IDMapperService (BridgeDb Server 2.3.1 API)

java.lang.Object
- org.restlet.Restlet
- - org.restlet.Application
  - - org.bridgedb.server.IDMapperService

All Implemented Interfaces:

org.restlet.Uniform
```
public class IDMapperService
extends org.restlet.Application
```
Server component for ID mapping.
Use -DserverURL=http:// to change the URL to the server. It defaults to http://bridgedb.org/wiki/BridgeWebservice and must be overwritten for custom installations.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`CONF_GDBS`
`File`	`configFile`
`static String`	`PAR_DATASOURCES`
`static String`	`PAR_DEST_SYSTEM`
`static String`	`PAR_ID`
`static String`	`PAR_ORGANISM`
`static String`	`PAR_QUERY`
`static String`	`PAR_SOURCE_SYSTEM`
`static String`	`PAR_SYSTEM`
`static String`	`PAR_TARGET_ATTR_NAME`
`static String`	`PAR_TARGET_LIMIT`
`static String`	`PAR_TARGET_SYSTEM`
`static String`	`URL_ATTRIBUTE_SEARCH` URL pattern for searching by attribute.
`static String`	`URL_ATTRIBUTE_SET` URL pattern for getting the supported attribute set.
`static String`	`URL_ATTRIBUTES` URL pattern for getting attributes of an xref.
`static String`	`URL_BACK_PAGE_TEXT` URL pattern for getting backpage HTML.
`static String`	`URL_CONFIG` URL pattern for getting the server configuration.
`static String`	`URL_CONTENTS` URL pattern for getting a list of species loaded in the server.
`static String`	`URL_DATASOURCES` URL pattern for getting the datasources.txt file
`static String`	`URL_HOME` URL pattern to redirect to home page.
`static String`	`URL_IS_FREE_SEARCH_SUPPORTED` URL pattern for finding out if free search is supported.
`static String`	`URL_IS_MAPPING_SUPPORTED` URL pattern to find out if a mapping is supported.
`static String`	`URL_NO_MATCH` URL pattern to catch a misformed query.
`static String`	`URL_PROPERTIES` URL pattern for getting IDMapper properties.
`static String`	`URL_SEARCH` URL pattern for searching xrefs.
`static String`	`URL_SUPPORTED_SOURCE_DATASOURCES` URL pattern for getting the supported source datasources for this database.
`static String`	`URL_SUPPORTED_TARGET_DATASOURCES` URL pattern for getting the supported target datasources for this database.
`static String`	`URL_XREF_EXISTS` URL pattern for finding out if an xref exists in the database.
`static String`	`URL_XREFS` URL pattern for mapping xrefs.

Constructor Summary

Constructors
Constructor and Description

IDMapperService(File aConfigFile, boolean transitive)

Constructors
Constructor and Description
`IDMapperService(File aConfigFile, boolean transitive)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method and Description

org.restlet.Restlet createRoot()

GdbProvider getGdbProvider()

void start()
- Methods inherited from class org.restlet.Application
  createInboundRoot, createOutboundRoot, getConnectorService, getConverterService, getCurrent, getDecoderService, getFinderClass, getInboundRoot, getMetadataService, getOutboundRoot, getRangeService, getRole, getRoles, getRoot, getServices, getStatusService, getTaskService, getTunnelService, handle, setClientRoot, setConnectorService, setContext, setConverterService, setCurrent, setDecoderService, setFinderClass, setInboundRoot, setInboundRoot, setMetadataService, setOutboundRoot, setRangeService, setRoles, setRoot, setRoot, setStatusService, setTaskService, setTunnelService, stop
- Methods inherited from class org.restlet.Restlet
  finalize, getApplication, getAuthor, getContext, getDescription, getLogger, getName, getOwner, isStarted, isStopped, setAuthor, setDescription, setName, setOwner
- Methods inherited from class java.lang.Object
  clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`org.restlet.Restlet`	`createRoot()`
`GdbProvider`	`getGdbProvider()`
`void`	`start()`

- Field Detail
  - CONF_GDBS
```
public static final String CONF_GDBS
```
    See Also:
    
    Constant Field Values
  - PAR_ORGANISM
```
public static final String PAR_ORGANISM
```
    See Also:
    
    Constant Field Values
  - PAR_ID
```
public static final String PAR_ID
```
    See Also:
    
    Constant Field Values
  - PAR_SYSTEM
```
public static final String PAR_SYSTEM
```
    See Also:
    
    Constant Field Values
  - PAR_QUERY
```
public static final String PAR_QUERY
```
    See Also:
    
    Constant Field Values
  - PAR_DATASOURCES
```
public static final String PAR_DATASOURCES
```
    See Also:
    
    Constant Field Values
  - PAR_TARGET_SYSTEM
```
public static final String PAR_TARGET_SYSTEM
```
    See Also:
    
    Constant Field Values
  - PAR_TARGET_ATTR_NAME
```
public static final String PAR_TARGET_ATTR_NAME
```
    See Also:
    
    Constant Field Values
  - PAR_TARGET_LIMIT
```
public static final String PAR_TARGET_LIMIT
```
    See Also:
    
    Constant Field Values
  - PAR_SOURCE_SYSTEM
```
public static final String PAR_SOURCE_SYSTEM
```
    See Also:
    
    Constant Field Values
  - PAR_DEST_SYSTEM
```
public static final String PAR_DEST_SYSTEM
```
    See Also:
    
    Constant Field Values
  - configFile
```
public final File configFile
```
  - URL_HOME
```
public static final String URL_HOME
```
    URL pattern to redirect to home page.
    {blank}
    
    See Also:
    
    Constant Field Values
  - URL_NO_MATCH
```
public static final String URL_NO_MATCH
```
    URL pattern to catch a misformed query.
    {unmatched patter}
    See Also: Constant Field Values
  URL_XREFS public static final String URL_XREFS URL pattern for mapping xrefs. /{organism}/xrefs/{system}/{id}[?dataSource={dsName}] See Also: IDMapper.mapID(org.bridgedb.Xref, org.bridgedb.DataSource...), Constant Field Values URL_SEARCH public static final String URL_SEARCH URL pattern for searching xrefs. /{organism}/search/{query}[?limit={limit}] See Also: IDMapper.freeSearch(String, int), Constant Field Values URL_XREF_EXISTS public static final String URL_XREF_EXISTS URL pattern for finding out if an xref exists in the database. /{organism}/xrefExists/{system}/{id} See Also: IDMapper.xrefExists(org.bridgedb.Xref), Constant Field Values URL_PROPERTIES public static final String URL_PROPERTIES URL pattern for getting IDMapper properties. Returns tab delimited text with a property on each line, where the first column is the property key, the second is the property value. /{organism}/properties See Also: IDMapperCapabilities.getKeys(), IDMapperCapabilities.getProperty(String), Constant Field Values URL_SUPPORTED_SOURCE_DATASOURCES public static final String URL_SUPPORTED_SOURCE_DATASOURCES URL pattern for getting the supported source datasources for this database. /{organism}/sourceDataSources See Also: IDMapperCapabilities.getSupportedSrcDataSources(), Constant Field Values URL_SUPPORTED_TARGET_DATASOURCES public static final String URL_SUPPORTED_TARGET_DATASOURCES URL pattern for getting the supported target datasources for this database. /{organism}/targetDataSources See Also: IDMapperCapabilities.getSupportedTgtDataSources(), Constant Field Values URL_IS_FREE_SEARCH_SUPPORTED public static final String URL_IS_FREE_SEARCH_SUPPORTED URL pattern for finding out if free search is supported. /{organism}/isFreeSearchSupported See Also: IDMapperCapabilities.isFreeSearchSupported(), Constant Field Values URL_IS_MAPPING_SUPPORTED public static final String URL_IS_MAPPING_SUPPORTED URL pattern to find out if a mapping is supported. /{organism}/isMappingSupported/{source_system}/{target_system} See Also: IDMapperCapabilities.isMappingSupported(org.bridgedb.DataSource, org.bridgedb.DataSource), Constant Field Values URL_ATTRIBUTE_SEARCH public static final String URL_ATTRIBUTE_SEARCH URL pattern for searching by attribute. Returns tab delimited text with an xref result on each line, where the first column is the identifier, the second column is the datasource and the third column is the attribute value. /{organism}/attributeSearch/{query}?[limit={limit}][&attrName={attrName}] See Also: AttributeMapper.freeAttributeSearch(String, String, int), Constant Field Values URL_ATTRIBUTES public static final String URL_ATTRIBUTES URL pattern for getting attributes of an xref. If attrName is supplied, this method returns plain text with an attribute value on each line. If attrName is not supplied, this method returns tab delimited text with an attribute key-value pair on each line. /{organism}/attributes/{system}/{id}[?attrName={attrName}] See Also: AttributeMapper.getAttributes(org.bridgedb.Xref, String), AttributeMapper.getAttributes(org.bridgedb.Xref), Constant Field Values URL_ATTRIBUTE_SET public static final String URL_ATTRIBUTE_SET URL pattern for getting the supported attribute set. /{organism}/attributeSet See Also: AttributeMapper.getAttributeSet(), Constant Field Values URL_CONFIG public static final String URL_CONFIG URL pattern for getting the server configuration. /config See Also: Config.getConfig(), Constant Field Values URL_CONTENTS public static final String URL_CONTENTS URL pattern for getting a list of species loaded in the server. /contents See Also: Contents.getContents(), Constant Field Values URL_BACK_PAGE_TEXT public static final String URL_BACK_PAGE_TEXT URL pattern for getting backpage HTML. URL: /{organism}/backPageText/{system}/{id} See Also: Constant Field Values URL_DATASOURCES public static final String URL_DATASOURCES URL pattern for getting the datasources.txt file See Also: Constant Field Values
Constructor Detail IDMapperService public IDMapperService(File aConfigFile, boolean transitive) Method Detail start public void start() throws Exception Overrides: start in class org.restlet.Application Throws: Exception createRoot public org.restlet.Restlet createRoot() Overrides: createRoot in class org.restlet.Application getGdbProvider public GdbProvider getGdbProvider()

Class IDMapperService

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.restlet.Application

Methods inherited from class org.restlet.Restlet

Methods inherited from class java.lang.Object

Field Detail

CONF_GDBS

PAR_ORGANISM

PAR_ID

PAR_SYSTEM

PAR_QUERY

PAR_DATASOURCES

PAR_TARGET_SYSTEM

PAR_TARGET_ATTR_NAME

PAR_TARGET_LIMIT

PAR_SOURCE_SYSTEM

PAR_DEST_SYSTEM

configFile

URL_HOME

URL_NO_MATCH

URL_XREFS

URL_SEARCH

URL_XREF_EXISTS

URL_PROPERTIES

URL_SUPPORTED_SOURCE_DATASOURCES

URL_SUPPORTED_TARGET_DATASOURCES

URL_IS_FREE_SEARCH_SUPPORTED

URL_IS_MAPPING_SUPPORTED

URL_ATTRIBUTE_SEARCH

URL_ATTRIBUTES

URL_ATTRIBUTE_SET

URL_CONFIG

URL_CONTENTS

URL_BACK_PAGE_TEXT

URL_DATASOURCES

Constructor Detail

IDMapperService

Method Detail

start

createRoot

getGdbProvider