[ome-users] OMERO 5 Flex Import Problem
Christophe TREFOIS
christophe.trefois at uni.lu
Thu Nov 28 13:41:01 GMT 2013
Dear Josh,
Please CC me in the ticket on trac.
I will send you the Blitz log files. Where should I send them to ?
How can I check what is imported? The screen in the Insight is empty after the failed import and I cannot see any images.
It seems to upload some items before failing.
The time it takes is a few minutes. The stages it goes through is:
- Scanning
- Uploading xx / 1 GB (Processing: Pending...)
- Upload 1GB / 1 GB
- Processing: Import Metadata -> Failed to import Metadata --> Failed...
Thank you for your help,
--
Christophe
................................................................................
Christophe TREFOIS
PhD Student
Ing. Sys. Com. Dipl. EPF
Luxembourg Centre for Systems Biomedicine
UNIVERSITY OF LUXEMBOURG
CAMPUS LIMPERTSBERG
162a, avenue de la Faïencerie
L-1511 Luxembourg
T +352 46 66 44 6124
F +352 46 66 44 6949
www.lcsb.lu
________________________________________
From: Josh Moore [josh at glencoesoftware.com]
Sent: Monday, November 25, 2013 11:56 AM
To: Christophe TREFOIS
Cc: melissa at glencoesoftware.com; Alexander SKUPIN; ome-users at lists.openmicroscopy.org.uk; Jake LIN
Subject: Re: [ome-users] OMERO 5 Flex Import Problem
Hi Christophe,
On Nov 20, 2013, at 7:06 PM, Christophe TREFOIS wrote:
> Hi Melissa,
>
> Now the error log reads the following:
> ...
> 2013-11-20 15:46:13,802 ERROR [.openmicroscopy.shoola.env.ui.FileLoader] (entQueue-0) Data Retrieval Failure: java.lang.NullPointerException
> ...
As you may have seen, this error has been filed as https://trac.openmicroscopy.org.uk/ome/ticket/11743#comment:3
which I can CC you on if you'd like.
> Is it possible to see the details of the variables at this step?
If you could send us the contents of your server logs (var/log/Blitz-*.log), we might be
able to tell what happened.
> I mean, I used a \\\\ path in the .ini file for the flex import, but the VM runs on Linux.
>
> Is the Linux VM trying to open a connection to the \\\\ or is it the OMERO Importer?
> Also, does the OMERO Importer use the saved network credentials of Windows or not.
> What I mean is that the network shares are mounted with a specific user/password and
> are accessible by simply typing the IP in the explorer bar as well (using the saved
> mapped credentials)?
Without knowing more, I'd say that this isn't the issue. The problems you've run in
to as I understand them are:
* DNS exception: something spurious happened at the network level
* NullPointerException: the size of a file hadn't been filled in yet.
Have you checked how much of the data imported despite the latest error? How
long after starting the import did it take until it occurred? Could you try
to reproduce?
> Thank you for your feedback on this,
And thanks for all your help.
Cheers,
~Josh.
> ________________________________________
> From: Josh Moore [josh at glencoesoftware.com]
> Sent: Monday, November 18, 2013 9:16 PM
> To: Christophe TREFOIS
> Cc: melissa at glencoesoftware.com; Alexander SKUPIN; ome-users at lists.openmicroscopy.org.uk; Jake LIN
> Subject: Re: [ome-users] OMERO 5 Flex Import Problem
>
> On Nov 18, 2013, at 7:17 PM, Christophe TREFOIS wrote:
>
>> Hi Melissa,
>
> Hi Christophe,
>
>> 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.
>
> there is another on-going discussion[1] about long-running imports which fail with a connection error
> similar to yours. We're currently looking into this. Though I'm not sure it will help, you may try the
> same with a CLI import if you have it installed. Otherwise, we'll keep you posted.
>
>
> Cheers,
> ~Josh
>
>
> [1] https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7351&p=13145#p13145
> Note: not all of this thread pertains
>
>
> P.S. one difference in your log file from QA 7711 is that your connection error mentions a DNSError:
>
> 013-11-14 13:38:58,545 DEBUG [openmicroscopy.shoola.env.data.Connector] (1-thread-1) Failed encrypted keep alive:Ice.DNSException
> error = 0
> host = "decepticon"
>
> in case there was any network event that you know of.
>
>
>> 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.
>> | > > >
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