[ome-devel] still some problems

[Bernd Jagla]

As I mentioned earlier it is working better, but still not perfectly.

I think I am stuck again with some weird configuration maybe but that should
not be the case because the rest of the system is working fine, the
installed when through without any complains and otherwise I don't see much
of a problem.

I deleted everything under /OME, dropped the ome db, and reinstalled (using
-y) and still have problems:

I also included the "compound importer.ome" for you guys to test

I still have the following problem:

I really hope you can help me THANKS!!!

(more comments between the "===")

======================================
[bernd at BERND-HOME ~]$ ome import test/Ai_compound_import.ome
Please login to OME:
Username? bernd
Password? 
Great, you're in.

Importing files
         1/4: [IN PROGRESS] Starting import
OME::Tasks::LSIDManager::getRemoteObject() is not implemented. at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportExport/ModuleImport.pm
line 183
Deleting compound_import.ome
Error calling DeleteFile with PixelsID=0: Deletion supported from local
connections only
Exiting...
         3/4: [DIED] Importing
Exiting...
[bernd at BERND-HOME ~]$ ome -v
OME commander, version 2.7.0

'-v' is an unknown command.

For a list of available commands:
ome help 
[bernd at BERND-HOME ~]$ which ome
/usr/local/bin/ome
[bernd at BERND-HOME ~]$ set | grep PERL
PERL5LIB=/home/bernd/allOMEs/06_08_18/OME/src/perl2:/home/bernd/allOMEs/06_0
8_18/OME/src/perl2/OME:/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Import
Engine
==========================================

I added the INCell importer into CoreDatabseTablesTask.pm and have the files
stored under OME/ImportEngine/INCellRunXML.pm

I also don't see my new importer in the help:

======================================
[bernd at BERND-HOME ~]$ ome help import
OME commander, version 2.7.0

Usage:
    ome import [<options>] [<list of files>]

This utility imports files into OME database and runs the import analysis 
chain against them.

The files can be proprietary format image files or OME XML files that define

OME objects.

Options:

  -d, --dataset (<id> | <name>) 
      Specify which dataset images should be imported into. If you don't
      own an unlocked dataset with the specified name, a new one will be
      created for you. If you are importing OME Semantic Type Definitions,
      Analysis Modules, or Chains this parameter is unnecessary. If you
      import images, but don't specify a dataset, a new dataset called
      '<time_stamp> Import Dataset' will be created for you.

  -D, --description
      Use this flag if you want to give a description to your new dataset.

  -i, --format
      Suggests the image formats. The Import Engine first checks if the
images
      are of the specified format, if not it reverts to default behaviour
and
      tries to discover the image formats. This speeds up import times for
      common images such as TIFFs.

      Permitted Values:
      OME::ImportEngine::OMETIFFreader
      OME::ImportEngine::MetamorphHTDFormat
      OME::ImportEngine::DVreader
      OME::ImportEngine::STKreader
      OME::ImportEngine::BioradReader
      OME::ImportEngine::LSMreader
      OME::ImportEngine::TIFFreader
      OME::ImportEngine::BMPreader
      OME::ImportEngine::DICOMreader
      OME::ImportEngine::XMLreader

  -r, --reimport
      Reimports images which are already in the database.  This should
      only be used for testing purposes. This flag is ignored for OME
      XML files.

Exiting...
[bernd at BERND-HOME ~]$
=================================================

Next I tried to check if all the perl modules are compiling correctly, so I
executed the following command under src/perl5

find . -name "*.pm" -exec perl -c {} \; >& perl-c.out

The output is attached to this message.

Regarding the Matlab problems: I am not sure if I installed ome with Matlab
support, but it is most likely that not. (Is there a way of checking without
running the installer again? That's why I believe those errors are not
important.


Then there is something wrong with " SVG/TT/Graph/TimeSeries.pm" and "
OME::ImportExport::HierarchyExport::ODBC2XML_timestamp" and some other
things I consider not so important.

Important is that none of my functions seem to fail...

Thanks,

Bernd

 
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