Examples with NetworkTableReader org.cytoscape.tableimport.internal.reader.NetworkTableReader used on opensource projects

Example 1 with NetworkTableReader

use of org.cytoscape.tableimport.internal.reader.NetworkTableReader in project cytoscape-impl by cytoscape.

the class ImportNetworkTableReaderTask method run.

@Override
public void run(TaskMonitor tm) throws Exception {
    tm.setTitle("Loading network from table");
    tm.setProgress(0.0);
    tm.setStatusMessage("Loading network...");
    Workbook workbook = null;
    // Load Spreadsheet data for preview.
    if (fileType != null && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) && workbook == null) {
        try {
            workbook = WorkbookFactory.create(is);
        } catch (InvalidFormatException e) {
            throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?", e);
        } finally {
            if (is != null)
                is.close();
        }
    }
    try {
        if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
            String networkName = ntmp.getName();
            if (networkName == null)
                networkName = workbook.getSheetName(0);
            final Sheet sheet = workbook.getSheet(networkName);
            reader = new ExcelNetworkSheetReader(networkName, sheet, ntmp, nMap, rootNetwork, serviceRegistrar);
        } else {
            reader = new NetworkTableReader(inputName, is, ntmp, nMap, rootNetwork, serviceRegistrar);
        }
    } catch (Exception ioe) {
        tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
        return;
    }
    loadNetwork(tm);
    tm.setProgress(1.0);
}

Example 2 with NetworkTableReader

use of org.cytoscape.tableimport.internal.reader.NetworkTableReader in project cytoscape-impl by cytoscape.

the class LoadNetworkReaderTask method run.

@Override
public void run(final TaskMonitor tm) throws Exception {
    tm.setTitle("Loading network from table");
    tm.setProgress(0.0);
    tm.setStatusMessage("Loading network...");
    taskMonitor = tm;
    final List<String> attrNameList = new ArrayList<>();
    int colCount;
    String[] attributeNames;
    final CyNetworkReaderManager networkReaderManager = serviceRegistrar.getService(CyNetworkReaderManager.class);
    if (is != null)
        netReader = networkReaderManager.getReader(is, inputName);
    if (netReader == null)
        netReader = networkReaderManager.getReader(uri, inputName);
    if (netReader instanceof CombineReaderAndMappingTask) {
        Workbook workbook = null;
        // Load Spreadsheet data for preview.
        if (fileType != null && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) && workbook == null) {
            try {
                workbook = WorkbookFactory.create(new FileInputStream(tempFile));
            } catch (InvalidFormatException e) {
                // e.printStackTrace();
                throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?", e);
            } finally {
            }
        }
        netReader = null;
        if (startLoadRow > 0)
            startLoadRow--;
        final int startLoadRowTemp = firstRowAsColumnNames ? 0 : startLoadRow;
        previewPanel.updatePreviewTable(workbook, fileType, tempFile.getAbsolutePath(), new FileInputStream(tempFile), delimiters.getSelectedValues(), null, startLoadRowTemp);
        colCount = previewPanel.getPreviewTable().getColumnModel().getColumnCount();
        Object curName = null;
        if (firstRowAsColumnNames) {
            previewPanel.setFirstRowAsColumnNames();
            startLoadRow++;
        }
        final SourceColumnSemantic[] types = previewPanel.getTypes();
        for (int i = 0; i < colCount; i++) {
            curName = previewPanel.getPreviewTable().getColumnModel().getColumn(i).getHeaderValue();
            if (attrNameList.contains(curName)) {
                int dupIndex = 0;
                for (int idx = 0; idx < attrNameList.size(); idx++) {
                    if (curName.equals(attrNameList.get(idx))) {
                        dupIndex = idx;
                        break;
                    }
                }
                if (!TypeUtil.allowsDuplicateName(ImportType.NETWORK_IMPORT, types[i], types[dupIndex])) {
                    // TODO add message to user (Duplicate Column Name Found)
                    return;
                }
            }
            if (curName == null)
                attrNameList.add("Column " + i);
            else
                attrNameList.add(curName.toString());
        }
        attributeNames = attrNameList.toArray(new String[attrNameList.size()]);
        final SourceColumnSemantic[] typesCopy = Arrays.copyOf(types, types.length);
        final AttributeDataType[] dataTypes = previewPanel.getDataTypes();
        final AttributeDataType[] dataTypesCopy = Arrays.copyOf(dataTypes, dataTypes.length);
        AttributeDataType[] tunableDataTypes = null;
        if (dataTypeList != null && !dataTypeList.trim().isEmpty())
            tunableDataTypes = TypeUtil.parseDataTypeList(dataTypeList);
        if (tunableDataTypes != null && tunableDataTypes.length > 0)
            System.arraycopy(tunableDataTypes, 0, dataTypesCopy, 0, Math.min(tunableDataTypes.length, dataTypesCopy.length));
        SourceColumnSemantic[] tunableColumnTypes = null;
        if (columnTypeList != null && !columnTypeList.trim().isEmpty()) {
            tunableColumnTypes = TypeUtil.parseColumnTypeList(columnTypeList);
        }
        if (tunableColumnTypes != null && tunableColumnTypes.length > 0) {
            System.arraycopy(tunableColumnTypes, 0, typesCopy, 0, Math.min(tunableColumnTypes.length, typesCopy.length));
            // Set the source and target interaction columns
            int index = 1;
            for (SourceColumnSemantic scs : tunableColumnTypes) {
                if (scs.equals(SourceColumnSemantic.SOURCE))
                    indexColumnSourceInteraction = index;
                else if (scs.equals(SourceColumnSemantic.TARGET))
                    indexColumnTargetInteraction = index;
                index++;
            }
        }
        if (nogui) {
            // Handle the validation
            nogui = false;
            ValidationState state = getValidationState(new StringBuffer(80));
            switch(state) {
                case INVALID:
                    tm.showMessage(TaskMonitor.Level.ERROR, "Source column must be specified");
                    return;
                case REQUEST_CONFIRMATION:
                    tm.showMessage(TaskMonitor.Level.WARN, "Target column is not specified.  No edges will be created");
            }
            nogui = true;
        }
        String[] listDelimiters = previewPanel.getListDelimiters();
        if (listDelimiters == null || listDelimiters.length == 0) {
            listDelimiters = new String[dataTypes.length];
            if (delimitersForDataList.getSelectedValue() != null)
                Arrays.fill(listDelimiters, delimitersForDataList.getSelectedValue());
        }
        if (indexColumnSourceInteraction > 0)
            indexColumnSourceInteraction--;
        if (indexColumnTargetInteraction > 0)
            indexColumnTargetInteraction--;
        if (indexColumnTypeInteraction > 0)
            indexColumnTypeInteraction--;
        networkName = previewPanel.getSourceName();
        ntmp = new NetworkTableMappingParameters(networkName, delimiters.getSelectedValues(), listDelimiters, attributeNames, dataTypesCopy, typesCopy, indexColumnSourceInteraction, indexColumnTargetInteraction, indexColumnTypeInteraction, defaultInteraction, startLoadRow, null);
        try {
            if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
                final Sheet sheet = workbook.getSheet(networkName);
                reader = new ExcelNetworkSheetReader(networkName, sheet, ntmp, nMap, rootNetwork, serviceRegistrar);
            } else {
                networkName = this.inputName;
                reader = new NetworkTableReader(networkName, new FileInputStream(tempFile), ntmp, nMap, rootNetwork, serviceRegistrar);
            }
        } catch (Exception ioe) {
            tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read network: " + ioe.getMessage());
            return;
        }
        loadNetwork(tm);
        tm.setProgress(1.0);
    } else {
        networkName = this.inputName;
        insertTasksAfterCurrentTask(netReader);
    }
}