEP
                        + (val.groupNest == null ? "" : String.join(SEP, val.groupNest));
                if (gotAnnot.contains(hash))
                    continue;

                JSONObject obj = new JSONObject();
                obj.put("propURI", ModelSchema.expandPrefix(val.propURI));
                obj.put("groupNest", new JSONArray(expandPrefixes(val.groupNest)));
                obj.put("valueURI", ModelSchema.expandPrefix(val.valueURI));
                jsonAnnot.put(obj);
                gotAnnot.add(hash);
                linesProcessed.add(key + ": " + data);
            }
            continue;
        }

        Literal lit = findLiteral(key, data);
        if (lit != null) {
            String hash = lit.propURI + SEP + (lit.groupNest == null ? "" : String.join(SEP, lit.groupNest))
                    + SEP + data;
            if (gotLiteral.contains(hash))
                continue;

            JSONObject obj = new JSONObject();
            obj.put("propURI", ModelSchema.expandPrefix(lit.propURI));
            obj.put("groupNest", new JSONArray(expandPrefixes(lit.groupNest)));
            obj.put("valueLabel", data);
            jsonAnnot.put(obj);
            gotLiteral.add(hash);
            linesProcessed.add(key + ": " + data);

            continue;
        }

        Reference ref = findReference(key, data);
        if (ref != null) {
            Pattern ptn = Pattern.compile(ref.valueRegex);
            Matcher m = ptn.matcher(data);
            if (!m.matches() || m.groupCount() < 1)
                throw new IOException(
                        "Pattern /" + ref.valueRegex + "/ did not match '" + data + "' to produce a group.");

            JSONObject obj = new JSONObject();
            obj.put("propURI", ModelSchema.expandPrefix(ref.propURI));
            obj.put("groupNest", new JSONArray(expandPrefixes(ref.groupNest)));
            obj.put("valueLabel", ref.prefix + m.group(1));
            jsonAnnot.put(obj);
            linesProcessed.add(key + ": " + data);

            continue;
        }

        // probably shouldn't get this far, but just in case
        linesSkipped.add(key + ": " + data);
    }

    // annotation collapsing: sometimes there's a branch sequence that should exclude parent nodes
    for (int n = 0; n < jsonAnnot.length(); n++) {
        JSONObject obj = jsonAnnot.getJSONObject(n);
        String propURI = obj.getString("propURI"), valueURI = obj.optString("valueURI");
        if (valueURI == null)
            continue;
        String[] groupNest = obj.getJSONArray("groupNest").toStringArray();
        Schema.Assignment[] assnList = schema.findAssignmentByProperty(ModelSchema.expandPrefix(propURI),
                groupNest);
        if (assnList.length == 0)
            continue;
        SchemaTree tree = treeCache.get(assnList[0]);
        if (tree == null)
            continue;

        Set<String> exclusion = new HashSet<>();
        for (SchemaTree.Node node = tree.getNode(valueURI); node != null; node = node.parent)
            exclusion.add(node.uri);
        if (exclusion.size() == 0)
            continue;

        for (int i = jsonAnnot.length() - 1; i >= 0; i--)
            if (i != n) {
                obj = jsonAnnot.getJSONObject(i);
                if (!obj.has("valueURI"))
                    continue;
                if (!propURI.equals(obj.getString("propURI")))
                    continue;
                if (!Objects.deepEquals(groupNest, obj.getJSONArray("groupNest").toStringArray()))
                    continue;
                if (!exclusion.contains(obj.getString("valueURI")))
                    continue;
                jsonAnnot.remove(i);
            }
    }

    /*String text = "";
    if (linesBlock.size() > 0) text += String.join("\n", linesBlock) + "\n\n";
    if (linesSkipped.size() > 0) text += "SKIPPED:\n" + String.join("\n", linesSkipped) + "\n\n";
    text += "PROCESSED:\n" + String.join("\n", linesProcessed);*/

    List<String> sections = new ArrayList<>();
    if (linesTitle.size() > 0)
        sections.add(String.join(" / ", linesTitle));
    if (linesBlock.size() > 0)
        sections.add(String.join("\n", linesBlock));
    sections.add("#### IMPORTED ####");
    if (linesSkipped.size() > 0)
        sections.add("SKIPPED:\n" + String.join("\n", linesSkipped));
    if (linesProcessed.size() > 0)
        sections.add("PROCESSED:\n" + String.join("\n", linesProcessed));
    String text = String.join("\n\n", sections);

    JSONObject assay = new JSONObject();
    assay.put("uniqueID", uniqueID);
    assay.put("text", text);
    assay.put("schemaURI", schema.getSchemaPrefix());
    assay.put("annotations", jsonAnnot);
    return assay;
}