Examples with Annotation annis.model.Annotation used on opensource projects

Example 41 with Annotation

use of annis.model.Annotation in project ANNIS by korpling.

the class AnnotatedSpanExtractor method mapRow.

@Override
public AnnotatedSpan mapRow(ResultSet resultSet, int rowNum) throws SQLException {
    long id = resultSet.getLong("id");
    String coveredText = resultSet.getString("span");
    Array arrayAnnotation = resultSet.getArray("annotations");
    ResultSetMetaData rsMeta = resultSet.getMetaData();
    Array arrayMeta = null;
    for (int i = 1; i <= rsMeta.getColumnCount(); i++) {
        if ("metadata".equals(rsMeta.getColumnName(i))) {
            arrayMeta = resultSet.getArray(i);
            break;
        }
    }
    List<Annotation> annotations = extractAnnotations(arrayAnnotation);
    List<Annotation> metaData = arrayMeta == null ? new LinkedList<Annotation>() : extractAnnotations(arrayMeta);
    // create key
    Array sqlKey = resultSet.getArray("key");
    Validate.isTrue(!resultSet.wasNull(), "Match group identifier must not be null");
    Validate.isTrue(sqlKey.getBaseType() == Types.BIGINT, "Key in database must be from the type \"bigint\" but was \"" + sqlKey.getBaseTypeName() + "\"");
    List<Long> key = Arrays.asList((Long[]) sqlKey.getArray());
    return new AnnotatedSpan(id, coveredText, annotations, metaData, key);
}

Example 42 with Annotation

use of annis.model.Annotation in project ANNIS by korpling.

the class AomAnnotateExtractor method extractData.

@Override
public List<AnnotationGraph> extractData(ResultSet resultSet) throws SQLException, DataAccessException {
    TableAccessStrategy tableAccessStrategy = outerQueryTableAccessStrategy;
    // function result
    List<AnnotationGraph> graphs = new LinkedList<>();
    // fn: match group -> annotation graph
    Map<List<Long>, AnnotationGraph> graphByMatchGroup = new HashMap<>();
    // fn: node id -> node
    Map<Long, AnnisNode> nodeById = new HashMap<>();
    // fn: edge pre order value -> edge
    Map<Long, Edge> edgeByRankID = new HashMap<>();
    // maps span that are continous to their coverage component
    Map<List<Long>, Map<Long, ComponentEntry>> keyToSpanToComponent = new HashMap<>();
    int rowNum = 0;
    while (resultSet.next()) {
        // process result by match group
        // match group is identified by the ids of the matched
        // nodes
        Array sqlKey = resultSet.getArray("key");
        Validate.isTrue(!resultSet.wasNull(), "Match group identifier must not be null");
        Validate.isTrue(sqlKey.getBaseType() == Types.BIGINT, "Key in database must be from the type \"bigint\" but was \"" + sqlKey.getBaseTypeName() + "\"");
        Long[] keyArray = (Long[]) sqlKey.getArray();
        List<Long> key = Arrays.asList(keyArray);
        if (!graphByMatchGroup.containsKey(key)) {
            log.debug("starting annotation graph for match: " + key);
            Map<Long, ComponentEntry> spans = new HashMap<>();
            AnnotationGraph graph = new AnnotationGraph();
            graphs.add(graph);
            graphByMatchGroup.put(key, graph);
            keyToSpanToComponent.put(key, spans);
            // clear mapping functions for this graph
            // assumes that the result set is sorted by key, pre
            nodeById.clear();
            edgeByRankID.clear();
            // set the matched keys
            for (Long l : key) {
                if (l != null) {
                    graph.addMatchedNodeId(l);
                }
            }
        }
        AnnotationGraph graph = graphByMatchGroup.get(key);
        Map<Long, ComponentEntry> spanToComponent = keyToSpanToComponent.get(key);
        graph.setDocumentName(new DocumentNameMapRow().mapRow(resultSet, rowNum));
        Array path = resultSet.getArray("path");
        graph.setPath((String[]) path.getArray());
        // get node data
        AnnisNode node = mapNode(resultSet, tableAccessStrategy, spanToComponent);
        // add node to graph if it is new, else get known copy
        long id = node.getId();
        if (!nodeById.containsKey(id)) {
            log.debug("new node: " + id);
            nodeById.put(id, node);
            graph.addNode(node);
        } else {
            node = nodeById.get(id);
        }
        // we now have the id of the node and the general key,
        // so we can
        // add the matched node index to the graph (if matched)
        long matchIndex = 1;
        // node.setMatchedNodeInQuery(null);
        for (Long l : key) {
            if (l != null) {
                if (id == l) {
                    node.setMatchedNodeInQuery(matchIndex);
                    break;
                }
                matchIndex++;
            }
        }
        // get edge data
        Edge edge = mapEdge(resultSet, tableAccessStrategy);
        // add edge to graph if it is new, else get known copy
        long rank_id = edge.getId();
        if (!edgeByRankID.containsKey(rank_id)) {
            // fix source references in edge
            edge.setDestination(node);
            fixNodes(edge, edgeByRankID, nodeById);
            // add edge to src and dst nodes
            node.addIncomingEdge(edge);
            AnnisNode source = edge.getSource();
            if (source != null) {
                source.addOutgoingEdge(edge);
            }
            log.debug("new edge: " + edge);
            edgeByRankID.put(edge.getId(), edge);
            graph.addEdge(edge);
        } else {
            edge = edgeByRankID.get(rank_id);
        }
        // add annotation data
        Annotation nodeAnnotation = mapAnnotation(resultSet, tableAccessStrategy, TableAccessStrategy.NODE_ANNOTATION_TABLE);
        if (nodeAnnotation != null) {
            node.addNodeAnnotation(nodeAnnotation);
        }
        Annotation edgeAnnotation = mapAnnotation(resultSet, tableAccessStrategy, TableAccessStrategy.EDGE_ANNOTATION_TABLE);
        if (edgeAnnotation != null) {
            edge.addAnnotation(edgeAnnotation);
        }
        rowNum++;
    }
    // remove edges from the graph with a source node inside the match
    for (Entry<List<Long>, AnnotationGraph> entry : graphByMatchGroup.entrySet()) {
        AnnotationGraph graph = entry.getValue();
        ListIterator<Edge> itEdge = graph.getEdges().listIterator();
        while (itEdge.hasNext()) {
            Edge edge = itEdge.next();
            if (edge.getSource() == null) {
                edge.getDestination().getIncomingEdges().remove(edge);
                itEdge.remove();
            }
        }
        Map<Long, ComponentEntry> spans = keyToSpanToComponent.get(entry.getKey());
        // filter out the continuous spans by finding all discontinuous spans
        // discontinuos spans will have a an entry for token
        createMissingSpanningRelations(graph, spans, nodeById);
    }
    return graphs;
}

Example 43 with Annotation

use of annis.model.Annotation in project ANNIS by korpling.

the class WekaHelper method exportArffHeader.

public static SortedMap<Integer, SortedSet<String>> exportArffHeader(Iterator<AnnotatedMatch> matches, PrintWriter w) {
    // header: relation name (unused)
    w.append("@relation name\n");
    w.append("\n");
    // figure out what annotations are used at each match position
    SortedMap<Integer, SortedSet<String>> columnsByNodePos = new TreeMap<>();
    while (matches.hasNext()) {
        AnnotatedMatch match = matches.next();
        for (int j = 0; j < match.size(); ++j) {
            AnnotatedSpan span = match.get(j);
            if (columnsByNodePos.get(j) == null) {
                columnsByNodePos.put(j, new TreeSet<String>());
            }
            for (Annotation annotation : span.getAnnotations()) {
                columnsByNodePos.get(j).add("anno_" + annotation.getQualifiedName());
            }
            for (Annotation meta : span.getMetadata()) {
                columnsByNodePos.get(j).add("meta_" + meta.getQualifiedName());
            }
        }
    }
    // print column names and data types
    int count = columnsByNodePos.keySet().size();
    for (int j = 0; j < count; ++j) {
        w.append("@attribute ").append(fullColumnName(j + 1, "id")).append(" string\n");
        w.append("@attribute ").append(fullColumnName(j + 1, "span")).append(" string\n");
        SortedSet<String> annotationNames = columnsByNodePos.get(j);
        for (String name : annotationNames) {
            w.append("@attribute ").append(fullColumnName(j + 1, name)).append(" string\n");
        }
    }
    return columnsByNodePos;
}