Example usage for org.apache.commons.configuration ConfigurationException ConfigurationException

Introduction

In this page you can find the example usage for org.apache.commons.configuration ConfigurationException ConfigurationException.

Prototype

public ConfigurationException(Throwable cause)

Source Link

Document

Constructs a new ConfigurationException with specified nested Throwable.

Usage

From source file:ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher.java

@Override
protected void initConfig() {
    localBasePath = Settings.getString("arrayExpress.local.datafile.basepath");
    remoteBaseDir = Settings.getString("arrayExpress.experiments.baseDir");

    if (localBasePath == null || localBasePath.length() == 0)
        throw new RuntimeException(new ConfigurationException("localBasePath was null or empty"));
    if (remoteBaseDir == null || remoteBaseDir.length() == 0)
        throw new RuntimeException(new ConfigurationException("baseDir was null or empty"));

}

From source file:ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher.java

@Override
protected void initConfig() {
    this.localBasePath = Settings.getString("geo.local.datafile.basepath");
    this.remoteBaseDir = Settings.getString("geo.remote.platformDir");
    if (StringUtils.isBlank(remoteBaseDir)) {
        throw new RuntimeException(
                new ConfigurationException("geo.remote.platformDir was not defined in resource bundle"));
    }/* w  w w  .j av  a 2s.  c  om*/

}

From source file:ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher.java

@Override
public void initConfig() {
    localBasePath = Settings.getString("geo.local.datafile.basepath");
    remoteBaseDir = Settings.getString("geo.remote.rawDataDir");

    if (localBasePath == null || localBasePath.length() == 0)
        throw new RuntimeException(new ConfigurationException("localBasePath was null or empty"));
    if (remoteBaseDir == null || remoteBaseDir.length() == 0)
        throw new RuntimeException(new ConfigurationException("baseDir was null or empty"));

}

From source file:ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher.java

@Override
protected void initConfig() {

    localBasePath = Settings.getString("ncbi.local.homologene.basepath");
    remoteBaseDir = Settings.getString("ncbi.remote.homologene.basedir");

    if (localBasePath == null || localBasePath.length() == 0)
        throw new RuntimeException(new ConfigurationException("localBasePath was null or empty"));
    if (remoteBaseDir == null || remoteBaseDir.length() == 0)
        throw new RuntimeException(new ConfigurationException("baseDir was null or empty"));

}

From source file:ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher.java

@Override
public void initConfig() {
    this.localBasePath = Settings.getString("ncbi.local.datafile.basepath");
    this.remoteBaseDir = Settings.getString("ncbi.remote.gene.basedir");

    if (remoteBaseDir == null)
        throw new RuntimeException(new ConfigurationException("Failed to get basedir"));
    if (localBasePath == null)
        throw new RuntimeException(new ConfigurationException("Failed to get localBasePath"));

}

From source file:ubic.gemma.core.loader.genome.taxon.TaxonFetcher.java

@Override
public void initConfig() {
    this.localBasePath = Settings.getString("ncbi.local.datafile.basepath");
    this.remoteBaseDir = Settings.getString("ncbi.remote.taxon.basedir");

    if (remoteBaseDir == null)
        throw new RuntimeException(new ConfigurationException("Failed to get basedir"));
    if (localBasePath == null)
        throw new RuntimeException(new ConfigurationException("Failed to get localBasePath"));
}

From source file:ubic.gemma.core.loader.protein.biomart.BiomartEnsemblNcbiFetcher.java

/**
 * Configure the URL for biomart//from   w  w  w  .j  a  v  a 2 s .c om
 *
 * @throws RuntimeException (ConfigurationException) one of the file download paths in the properties file was not configured
 *                          correctly.
 */
private void initConfig() {

    urlBiomartService = Settings.getString(BIOMARTPATH);
    if (urlBiomartService == null || urlBiomartService.length() == 0)
        throw new RuntimeException(new ConfigurationException(BIOMARTPATH + " was null or empty"));
}

From source file:ubic.gemma.core.loader.protein.string.StringProteinFileFetcher.java

/**
 * Sets the paths of the remote files to download as set in the project properties files
 *
 * @throws RuntimeException (ConfigurationException) one of the file download paths in the properties file was not configured
 *                          correctly./*from   www  .ja  v  a 2s .  c  o  m*/
 */
@SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
@Override
public void initConfig() {
    stringProteinFileName = Settings.getString(StringProteinFileFetcher.INTERACTION);
    if (stringProteinFileName == null || stringProteinFileName.length() == 0)
        throw new RuntimeException(
                new ConfigurationException(StringProteinFileFetcher.INTERACTION + " was null or empty"));
}

From source file:ubic.gemma.core.loader.protein.StringProteinProteinInteractionConverter.java

/**
 * @param ensembl2ncbi Map of ensembl peptide ids to entrez/ncbi id genes.
 *//*from  w  w w .ja  v a 2s . c o m*/
public StringProteinProteinInteractionConverter(Map<String, Ensembl2NcbiValueObject> ensembl2ncbi) {
    this.ensembl2ncbi = ensembl2ncbi;

    StringProteinProteinInteractionConverter.stringVersion = Settings.getString("protein.string.version");
    StringProteinProteinInteractionConverter.stringUrl = Settings.getString("protein.string.linksurl");
    if (StringProteinProteinInteractionConverter.stringUrl == null
            || StringProteinProteinInteractionConverter.stringUrl.length() == 0)
        throw new RuntimeException(new ConfigurationException("stringUrl was null or empty"));
    if (StringProteinProteinInteractionConverter.stringVersion == null
            || StringProteinProteinInteractionConverter.stringVersion.length() == 0)
        throw new RuntimeException(new ConfigurationException("stringVersion was null or empty"));
}

From source file:ubic.gemma.loader.expression.arrayExpress.DataFileFetcher.java

/**
 * @throws ConfigurationException//from  w w  w  .j  a v  a 2s  . co  m
 */
@Override
public void initConfig() {

    localBasePath = ConfigUtils.getString("arrayExpress.local.datafile.basepath");
    remoteBaseDir = ConfigUtils.getString("arrayExpress.experiments.baseDir");

    if (localBasePath == null || localBasePath.length() == 0)
        throw new RuntimeException(new ConfigurationException("localBasePath was null or empty"));
    if (remoteBaseDir == null || remoteBaseDir.length() == 0)
        throw new RuntimeException(new ConfigurationException("baseDir was null or empty"));

}