uk.ac.ebi.arrayexpress2.magetab.handler.idf

Class IDFReadHandler

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler

uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler

All Implemented Interfaces:

Handler, ReadHandler<String,String[],IDF>

Direct Known Subclasses:

AccessionHandler, CommentHandler, DateOfExperimentHandler, ExperimentalDesignHandler, ExperimentalDesignTermAccessionHandler, ExperimentalDesignTermSourceRefHandler, ExperimentalFactorNameHandler, ExperimentalFactorTermAccessionHandler, ExperimentalFactorTermSourceRefHandler, ExperimentalFactorTypeHandler, ExperimentDescriptionHandler, InvestigationTitleHandler, MAGETABVersionHandler, NormalizationTermAccessionHandler, NormalizationTermSourceRefHandler, NormalizationTypeHandler, PersonAddressHandler, PersonAffiliationHandler, PersonEmailHandler, PersonFaxHandler, PersonFirstNameHandler, PersonLastNameHandler, PersonMidInitialsHandler, PersonPhoneHandler, PersonRolesHandler, PersonRolesTermAccessionHandler, PersonRolesTermSourceRefHandler, ProtocolContactHandler, ProtocolDescriptionHandler, ProtocolHardwareHandler, ProtocolNameHandler, ProtocolParametersHandler, ProtocolSoftwareHandler, ProtocolTermAccessionHandler, ProtocolTermSourceRefHandler, ProtocolTypeHandler, PublicationAuthorListHandler, PublicationDoiHandler, PublicationStatusHandler, PublicationStatusTermAccessionHandler, PublicationStatusTermSourceRefHandler, PublicationTitleHandler, PublicReleaseDateHandler, PubMedIdHandler, QualityControlTermAccessionHandler, QualityControlTermSourceRefHandler, QualityControlTypeHandler, ReplicateTermAccessionHandler, ReplicateTermSourceRefHandler, ReplicateTypeHandler, SDRFFileHandler, TermSourceFileHandler, TermSourceNameHandler, TermSourceVersionHandler

public abstract class IDFReadHandler
extends AbstractHandler
implements ReadHandler<String,String[],IDF>

An abstract implementation of a ReadHandler for reading data from IDF file into an MAGETABInvestigation. This contains most of the boilerplate code, so that specific handlers only need define the header they can read, the maximum number of values allowed on the line marked by this tag, and how to set the field on the MAGETABInvestigation object.

Author:

Tony Burdett

Field Summary

Fields inherited from class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler

listeners

Constructor Summary

Constructors

Constructor and Description
IDFReadHandler()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canRead(Object header) Determine whether this handler can read the supplied header.
protected abstract boolean	canReadHeader(String header) Determine whether this handler can read the data referenced by this header.
int	getAllowedLength() Get the legal number of data entries for this type of handler, as specified by the MAGE-TAB specification.
void	read(String header, String[] data, IDF idf, int lineNumber, int columnNumber) Invoke this read handler.
protected abstract void	readValue(IDF idf, String value, int lineNumber, String... types) Performs the unit of work to read the data into the internal MAGE-TAB investigation.

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler

accept, addListener, fireHandlingFailedEvent, fireHandlingStartedEvent, fireHandlingSucceededEvent, getListeners, getLog, removeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.arrayexpress2.magetab.handler.Handler

accept, addListener, getListeners, removeListener

Constructor Detail

IDFReadHandler

public IDFReadHandler()

Method Detail

canRead

public boolean canRead(Object header)

Description copied from interface: ReadHandler

Determine whether this handler can read the supplied header. Typically, the data will be a String or String array depending on whether IDF, SDRF or ADF is being read, although the general framework can be extended to parse any data type.

This header should be passed to the handler prior to reading to determine whether this handler can handle it

Specified by:

canRead in interface ReadHandler<String,String[],IDF>

Parameters:

header - the data that will be validated

Returns:

true if this handler can handle this tag, false otherwise

getAllowedLength

public int getAllowedLength()

Get the legal number of data entries for this type of handler, as specified by the MAGE-TAB specification. Usually, this will not be set unless there is a specific cardinality=1 requirement (only found in some places in the IDF spec).

If the allowed length is -1 (the default) this means the cardinality is unrestricted

Returns:

the allowed length

read

public void read(String header,
        String[] data,
        IDF idf,
        int lineNumber,
        int columnNumber)
          throws ParseException

Invoke this read handler. This will read the supplied data assigned to this handler into the MAGETABInvestigation object.

This abstract implementation delegates the responsibility for setting the correct fields to concrete implementations via readValue(uk.ac.ebi.arrayexpress2.magetab.datamodel.IDF, String, int, String...). This method itself governs the update of progress tracking and status information. Before this handler has completed reading, the status of the current task index is updated to Status.COMPLETE if everything succeeded, or Status.FAILED otherwise

Specified by:

read in interface ReadHandler<String,String[],IDF>

Parameters:

header - the header identifying the type of the data

data - the data to be read

idf - the object that the data will be read into

lineNumber - the line number of the field this data was read from

columnNumber - the column number of the field this data was read from

Throws:

ParseException - if the handler failed to read data from it's source

canReadHeader

protected abstract boolean canReadHeader(String header)

Determine whether this handler can read the data referenced by this header. Typically, the header in an IDF file (or ADF header) is the first token on any given line, and the header in an SDRF file (or ADF graph part) is the column heading for each tab-separated column. Other types of data referencing can be supplied - for example, an XML type reader might pass the tag qname as the header.

The header should be passed to the handler prior to reading to determine whether this handler can handle this line.

Parameters:

header - the first token on a line, or the column heading, which is the string describing this line contents

Returns:

true if this handler can handle this tag, false otherwise

readValue

protected abstract void readValue(IDF idf,
             String value,
             int lineNumber,
             String... types)
                           throws ParseException

Performs the unit of work to read the data into the internal MAGE-TAB investigation. Override this method in implementations, so that you don't need to implement status updating and checking code.

This method is passed the investigation to read into, the next value that should be read and (optionally) the type. The type parameter will normally be zero or one value indicating the absence or presence of a type variable on the header.

Parameters:

idf - the IDF to read data into

value - the value to read into the cache

lineNumber - the line number this data is read from

types - a single string representing the type, if present. Should not normally be greater than 1 element long @throws ParseException if the header cannot be parsed or there was an error reading the value

Throws:

ParseException - if the supplied data could not be parsed