DiseasePanel.java

/*
 * Copyright 2015-2016 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.opencga.catalog.models;

import org.opencb.opencga.catalog.models.acls.AbstractAcl;
import org.opencb.opencga.catalog.models.acls.permissions.DiseasePanelAclEntry;

import java.util.Collections;
import java.util.List;

/**
 * Created by pfurio on 01/06/16.
 */
public class DiseasePanel extends AbstractAcl<DiseasePanelAclEntry> {

    private long id;
    private String name;
    private String disease;
    private String description;

    private List<String> genes;
    private List<String> regions;
    private List<String> variants;

    private PanelStatus status;
//    private List<DiseasePanelAclEntry> acl;


    public DiseasePanel() {
    }

    public DiseasePanel(long id, String name, String disease, String description, List<String> genes, List<String> regions,
                        List<String> variants, PanelStatus status) {
        this.id = id;
        this.name = name;
        this.disease = disease;
        this.description = description;
        this.genes = genes;
        this.regions = regions;
        this.variants = variants;
        this.acl = Collections.emptyList();
        this.status = status;
    }

    public DiseasePanel(long id, String name, String disease, String description, List<String> genes, List<String> regions,
                        List<String> variants, PanelStatus status, List<DiseasePanelAclEntry> acl) {
        this.id = id;
        this.name = name;
        this.disease = disease;
        this.description = description;
        this.genes = genes;
        this.regions = regions;
        this.variants = variants;
        this.status = status;
        this.acl = acl;
    }


    public static class PanelStatus extends Status {

        public static final String ARCHIVED = "ARCHIVED";

        public PanelStatus(String status, String message) {
            if (isValid(status)) {
                init(status, message);
            } else {
                throw new IllegalArgumentException("Unknown status " + status);
            }
        }

        public PanelStatus(String status) {
            this(status, "");
        }

        public PanelStatus() {
            this(READY, "");
        }

        public static boolean isValid(String status) {
            if (Status.isValid(status)) {
                return true;
            }
            if (status != null && (status.equals(ARCHIVED))) {
                return true;
            }
            return false;
        }
    }

    @Override
    public String toString() {
        final StringBuilder sb = new StringBuilder("DiseasePanel{");
        sb.append("id=").append(id);
        sb.append(", name='").append(name).append('\'');
        sb.append(", disease='").append(disease).append('\'');
        sb.append(", description='").append(description).append('\'');
        sb.append(", genes=").append(genes);
        sb.append(", regions=").append(regions);
        sb.append(", variants=").append(variants);
        sb.append(", status=").append(status);
        sb.append(", acl=").append(acl);
        sb.append('}');
        return sb.toString();
    }

    public long getId() {
        return id;
    }

    public DiseasePanel setId(long id) {
        this.id = id;
        return this;
    }

    public String getName() {
        return name;
    }

    public DiseasePanel setName(String name) {
        this.name = name;
        return this;
    }

    public String getDisease() {
        return disease;
    }

    public DiseasePanel setDisease(String disease) {
        this.disease = disease;
        return this;
    }

    public String getDescription() {
        return description;
    }

    public DiseasePanel setDescription(String description) {
        this.description = description;
        return this;
    }

    public List<String> getGenes() {
        return genes;
    }

    public DiseasePanel setGenes(List<String> genes) {
        this.genes = genes;
        return this;
    }

    public List<String> getRegions() {
        return regions;
    }

    public DiseasePanel setRegions(List<String> regions) {
        this.regions = regions;
        return this;
    }

    public List<String> getVariants() {
        return variants;
    }

    public DiseasePanel setVariants(List<String> variants) {
        this.variants = variants;
        return this;
    }

    public PanelStatus getStatus() {
        return status;
    }

    public DiseasePanel setStatus(PanelStatus status) {
        this.status = status;
        return this;
    }

    public DiseasePanel setAcl(List<DiseasePanelAclEntry> acl) {
        this.acl = acl;
        return this;
    }

}