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

java.lang.Object
  java.io.Writer
      uk.ac.ebi.microarray.zooma.reports.ReportWriter

All Implemented Interfaces:

java.io.Closeable, java.io.Flushable, java.lang.Appendable

Direct Known Subclasses:

TextReportWriter

public class ReportWriter
extends java.io.Writer

A writer implementation that writes all output lines supplied into a buffer, alphabetically sorts them, and flushes them to file when this writer is closed.

Author:

Tony Burdett

Field Summary

Fields inherited from class java.io.Writer

lock

Constructor Summary

ReportWriter(java.io.File file)
Creates a ReportWriter that buffers written lines, sorting them alphabetically.

Method Summary

void	close() Writes the header, the footer, and the content of the buffer to disk.
ReportWriter	endReport(int exitCode) Finalises the report, setting the exit code of the process, sorting alphabetically and flushing to disk.
protected java.lang.String	extractOntologyTermFromURI(java.lang.String termURI)
protected java.lang.String	fetchOntologyName(uk.ac.ebi.ontocat.OntologyTerm term) Fetches the name of the ontology for the supplied term.
void	flush() Sorts the current buffer of report output, and flushes everything to a temporary file.
protected org.slf4j.Logger	getLog()
protected java.lang.String	lookupVersionFromMavenProperties() Retrieves the version number of the application, by locating the version property from the automatically generated maven pom.properties file.
ReportWriter	startReport() Initialises the report, setting useful information about the outcome such as start time, working directory etc.
void	write(char[] cbuf, int off, int len)
protected void	writeReportFooter(java.io.PrintWriter writer) Writes the footer of the report into the supplied print writer
protected void	writeReportHeader(java.io.PrintWriter writer) Writes the header of the report into the supplied print writer.

Methods inherited from class java.io.Writer

append, append, append, write, write, write, write

Methods inherited from class java.lang.Object

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

Constructor Detail

ReportWriter

public ReportWriter(java.io.File file)

Creates a ReportWriter that buffers written lines, sorting them alphabetically. The file is only created on completion, once this writer is closed.

Parameters:

file - the file to write the report to

Method Detail

getLog

protected org.slf4j.Logger getLog()

startReport

public ReportWriter startReport()
                         throws java.io.IOException

Initialises the report, setting useful information about the outcome such as start time, working directory etc.

Returns:

a reference to this report writer

Throws:

java.io.IOException - if something failed whilst creating the file

endReport

public ReportWriter endReport(int exitCode)
                       throws java.io.IOException

Finalises the report, setting the exit code of the process, sorting alphabetically and flushing to disk.

Parameters:

exitCode - the exit code that our mapping process should return

Returns:

a reference to this report writer

Throws:

java.io.IOException - if writing to the file failed

write

public void write(char[] cbuf,
                  int off,
                  int len)
           throws java.io.IOException

Specified by:

write in class java.io.Writer

Throws:

java.io.IOException

flush

public void flush()
           throws java.io.IOException

Sorts the current buffer of report output, and flushes everything to a temporary file.

Specified by:

flush in interface java.io.Flushable

Specified by:

flush in class java.io.Writer

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Writes the header, the footer, and the content of the buffer to disk. This method also flushes and closes the temporary file.

Specified by:

close in interface java.io.Closeable

Specified by:

close in class java.io.Writer

Throws:

java.io.IOException - if closing this writer failed

writeReportHeader

protected void writeReportHeader(java.io.PrintWriter writer)

Writes the header of the report into the supplied print writer. If you require columns headers at the top of your report, you should extend this method, calling super.writeReportHeader() first followed by writer.println(<my line here>);

Parameters:

writer - the writer to write the header data to

writeReportFooter

protected void writeReportFooter(java.io.PrintWriter writer)

Writes the footer of the report into the supplied print writer

Parameters:

writer - the writer to write the footer data into

lookupVersionFromMavenProperties

protected java.lang.String lookupVersionFromMavenProperties()

Retrieves the version number of the application, by locating the version property from the automatically generated maven pom.properties file.

Returns:

the application version number

fetchOntologyName

protected java.lang.String fetchOntologyName(uk.ac.ebi.ontocat.OntologyTerm term)

Fetches the name of the ontology for the supplied term. This is a convenience method. If the label of the ontology attached to the given term could not be determined, the ontology accession is used.

Parameters:

term - the term we want the ontology name for

Returns:

the ontology name, or accession if the name was null

extractOntologyTermFromURI

protected java.lang.String extractOntologyTermFromURI(java.lang.String termURI)