2012-01-17 09:57:02,615 0 [ main] WARN loci.formats.services.OMEXMLService - Could not transform version OME-XML.
??? Java exception occurred:
java.lang.AbstractMethodError: ome.formats.OMEROMetadataStoreClient.setImageAcquiredDate(Ljava/lang/String;I)V
at loci.formats.meta.FilterMetadata.setImageAcquiredDate(FilterMetadata.java:1223)
at loci.formats.MetadataTools.setDefaultCreationDate(MetadataTools.java:317)
at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:191)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:121)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:85)
at loci.formats.in.BaseTiffReader.initMetadataStore(BaseTiffReader.java:392)
at loci.formats.in.TiffReader.initMetadataStore(TiffReader.java:210)
at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:84)
at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:502)
at loci.formats.FormatReader.setId(FormatReader.java:1072)
at loci.formats.ImageReader.setId(ImageReader.java:677)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:189)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:313)
JakeNewman wrote:Ok, I've done that. And so the OMEWrapper class now asks for an ImportConfig object. Is there anyway I could use the CommandLineImporter.java to do what I want? Is it *just* a case of setting up an ImportConfig and giving it the required paths?
import ome.formats.importer.ImportConfig;
import ome.formats.importer.cli.*;
import org.apache.commons.logging.*;
import org.apache.log4j.*;
import org.ini4j.*;
import loci.formats.in.*;
public class JavaApplication2 {
public static void main(String[] args) throws Exception {
ImportConfig config = new ImportConfig();
config.email.set("");
config.sendFiles.set(true);
config.sendReport.set(false);
config.contOnError.set(false);
config.debug.set(false);
config.hostname.set("omero.institution.ac.uk");
config.username.set("user");
config.password.set("pass");
config.port.set(Integer.parseInt("4064"));
config.targetId.set(Long.parseLong("908"));
CommandLineImporter c = null;
String[] inputImg = new String[1];
inputImg[0] = "/Users/jacobnewman/Desktop/newIMGwithXML";
c = new CommandLineImporter(config, inputImg, false);
int rc = c.start();
c.cleanup();
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