Package ubic.gemma.core.loader.expression.simple

Class ExperimentalDesignImporterImpl

java.lang.Object

ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl

All Implemented Interfaces:

ExperimentalDesignImporter

@Service
public class ExperimentalDesignImporterImpl
extends Object
implements ExperimentalDesignImporter

See interface for docs.

Author:

Paul

Field Summary

Fields

Modifier and Type	Field	Description
static String	EXPERIMENTAL_FACTOR_DESCRIPTION_LINE_INDICATOR

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignImporterImpl()

Method Summary

Modifier and Type	Method	Description
void	importDesign(ExpressionExperiment experiment, InputStream is)	This is the main builder director method of the application: It processes the input file containing information about the experimental design for a given expression experiment.

Methods inherited from class java.lang.Object

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

Field Detail

EXPERIMENTAL_FACTOR_DESCRIPTION_LINE_INDICATOR

public static final String EXPERIMENTAL_FACTOR_DESCRIPTION_LINE_INDICATOR

See Also:

Constant Field Values

Constructor Detail

ExperimentalDesignImporterImpl

public ExperimentalDesignImporterImpl()

Method Detail

importDesign

@Transactional
public void importDesign(ExpressionExperiment experiment,
                         InputStream is)
                  throws IOException

Description copied from interface: ExperimentalDesignImporter

This is the main builder director method of the application: It processes the input file containing information about the experimental design for a given expression experiment. There are 3 main steps in the workflow:

Step1 - validate the the 3 components of the file which should contain: The first component is the experimental factor lines marked with a $# there are as many lines as experimental factors - (experimentalFactorLines). Then one line containing header information indicating the order of the experimental factors in the file - sampleHeaderLine Finally factor values, the first column of which is the sample or biomaterial ids and thereafter factor values.

Step 2 the file components are mapped to objects to populate the experimental design, before addition of objects to the composite existing values are checked for. The expression experiment composite: ExpressionExperiments have an experimental design which have experimental factors. Experimental factors have factor values. BioMaterials have factor values. Bioassays have biomaterials, bioassays are in an expression experiment which completes the circle.

Step 3 on successful validation and object creation the experimental design is persisted following a strict order, expression factors first then biomaterial details.

Specified by:

importDesign in interface ExperimentalDesignImporter

Parameters:

experiment - the one to add the experimental design

is - File to process

Throws:

IOException - when IO problems occur.

See Also:

#importDesign(ubic.gemma.model.expression.experiment .ExpressionExperiment, java.io.InputStream, boolean)