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

Example 1 with DefaultAttributeTableReader

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

the class LoadTableReaderTask method run.

@Override
public void run(final TaskMonitor tm) throws Exception {
    tm.setTitle("Loading table data");
    tm.setProgress(0.0);
    tm.setStatusMessage("Loading table...");
    List<String> attrNameList = new ArrayList<>();
    int colCount;
    String[] attributeNames;
    Workbook workbook = null;
    // Load Spreadsheet data for preview.
    try {
        if (fileType != null && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) && workbook == null) {
            try {
                workbook = WorkbookFactory.create(isStart);
            } catch (InvalidFormatException e) {
                e.printStackTrace();
                throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?");
            } finally {
                if (isStart != null)
                    isStart.close();
            }
        }
    } catch (Exception ioe) {
        tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
        return;
    }
    if (startLoadRow > 0)
        startLoadRow--;
    final int startLoadRowTemp = firstRowAsColumnNames ? 0 : startLoadRow;
    previewPanel.updatePreviewTable(workbook, fileType, inputName, isStart, delimiters.getSelectedValues(), null, startLoadRowTemp);
    colCount = previewPanel.getPreviewTable().getColumnModel().getColumnCount();
    Object curName = null;
    if (firstRowAsColumnNames) {
        previewPanel.setFirstRowAsColumnNames();
        startLoadRow++;
    }
    final String sourceName = previewPanel.getSourceName();
    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.TABLE_IMPORT, types[i], types[dupIndex])) {
                // TODO add message to user
                return;
            }
        }
        if (curName == null)
            attrNameList.add("Column " + i);
        else
            attrNameList.add(curName.toString());
    }
    attributeNames = attrNameList.toArray(new String[0]);
    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));
    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 (keyColumnIndex > 0)
        keyColumnIndex--;
    amp = new AttributeMappingParameters(sourceName, delimiters.getSelectedValues(), listDelimiters, keyColumnIndex, attributeNames, dataTypesCopy, typesCopy, startLoadRow, null);
    if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
        // Fixed bug# 1668, Only load data from the first sheet, ignore the rest sheets
        // UPDATE: From the user perspective it makes more sense to get the selected tab/sheet than the first one.
        final Sheet sheet = workbook.getSheet(sourceName);
        if (sheet != null) {
            reader = new ExcelAttributeSheetReader(sheet, amp, serviceRegistrar);
            loadAnnotation(tm);
        }
    } else {
        reader = new DefaultAttributeTableReader(null, amp, this.isEnd, serviceRegistrar);
        loadAnnotation(tm);
    }
}

Example 2 with DefaultAttributeTableReader

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

the class ImportAttributeTableReaderTask method run.

@Override
public void run(TaskMonitor tm) throws Exception {
    tm.setTitle("Loading table data");
    tm.setProgress(0.0);
    tm.setStatusMessage("Loading table...");
    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) {
            e.printStackTrace();
            throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?");
        } finally {
            if (is != null)
                is.close();
        }
    }
    if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
        // Fixed bug# 1668, Only load data from the first sheet, ignore the rest sheets
        // UPDATE: From the user perspective it makes more sense to get the selected tab/sheet instead.
        String networkName = amp.getName();
        if (networkName == null)
            networkName = workbook.getSheetName(0);
        final Sheet sheet = workbook.getSheet(networkName);
        if (sheet != null) {
            reader = new ExcelAttributeSheetReader(sheet, amp, serviceRegistrar);
            loadAnnotation(tm);
        }
    } else {
        try {
            reader = new DefaultAttributeTableReader(null, amp, this.is, serviceRegistrar);
            loadAnnotation(tm);
        } catch (Exception ioe) {
            tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
        }
    }
}