@Parameters({"target"})
@BeforeClass
public void setUp(String target) throws Exception {
log.info("METADATA VALIDATOR TARGET: " + target);
sf = new TestServiceFactory().proxy();
config = new ImportConfig();
// Let the user know at what level we're logging
ch.qos.logback.classic.Logger lociLogger =
(ch.qos.logback.classic.Logger) LoggerFactory.getLogger("loci");
ch.qos.logback.classic.Logger omeLogger =
(ch.qos.logback.classic.Logger) LoggerFactory.getLogger("ome.formats");
log.info(
String.format(
"Log levels -- Bio-Formats: %s OMERO.importer: %s",
lociLogger.getLevel(), omeLogger.getLevel()));
store = new OMEROMetadataStoreClient();
store.initialize(sf);
store.setEnumerationProvider(new TestEnumerationProvider());
store.setInstanceProvider(new BlitzInstanceProvider(store.getEnumerationProvider()));
minimalStore = new OMEROMetadataStoreClient();
minimalStore.initialize(sf);
minimalStore.setEnumerationProvider(new TestEnumerationProvider());
minimalStore.setInstanceProvider(
new BlitzInstanceProvider(minimalStore.getEnumerationProvider()));
wrapper = new OMEROWrapper(config);
wrapper.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));
minimalWrapper = new OMEROWrapper(config);
minimalWrapper.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM));
wrapper.setMetadataStore(store);
store.setReader(wrapper.getImageReader());
minimalStore.setReader(minimalWrapper.getImageReader());
}
/** opens the file using the {@link FormatReader} instance */
private void open(OMEROWrapper reader, OMEROMetadataStoreClient store, CheckedPath targetFile)
throws FormatException, IOException {
// reader.close(); This instance is no longer re-used
reader.setMetadataStore(store);
reader.setMinMaxStore(store);
store.setReader(reader.getImageReader());
targetFile.bfSetId(reader);
// reset series count
if (log.isDebugEnabled()) {
log.debug("Image Count: " + reader.getImageCount());
}
}