FeatureTableImportModule.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 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 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 3 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 MZmine 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.modules.featuretableimport;

import java.io.File;
import java.util.Collection;
import java.util.List;

import javax.annotation.Nonnull;

import org.apache.commons.io.FilenameUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.google.common.base.Strings;

import io.github.msdk.MSDKMethod;
import io.github.msdk.datamodel.datastore.DataPointStore;
import io.github.msdk.datamodel.datastore.DataPointStoreFactory;
import io.github.msdk.datamodel.featuretables.FeatureTable;
import io.github.msdk.io.csv.CsvFileImportMethod;
import io.github.msdk.io.mztab.MzTabFileImportMethod;
import io.github.mzmine.gui.MZmineGUI;
import io.github.mzmine.modules.MZmineProcessingModule;
import io.github.mzmine.modules.rawdata.rawdataimport.RawDataImportParameters;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.project.MZmineProject;
import io.github.mzmine.taskcontrol.MSDKTask;
import javafx.concurrent.Task;

/**
 * Feature table import module
 */
public class FeatureTableImportModule implements MZmineProcessingModule {

  private Logger logger = LoggerFactory.getLogger(this.getClass());

  @Nonnull
  private static final String MODULE_NAME = "Feature table import";
  @Nonnull
  private static final String MODULE_DESCRIPTION =
      "This module imports feature tables into the project.";

  @Override
  public @Nonnull String getName() {
    return MODULE_NAME;
  }

  @Override
  public @Nonnull String getDescription() {
    return MODULE_DESCRIPTION;
  }

  @Override
  public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
      @Nonnull Collection<Task<?>> tasks) {

    final List<File> fileNames =
        parameters.getParameter(FeatureTableImportParameters.fileNames).getValue();
    final String removePrefix =
        parameters.getParameter(RawDataImportParameters.removePrefix).getValue();
    final String removeSuffix =
        parameters.getParameter(RawDataImportParameters.removeSuffix).getValue();

    if (fileNames == null) {
      logger.warn("Feature table import module started with no filenames");
      return;
    }

    for (File fileName : fileNames) {

      if ((!fileName.exists()) || (!fileName.canRead())) {
        MZmineGUI.displayMessage("Cannot read file " + fileName);
        logger.warn("Cannot read file " + fileName);
        continue;
      }

      DataPointStore dataStore = DataPointStoreFactory.getTmpFileDataStore();

      // Find file extension and initiate corresponding import method
      String fileExtension = FilenameUtils.getExtension(fileName.getAbsolutePath());
      MSDKMethod<?> method = null;
      switch (fileExtension.toUpperCase()) {
        default:
        case "CSV":
          method = new CsvFileImportMethod(fileName, dataStore);
          break;
        case "MZTAB":
          method = new MzTabFileImportMethod(fileName, dataStore);
          break;
      }
      final MSDKMethod<?> finalMethod = method;

      MSDKTask newTask =
          new MSDKTask("Importing feature table file", fileName.getName(), finalMethod);
      newTask.setOnSucceeded(e -> {
        FeatureTable featureTable = (FeatureTable) finalMethod.getResult();
        if (featureTable == null)
          return;

        // Remove common prefix
        if (!Strings.isNullOrEmpty(removePrefix)) {
          String name = featureTable.getName();
          if (removePrefix != null && name.startsWith(removePrefix))
            name = name.substring(removePrefix.length());
          featureTable.setName(name);
        }

        // Remove common suffix
        if (!Strings.isNullOrEmpty(removeSuffix)) {
          String suffix = removeSuffix;
          if (suffix.equals(".*"))
            suffix = "." + fileExtension;
          String name = featureTable.getName();
          if (name.endsWith(suffix))
            name = name.substring(0, name.length() - suffix.length());
          featureTable.setName(name);
        }

        project.addFeatureTable(featureTable);
      });

      tasks.add(newTask);

    }

  }

  @Override
  public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
    return FeatureTableImportParameters.class;
  }
}