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    • org.bridgedb.uri.ws.server.3.1.4.source-code.api.vm Maven / Gradle / Ivy

    The newest version!
    Supported services include:
    

    
    
    mapID
    
    
    List the Xrefs that map to these Xrefs
    

    
    xrefExists
    
    
    State if the Xref is know to the Mapping Service or not
    

    
    freeSearch
    
    
    Searches for Xrefs that have this id.
    

    
    getCapabilities
    
    
    Gives the Capabilitles as defined by BridgeDb.
    

    
    Close()
    
    
    Not supported as clients should not be able to close the server.
    

    
    isConnected
    
    
    Not supported as Close() is not allowed
    

    
    isFreeSearchSupported
    
    
    Returns True as freeSearch and URLSearch are supported.
    

    
    getSupportedSrcDataSources
    
    
    Returns Supported Source (BridgeDb) DataSource(s).
    

    
    getSupportedTgtDataSources
    
    
    Returns Supported Target (BridgeDb) DataSource(s).
    

    
    isMappingSupported
    
    
    States if two DataSources are mapped at least once.
    

    
    property/key
    
    
    Returns The property value for this key.
    

    
    getKeys
    
    
    Returns The keys and their property value.
    

    
    map
    
    
    List the full mappings to this URI (or Xref)
    

    
    mapUri
    
    
    List the URIs that map to this/these URIs
    

    
    mapUriRDF
    
    
    Same data as mapURI but presented as RDF.
    

    
    mapBySet
    
    
    DEPRECATED: Use map which gives the required information and more.
    

    
    mapBySetRDF
    
    
    DEPRECATED: Use mapUriRDF which gives the required information.
    

    
    UriExists
    
    
    State if the URI is know to the Mapping Service or not
    

    
    UriSearch
    
    
    Searches for URIs that have this ending.
    

    
    dataSource
    
    
    Returns the DataSource and associated UriSpace(s) with a specific id
    

    
    toUris
    
    
    Returns the URIs associated with a Xref (specified as id and code)
    

    
    toXref
    
    
    Retrns the Xref for this URI
    

    
    SourceInfos
    
    
    Brings up a table of all the Sources in the system.
    

    
    SourceTargetInfos
    
    
    Brings up a table of all the Targets for a particular Source.
    

    
    mappingSet
    
    
    Brings up a table of all the mappings in the system for a particular Source and Target.
    

    
    mappingSet/id
    
    
    Provides the metadata for one mapping set
    

    
    mappingSetRDF
    
    
    Same data as mappingSet/id but presented as RDF.
    

    
    mappingSetRDF/id
    
    
    Same data as mappingSet/id but presented as RDF.
    

    
    Lens
    
    
    Brings up a list of the Supported Lens
    

    
    LensRDF
    
    
    Brings up the supported Lens in RDF format
    

    


    Parameters 
    
The following parameters may be applicable to the methods.
See the individual method description for which are required and which are optional.
Their behaviour is consistent across all methods, unless stated otherwise

    BridgeDb Parameters
    


    id and code
    

      
    
    • Limits the results to ones with this/these Xrefs.
      • 
    
    • code is the SystemCode of the Xref's DataSource)
      • 
    
    • id is the identifier part of the Xref
      • 
    
    • Typically There can be multiple "id" and "code" values
        
        
            
      • There must be at least one of each.
        • 
            
      • There must be the same number of each.
        • 
            
      • They will be paired by order.
        • 
            
      • If multiple Xref's have the same DataSource their code must be repeated.
        • 
        
      
    
      • 
    
    • Note: Other methods may obtain a different id by following the method name with a slash // id. These do not require a "code"
      • 

    


    key
    

      
    
    • Selects which property to return.
      • 
    
    • Only one key parameter is supported.
      • 

    


    limit
    

      
    
    • Limits the number of results.
      • 
    
    • Must be a positive Integer in String Format
      • 
    
    • If less than limit results are available limit will have no effect.
      • 
    
    • Only one limit parameter is supported.
      • 
    
    • If no limit is set a default limit will be used.
      • 
    
    • If too high a limit is set the default limit will be used.
      • 
    
    • To obtain a full data dump please contact the admins.
      • 

    


    sourceCode
    

      
    
    • Limits the results to ones with those Source Xref's DataSource has this sysCode.
      • 
    
    • String Format
      • 
    
    • Typically there must be exactly one sourceCode when used.
      • 

    


    targetCode
    

      
    
    • Limits the results to ones with those Target Xref's DataSource has this sysCode.
      • 
    
    • String Format
    • Typically there can but need not be more than one.
      • 

    


    text
    

      
    
    • A bit of text that will be searched for.
      • 
    
    • String Format
      • 
    
    • Only one text parameter is supported.
      • 
    
    • Note this is for searching for text in Identifiers not for mapping between text and Identifiers.
      • 

    


    Ops Extension Parameters
    


    Uri
    

      
    
    • Limits the results to ones with this URI.
      • 
    
    • String Format
      • 
    
    • Do NOT include the < and > seen around URIs in RDF
      • 
    
    • Only one Uri parameters is supported.
      • 

    


    baseUri
    

      
    
    • Used for methods that return RDF.
      • 
    
    • Changes the base of any URIs that refer to the IMS
      • 
    
    • Should be used if the IMS services are used Vai another service
      • 
    
    • The baseUri should include the service name and the final / but not the method name
    
        
        
      • So if calling http://localhost:8080/BridgeDb/mapUriRDF?... the baseUri would be http://www.example.com/MyBridgeDb/
        • 
        
      • This allows http://www.example.com/MyBridgeDb/ to forward any calls to its BridgeDb service.
        • 
    
          

    


    lensUri
    

      
    
    • Determines which types of results are returned
      • 
    
    • If not provided the default lens is used. Except in the Lens
      • 
    
    •  Use Lens  method to get a list of the Lens.
      • 

    


    lensGroup
    

      
    
    • If not provided the public groups is used 
      • 
    
    • A list of the current groups is available from /BridgeDb/lensGroup
      • 

    


    linksetInfo
    



    overridePredicateURI
    

      
  
    • Override the link predicate URI returned by mapUri and mapUriRDF
      • 
  
    • The default (if the parameter is not given or is an empty string) is to return links using the predicates from the original linksets
      • 
  
    • Parameter must be an absolute URI of the term to use, e.g. http://www.w3.org/2004/02/skos/core#exactMatch or 
  	http://www.w3.org/2002/07/owl#sameAs
      • 
  
    • If combined with linksetInfo=true, the returned linkset info will describe
   derived linksets with the overridden void:linkPredicate
      • 

    



    graph
    

      
    
    • Limits the results to ones required for this OpenRdf context/graph.
      • 
    
    • This works by looking up the required targetUriPattern(s) in the graph.properties configuration file.
      • 
    
    • There can only one parameter graph and ONLY if NO paramters targetUriPattern are supplied.
      • 

    


    targetUriPattern
    

      
    
    • Limits the results to ones with URIs with this pattern.
      • 
    
    • The URI pattern must match on of the Patterns specified in the System.
      • 
    
    • String Format
      • 
    
    • Do NOT include the < and > seen around URIs in RDF
      • 
    
    • There are two supported formats 
        
        
            
      • prefix$idpostfix 
                
          
                    
        • Only selects URIs which have exactlty that pattern
          • 
                    
        • Must be exactly a known pattern or an exception is thrown.
          • 
                    
        • Where $id represent the id part of the URI
        • The whole postfix part must be provided.
          • 
                    
        • It the pattern has nothing after the $id no postfix is included.
          • 
                
        
            
        • 
            
      • startsWith 
                
          
                    
        • Returns any URIs whose prefixt start with the provided pattern.
          • 
                    
        • Can not include any part of the id section of the URI.
          • 
                    
        • For example targetUriPattern=http://identifiers.org returns all indentifiers.org URIs
          • 
                
               
            
        • 
            
      • No wildcard or regex support is currently available.
        • 
            
      • An Empty String is considered a null and returns an empty set
        • 
        
      
    
      • 
    
    • Typically there can but need not be more than one.
        
        
            
      • Each TargetURI is added as a new paramter
        • 
            
      • In the format targetUriPattern=target1&targetUriPattern=target12&
        • 
            
      • See: mapUri for a working example
        • 
        
      
    
      • 

    


    targetCode
    

      
    
    • Acts in exactly the same way as non URI based methods.
      • 
    
    • Note: If both targetUriPattern and  targetCode are specified the result is the union of results of running this method twice with each parameter individually.
      • 
    
    • String Format
      • 
    
    • Typically there can but need not be more than one.
      • 

    


    rdfFormat
    

      
    
    • Specifies the RDF format that should be used.
        
        
            
      • WARNING: Not all RDF formats supports contexts/graphs.
        • 
            
      • So some formats will not have the mappings in Set contexts.
        • 
        
      
    
      • 
    
    • String Format
      • 
    
    • Legal values are:
        
        
            #foreach ($rdfFormat in $rdfFormats)
                
      • $rdfFormat.getName()
                #if ($rdfFormat.supportsContexts())
                      (Supports Context)
                #end
                
        • 
            #end
          
      
    
      • 
    
    • Only one format can be specified.
      • 
    
    • The default format $rdfDefaultFormat is used if  MediaType.TEXT_PLAIN is requested
      • 

    


    includeXrefResults
    

      
    
    • Ask for the results to include Bridgb Xref results.
      • 
    
    • Only effects calls that would not naturally return Xref results
        
        
            
      • Always considered true for any call with 
        • 
            
      • id and code paramtered set
        • 
            
      • Always considered true for any call with targetCode  paramters set
        • 
            
      • For transitives also allows the Via information to be added.
        • 
            
      • In all other cases defaults to false.
        • 
        
      
    
      • 

    


    includeUriResults
    

      
    
    • Ask for the results to include URI results.
      • 
    
    • Only effects calls that would not naturally return URI results
        
        
            
      • Always considered true for any call with Uri paramter set
        • 
            
      • Always considered true for any call with graph paramters set
        • 
            
      • Always considered true for any call with targetUriPattern paramters set
        • 
            
      • In all other cases defaults to false.
        • 
        
      
    
      • 

    


    Implementations of BridgeDb's IDMapper methods
    


    mapID
    

      
    
    • List the Xrefs that map to these Xrefs
      • 
    
    • Implements:  Map<Xref, Set<Xref>> mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources)
      • 
    
    • Implements:  Set<Xref> mapID(Xref srcXrefs, DataSource... tgtDataSources)
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will a html formated page.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Required arguements: (Only Source Xref considered)
        
    
      • 
    
    • Optional arguments
        
    
      • 
    
    • Xref Example: 
            mapID?id=$id2&code=$code2&id=$id1&code=$code1
      • 
    
    • Target Code: 
            mapID?id=$id2&code=$code2&id=$id1&code=$code1&targetCode=$targetCode1
      • 

    


    xrefExists
    

      
    
    • Implements:  boolean xrefExists(Xref xref)
      • 
    
    • State if the Xref is know to the Mapping Service or not
      • 
    
    • This method is available for media types XML and JSON.
        
        
            
      • Status 204 (no Content) is never returned.
        • 
        
      
    
      • 
    
    • There is not media type HTML.
      • 
    
    • Required arguements: (Considers both Source and target Xrefs
        
        
            
      • id
        • 
            
      • code
        • 
            
      • Currently only a single id and single code supported.
        • 
        
      
    
      • 
    
    • Example: 
            xrefExists?id=$id2?id=Cs
      • 

    


    freeSearch
    

      
    
    • Searches for Xrefs that have this id.
      • 
    
    • Implements:  Set<Xref> freeSearch (String text, int limit)
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML result in a framed page.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Required arguements:
        
    
      • 
    
    • Example: 
            freeSearch?text=$id2&limit=5
      • 

    


    getCapabilities
    

      
    
    • Implements:  IDMapperCapabilities getCapabilities()
      • 
    
    • Gives the Capabilitles as defined by BridgeDb.
      • 
    
    • This method is available for media types XML and JSON.
        
        
            
      • Status 204 (no Content) is never returned.
        • 
        
      
    
      • 
    
    • There is not media type HTML.
      • 
    
    • Example: getCapabilities
      • 

    


    Other IDMapper Functions
    

    
    
    Close()
    
    
    Not supported as clients should not be able to close the server.
    
    
    isConnected
    
    
    Not supported as Close() is not allowed
    

    


    Implementations of BridgeDb's IDMapperCapabilities methods
    


    isFreeSearchSupported
    

      
    
    • Implements:  boolean isFreeSearchSupported()
      • 
    
    • Returns True as freeSearch and URISearch are supported.
      • 
    
    • This method is available for media types XML and JSON.
        
        
            
      • Status 204 (no Content) is never returned.
        • 
        
      
    
      • 
    
    • There is not media type HTML.
      • 
    
    • Example: isFreeSearchSupported
      • 

    


    getSupportedSrcDataSources
    

      
    
    • Implements:  Set<DataSource>  getSupportedSrcDataSources()
      • 
    
    • Returns Supported Source (BridgeDb) DataSource(s).
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML result in a framed page.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Example: getSupportedSrcDataSources
      • 

    


    getSupportedTgtDataSources
    

      
    
    • Implements:  Set<DataSource>  getSupportedTgtDataSources()
      • 
    
    • Returns Supported Target (BridgeDb) DataSource(s).
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will a html formated page.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Example: getSupportedTgtDataSources
      • 

    


    isMappingSupported
    



    property/key
    

      
    
    • Implements:  String getProperty(String key)
      • 
    
    • Returns The property value for this key.
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will a html formated page.
        
        
            
      • An warning page is returned if no data available
        • 
        
      
    
      • 
    
    • Required arguements:
        
        
            
      • Place the actual key after the /
        • 
        
      
    
      • 
    
    • Example: property/LastUpdates
      • 

    


    getKeys
    

      
    
    • Implements:  Set<string> getKeys()
      • 
    
    • Returns The keys and their property value.
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will a html formated page.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Example: getKeys
      • 

    


    URI based methods
    


    map
    



    mapUri
    



    mapUriRDF
    
mapBySet

      
    
    • DEPRECATED: Use map which gives the required information and more
      • 

    


    mapBySetRDF
    

      
    
    • DEPRECATED: Use mapUriRDF which gives the required information.
      • 

    


    UriExists
    

      
    
    • State if the URI is know to the Mapping Service or not
      • 
    
    • This method is available for media types XML and JSON.
        
        
            
      • Status 204 (no Content) is never returned.
        • 
        
      
    
      • 
    
    • There is not media type HTML.
      • 
    
    • Required arguements:
        
        
            
      • Uri
                
          
                    
        • Currently limited to single URI
          • 
                
        
            
        • 
        
      
    
      • 
    
    • Example: 
            UriExists?Uri=$uri2
      • 

    


    UriSearch
    

      
    
    • Searches for URIs that have this ending.
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will a html formated page.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Required arguements:
        
    
      • 
    
    • Example: UriSearch?text=$id2&limit=5
      • 

    


    dataSource/id
    

      
    
    • Obtain a dataSource
      • 
    
    • This method is available for media types XML and JSON.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will return XML Format.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Required arguements: 
        
        
            
      • Returns the DataSource and associated UriSpace(s) with a specific id.
        
      
    
      • 
    
    • Example: dataSource/$code1
      • 

    


    toUris
    

      
    
    • Returns the URIs associated with a Xref
      • 
    
    • This method is available for media types XML and JSON.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will return XML Format.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Required arguements: 
        
    
      • 
    
    • Example: toUris?id=$id2&code=$code2
      • 

    


    toXref
    

      
    
    • Retrns the Xref for this URI
      • 
    
    • This method is available for media types XML, JSON and HTML.
        
        
            
      • Status 204 (no Content) is return if no data available.
        • 
        
      
    
      • 
    
    • Request for media type HTML will a html formated page.
        
        
            
      • An warning page is returned if no data available.
        • 
        
      
    
      • 
    
    • Required arguements:
        
    
      • 
    
    • Example: toXref?Uri=$uri2
      • 

    


    Support methods
    SourceInfos
    



    SourceTargetInfos
    



    mappingSet
    



    mappingSetRDF
    



    graphviz
    
This method will now always throw an Exception! It did not scale.


    Lens
    



    LensRDF




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