edu.umn.msi.tropix.jobs.activities.factories.GalaxySupportImpl.java Source code

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Here is the source code for edu.umn.msi.tropix.jobs.activities.factories.GalaxySupportImpl.java

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.jobs.activities.factories;

import java.util.List;

import javax.annotation.ManagedBean;
import javax.inject.Inject;

import com.google.common.collect.Lists;

import edu.umn.msi.tropix.files.PersistentModelStorageDataFactory;
import edu.umn.msi.tropix.galaxy.GalaxyDataUtils;
import edu.umn.msi.tropix.galaxy.GalaxyDataUtils.ParamVisitor;
import edu.umn.msi.tropix.galaxy.tool.Param;
import edu.umn.msi.tropix.galaxy.tool.ParamType;
import edu.umn.msi.tropix.galaxy.tool.Tool;
import edu.umn.msi.tropix.galaxy.inputs.Input;
import edu.umn.msi.tropix.galaxy.inputs.RootInput;
import edu.umn.msi.tropix.grid.credentials.Credential;
import edu.umn.msi.tropix.storage.client.ModelStorageData;

@ManagedBean
class GalaxySupportImpl implements GalaxySupport {
    private final PersistentModelStorageDataFactory persistentModelStorageDataFactory;

    @Inject
    GalaxySupportImpl(final PersistentModelStorageDataFactory persistentModelStorageDataFactory) {
        this.persistentModelStorageDataFactory = persistentModelStorageDataFactory;
    }

    public List<GalaxyInputFile> prepareInputFiles(final Tool tool, final RootInput rootInput,
            final Credential credential) {
        final List<GalaxyInputFile> files = Lists.newLinkedList();
        GalaxyDataUtils.visitParams(tool, rootInput, new ParamVisitor() {
            public void visit(final String key, final Input fileInput, final Param param) {
                final ParamType paramType = param.getType();
                if (paramType != ParamType.DATA) {
                    return;
                }
                final String fileId = fileInput.getValue();
                final ModelStorageData data = persistentModelStorageDataFactory.getPersistedStorageData(fileId,
                        credential);
                final String fileName = data.getTropixFile().getName();
                fileInput.setValue(fileName);
                final GalaxyInputFile fileSummary = new GalaxyInputFile(fileName, data.prepareDownloadResource());
                files.add(fileSummary);
            }
        });
        return files;
    }

}