public class CellBaseConfiguration extends Object
Modifier and Type | Class and Description |
---|---|
static class |
CellBaseConfiguration.ConfigurationFileFormat |
Modifier and Type | Field and Description |
---|---|
static String |
CELLBASE_DATABASES_MONGODB_HOST |
static String |
CELLBASE_DATABASES_MONGODB_OPTIONS_PREFIX |
static String |
CELLBASE_DATABASES_MONGODB_PASSWORD |
static String |
CELLBASE_DATABASES_MONGODB_USER |
static String |
CELLBASE_PREFIX |
Constructor and Description |
---|
CellBaseConfiguration() |
public static final String CELLBASE_PREFIX
public static final String CELLBASE_DATABASES_MONGODB_HOST
public static final String CELLBASE_DATABASES_MONGODB_USER
public static final String CELLBASE_DATABASES_MONGODB_PASSWORD
public static final String CELLBASE_DATABASES_MONGODB_OPTIONS_PREFIX
public static CellBaseConfiguration load(Path configurationPath) throws IOException
IOException
public static CellBaseConfiguration load(InputStream configurationInputStream) throws IOException
IOException
public static CellBaseConfiguration load(InputStream configurationInputStream, CellBaseConfiguration.ConfigurationFileFormat format) throws IOException
IOException
public void serialize(OutputStream configurationOututStream) throws IOException
IOException
protected static void overwriteEnvVariables(CellBaseConfiguration configuration)
protected static void overwriteEnvVariables(CellBaseConfiguration configuration, Map<String,String> envVariables)
public String getVersion()
public void setVersion(String version)
public String getApiVersion()
public void setApiVersion(String apiVersion)
public String getWiki()
public void setWiki(String wiki)
public String getMaintenanceFlagFile()
public void setMaintenanceFlagFile(String maintenanceFlagFile)
public String getMaintainerContact()
public void setMaintainerContact(String maintainerContact)
public Databases getDatabases()
public CellBaseConfiguration setDatabases(Databases databases)
public String getDefaultOutdir()
public void setDefaultOutdir(String defaultOutdir)
public DownloadProperties getDownload()
public void setDownload(DownloadProperties download)
public SpeciesProperties getSpecies()
public void setSpecies(SpeciesProperties species)
public SpeciesConfiguration getSpeciesConfig(String id)
id
- shortName for species, e.g. hsapienspublic List<SpeciesConfiguration> getAllSpecies()
public ServerProperties getServer()
public void setServer(ServerProperties server)
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