helpers.OpenBisFunctions.java Source code

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Here is the source code for helpers.OpenBisFunctions.java

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/*******************************************************************************
 * QBiC Project qNavigator enables users to manage their projects. Copyright (C) "2016? Christopher
 * Mohr, David Wojnar, Andreas Friedrich
 *
 * 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/>.
 *******************************************************************************/
package helpers;

import java.util.ArrayList;
import java.util.List;

import org.apache.commons.lang3.text.WordUtils;

import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm;

public class OpenBisFunctions {

    /**
     * Returns the 4 or 5 character project prefix used for samples in openBIS.
     * 
     * @param sample sample ID starting with a standard project prefix.
     * @return Project prefix of the sample
     */
    public static String getProjectPrefix(String sample) {
        if (Utils.isInteger("" + sample.charAt(4)))
            return sample.substring(0, 4);
        else
            return sample.substring(0, 5);
    }

    public static double statusToDoubleValue(String status) {

        double value = 0.0;

        switch (status) {
        case "STARTED":
            value = 0.25;
            break;
        case "RUNNING":
            value = 0.5;
            break;
        case "FINISHED":
            value = 1.0;
            break;

        }
        return value;
    }

    /**
     * Function to list the vocabulary terms for a given property which has been added to openBIS. The
     * property has to be a Controlled Vocabulary Property.
     * 
     * @param property the property type
     * @return list of the vocabulary terms of the given property
     */
    public static List<String> listVocabularyTermsForProperty(PropertyType property) {
        List<String> terms = new ArrayList<String>();
        ControlledVocabularyPropertyType controlled_vocab = (ControlledVocabularyPropertyType) property;
        for (VocabularyTerm term : controlled_vocab.getTerms()) {
            terms.add(term.getLabel().toString());
        }
        return terms;
    }

    /**
     * Function to get the label of a CV item for some property
     * 
     * @param propertyType the property type
     * @param propertyValue the property value
     * @return Label of CV item
     */
    public static String getCVLabelForProperty(PropertyType propertyType, String propertyValue) {
        ControlledVocabularyPropertyType controlled_vocab = (ControlledVocabularyPropertyType) propertyType;

        for (VocabularyTerm term : controlled_vocab.getTerms()) {
            if (term.getCode().equals(propertyValue)) {
                return term.getLabel();
            }
        }
        throw new IllegalArgumentException();
    }

    /**
     * Function to retrieve all properties which have been assigned to a specific entity type
     * 
     * @param entity_type entitiy type
     * @return list of properties which are assigned to the entity type
     */
    public static List<PropertyType> listPropertiesForType(EntityType entity_type) {
        List<PropertyType> property_types = new ArrayList<PropertyType>();
        List<PropertyTypeGroup> props = entity_type.getPropertyTypeGroups();
        for (PropertyTypeGroup pg : props) {
            for (PropertyType prop_type : pg.getPropertyTypes()) {
                property_types.add(prop_type);
            }
        }
        return property_types;
    }

    /**
     * Function to transform openBIS entity type to human readable text. Performs String replacement
     * and does not query openBIS!
     * 
     * @param entityCode the entity code as string
     * @return entity code as string in human readable text
     */
    public static String openBIScodeToString(String entityCode) {
        entityCode = WordUtils.capitalizeFully(entityCode.replace("_", " ").toLowerCase());
        String edit_string = entityCode.replace("Ngs", "NGS").replace("Hla", "HLA").replace("Rna", "RNA")
                .replace("Dna", "DNA").replace("Ms", "MS");
        if (edit_string.startsWith("Q ")) {
            edit_string = edit_string.replace("Q ", "");
        }
        return edit_string;
    }

}