phenote.dataadapter.ncbi
Class PubMedAdapter

java.lang.Object
  phenote.dataadapter.ncbi.PubMedAdapter

All Implemented Interfaces:

NCBIDataAdapterI

public class PubMedAdapter
extends java.lang.Object
implements NCBIDataAdapterI

This adapter will utilize the NCBI RESTful toolkit to query OMIM IDs and return some formatted information.

In the future we should probably use their SOAP toolkit.

This is the basis for what will become a generic class for ncbi lookup tools

Probably should be OMIMAdapter extends NCBIDataAdapterI or something

Author:

Nicole Washington

Field Summary

Fields inherited from interface phenote.dataadapter.ncbi.NCBIDataAdapterI

ncbiURL

Constructor Summary

PubMedAdapter()

Method Summary

java.lang.String	getLookupButtonImage() The label that gets displayed on the lookup button.
java.lang.String	getName()
java.lang.String	getOMIMbyID(java.lang.String id)
java.util.List<java.lang.String>	getQueryableGroups() returns a list of group strings of groups that can be queried for with query method
boolean	isFieldQueryable(java.lang.String field) return true if data adapter can query for the char field
org.obo.datamodel.Instance	query(java.lang.String id)
java.lang.String	query(java.lang.String id, java.lang.String database) Throws exception if query fails, and no data to return Query with query string of type field for group

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PubMedAdapter

public PubMedAdapter()

Method Detail

getQueryableGroups

public java.util.List<java.lang.String> getQueryableGroups()

Description copied from interface: NCBIDataAdapterI

returns a list of group strings of groups that can be queried for with query method

Specified by:

getQueryableGroups in interface NCBIDataAdapterI

getOMIMbyID

public java.lang.String getOMIMbyID(java.lang.String id)

isFieldQueryable

public boolean isFieldQueryable(java.lang.String field)

return true if data adapter can query for the char field

Specified by:

isFieldQueryable in interface NCBIDataAdapterI

query

public java.lang.String query(java.lang.String id,
                              java.lang.String database)

Description copied from interface: NCBIDataAdapterI

Throws exception if query fails, and no data to return Query with query string of type field for group

Specified by:

query in interface NCBIDataAdapterI

query

public org.obo.datamodel.Instance query(java.lang.String id)

Specified by:

query in interface NCBIDataAdapterI

getLookupButtonImage

public java.lang.String getLookupButtonImage()

Description copied from interface: NCBIDataAdapterI

The label that gets displayed on the lookup button. Different functions might have different buttons in the future.

Specified by:

getLookupButtonImage in interface NCBIDataAdapterI

getName

public java.lang.String getName()

Specified by:

getName in interface NCBIDataAdapterI