de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java
/*******************************************************************************
* Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
*
* 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/>.
*
* Contributors:
* Department Biological Safety - BfR
*******************************************************************************/
package de.bund.bfr.knime.pmm.microbialdataedit;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.knime.core.data.DataTableSpec;
import org.knime.core.node.BufferedDataContainer;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.CanceledExecutionException;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeModel;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
import de.bund.bfr.knime.pmm.common.AgentXml;
import de.bund.bfr.knime.pmm.common.MatrixXml;
import de.bund.bfr.knime.pmm.common.MdInfoXml;
import de.bund.bfr.knime.pmm.common.MiscXml;
import de.bund.bfr.knime.pmm.common.PmmXmlDoc;
import de.bund.bfr.knime.pmm.common.generictablemodel.KnimeRelationReader;
import de.bund.bfr.knime.pmm.common.generictablemodel.KnimeTuple;
import de.bund.bfr.knime.pmm.common.pmmtablemodel.SchemaFactory;
import de.bund.bfr.knime.pmm.common.pmmtablemodel.TimeSeriesSchema;
/**
* This is the model implementation of MicrobialDataEdit.
*
*
* @author Christian Thoens
*/
public class MicrobialDataEditNodeModel extends NodeModel {
private SettingsHelper set;
/**
* Constructor for the node model.
*/
protected MicrobialDataEditNodeModel() {
super(1, 1);
set = new SettingsHelper();
}
/**
* {@inheritDoc}
*/
@Override
protected BufferedDataTable[] execute(final BufferedDataTable[] inData,
final ExecutionContext exec) throws Exception {
KnimeRelationReader reader = new KnimeRelationReader(
SchemaFactory.createDataSchema(), inData[0]);
List<KnimeTuple> tuples = new ArrayList<>();
while (reader.hasMoreElements()) {
tuples.add(reader.nextElement());
}
BufferedDataContainer container = exec
.createDataContainer(SchemaFactory.createDataSchema()
.createSpec());
for (KnimeTuple tuple : tuples) {
String combaseID = tuple.getString(TimeSeriesSchema.ATT_COMBASEID);
int condID = tuple.getInt(TimeSeriesSchema.ATT_CONDID);
String id;
if (combaseID != null) {
id = combaseID + " (" + condID + ")";
} else {
id = condID + "";
}
if (set.getAgents().containsKey(id)) {
PmmXmlDoc agentXml = new PmmXmlDoc();
AgentXml agent = set.getAgents().get(id);
if (agent != null) {
agentXml.add(agent);
} else {
agentXml.add(new AgentXml());
}
tuple.setValue(TimeSeriesSchema.ATT_AGENT, agentXml);
}
if (set.getAgentDetails().containsKey(id)) {
PmmXmlDoc agentXml = tuple
.getPmmXml(TimeSeriesSchema.ATT_AGENT);
((AgentXml) agentXml.get(0)).detail = set.getAgentDetails().get(id);
tuple.setValue(TimeSeriesSchema.ATT_AGENT, agentXml);
}
if (set.getMatrices().containsKey(id)) {
PmmXmlDoc matrixXml = new PmmXmlDoc();
MatrixXml matrix = set.getMatrices().get(id);
if (matrix != null) {
matrixXml.add(matrix);
} else {
matrixXml.add(new MatrixXml());
}
tuple.setValue(TimeSeriesSchema.ATT_MATRIX, matrixXml);
}
if (set.getMatrixDetails().containsKey(id)) {
PmmXmlDoc matrixXml = tuple
.getPmmXml(TimeSeriesSchema.ATT_MATRIX);
((MatrixXml) matrixXml.get(0)).detail = set.getMatrixDetails()
.get(id);
tuple.setValue(TimeSeriesSchema.ATT_MATRIX, matrixXml);
}
if (set.getComments().containsKey(id)) {
PmmXmlDoc infoXml = tuple
.getPmmXml(TimeSeriesSchema.ATT_MDINFO);
((MdInfoXml) infoXml.get(0)).comment = set.getComments().get(
id);
tuple.setValue(TimeSeriesSchema.ATT_MDINFO, infoXml);
}
if (set.getQualityScores().containsKey(id)) {
PmmXmlDoc infoXml = tuple
.getPmmXml(TimeSeriesSchema.ATT_MDINFO);
((MdInfoXml) infoXml.get(0)).qualityScore = set
.getQualityScores().get(id);
tuple.setValue(TimeSeriesSchema.ATT_MDINFO, infoXml);
}
if (set.getChecks().containsKey(id)) {
PmmXmlDoc infoXml = tuple
.getPmmXml(TimeSeriesSchema.ATT_MDINFO);
((MdInfoXml) infoXml.get(0))
.checked = set.getChecks().get(id);
tuple.setValue(TimeSeriesSchema.ATT_MDINFO, infoXml);
}
if (set.getTimeSeries().containsKey(id)) {
PmmXmlDoc timeSeriesXml = new PmmXmlDoc();
timeSeriesXml.getElementSet().addAll(
set.getTimeSeries().get(id));
tuple.setValue(TimeSeriesSchema.ATT_TIMESERIES, timeSeriesXml);
}
if (set.getReferences().containsKey(id)) {
PmmXmlDoc refXml = new PmmXmlDoc();
refXml.getElementSet().addAll(set.getReferences().get(id));
tuple.setValue(TimeSeriesSchema.ATT_LITMD, refXml);
}
PmmXmlDoc miscXml = new PmmXmlDoc();
for (int miscID : set.getConditions().keySet()) {
MiscXml misc = new MiscXml(set.getConditions().get(miscID));
misc.value = set.getConditionValues().get(miscID).get(id);
misc.unit = set.getConditionUnits().get(miscID).get(id);
misc.origUnit = set.getConditionUnits().get(miscID).get(id);
miscXml.add(misc);
}
for (int miscID : set.getAddedConditions().keySet()) {
if (set.getConditions().containsKey(miscID)) {
continue;
}
MiscXml misc = new MiscXml(set.getAddedConditions().get(miscID));
misc.value = set.getAddedConditionValues().get(miscID).get(id);
misc.unit = set.getAddedConditionUnits().get(miscID).get(id);
miscXml.add(misc);
}
tuple.setValue(TimeSeriesSchema.ATT_MISC, miscXml);
container.addRowToTable(tuple);
}
container.close();
return new BufferedDataTable[] { container.getTable() };
}
/**
* {@inheritDoc}
*/
@Override
protected void reset() {
}
/**
* {@inheritDoc}
*/
@Override
protected DataTableSpec[] configure(final DataTableSpec[] inSpecs)
throws InvalidSettingsException {
if (!SchemaFactory.createDataSchema().conforms(inSpecs[0])
|| SchemaFactory.createM1Schema().conforms(inSpecs[0])) {
throw new InvalidSettingsException("Wrong input");
}
if (set.getTimeSeries().isEmpty()) {
throw new InvalidSettingsException("Node has to be configured");
}
return new DataTableSpec[] { SchemaFactory.createDataSchema()
.createSpec() };
}
/**
* {@inheritDoc}
*/
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
set.saveSettings(settings);
}
/**
* {@inheritDoc}
*/
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings)
throws InvalidSettingsException {
set.loadSettings(settings);
}
/**
* {@inheritDoc}
*/
@Override
protected void validateSettings(final NodeSettingsRO settings)
throws InvalidSettingsException {
}
/**
* {@inheritDoc}
*/
@Override
protected void loadInternals(final File internDir,
final ExecutionMonitor exec) throws IOException,
CanceledExecutionException {
}
/**
* {@inheritDoc}
*/
@Override
protected void saveInternals(final File internDir,
final ExecutionMonitor exec) throws IOException,
CanceledExecutionException {
}
}