/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.modules;
import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;
import static com.google.common.base.Preconditions.checkState;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.annotations.LocalOnly;
import fr.ens.biologie.genomique.eoulsan.annotations.ReuseModuleInstance;
import fr.ens.biologie.genomique.eoulsan.checkers.CheckStore;
import fr.ens.biologie.genomique.eoulsan.checkers.Checker;
import fr.ens.biologie.genomique.eoulsan.core.DataUtils;
import fr.ens.biologie.genomique.eoulsan.core.InputPorts;
import fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder;
import fr.ens.biologie.genomique.eoulsan.core.OutputPort;
import fr.ens.biologie.genomique.eoulsan.core.OutputPorts;
import fr.ens.biologie.genomique.eoulsan.core.Parameter;
import fr.ens.biologie.genomique.eoulsan.core.TaskContext;
import fr.ens.biologie.genomique.eoulsan.core.TaskResult;
import fr.ens.biologie.genomique.eoulsan.core.TaskStatus;
import fr.ens.biologie.genomique.eoulsan.core.Version;
import fr.ens.biologie.genomique.eoulsan.data.Data;
import fr.ens.biologie.genomique.eoulsan.data.DataFormat;
/**
* This class is a module that launch checkers.
* @author Laurent Jourdren
* @since 2.0
*/
@LocalOnly
@ReuseModuleInstance
public class CheckerModule extends AbstractModule {
public static final String MODULE_NAME = "checker";
private static CheckerModule instance;
private final Map<DataFormat, Checker> checkers = new HashMap<>();
private final Map<DataFormat, Set<Parameter>> checkerConfiguration =
new HashMap<>();
private InputPorts inputPorts = InputPortsBuilder.noInputPort();
private boolean inputPortsConfigured;
/**
* Configure input port of the checker from the output ports of the design
* step.
* @param designOutputPorts output ports of the design step
*/
void configureInputPorts(final OutputPorts designOutputPorts) {
checkState(!this.inputPortsConfigured,
"inputPorts has been already configured");
final InputPortsBuilder builder = new InputPortsBuilder();
for (OutputPort port : designOutputPorts) {
final String portName = port.getName();
final DataFormat format = port.getFormat();
if (format.isChecker()) {
if (!this.checkers.containsKey(format)) {
builder.addPort(portName, true, format);
this.checkers.put(format, format.getChecker());
}
}
}
this.inputPorts = builder.create();
this.inputPortsConfigured = true;
}
/**
* This method allow to configure a checker from the configure method of other
* steps, that's why this method is static.
* @param format checker format to configure
* @param parameters parameter of the checker
*/
public static final void configureChecker(final DataFormat format,
final Set<Parameter> parameters) {
checkNotNull(format, "format argument cannot be null");
checkNotNull(parameters, "parameter argument cannot be null");
checkArgument(format.isChecker(),
"No checker exists for format: " + format.getName());
checkState(instance != null,
"Instance of CheckerModule has not been yet created");
instance.checkerConfiguration.put(format, Sets.newHashSet(parameters));
}
//
// Module methods
//
@Override
public String getName() {
return MODULE_NAME;
}
@Override
public Version getVersion() {
return Globals.APP_VERSION;
}
@Override
public InputPorts getInputPorts() {
return this.inputPorts;
}
@Override
public TaskResult execute(final TaskContext context,
final TaskStatus status) {
// Get the CheckStore
final CheckStore checkStore = CheckStore.getCheckStore();
int count = 0;
try {
final List<Checker> checkerList = createDependenciesList();
// For all input ports of the step
for (Checker checker : checkerList) {
// Get the format of the checker
final DataFormat format = checker.getFormat();
// Configure checker if specific configuration exists
if (this.checkerConfiguration.containsKey(format)) {
checker.configure(this.checkerConfiguration.get(format));
}
for (Data data : context.getInputData(format).getListElements()) {
context.getLogger()
.info("Start checker "
+ checker.getName() + " to check: "
+ DataUtils.getDataFiles(data));
// Check the data
checker.check(data, checkStore);
context.getLogger()
.info("End of checker "
+ checker.getName() + " to check: "
+ DataUtils.getDataFiles(data));
}
count++;
status.setProgress(((double) count) / checkerList.size());
}
} catch (EoulsanException e) {
return status.createTaskResult(e);
} finally {
// Clear the checker
this.checkers.clear();
this.checkerConfiguration.clear();
}
return status.createTaskResult();
}
/**
* Create the dependencies list of the checker.
* @return a list of Checker object correctly ordered to avoid missing
* dependencies
* @throws EoulsanException if dependencies order cannot be defined
*/
private List<Checker> createDependenciesList() throws EoulsanException {
List<Checker> list = Lists.newArrayList(this.checkers.values());
List<Checker> result = new ArrayList<>();
final Map<Checker, Set<Checker>> dependencies = new HashMap<>();
final Set<Checker> added = new HashSet<>();
// Create the dependencies map
for (Checker c : list) {
if (c == null) {
continue;
}
final Set<Checker> deps = new HashSet<>();
for (DataFormat format : c.getCheckersRequired()) {
if (this.checkers.containsKey(format)) {
deps.add(this.checkers.get(format));
}
}
if (deps.size() == 0) {
result.add(c);
added.add(c);
} else {
dependencies.put(c, deps);
}
}
// Resolve dependencies
while (result.size() != list.size()) {
final Set<Checker> toRemove = new HashSet<>();
for (Map.Entry<Checker, Set<Checker>> e : dependencies.entrySet()) {
e.getValue().removeAll(added);
if (e.getValue().size() == 0) {
toRemove.add(e.getKey());
}
}
if (toRemove.size() == 0) {
throw new EoulsanException("Unable to resolve checker dependencies");
}
for (Checker c : toRemove) {
dependencies.remove(c);
result.add(c);
added.add(c);
}
}
return result;
}
//
// Constructor
//
/**
* Public constructor.
*/
public CheckerModule() {
checkState(instance == null,
"Instance of CheckerModule has been already created");
instance = this;
}
}