[ome-users] OMERO 5 Flex Import Problem
Christophe TREFOIS
christophe.trefois at uni.lu
Mon Nov 18 18:17:41 GMT 2013
Hi Melissa,
I'll try again but this was on a LAN with the provided VM box (not on the same machine but in the same floor).
So I hardly think the real issue is a connection one. However, I'll try again and let you know.
Thanks,
| -----Original Message-----
| From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of
| Melissa Linkert
| Sent: lundi 18 novembre 2013 17:21
| 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 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\OperaA
| > > > rchi
| > > > 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\OperaA
| > > > rchi
| > > > 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\OperaA
| > > > rchi
| > > > 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
| >
More information about the ome-users
mailing list