uk.ac.ebi.microarray.zooma.reports
Class TextReports

java.lang.Object
  uk.ac.ebi.microarray.zooma.reports.TextReports

@ZoomaMappingGenerator(mode="text")
public class TextReports
extends java.lang.Object

A zooma mode that generates a text report in the specified directory given a list of text values to map.

There are two modes of operation: the production of a list of

Author:

Tony Burdett

Constructor Summary

TextReports()

Method Summary

boolean	generateAllPossibleMappings(java.lang.String reportDirectory, java.lang.String valuesFile) Generate a report describing possible terms, matched from a host of different ontologies, that could be used as mappings for the supplied terms.
boolean	generateMappingsToSingleOntology(java.lang.String reportDirectory, java.lang.String valuesFile, java.lang.String ontologyName) Generates a report describing the mappings that match exactly against the supplied ontology.
protected org.slf4j.Logger	getLog()
TextReportingMapper	getMapper()

Methods inherited from class java.lang.Object

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

Constructor Detail

TextReports

public TextReports()

Method Detail

getLog

protected org.slf4j.Logger getLog()

getMapper

public TextReportingMapper getMapper()

generateMappingsToSingleOntology

@ZoomaMappingOperation(operation="single",
                       shortName="s",
                       description="Maps supplied values to a single named ontology (identified in the config file)")
public boolean generateMappingsToSingleOntology(@ZoomaMappingArgument(name="report-directory",shortName="d",description="The directory in which reports will be written",required=false)
                                                                                                   java.lang.String reportDirectory,
                                                                                                   @ZoomaMappingArgument(name="values",shortName="v",description="Path to a file containing the values to map")
                                                                                                   java.lang.String valuesFile,
                                                                                                   @ZoomaMappingArgument(name="ontology",shortName="o",description="The name of the ontology (from the config file) to map against")
                                                                                                   java.lang.String ontologyName)

Generates a report describing the mappings that match exactly against the supplied ontology. This mode uses an exact matching algorithm to return mapping between text values to ontology terms, where only exact matches to labels or synonyms of the ontology term are mapped.

This method generates a report based on every single provided in the valuesFile argument.

Parameters:

reportDirectory - the directory in which to write the error report

valuesFile - the file containing the input text values to map to your ontology

ontologyName - the name of the ontology to map against

Returns:

true if the report is generated successfully, false otherwise

generateAllPossibleMappings

@ZoomaMappingOperation(operation="all",
                       shortName="a",
                       description="Maps supplied values against terms from a wide variety of ontologies")
public boolean generateAllPossibleMappings(@ZoomaMappingArgument(name="report-directory",shortName="d",description="The directory in which reports will be written.  If unspecified, defaults to the current working directory.",required=false)
                                                                                              java.lang.String reportDirectory,
                                                                                              @ZoomaMappingArgument(name="values",shortName="v",description="Path to a file containing the values to map")
                                                                                              java.lang.String valuesFile)

Generate a report describing possible terms, matched from a host of different ontologies, that could be used as mappings for the supplied terms.

This method uses query expansion derived from the methods used by OntoCAT to return potential hits. These matches are therefore often host-dependent: OntoCAT federates queries to BioPortal and OLS, as well as implementing logic to broaden matches against locally held files. Of the possible hits returned, this method uses configured rankings and preferences to narrow down the list of mappings as much as possible. Therefore, this report may contain some perfect mappings, and others that map to a variety of terms.

Parameters:

reportDirectory - the directory in which to generate the report

valuesFile - the file containing the input text values to map to your ontology

Returns:

true if the report generates successfully, false otherwise