uk.ac.ebi.adfconverter.common.configuration.ADFConverterConfiguration
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java.lang.Object
Allows the configuration of ADFConverter from an external file
All option values admit variable substitution. The
syntax of variable substitution is similar to that of Unix
shells. The string between an opening "${" and
closing "}" is interpreted as a key. The value of
the substituted variable can be defined as a system property or in
the configuration file itself. The value of the key is first
searched in the system properties, and if not found there, it is
then searched in the configuration file being parsed. The
corresponding value replaces the ${variableName} sequence. For
example, if java.home system property is set to
/home/xyz, then every occurrence of the sequence
${java.home} will be interpreted as
/home/xyz.
#ADF MAGEML Tool property file
#
# This file contains configuration properties for the ADF MAGE-ML Tool.
# They set behaviour for the different modules, but most of them can be overridded
# by the command-line.
#
# List of possible properties:
#
# The common module:
# adfconverter.common.loggingLevel : set the logging level for the treatment log (not the global tool log):
# DEBUG, INFO, WARN, ERROR, FATAL (log4j level). The global tool log level is set to info.
# adfconverter.common.logger.logType : set the type of the application output: console on the standard output, file exporting in a file
# adfconverter.common.logger.OUTPUTTYPE.format : for a given output type (console, file), set the format of each output line
# ( from log4j) : FORMATTYPE, ASSOCIATEDVALUE (ex: pattern: ,%-5p %x : %m%
# adfconverter.common.logger.applicationLogFile : set the file for the application log
# (should be rename adfconverter.common.logger.file.filename)
#
# The Checker module:
# adfconverter.checker.AccessionNumberCheckingEnable: set if the database accession number checking is enable (check accession number# against pattern provided in the approved database file
# adfconverter.checker.OntologyCheckerEnable: set if the Ontology term checking is enable
# (check if a term belong to the MGED Ontology, using the MGED Ontology in DAML+OIL from the MGED web site)
# adfconverter.checker.strictMode: set array design strict checking
# adfconverter.checker.doCurationToFile: set curated data file saving (save corrected data in a correct structure)
# adfconverter.checker.database.linkseparator: inner variable, should not be modified ( should be removed from configuration file)
#
# adfconverter.checker.stepByStepMode: set step by step array design checking
# adfconverter.checker.ApprovedDBFilePath: path to the ArrayExpress approved database file
# adfconverter.checker.ApprovedDBFileStructureDescriptionPath: path the file description file
# (should be removed from the configuration file)
# adfconverter.checker.FileDescriptionDirectory: path to the directory containing file structure description
# adfconverter.checker.MGEDOntologyFile: path to the MGED Ontology file ( in DAML+OIL format)
# adfconverter.checker.ADFMGEDOntologyLinks: path to the file containing link between ADF name, MGED Ontology category
# and MAGE object (MAGE Java class)
# adfconverter.checker.ADFMGEDOntologyLinksStructure: path to the file containing the structure description for the link file
# adfconverter.checker.duplicateCheckingEnable: set it the duplicate checking is enable (for ADF, checking of duplicate features,
# reporters, CompositeSequence. if disabled, the checking should be faster
#
# The conversion module
# //MAGE Identifier generation
# The user can generate MAGE identifiers following its own rules:
# The user can creatre variable used in generation rules. The user specifies a general rule and can add a rule per MAGE Object type.
# adfconverter.converter.identifier.VARIABLENAME : set a rule variable value.
# There are several inner variables, which can be used in rules:
# #DBName, add the corresponding database tag,
# #objectType, add the object type of the current object
# #objectTypeInitial, add the first letter of the object type name
# #objectNumber, add object number with the same object type
# adfconverter.converter.identifier.rule: set the common rule for identifier identifier
# adfconverter.converter.identifier.rule.OBJECTTYPE: set a specific rule for the given object type
#
# adfconverter.converter.assigned_geneTypeValue: set the ontology value corresponding to the ADF assigned gene ( should be removed?)
# adfconverter.converter.groupSeparator: set the separator between the groupname and group value
# adfconverter.converter.dtdPath: path to the version 1.1 MAGE DTD file
# adfconverter.converter.dtdpublicdoctype: set the the public doctype for generated MAGE-ML file
# adfconverter.converter.dtdsystemdoctype: set the system public doctype
# adfconverter.converter.UnsupportedArrayDesigns: set unsupported identifier prefix list (separator= ',') ( should be removed?)
#
#
#
# The Exporter module
# adfconverter.exporter.ADFOutputFileFormat: set default output for generated ADF ( can be text or workbook)
#
#
# The network properties
# adfconverter.network.proxySet: indicates if a proxy is needed for http connection ( true or false)
# adfconverter.network.proxyHost: set http proxy hostname or network address (only use if proxySet sets to true)
# adfconverter.network.proxyPort: set http proxy host port (only use if proxySet sets to true)
# adfconverter.network.proxyUser: set proxy user, if needed- optional (only use if proxySet sets to true)
# adfconverter.network.proxyPassword: set user passwork, if needed - optional (only use if proxySet sets to true)
#
# adfconverter.network.ftpProxySet: indicates if a proxy is needed for ftp connection ( true or false)
# adfconverter.network.ftpProxyHost: set ftp proxy hostname or network address (only use if ftpProxySet sets to true)
# adfconverter.network.ftpProxyPort: set ftp proxy host port (only use if ftpProxySet sets to true)
TODO have unsaveable properties
TODO add and remove properties
TODO add mandatory properties
| Field Summary | |
static java.lang.String |
CheckerPREFIX
Definition of the adfconverter property name sub prefix for the checker module: checker. |
static java.lang.String |
commonPREFIX
Definition of the adfconverter property name sub prefix for the common module: common. |
static java.lang.String |
conversionPREFIX
Definition of the adfconverter property name sub prefix for the conversion module: converter. |
static java.lang.String |
exporterPREFIX
Definition of the adfconverter property name sub prefix for exporter module: exporter. |
static java.lang.String |
identifierPREFIX
Definition of the adfconverter property name sub prefix for the identifier submodule (for identifier generation): identifier. |
static java.lang.String |
loggerPREFIX
Definition of the adfconverter property name sub prefix for logging module: logger. |
static java.lang.String |
networkPREFIX
Definition of the adfconverter property name sub prefix for network module: network. |
static java.lang.String |
PREFIX
Definition of the adfconverter property name prefix: adfconverter. |
static java.lang.String |
rulePREFIX
Definition of the adfconverter property name sub prefix for identifier generation rules: rule. |
| Constructor Summary | |
ADFConverterConfiguration()
Constructor of the ADFConverterConfiguration init list of mandatory properties |
|
| Method Summary | |
static void |
addProperty(java.lang.String name,
java.lang.String value)
Adds a property to the configuration |
static void |
doConfigure(java.util.Properties props)
Read configuration options from properties. |
static void |
doConfigure(java.lang.String configFileName,
boolean useDefaultConfiguration)
Read configuration from a file. |
static void |
doConfigure(java.net.URL configURL)
Read configuration options from url configURL. |
static java.lang.String |
getCheckerProperty(java.lang.String name)
Retrieves a Checker configuration property value |
static java.lang.String |
getCommonProperty(java.lang.String name)
Retrieves a commom configuration property value |
static java.util.Properties |
getConversionProperties()
Retrieves all properties for the converter |
static java.lang.String |
getConversionProperty(java.lang.String name)
Retrieves a Conversion configuration property value |
static java.util.Properties |
getExporterProperties()
Retrieves the properties corresponding to the exporter module |
static java.util.Properties |
getIdentifierProperties()
Retrieves all properties of the identifier generation |
static java.util.Properties |
getLoggerProperties()
Retrieves all properties corresponding to the logging module |
static java.lang.String |
getNetworkProperty(java.lang.String name)
Retrieves a Conversion configuration property value |
static java.lang.String |
getProperty(java.lang.String name)
Retrieves a configuration property value |
static void |
removeProperty(java.lang.String name)
Removes a property from configuration property list |
static void |
WriteConfiguration()
Writes the current configuration in the configuration file |
| Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
public static final java.lang.String CheckerPREFIX
public static final java.lang.String commonPREFIX
public static final java.lang.String conversionPREFIX
public static final java.lang.String exporterPREFIX
public static final java.lang.String identifierPREFIX
public static final java.lang.String loggerPREFIX
public static final java.lang.String networkPREFIX
public static final java.lang.String PREFIX
public static final java.lang.String rulePREFIX
| Constructor Detail |
public ADFConverterConfiguration()
| Method Detail |
public static void addProperty(java.lang.String name,
java.lang.String value)
name - the property namevalue - the value associated to the property name
public static void doConfigure(java.util.Properties props)
throws ConfigurationMissingConfException
properties.
props - the application properties to set
ConfigurationMissingConfException - if an error occurs during runtime
public static void doConfigure(java.lang.String configFileName,
boolean useDefaultConfiguration)
throws ConfigurationMissingConfException
The configuration file consists of statements in the format
key=value. The syntax of different configuration
elements are discussed below.
Use the # or ! characters at the
beginning of a line for comments.
configFileName - The name of the configuration file where the
configuration information is stored.useDefaultConfiguration - indicates if the default configuration must be used
ConfigurationMissingConfException - - if an error occurred when reading from the input stream.
java.lang.IllegalArgumentException - - if the input stream contains a malformed Unicode escape sequence.
public static void doConfigure(java.net.URL configURL)
throws ConfigurationMissingConfException
configURL.
configURL - the url of the config file
ConfigurationMissingConfException - if an error occurs during runtimepublic static java.lang.String getCheckerProperty(java.lang.String name)
name - the name of the property to retrieve
public static java.lang.String getCommonProperty(java.lang.String name)
name - the name of the property to retrieve
public static java.util.Properties getConversionProperties()
public static java.lang.String getConversionProperty(java.lang.String name)
name - the name of the property to retrieve
public static java.util.Properties getExporterProperties()
public static java.util.Properties getIdentifierProperties()
public static java.util.Properties getLoggerProperties()
public static java.lang.String getNetworkProperty(java.lang.String name)
name - the name of the property to retrieve
public static java.lang.String getProperty(java.lang.String name)
name - the name of the property to retrieve
public static void removeProperty(java.lang.String name)
name - the name of the property to removepublic static void WriteConfiguration()
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