[ome-users] OMERO 5 Flex Import Problem
Josh Moore
josh at glencoesoftware.com
Fri Nov 29 15:01:30 GMT 2013
On Nov 28, 2013, at 2:41 PM, Christophe TREFOIS wrote:
> Dear Josh,
Hi Christophe,
> Please CC me in the ticket on trac.
Done.
> I will send you the Blitz log files. Where should I send them to ?
You can upload arbitrary files, zipped, to http://qa.openmicroscopy.org.uk
> How can I check what is imported? The screen in the Insight is empty after the failed import and I cannot see any images.
If no Plates show up in the left-panel browser after you refresh it, then the import can't be considered successful.
> 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,
And you for yours.
Cheers,
~Josh
> --
> 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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