org.impressivecode.depress.matcher.commonmarker.MarkerInputTransformer.java Source code

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Here is the source code for org.impressivecode.depress.matcher.commonmarker.MarkerInputTransformer.java

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/*
 ImpressiveCode Depress Framework
 Copyright (C) 2013  ImpressiveCode contributors
    
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
    
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
    
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package org.impressivecode.depress.matcher.commonmarker;

import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;
import static org.impressivecode.depress.common.DataTableSpecUtils.findMissingColumnSubset;
import static org.impressivecode.depress.scm.common.SCMAdapterTableFactory.RESOURCE_NAME;

import java.util.List;
import java.util.Set;

import org.impressivecode.depress.common.InputTransformer;
import org.impressivecode.depress.common.TableCellReader;
import org.knime.core.data.DataColumnSpec;
import org.knime.core.data.DataRow;
import org.knime.core.data.DataTable;
import org.knime.core.data.DataTableSpec;
import org.knime.core.data.RowIterator;
import org.knime.core.node.InvalidSettingsException;

import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;

/**
 * 
 * @author Marek Majchrzak, ImpressiveCode
 * 
 */
public class MarkerInputTransformer implements InputTransformer<MarkerDataType> {

    private DataTableSpec minimalTableSpec;
    private DataTableSpec inputTableSpec;
    private DataTableSpec minimalOrTableSpec;

    public MarkerInputTransformer() {
    }

    @Override
    public List<MarkerDataType> transform(final DataTable inTable) {
        checkNotNull(this.minimalTableSpec, "Minimal DataTableSpec hat to be set");
        checkNotNull(this.inputTableSpec, "Input DataTableSpec hat to be set");
        checkNotNull(inTable, "InTable has to be set");
        List<MarkerDataType> markerData = Lists.newArrayListWithExpectedSize(1000);
        RowIterator iterator = inTable.iterator();
        while (iterator.hasNext()) {
            markerData.add(transformRow(iterator.next()));
        }
        return markerData;
    }

    @Override
    public MarkerDataType transformRow(final DataRow row) {
        TableCellReader reader = new TableCellReader(this.inputTableSpec, row);
        MarkerDataType marker = new MarkerDataType();
        marker.setResourceName(reader.stringOptional(RESOURCE_NAME));
        marker.setMarkers(reader.stringSetOptional(MarkerAdapterTableFactory.MARKER));
        marker.setActivityMarkers(reader.stringSetOptional(MarkerAdapterTableFactory.AM_MARKER));
        marker.setExtendedMarkers(reader.stringSetOptional(MarkerAdapterTableFactory.EXT_MARKER));
        return marker;
    }

    @Override
    public InputTransformer<MarkerDataType> validate() throws InvalidSettingsException {
        checkArgument(this.minimalTableSpec != null || this.minimalOrTableSpec != null,
                "Minimal or MinimalOr DataTableSpec has to be set");
        checkNotNull(this.inputTableSpec, "Input DataTableSpec hat to be set");

        if (this.minimalTableSpec != null) {
            Set<String> missing = findMissingColumnSubset(this.inputTableSpec, this.minimalTableSpec);
            if (!missing.isEmpty()) {
                throw new InvalidSettingsException(
                        "Markers input data table does not contain required columns. Missing: "
                                + Iterables.toString(missing));
            }
        }

        if (this.minimalOrTableSpec != null) {
            Set<String> missing = findMissingColumnSubset(this.inputTableSpec, this.minimalOrTableSpec);
            if (missing.size() == this.minimalOrTableSpec.getNumColumns()) {
                throw new InvalidSettingsException(
                        "Markers data table does not contain required columns. Should has at least one of: "
                                + Iterables.toString(missing));
            }
        }

        return this;
    }

    @Override
    public InputTransformer<MarkerDataType> setMinimalSpec(final DataTableSpec spec) {
        this.minimalTableSpec = spec;
        return this;
    }

    @Override
    public InputTransformer<MarkerDataType> setInputSpec(final DataTableSpec spec) {
        this.inputTableSpec = spec;
        return this;
    }

    @Override
    public InputTransformer<MarkerDataType> setMinimalOrSpec(final DataColumnSpec... orSpec) {
        this.minimalOrTableSpec = new DataTableSpec(orSpec);
        return this;
    }
}