Bug: OMERO ImageJ plugin update

[saloynton]

Based on the problem in #6598 the loci plugin shall be updated.
Currently the OMERO image J plugin interact with BF using ome-tiff. Better to easier pass the user credentials, ideally session id.

[jburel <j.burel@…>]

(In [82869c6107664b7599fd9eb28d90d018c01ca993/ome.git] on branch develop) Update plugin to use the new omero reader. (close #6599)

[Chris Allan <callan@…>]

(In [80dc268acb51dc003ca3429becdcbc6a687ff115/ome.git] on branch develop) Rervting addition of ome-io dependency. (See #6599)

JAR dependency added in 82869c6107664b7599fd9eb28d90d018c01ca993. Not
sure why this was added but it causes build and packaging problems as the
JAR includes old OMERO classes.

[jburel]

we will either need ome-io or ome-tools in order for the plugin to work. We already assume that loci-tools is installed, which is already a problem reported.

[cxallan]

What classes are needed Jean-Marie? The plug-in seems to build fine without ome-io.jar at all. Current listing of ome-io.jar from [9aceede8ee80ab5cd933668689378d26510e651b/bioformats.git]:

$ unzip -l ome-io.jar
Archive:  ome-io.jar
  Length     Date   Time    Name
 --------    ----   ----    ----
        0  09-09-11 14:01   META-INF/
      277  09-09-11 14:01   META-INF/MANIFEST.MF
        0  09-09-11 14:01   loci/
        0  09-09-11 14:01   loci/ome/
        0  09-09-11 14:01   loci/ome/io/
        0  09-09-11 14:01   loci/ome/io/services/
     2132  09-09-11 14:01   loci/ome/io/OMECredentials.class
     9687  09-09-11 14:01   loci/ome/io/OMEReader.class
    16085  09-09-11 14:01   loci/ome/io/OMEUtils.class
    17141  09-09-11 14:01   loci/ome/io/OMEWriter.class
    11547  09-09-11 14:01   loci/ome/io/OmeroReader.class
    62164  06-29-11 11:02   loci/ome/io/ome-logo.png
      344  09-09-11 14:01   loci/ome/io/services/OMEReaderWriterService.class
     1182  09-09-11 14:01   loci/ome/io/services/OMEReaderWriterServiceImpl.class
 --------                   -------
   120559                   14 files

[jburel]

The plugin will build but won't work.
We need to remove

import org.openmicroscopy.ds.dto.Image;
in OMEReaderWriterServiceImpl

It seems to be the only one

[jburel]

I did not notice this import before

[jburel]

OmeroReader is the class that will be used by LociImporter plugin when reading the image

[cxallan]

Can look at that later then because ome-io.jar isn't even going to satisfy that dependency. We'd need ome-tools.jar which contains the old OMERO classes, Ice classes and all sorts of dangerous stuff for us to have on our CLASSPATH.

[jburel]

some cleaning required. not sure the ome-tools will be required but we need to check.OmeroReader? was just the indication of what is invoked in order to read.

[jburel]

Testing the plug-in again. Adding ome-io is actually enough to get it working in imageJ.
The cleaning of !OMEReaderWriterServiceImpl should actually be enough.
+omero_client dependency issue.

Maybe Need to think of different strategy for the plug-in i.e. manual solution, not ideal but with time running out..

[Chris Allan <callan@…>]

(In [6df77fa938677a1018d632ee03658c0ca4bce685/ome.git] on branch develop) Adding ome-io.jar to the set of included JARs. (See #6599)

[Chris Allan <callan@…>]

(In [0770caca501863f947ee4e7beae4f1c14ffcd774/ome.git] on branch develop) Revert "Rervting addition of ome-io dependency. (See #6599)"

This reverts commit 80dc268acb51dc003ca3429becdcbc6a687ff115. New
OmeroReader? usage requires the ome-io.jar as per discussion in #6599.

[Chris Allan <callan@…>]

(In [6438cf3f8e828ee8e0d59f6d8cc67d9264ebfaea/ome.git] on branch develop) Re-adding ome-io.jar to the Bio-Formats JAR set. (See #6599)

[jburel <j.burel@…>]

(In [e19a983da28bbc010d359fc5e7938c0ba5290fad/ome.git] on branch develop) Remove IJ debug flag (see #6599)