[ome-users] OMERO 5 Flex Import Problem
Josh Moore
josh at glencoesoftware.com
Tue Dec 3 18:30:05 GMT 2013
On Nov 29, 2013, at 4:01 PM, Josh Moore wrote:
> On Nov 28, 2013, at 2:41 PM, Christophe TREFOIS wrote:
>
>> 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
Thanks for the log file. I did find a bug in the flex support and filed
https://trac.openmicroscopy.org.uk/ome/ticket/11781
We'll look into getting a fix into the upcoming 5.0.0-beta2 release.
Thanks for all your help in tracking this down!
~Josh
>> 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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