Examples with SDocument org.corpus_tools.salt.common.SDocument used on opensource projects

Example 1 with SDocument

use of org.corpus_tools.salt.common.SDocument in project ANNIS by korpling.

the class CorefVisualizer method writeOutput.

/**
 * writes Output for the CorefVisualizer
 * @param writer writer to write with
 */
@Override
public void writeOutput(VisualizerInput input, Writer w) {
    // root html element
    Html html = new Html();
    Head head = new Head();
    Body body = new Body();
    html.removeXmlns();
    html.appendChild(head);
    html.appendChild(body);
    try {
        LinkedList<String> fonts = new LinkedList<String>();
        if (input.getFont() != null) {
            Link linkFont = new Link();
            linkFont.setHref(input.getFont().getUrl());
            head.appendChild(linkFont);
            fonts.add(input.getFont().getName());
        }
        fonts.add("serif");
        Link linkJQueryUI = new Link();
        linkJQueryUI.setHref(input.getResourcePath("coref/jquery-ui-1.11.4.custom/jquery-ui.min.css"));
        linkJQueryUI.setRel("stylesheet");
        linkJQueryUI.setType("text/css");
        head.appendChild(linkJQueryUI);
        Link linkJQueryUIStructure = new Link();
        linkJQueryUIStructure.setHref(input.getResourcePath("coref/jquery-ui-1.11.4.custom/jquery-ui.structure.min.css"));
        linkJQueryUIStructure.setRel("stylesheet");
        linkJQueryUIStructure.setType("text/css");
        head.appendChild(linkJQueryUIStructure);
        Script scriptJquery = new Script("text/javascript");
        scriptJquery.setSrc(input.getResourcePath("coref/jquery.js"));
        head.appendChild(scriptJquery);
        Script scriptUI = new Script("text/javascript");
        scriptUI.setSrc(input.getResourcePath("coref/jquery-ui-1.11.4.custom/jquery-ui.min.js"));
        head.appendChild(scriptUI);
        Link linkCoref = new Link();
        linkCoref.setHref(input.getResourcePath("coref/coref.css"));
        linkCoref.setRel("stylesheet");
        linkCoref.setType("text/css");
        head.appendChild(linkCoref);
        Script scriptCoref = new Script("text/javascript");
        scriptCoref.setSrc(input.getResourcePath("coref/CorefVisualizer.js"));
        head.appendChild(scriptCoref);
        body.setStyle("font-family: '" + StringUtils.join(fonts, "', '") + "';");
        // get Info
        globalIndex = 0;
        tokensOfNode = new HashMap<String, List<String>>();
        referentList = new LinkedList<TReferent>();
        komponent = new LinkedList<TComponent>();
        referentOfToken = new HashMap<String, HashMap<Long, Integer>>();
        componentOfToken = new HashMap<String, List<Long>>();
        componenttype = new LinkedList<TComponenttype>();
        SDocument saltDoc = input.getDocument();
        SDocumentGraph saltGraph = saltDoc.getDocumentGraph();
        if (saltGraph == null) {
            body.setText("An Error occured: Could not get Graph of Result (Graph == null).");
            return;
        }
        List<SRelation<SNode, SNode>> edgeList = saltGraph.getRelations();
        if (edgeList == null) {
            return;
        }
        for (SRelation rawRel : edgeList) {
            if (includeEdge(rawRel, input.getNamespace())) {
                SPointingRelation rel = (SPointingRelation) rawRel;
                String relType = componentNameForRelation(rel);
                visitedNodes = new LinkedList<String>();
                // got type for this?
                boolean gotIt = false;
                int componentnr;
                for (componentnr = 0; componentnr < componenttype.size(); componentnr++) {
                    if (componenttype.get(componentnr) != null && componenttype.get(componentnr).type != null && componenttype.get(componentnr).nodeList != null && componenttype.get(componentnr).type.equals(relType) && componenttype.get(componentnr).nodeList.contains(rel.getSource().getId())) {
                        gotIt = true;
                        break;
                    }
                }
                TComponent currentComponent;
                TComponenttype currentComponenttype;
                if (gotIt) {
                    currentComponent = komponent.get(componentnr);
                    currentComponenttype = componenttype.get(componentnr);
                } else {
                    currentComponenttype = new TComponenttype();
                    currentComponenttype.type = relType;
                    componenttype.add(currentComponenttype);
                    componentnr = komponent.size();
                    currentComponent = new TComponent();
                    currentComponent.type = relType;
                    currentComponent.tokenList = new LinkedList<String>();
                    komponent.add(currentComponent);
                    currentComponenttype.nodeList.add(rel.getSource().getId());
                }
                TReferent ref = new TReferent();
                ref.annotations = new HashSet<SerializableAnnotation>();
                for (SAnnotation anno : rel.getAnnotations()) {
                    ref.annotations.add(new SerializableAnnotation(anno));
                }
                ref.component = componentnr;
                referentList.add(ref);
                List<String> currentTokens = getAllTokens(rel.getSource(), componentNameForRelation(rel), currentComponenttype, componentnr, input.getNamespace());
                // neu
                setReferent(rel.getTarget(), globalIndex, 0);
                // neu
                setReferent(rel.getSource(), globalIndex, 1);
                for (String s : currentTokens) {
                    if (!currentComponent.tokenList.contains(s)) {
                        currentComponent.tokenList.add(s);
                    }
                }
                globalIndex++;
            }
        }
        colorlist = new HashMap<Integer, Integer>();
        // A list containing all the generated HTML elements, one list entry
        // for each text.
        List<List<Node>> nodesPerText = new LinkedList<List<Node>>();
        // write output for each text separatly
        List<STextualDS> texts = saltGraph.getTextualDSs();
        if (texts != null && !texts.isEmpty()) {
            for (STextualDS t : texts) {
                DataSourceSequence<Integer> sequence = new DataSourceSequence<>(t, 0, (t.getText() != null) ? t.getText().length() : 0);
                List<SToken> token = saltGraph.getSortedTokenByText(saltGraph.getTokensBySequence(sequence));
                if (token != null) {
                    boolean validText = true;
                    if (Boolean.parseBoolean(input.getMappings().getProperty("hide_empty", "false"))) {
                        validText = false;
                        // check if the text contains any matching annotations
                        for (SToken tok : token) {
                            /* 
                 * The token is only added to this map if an valid edge
                 * (according to the resolver trigger) conntected to 
                 * this token was found.
                 */
                            if (referentOfToken.get(tok.getId()) != null && !referentOfToken.get(tok.getId()).isEmpty()) {
                                validText = true;
                                break;
                            }
                        }
                    }
                    if (validText) {
                        List<Node> nodes = outputSingleText(token, input);
                        nodesPerText.add(nodes);
                    }
                }
            }
            // end for each STexutalDS
            /* 
         * Append the generated output to the body, wrap in table if necessary. 
         */
            // present all texts as columns side by side if using multiple texts
            Table tableTexts = new Table();
            Tr trTextRow = new Tr();
            trTextRow.setCSSClass("textRow");
            // only append wrapper table if we have multiple texts
            if (nodesPerText.size() > 1) {
                body.appendChild(tableTexts);
                tableTexts.appendChild(trTextRow);
            }
            for (List<Node> nodes : nodesPerText) {
                // multi-text mode?
                if (nodesPerText.size() > 1) {
                    Td tdSingleText = new Td();
                    trTextRow.appendChild(tdSingleText);
                    tdSingleText.setCSSClass("text");
                    tdSingleText.appendChild(nodes);
                } else {
                    body.appendChild(nodes);
                }
            }
        } else {
            Text errorTxt = new Text("Could not find any texts for the " + input.getNamespace() + " node namespace (layer).");
            body.appendChild(errorTxt);
        }
        // write HTML4 transitional doctype
        w.append(new Doctype(DocumentType.HTMLTransitional).write());
        // append the html tree
        w.append(html.write());
    } catch (IOException ex) {
        log.error(null, ex);
    }
}

Example 2 with SDocument

use of org.corpus_tools.salt.common.SDocument in project ANNIS by korpling.

the class QueryDaoImpl method exportCorpus.

@Override
@Transactional(readOnly = true)
public void exportCorpus(String toplevelCorpus, File outputDirectory) {
    // check if the corpus really exists
    mapCorpusNameToId(toplevelCorpus);
    SaltProject corpusProject = SaltFactory.createSaltProject();
    SCorpusGraph corpusGraph = SaltFactory.createSCorpusGraph();
    corpusGraph.setSaltProject(corpusProject);
    SCorpus rootCorpus = corpusGraph.createCorpus(null, toplevelCorpus);
    // add all root metadata
    for (Annotation metaAnno : listCorpusAnnotations(toplevelCorpus)) {
        rootCorpus.createMetaAnnotation(metaAnno.getNamespace(), metaAnno.getName(), metaAnno.getValue());
    }
    File documentRootDir = new File(outputDirectory, toplevelCorpus);
    if (!outputDirectory.exists()) {
        if (!outputDirectory.mkdirs()) {
            log.warn("Could not create output directory \"{}\" for exporting the corpus", outputDirectory.getAbsolutePath());
        }
    }
    List<Annotation> docs = listDocuments(toplevelCorpus);
    int i = 1;
    for (Annotation docAnno : docs) {
        log.info("Loading document {} from database ({}/{})", docAnno.getName(), i, docs.size());
        SaltProject docProject = retrieveAnnotationGraph(toplevelCorpus, docAnno.getName(), null);
        if (docProject != null && docProject.getCorpusGraphs() != null && !docProject.getCorpusGraphs().isEmpty()) {
            List<Annotation> docMetaData = listCorpusAnnotations(toplevelCorpus, docAnno.getName(), true);
            SCorpusGraph docCorpusGraph = docProject.getCorpusGraphs().get(0);
            // TODO: we could re-use the actual corpus structure instead of just adding a flat list of documents
            if (docCorpusGraph.getDocuments() != null) {
                for (SDocument doc : docCorpusGraph.getDocuments()) {
                    log.info("Removing SFeatures from {} ({}/{})", docAnno.getName(), i, docs.size());
                    // remove all ANNIS specific features that require a special Java class
                    SDocumentGraph graph = doc.getDocumentGraph();
                    if (graph != null) {
                        if (graph.getNodes() != null) {
                            for (SNode n : graph.getNodes()) {
                                n.removeLabel(AnnisConstants.ANNIS_NS, AnnisConstants.FEAT_RELANNIS_NODE);
                            }
                        }
                        if (graph.getRelations() != null) {
                            for (SRelation e : graph.getRelations()) {
                                e.removeLabel(AnnisConstants.ANNIS_NS, AnnisConstants.FEAT_RELANNIS_EDGE);
                            }
                        }
                    }
                    log.info("Saving document {} ({}/{})", doc.getName(), i, docs.size());
                    SaltUtil.saveDocumentGraph(graph, URI.createFileURI(new File(documentRootDir, doc.getName() + "." + SaltUtil.FILE_ENDING_SALT_XML).getAbsolutePath()));
                    SDocument docCopy = corpusGraph.createDocument(rootCorpus, doc.getName());
                    log.info("Adding metadata to document {} ({}/{})", doc.getName(), i, docs.size());
                    for (Annotation metaAnno : docMetaData) {
                        docCopy.createMetaAnnotation(metaAnno.getNamespace(), metaAnno.getName(), metaAnno.getValue());
                    }
                }
            }
        }
        i++;
    }
    // end for each document
    // save the actual SaltProject
    log.info("Saving corpus structure");
    File projectFile = new File(outputDirectory, SaltUtil.FILE_SALT_PROJECT);
    SaltXML10Writer writer = new SaltXML10Writer(projectFile);
    writer.writeSaltProject(corpusProject);
}

Example 3 with SDocument

use of org.corpus_tools.salt.common.SDocument in project ANNIS by korpling.

the class AutoSimpleRegexQuery method analyzingQuery.

@Override
public void analyzingQuery(SaltProject saltProject) {
    List<String> tokens = new ArrayList<>();
    for (SCorpusGraph g : saltProject.getCorpusGraphs()) {
        if (g != null) {
            for (SDocument doc : g.getDocuments()) {
                SDocumentGraph docGraph = doc.getDocumentGraph();
                List<SNode> sNodes = docGraph.getNodes();
                if (sNodes != null) {
                    for (SNode n : sNodes) {
                        if (n instanceof SToken) {
                            tokens.add(CommonHelper.getSpannedText((SToken) n));
                        }
                    }
                }
            }
        }
    }
    // try to find a word with which is contained twice with Capitalize letter.
    text = null;
    for (int i = 0; i < tokens.size(); i++) {
        for (int j = i + 1; j < tokens.size(); j++) {
            if (tokens.get(i).equalsIgnoreCase(tokens.get(j))) {
                if (tokens.get(i).length() > 1 && ((Character.isLowerCase(tokens.get(i).charAt(0)) && Character.isUpperCase(tokens.get(j).charAt(0))) || (Character.isLowerCase(tokens.get(j).charAt(0)) && Character.isUpperCase(tokens.get(i).charAt(0))))) {
                    text = tokens.get(i);
                    break;
                }
            }
        }
    }
    if (text != null) {
        Character upperLetter = Character.toUpperCase(text.charAt(0));
        Character lowerLetter = Character.toLowerCase(text.charAt(0));
        String rest = StringUtils.substring(text, -(text.length() - 1));
        finalAQL = "/[" + upperLetter + lowerLetter + "]" + rest + "/";
    } else {
        // select one random token from the result
        int tries = 10;
        int r = new Random().nextInt(tokens.size() - 1);
        text = tokens.get(r);
        while ("".equals(text) && tries > 0) {
            r = new Random().nextInt(tokens.size() - 1);
            text = tokens.get(r);
            tries--;
        }
        if (!"".equals(text) && text.length() > 1) {
            Character upperLetter = Character.toUpperCase(text.charAt(0));
            Character lowerLetter = Character.toLowerCase(text.charAt(0));
            String rest = StringUtils.substring(text, -(text.length() - 1));
            finalAQL = "/[" + upperLetter + lowerLetter + "]" + rest + "/";
        } else {
            finalAQL = "";
        }
    }
}

Example 4 with SDocument

use of org.corpus_tools.salt.common.SDocument in project ANNIS by korpling.

the class SaltAnnotateExtractor method addMatchInformation.

/**
 * Sets additional match (global) information about the matched nodes and
 * annotations.
 *
 * This will add the {@link AnnisConstants#FEAT_MATCHEDIDS) to all {@link SDocument} elements of the
 * salt project.
 *
 * @param p The salt project to add the features to.
 * @param matchGroup A list of matches in the same order as the corpus graphs
 * of the salt project.
 */
public static void addMatchInformation(SaltProject p, MatchGroup matchGroup) {
    int matchIndex = 0;
    for (Match m : matchGroup.getMatches()) {
        // get the corresponding SDocument of the salt project
        SCorpusGraph corpusGraph = p.getCorpusGraphs().get(matchIndex);
        SDocument doc = corpusGraph.getDocuments().get(0);
        setMatchedIDs(doc.getDocumentGraph(), m);
        matchIndex++;
    }
}

Example 5 with SDocument

use of org.corpus_tools.salt.common.SDocument in project ANNIS by korpling.

the class SaltBasedExporter method convertSaltProject.

/**
 * Iterates over all matches (modelled as corpus graphs) and calls {@link #convertText(de.hu_berlin.german.korpling.saltnpepper.salt.saltCommon.sDocumentStructure.SDocumentGraph, java.util.List, java.util.Map, int, java.io.Writer) } for
 * the single document graph.
 * @param p
 * @param annoKeys
 * @param args
 * @param alignmc
 * @param offset
 * @param out
 */
// invokes the createAdjacencyMatrix method, if nodeCount != null or outputText otherwise
private void convertSaltProject(SaltProject p, List<String> annoKeys, Map<String, String> args, boolean alignmc, int offset, Map<String, CorpusConfig> corpusConfigs, Writer out, Integer nodeCount) throws IOException, IllegalArgumentException {
    int recordNumber = offset;
    if (p != null && p.getCorpusGraphs() != null) {
        Map<String, String> spanAnno2order = null;
        boolean virtualTokenizationFromNamespace = false;
        Set<String> corpusNames = CommonHelper.getToplevelCorpusNames(p);
        if (!corpusNames.isEmpty()) {
            CorpusConfig config = corpusConfigs.get(corpusNames.iterator().next());
            if (config != null) {
                if ("true".equalsIgnoreCase(config.getConfig("virtual_tokenization_from_namespace"))) {
                    virtualTokenizationFromNamespace = true;
                } else {
                    String mappingRaw = config.getConfig("virtual_tokenization_mapping");
                    if (mappingRaw != null) {
                        spanAnno2order = new HashMap<>();
                        for (String singleMapping : Splitter.on(',').split(mappingRaw)) {
                            List<String> mappingParts = Splitter.on('=').splitToList(singleMapping);
                            if (mappingParts.size() >= 2) {
                                spanAnno2order.put(mappingParts.get(0), mappingParts.get(1));
                            }
                        }
                    }
                }
            }
        }
        for (SCorpusGraph corpusGraph : p.getCorpusGraphs()) {
            if (corpusGraph.getDocuments() != null) {
                for (SDocument doc : corpusGraph.getDocuments()) {
                    if (virtualTokenizationFromNamespace) {
                        TimelineReconstructor.removeVirtualTokenizationUsingNamespace(doc.getDocumentGraph());
                    } else if (spanAnno2order != null) {
                        // there is a definition how to map the virtual tokenization to a real one
                        TimelineReconstructor.removeVirtualTokenization(doc.getDocumentGraph(), spanAnno2order);
                    }
                    if (nodeCount != null) {
                        createAdjacencyMatrix(doc.getDocumentGraph(), args, recordNumber++, nodeCount);
                    } else {
                        outputText(doc.getDocumentGraph(), alignmc, recordNumber++, out);
                    }
                }
            }
        }
    }
}