/*
* 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.diffana;
import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import static fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder.DEFAULT_SINGLE_INPUT_PORT_NAME;
import static fr.ens.biologie.genomique.eoulsan.data.DataFormats.EXPRESSION_RESULTS_TSV;
import static fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule.DESEQ1_DOCKER_IMAGE;
import static java.util.Collections.unmodifiableSet;
import java.util.HashSet;
import java.util.Set;
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.core.InputPorts;
import fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder;
import fr.ens.biologie.genomique.eoulsan.core.Modules;
import fr.ens.biologie.genomique.eoulsan.core.Parameter;
import fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext;
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.design.Design;
import fr.ens.biologie.genomique.eoulsan.modules.AbstractModule;
import fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType;
import fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod;
import fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode;
import fr.ens.biologie.genomique.eoulsan.requirements.Requirement;
import fr.ens.biologie.genomique.eoulsan.util.r.RExecutor;
/**
* This class define the module of differential analysis in local mode.
* @since 1.0
* @author Laurent Jourdren
* @author Vivien Deshaies
*/
@LocalOnly
public class DiffAnaModule extends AbstractModule {
private static final String DISP_EST_METHOD_PARAMETER_NAME =
"disp.est.method";
private static final String DISP_EST_FIT_TYPE_PARAMETER_NAME =
"disp.est.fit.type";
private static final String DISP_EST_SHARING_MODE_PARAMETER_NAME =
"disp.est.sharing.mode";
private static final String MODULE_NAME = "diffana";
// parameters and there default values
private DispersionMethod dispEstMethod = DispersionMethod.POOLED;
private DispersionFitType dispEstFitType = DispersionFitType.LOCAL;
private DispersionSharingMode dispEstSharingMode =
DispersionSharingMode.MAXIMUM;
private Set<Requirement> requirements = new HashSet<>();
private RExecutor executor;
//
// Module methods
//
@Override
public String getName() {
return MODULE_NAME;
}
@Override
public Version getVersion() {
return Globals.APP_VERSION;
}
@Override
public String getDescription() {
return "This class compute the differential analysis for the experiment.";
}
@Override
public InputPorts getInputPorts() {
return new InputPortsBuilder()
.addPort(DEFAULT_SINGLE_INPUT_PORT_NAME, true, EXPRESSION_RESULTS_TSV)
.create();
}
@Override
public Set<Requirement> getRequirements() {
return unmodifiableSet(this.requirements);
}
@Override
public TaskResult execute(final TaskContext context,
final TaskStatus status) {
try {
final Design design = context.getWorkflow().getDesign();
// Launch differential analysis
final DiffAna diffana = new DiffAna(this.executor, design,
this.dispEstMethod, this.dispEstSharingMode, this.dispEstFitType);
diffana.run(context, context.getInputData(EXPRESSION_RESULTS_TSV));
// Write log file
return status.createTaskResult();
} catch (EoulsanException e) {
return status.createTaskResult(e,
"Error while analysis data: " + e.getMessage());
}
}
@Override
public void configure(final StepConfigurationContext context,
final Set<Parameter> stepParameters) throws EoulsanException {
// Parse R executor parameters
final Set<Parameter> parameters = new HashSet<>(stepParameters);
this.executor = RModuleCommonConfiguration.parseRExecutorParameter(context,
parameters, this.requirements, DESEQ1_DOCKER_IMAGE);
for (Parameter p : parameters) {
switch (p.getName()) {
case DISP_EST_METHOD_PARAMETER_NAME:
this.dispEstMethod =
DispersionMethod.getDispEstMethodFromName(p.getStringValue());
if (this.dispEstMethod == null) {
Modules.badParameterValue(context, p,
"Unknown dispersion estimation method");
}
break;
case DISP_EST_FIT_TYPE_PARAMETER_NAME:
this.dispEstFitType =
DispersionFitType.getDispEstFitTypeFromName(p.getStringValue());
if (this.dispEstFitType == null) {
Modules.badParameterValue(context, p,
"Unknown dispersion estimation fitType");
}
break;
case DISP_EST_SHARING_MODE_PARAMETER_NAME:
this.dispEstSharingMode = DispersionSharingMode
.getDispEstSharingModeFromName(p.getStringValue());
if (this.dispEstSharingMode == null) {
Modules.badParameterValue(context, p,
"Unknown dispersion estimation sharing mode");
}
break;
default:
Modules.unknownParameter(context, p);
}
}
// Log Step parameters
getLogger().info("In "
+ getName() + ", dispersion estimation method="
+ this.dispEstMethod.getName());
getLogger().info("In "
+ getName() + ", dispersion estimation sharing mode="
+ this.dispEstSharingMode.getName());
getLogger().info("In "
+ getName() + ", dispersion estimation fit type="
+ this.dispEstFitType.getName());
}
}