ome.formats

Class OMEROImportFixture

java.lang.Object

ome.formats.OMEROImportFixture

public class OMEROImportFixture
extends Object

test fixture for importing files without a GUI. Sample usage:

 OMEROMetadataStoreClient client = new OMEROMetadataStoreClient(sf);
 OMEROImportFixture fixture = new OMEROImportFixture(client);
 fixture.setUp();
 fixture.setFile(ResourceUtils.getFile("classpath:tinyTest.d3d.dv"));
 fixture.setName(name);
 fixture.doImport();
 List<Pixels> p = fixture.getPixels();
 fixture.tearDown();
 i.setName(name);
 i = userSave(i);
 

This class is not thread safe.

Since:

4.0

Author:

Josh Moore, josh.moore at gmx.de

See Also:

OMEROMetadataStoreClient

Field Summary

Fields

Modifier and Type	Field and Description
protected OMEROMetadataStoreClient	store

Constructor Summary

Constructors

Constructor and Description
OMEROImportFixture(OMEROMetadataStoreClient store, OMEROWrapper reader)

Method Summary

Methods

Modifier and Type	Method and Description
void	doImport() runs import by looping through all files and then calling: ImportLibrary#open(String) ImportLibrary#calculateImageCount(String) ImportLibrary#importMetadata() ImportLibrary#importData(long, String, ome.formats.testclient.ImportLibrary.Step)
List<omero.model.Pixels>	fullImport(File f, String name) Provides one complete import cycle.
List<omero.model.Pixels>	getPixels() Accessor for the created pixels.
void	setFile(File file)
void	setName(String name)
void	setUp() checks for the necessary fields and initializes the ImportLibrary
void	tearDown() sets ImportLibrary, OMEROMetadataStore, and file array to null.

Methods inherited from class java.lang.Object

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

Field Detail

store

protected OMEROMetadataStoreClient store

Constructor Detail

OMEROImportFixture

public OMEROImportFixture(OMEROMetadataStoreClient store,
                  OMEROWrapper reader)

Method Detail

setUp

public void setUp()
           throws Exception

checks for the necessary fields and initializes the ImportLibrary

Throws:

Exception

tearDown

public void tearDown()

sets ImportLibrary, OMEROMetadataStore, and file array to null. Also attempts to call FormatReader.close().

fullImport

public List<omero.model.Pixels> fullImport(File f,
                                  String name)
                                    throws Exception

Provides one complete import cycle.

Throws:

Exception

doImport

public void doImport()
              throws Exception

runs import by looping through all files and then calling:

• ImportLibrary#open(String)
• ImportLibrary#calculateImageCount(String)
• ImportLibrary#importMetadata()
• ImportLibrary#importData(long, String, ome.formats.testclient.ImportLibrary.Step)

Parameters:

step - an action to take per plane. not null.

Throws:

Exception

setFile

public void setFile(File file)

setName

public void setName(String name)

getPixels

public List<omero.model.Pixels> getPixels()
                                   throws Exception

Accessor for the created pixels. Should be called before the next call to doImport()

Throws:

Exception