com.ohnosequences.xml.model.mg7.MG7DataXML.java Source code

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Here is the source code for com.ohnosequences.xml.model.mg7.MG7DataXML.java

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/*
 * Copyright (C) 2010-2012  "Oh no sequences!"
 *
 * This is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero 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 Affero General Public License for more details.
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 */
package com.ohnosequences.xml.model.mg7;

import com.ohnosequences.xml.api.model.XMLElement;
import com.ohnosequences.xml.api.model.XMLElementException;
import org.jdom2.Element;

/**
 *
 * @author <a href="mailto:ppareja@ohnosequences.com">Pablo Pareja-Tobes</a>
 */
public class MG7DataXML extends XMLElement {

    public static final String TAG_NAME = "mg7_data";

    public static final String QUEUE_NAME_TAG_NAME = "queue_name";
    public static final String READS_PER_FILE_TAG_NAME = "reads_per_file";
    public static final String READ_PACKAGES_BUCKET_FOLDER_TAG_NAME = "read_packages_bucket_folder";
    public static final String BUCKET_TAG_NAME = "bucket";
    public static final String READS_BUCKET_FOLDER_TAG_NAME = "reads_bucket_folder";
    public static final String RESULTS_BUCKET_FOLDER_TAG_NAME = "results_bucket_folder";
    public static final String ERRORS_BUCKET_FOLDER_TAG_NAME = "errors_bucket_folder";

    public static final String INSTANCES_IDLE_TIME_IN_SECONDS_TAG_NAME = "instances_idle_time_in_seconds";
    public static final String INSTANCE_TYPE_TAG_NAME = "instance_type";

    public static final String BASE_FOLDER_TAG_NAME = "base_folder";
    public static final String BLAST_PATH_TAG_NAME = "blast_path";

    public static final String ERROR_FILE_SUFFIX_TAG_NAME = "error_file_suffix";

    public static final String PROJECT_PREFIX_TAG_NAME = "project_prefix";

    public static final String KEY_PAIR_NAME_TAG_NAME = "key_pair_name";

    public static final String NUMBER_OF_CONCURRENT_INSTANCES_TAG_NAME = "number_of_concurrent_instances";
    public static final String SPOT_INSTANCE_PRICE_TAG_NAME = "spot_instance_price";

    public static final String USER_DATA_FILE_TAG_NAME = "user_data_file";

    public static final String ERRORS_SNS_TOPIC_NAME_TAG_NAME = "errors_sns_topic_name";
    public static final String ERRORS_SNS_TOPIC_ARN_TAG_NAME = "errors_sns_topic_arn";

    public static final String RESULTS_DB_FOLDER = "results_db_folder";

    public static final String STORE_HITS_TAG_NAME = "store_hits";
    public static final String STORE_HSPS_TAG_NAME = "store_hsps";

    public static final String BLAST_NT_S3_FILE_TAG_NAME = "blast_nt_s3_file";

    public MG7DataXML() {
        super(new Element(TAG_NAME));
    }

    public MG7DataXML(Element elem) throws XMLElementException {
        super(elem);
        if (!elem.getName().equals(TAG_NAME)) {
            throw new XMLElementException(XMLElementException.WRONG_TAG_NAME, new XMLElement(elem));
        }
    }

    public MG7DataXML(String value) throws Exception {
        super(value);
        if (!root.getName().equals(TAG_NAME)) {
            throw new XMLElementException(XMLElementException.WRONG_TAG_NAME, new XMLElement(value));
        }
    }

    //----------------SETTERS-------------------
    public void setQueueName(String value) {
        setNodeText(QUEUE_NAME_TAG_NAME, value);
    }

    public void setReadsPerFile(String value) {
        setNodeText(READS_PER_FILE_TAG_NAME, value);
    }

    public void setReadPackagesBucketFolder(String value) {
        setNodeText(READ_PACKAGES_BUCKET_FOLDER_TAG_NAME, value);
    }

    public void setBucket(String value) {
        setNodeText(BUCKET_TAG_NAME, value);
    }

    public void setReadsBucketFolder(String value) {
        setNodeText(READS_BUCKET_FOLDER_TAG_NAME, value);
    }

    public void setResultsBucketFolder(String value) {
        setNodeText(RESULTS_BUCKET_FOLDER_TAG_NAME, value);
    }

    public void setErrorsBucketFolder(String value) {
        setNodeText(ERRORS_BUCKET_FOLDER_TAG_NAME, value);
    }

    public void setInstancesIdleTimeInSeconds(String value) {
        setNodeText(INSTANCES_IDLE_TIME_IN_SECONDS_TAG_NAME, value);
    }

    public void setInstanceType(String value) {
        setNodeText(INSTANCE_TYPE_TAG_NAME, value);
    }

    public void setBaseFolder(String value) {
        setNodeText(BASE_FOLDER_TAG_NAME, value);
    }

    public void setBlastPath(String value) {
        setNodeText(BLAST_PATH_TAG_NAME, value);
    }

    public void setErrorFileSufix(String value) {
        setNodeText(ERROR_FILE_SUFFIX_TAG_NAME, value);
    }

    public void setProjectPrefix(String value) {
        setNodeText(PROJECT_PREFIX_TAG_NAME, value);
    }

    public void setKeyPairName(String value) {
        setNodeText(KEY_PAIR_NAME_TAG_NAME, value);
    }

    public void setNumberOfConcurrentInstances(String value) {
        setNodeText(NUMBER_OF_CONCURRENT_INSTANCES_TAG_NAME, value);
    }

    public void setSpotInstancePrice(String value) {
        setNodeText(SPOT_INSTANCE_PRICE_TAG_NAME, value);
    }

    public void setUserDataFile(String value) {
        setNodeText(USER_DATA_FILE_TAG_NAME, value);
    }

    public void setErrorsSNSTopicName(String value) {
        setNodeText(ERRORS_SNS_TOPIC_NAME_TAG_NAME, value);
    }

    public void setErrorsSNSTopicArn(String value) {
        setNodeText(ERRORS_SNS_TOPIC_ARN_TAG_NAME, value);
    }

    public void setResultsDBFolder(String value) {
        setNodeText(RESULTS_DB_FOLDER, value);
    }

    public void setStoreHits(Boolean value) {
        setNodeText(STORE_HITS_TAG_NAME, String.valueOf(value));
    }

    public void setStoreHsps(Boolean value) {
        setNodeText(STORE_HSPS_TAG_NAME, String.valueOf(value));
    }

    public void setBlastNtS3File(String value) {
        setNodeText(BLAST_NT_S3_FILE_TAG_NAME, value);
    }

    //----------------GETTERS---------------------
    public String getQueueName() {
        return getNodeText(QUEUE_NAME_TAG_NAME);
    }

    public int getReadsPerFile() {
        return Integer.parseInt(getNodeText(READS_PER_FILE_TAG_NAME));
    }

    public String getReadPackagesBucketFolder() {
        return getNodeText(READ_PACKAGES_BUCKET_FOLDER_TAG_NAME);
    }

    public String getBucket() {
        return getNodeText(BUCKET_TAG_NAME);
    }

    public String getResultsBucketFolder() {
        return getNodeText(RESULTS_BUCKET_FOLDER_TAG_NAME);
    }

    public String getErrorsBucketFolder() {
        return getNodeText(ERRORS_BUCKET_FOLDER_TAG_NAME);
    }

    public String getReadsBucketFolder() {
        return getNodeText(READS_BUCKET_FOLDER_TAG_NAME);
    }

    public int getInstancesIdleTimeInSeconds() {
        return Integer.parseInt(getNodeText(INSTANCES_IDLE_TIME_IN_SECONDS_TAG_NAME));
    }

    public String getInstanceType() {
        return getNodeText(INSTANCE_TYPE_TAG_NAME);
    }

    public String getBaseFolder() {
        return getNodeText(BASE_FOLDER_TAG_NAME);
    }

    public String getBlastPath() {
        return getNodeText(BLAST_PATH_TAG_NAME);
    }

    public String getProjectPrefix() {
        return getNodeText(PROJECT_PREFIX_TAG_NAME);
    }

    public String getErroFileSufix() {
        return getNodeText(ERROR_FILE_SUFFIX_TAG_NAME);
    }

    public String getKeyPairName() {
        return getNodeText(KEY_PAIR_NAME_TAG_NAME);
    }

    public int getNumberOfConcurrentInstances() {
        return Integer.parseInt(getNodeText(NUMBER_OF_CONCURRENT_INSTANCES_TAG_NAME));
    }

    public String getSpotInstancePrice() {
        return getNodeText(SPOT_INSTANCE_PRICE_TAG_NAME);
    }

    public String getUserDataFile() {
        return getNodeText(USER_DATA_FILE_TAG_NAME);
    }

    public String getErrorsSNSTopicName() {
        return getNodeText(ERRORS_SNS_TOPIC_NAME_TAG_NAME);
    }

    public String getErrorsSNSTopicArn() {
        return getNodeText(ERRORS_SNS_TOPIC_ARN_TAG_NAME);
    }

    public String getResultsDBFolder() {
        return getNodeText(RESULTS_DB_FOLDER);
    }

    public boolean getStoreHits() {
        return Boolean.parseBoolean(getNodeText(STORE_HITS_TAG_NAME));
    }

    public boolean getStoreHsps() {
        return Boolean.parseBoolean(getNodeText(STORE_HSPS_TAG_NAME));
    }

    public String getBlastNtS3File() {
        return getNodeText(BLAST_NT_S3_FILE_TAG_NAME);
    }

}