[ome-users] OMERO 5 Flex Import Problem
Melissa Linkert
melissa at glencoesoftware.com
Mon Nov 18 16:21:13 GMT 2013
Hi Christophe,
> I used the online portal that you suggested.
Thank you for uploading the log file. The error messages in the log
(lines 8423 and beyond) suggest that the import failed because the
connection between Insight and the server was terminated. This can
happen for a few reasons, including a slow internet connection and
temporary unavailability of the server.
You might try importing the file again and see if that works; I don't
see anything in the log to suggest that it's a problem with the file
itself. If that doesn't work, please let us know and we'll investigate
further.
Regards,
-Melissa
On Thu, Nov 14, 2013 at 12:43:49PM +0000, Christophe TREFOIS wrote:
> Dear Melissa,
>
> I used the online portal that you suggested.
>
> Let us follow-up there.
>
> Thank you,
>
> ................................................................................
> Dipl.-Ing. Christophe TREFOIS
> Ing. Sys. Com. Dipl. EPF
> PhD Candidate
>
> Université du Luxembourg | University of Luxembourg
> Campus Belval | House of Biomedicine
> 7, avenue des Hauts-Fourneaux
> L-4362 Esch-sur-Alzette
> T +352 46 66 44 6124
> F +352 46 66 44 6949
> www.uni.lu/lcsb
>
> This message is confidential and may contain privileged information.
> It is intended for the named recipient only.
> If you receive it in error please notify me and permanently delete the original message and any copies.
>
> > -----Original Message-----
> > From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of
> > Melissa Linkert
> > Sent: Thursday, November 14, 2013 2:21 AM
> > To: Christophe TREFOIS
> > Cc: ome-users at lists.openmicroscopy.org.uk; Alexander SKUPIN; Jake LIN
> > Subject: Re: [ome-users] OMERO 5 Flex Import Problem
> >
> > Hi Christophe,
> >
> > > I tried using the new OMER 5.0 beta to import flex files from the
> > PerkinElmer Opera.
> > >
> > > I configure a CIA in the import.ini file and it starts to import correctly but
> > then fails on importing the metadata.
> > >
> > > I then used Insight -> Import and selected the corresponding .mea file.
> > Then I clicked Import.
> > >
> > > Here is an excerpt from the log file.
> >
> > Thank you for the report.
> >
> > Unfortunately, that piece of the log file doesn't show the import failure.
> > Could you please send the complete log file, either to the list or as a Zip file to
> > http://qa.openmicroscopy.org.uk/qa/upload/ ?
> > Alternately, you can try the import again and then click the button in the
> > error window to submit the error report directly from Insight.
> >
> > Regards,
> > -Melissa
> >
> > On Tue, Nov 12, 2013 at 05:47:58PM +0000, Christophe TREFOIS wrote:
> > > Dear all,
> > >
> > > I tried using the new OMER 5.0 beta to import flex files from the
> > PerkinElmer Opera.
> > >
> > > I configure a CIA in the import.ini file and it starts to import correctly but
> > then fails on importing the metadata.
> > >
> > > I then used Insight -> Import and selected the corresponding .mea file.
> > Then I clicked Import.
> > >
> > > Here is an excerpt from the log file.
> > >
> > > 2013-11-12 18:15:53,280 INFO [ ome.formats.importer.ImportConfig] (
> > Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
> > > 2013-11-12 18:15:53,280 INFO [
> > > ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader
> > > map values:
> > > \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchi
> > > veCol>
> > > 2013-11-12 18:15:53,285 INFO [ ome.formats.importer.util.IniFileLoader] (
> > Thread-22) Added Flex reader server map 'CIA-1' =
> > '\\10.79.2.101\hcs\OperaArchiveCol'.
> > > 2013-11-12 18:15:53,285 INFO [ ome.formats.importer.ImportConfig] (
> > Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June
> > 2013
> > > 2013-11-12 18:15:53,385 DEBUG
> > [penmicroscopy.shoola.util.NetworkChecker] ( Thread-22) Network status:
> > true (in 99 ms.)
> > > 2013-11-12 18:15:54,383 INFO [ ome.formats.importer.ImportConfig] (
> > Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
> > > 2013-11-12 18:15:54,383 INFO [
> > > ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader
> > > map values:
> > > \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchi
> > > veCol>
> > > 2013-11-12 18:15:54,386 INFO [ ome.formats.importer.util.IniFileLoader] (
> > Thread-22) Added Flex reader server map 'CIA-1' =
> > '\\10.79.2.101\hcs\OperaArchiveCol'.
> > > 2013-11-12 18:15:54,386 INFO [ ome.formats.importer.ImportConfig] (
> > Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June
> > 2013
> > > 2013-11-12 18:16:01,674 DEBUG [ ome.scifio.io.Location] ( Thread-
> > 22) Location.mapFile: embedded-stream.raw -> null
> > > 2013-11-12 18:16:01,980 INFO [ ome.formats.importer.ImportConfig] (
> > Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
> > > 2013-11-12 18:16:01,980 INFO [
> > > ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader
> > > map values:
> > > \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchi
> > > veCol>
> > > 2013-11-12 18:16:01,984 INFO [ ome.formats.importer.util.IniFileLoader] (
> > Thread-22) Added Flex reader server map 'CIA-1' =
> > '\\10.79.2.101\hcs\OperaArchiveCol'.
> > > 2013-11-12 18:16:01,984 INFO [ ome.formats.importer.ImportConfig] (
> > Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June
> > 2013
> > > 2013-11-12 18:16:01,986 INFO [ ome.formats.importer.ImportCandidates]
> > ( Thread-22) Depth: 4 Metadata Level: MINIMUM
> > > 2013-11-12 18:16:02,008 DEBUG [ ome.scifio.io.Location] ( Thread-
> > 22) Location.mapFile: embedded-stream.raw -> null
> > > 2013-11-12 18:16:02,182 INFO [ loci.formats.ImageReader] ( Thread-
> > 22) FlexReader initializing
> > V:\OperaDB_Backups\2013\2013_11\OperaDB_2013_Nov\Christophe
> > Trefois\CT 2013.11.08_Rotenone_Paraquat\Settings\Beads control\CT
> > 20131109_BeadsControl\Meas_01\Meas_01(2013-11-09_13-13-12).mea
> > > 2013-11-12 18:16:02,183 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Reading contents of .mea file
> > > 2013-11-12 18:16:02,183 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Parsing XML from .mea file
> > > 2013-11-12 18:16:03,094 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Looking for corresponding .res file
> > > 2013-11-12 18:16:03,094 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Looking for files that are in the same dataset as
> > V:\OperaDB_Backups\2013\2013_11\OperaDB_2013_Nov\Christophe
> > Trefois\CT 2013.11.08_Rotenone_Paraquat\Settings\Beads control\CT
> > 20131109_BeadsControl\Meas_01\Meas_01(2013-11-09_13-13-12).mea
> > > 2013-11-12 18:16:03,208 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Grouping together files in the same dataset
> > > 2013-11-12 18:16:34,782 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Parsing IFDs for well D6
> > > 2013-11-12 18:16:35,084 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Parsing .flex file (well D6)
> > > 2013-11-12 18:16:35,086 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Parsing XML in .flex file
> > > 2013-11-12 18:16:35,090 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Populating core metadata for well row 3, column 5
> > > 2013-11-12 18:16:35,090 INFO [ loci.formats.FormatHandler] (
> > Thread-22) Populating pixel scaling factors
> > > 2013-11-12 18:16:35,090 WARN [ loci.formats.FormatHandler] (
> > Thread-22) mismatch between image count, names and factors (count=9,
> > names=3, factors=3)
> > >
> > > Any help on this might be very helpful as I think I'm missing something
> > here...
> > >
> > > Thank you for your help.
> > >
> > >
> > >
> > > ................................................................................
> > >
> > > Dipl.-Ing. Christophe TREFOIS
> > > Ing. Sys. Com. Dipl. EPF
> > >
> > > PhD Candidate
> > >
> > >
> > > Université du Luxembourg | University of Luxembourg
> > >
> > > Campus Belval | House of Biomedicine
> > >
> > > 7, avenue des Hauts-Fourneaux
> > >
> > > L-4362 Esch-sur-Alzette
> > >
> > > T +352 46 66 44 6124
> > > F +352 46 66 44 6949
> > > www.uni.lu/lcsb<http://www.uni.lu/lcsb>
> > >
> > >
> > > This message is confidential and may contain privileged information.
> > > It is intended for the named recipient only.
> > > If you receive it in error please notify me and permanently delete the
> > original message and any copies.
> > >
> >
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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