Examples with Issue org.gephi.io.importer.api.Issue used on opensource projects

Example 11 with Issue

use of org.gephi.io.importer.api.Issue in project gephi by gephi.

the class ImporterGDF method importData.

private void importData(LineNumberReader reader) throws Exception {
    //Progress
    Progress.start(progressTicket);
    //Verify a node line exists and puts nodes and edges lines in arrays
    walkFile(reader);
    //Progress
    Progress.switchToDeterminate(progressTicket, nodeLines.size() + edgeLines.size());
    //Magix regex
    Pattern pattern = Pattern.compile("(?<=(?:,|^)\")(.*?)(?=(?<=(?:[^\\\\]))\",|\"$)|(?<=(?:,|^)')(.*?)(?=(?<=(?:[^\\\\]))',|'$)|(?<=(?:,|^))(?=[^'\"])(.*?)(?=(?:,|$))|(?<=,)($)");
    //Nodes
    for (String nodeLine : nodeLines) {
        if (cancel) {
            return;
        }
        //Create Node
        NodeDraft node = null;
        Matcher m = pattern.matcher(nodeLine);
        int count = 0;
        String id = "";
        while (m.find()) {
            int start = m.start();
            int end = m.end();
            if (start != end) {
                String data = nodeLine.substring(start, end);
                data = data.trim();
                if (!data.isEmpty() && !data.toLowerCase().equals("null")) {
                    if (count == 0) {
                        //Id
                        id = data;
                        if (node == null) {
                            node = container.factory().newNodeDraft(id);
                        }
                    } else if (count - 1 < nodeColumns.length) {
                        if (nodeColumns[count - 1] != null) {
                            setNodeData(node, nodeColumns[count - 1], data);
                        }
                    } else {
                        report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat7", id), Issue.Level.SEVERE));
                    }
                }
            }
            count++;
        }
        container.addNode(node);
        //Progress
        Progress.progress(progressTicket);
    }
    //Edges
    for (String edgeLine : edgeLines) {
        if (cancel) {
            return;
        }
        //Create Edge
        EdgeDraft edge = container.factory().newEdgeDraft();
        //Default to undirected unless stated
        edge.setDirection(EdgeDirection.UNDIRECTED);
        Matcher m = pattern.matcher(edgeLine);
        int count = 0;
        String id = "";
        while (m.find()) {
            int start = m.start();
            int end = m.end();
            if (start != end) {
                String data = edgeLine.substring(start, end);
                data = data.trim();
                if (!data.isEmpty() && !data.toLowerCase().equals("null")) {
                    if (count == 0) {
                        NodeDraft nodeSource = container.getNode(data);
                        edge.setSource(nodeSource);
                        id = data;
                    } else if (count == 1) {
                        NodeDraft nodeTarget = container.getNode(data);
                        edge.setTarget(nodeTarget);
                        id += "," + data;
                    } else if (count - 2 < edgeColumns.length) {
                        if (edgeColumns[count - 2] != null) {
                            setEdgeData(edge, edgeColumns[count - 2], data);
                        }
                    } else {
                        report.logIssue(new Issue(NbBundle.getMessage(ImporterGDF.class, "importerGDF_error_dataformat7", id), Issue.Level.SEVERE));
                    }
                }
            }
            count++;
        }
        container.addEdge(edge);
        //Progress
        Progress.progress(progressTicket);
    }
}

Example 12 with Issue

use of org.gephi.io.importer.api.Issue in project gephi by gephi.

the class ImporterEdgeList method getEdges.

private void getEdges(Connection connection) throws SQLException {
    //Factory
    ElementDraft.Factory factory = container.factory();
    //Properties
    PropertiesAssociations properties = database.getPropertiesAssociations();
    Statement s = connection.createStatement();
    ResultSet rs = null;
    try {
        rs = s.executeQuery(database.getEdgeQuery());
    } catch (SQLException ex) {
        report.logIssue(new Issue("Failed to execute Edge query", Issue.Level.SEVERE, ex));
        return;
    }
    findEdgeAttributesColumns(rs);
    ResultSetMetaData metaData = rs.getMetaData();
    int columnsCount = metaData.getColumnCount();
    while (rs.next()) {
        String id = null;
        for (int i = 0; i < columnsCount; i++) {
            String columnName = metaData.getColumnLabel(i + 1);
            EdgeProperties p = properties.getEdgeProperty(columnName);
            if (p != null && p.equals(EdgeProperties.ID)) {
                String ide = rs.getString(i + 1);
                if (ide != null) {
                    id = ide;
                }
            }
        }
        EdgeDraft edge;
        if (id != null) {
            edge = factory.newEdgeDraft(id);
        } else {
            edge = factory.newEdgeDraft();
        }
        for (int i = 0; i < columnsCount; i++) {
            String columnName = metaData.getColumnLabel(i + 1);
            EdgeProperties p = properties.getEdgeProperty(columnName);
            if (p != null) {
                injectEdgeProperty(p, rs, i + 1, edge);
            } else {
                //Inject edge attributes
                ColumnDraft col = container.getEdgeColumn(columnName);
                injectElementAttribute(rs, i + 1, col, edge);
            }
        }
        injectTimeIntervalProperty(edge);
        container.addEdge(edge);
    }
    rs.close();
    s.close();
}

Example 13 with Issue

use of org.gephi.io.importer.api.Issue in project gephi by gephi.

the class ImporterDL method readEdgelistRow.

private void readEdgelistRow(String row, int pointer, double startTime, double endTime) {
    StringTokenizer rowkonizer = new StringTokenizer(row);
    if (!rowkonizer.hasMoreTokens()) {
        return;
    }
    // should have three entries, int from, int to, weight
    String from = rowkonizer.nextToken();
    if (!rowkonizer.hasMoreTokens()) {
        return;
    }
    String to = rowkonizer.nextToken();
    double weight = 1.0;
    if (rowkonizer.hasMoreTokens()) {
        String weightParse = rowkonizer.nextToken();
        try {
            weight = Double.parseDouble(weightParse);
        } catch (Exception e) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_edgeparseweight", weightParse, getLineNumber(pointer)), Issue.Level.WARNING));
        }
    }
    NodeDraft sourceNode = container.getNode(from);
    NodeDraft targetNode = container.getNode(to);
    EdgeDraft edgeDraft = container.factory().newEdgeDraft();
    edgeDraft.setSource(sourceNode);
    edgeDraft.setTarget(targetNode);
    edgeDraft.setWeight((float) weight);
    container.addEdge(edgeDraft);
}

Example 14 with Issue

use of org.gephi.io.importer.api.Issue in project gephi by gephi.

the class ImporterDL method importData.

private void importData(LineNumberReader reader) throws Exception {
    //Progress
    Progress.start(progressTicket);
    List<String> lines = new ArrayList<>();
    for (; reader.ready(); ) {
        String line = reader.readLine();
        if (line != null && !line.isEmpty()) {
            lines.add(line);
        }
    }
    if (lines.isEmpty() || (!lines.get(0).startsWith("DL") && !lines.get(0).startsWith("dl"))) {
        report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_firstline"), Issue.Level.CRITICAL));
    }
    headerMap = new HashMap<>();
    readHeaderLine(lines.get(0).substring(2));
    int i = 1;
    for (; i < lines.size(); i++) {
        String line = lines.get(i).toLowerCase();
        if (line.trim().endsWith("data:") || line.trim().endsWith("labels:")) {
            break;
        } else {
            readHeaderLine(line);
        }
    }
    computeHeaders();
    if (lines.get(i).toLowerCase().trim().endsWith("labels:") && lines.size() > i + 1) {
        readLabels(lines.get(++i));
    }
    int dataLineStart = -1;
    for (; i < lines.size(); i++) {
        String line = lines.get(i).toLowerCase();
        if (line.trim().endsWith("data:")) {
            dataLineStart = i + 1;
            break;
        }
    }
    if (dataLineStart == -1) {
        report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_nodata"), Issue.Level.SEVERE));
    } else if (lines.size() > dataLineStart) {
        dataLineStartDelta = dataLineStart + 1;
        lines = lines.subList(dataLineStart, lines.size());
        if (format.equals(Format.FULLMATRIX)) {
            readeMatrixBlock(lines);
        } else if (format.equals(Format.EDGELIST1)) {
            readEdgelistBlock(lines);
        }
    }
}

Example 15 with Issue

use of org.gephi.io.importer.api.Issue in project gephi by gephi.

the class ImporterDL method readMatrixRow.

private void readMatrixRow(String line, int pointer, int row, int startTime, int endTime) {
    StringTokenizer rowkonizer = new StringTokenizer(line, " ");
    int from = row + 1;
    int to = 1;
    double weight = 0;
    while (rowkonizer.hasMoreTokens()) {
        String toParse = (String) rowkonizer.nextToken();
        if (to > numNodes) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_matrixentriescount", row, startTime, getLineNumber(pointer)), Issue.Level.SEVERE));
        }
        try {
            weight = Double.parseDouble(toParse);
        } catch (Exception e) {
            report.logIssue(new Issue(NbBundle.getMessage(ImporterDL.class, "importerDL_error_weightparseerror", toParse, startTime, getLineNumber(pointer)), Issue.Level.SEVERE));
        }
        if (weight != 0) {
            NodeDraft sourceNode = container.getNode("" + from);
            NodeDraft targetNode = container.getNode("" + to);
            EdgeDraft edgeDraft = container.factory().newEdgeDraft();
            edgeDraft.setSource(sourceNode);
            edgeDraft.setTarget(targetNode);
            edgeDraft.setWeight((float) weight);
            container.addEdge(edgeDraft);
        }
        to++;
    }
}