[ome-users] OMERO 5 Flex Import Problem
Christophe TREFOIS
christophe.trefois at uni.lu
Tue Dec 3 21:00:47 GMT 2013
Thanks for your help.
I'm looking forward to trying 5.0.0-beta2.
Let me know if you need additional information or if I can tryout a hotfix.
Best,
| -----Original Message-----
| From: Josh Moore [mailto:josh at glencoesoftware.com]
| Sent: mardi 3 décembre 2013 19:30
| To: Christophe TREFOIS
| Cc: Melissa Linkert; Alexander SKUPIN; OME Users; Jake LIN
| Subject: Re: [ome-users] OMERO 5 Flex Import Problem
|
|
| 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).me
| >>>> | > > a
| >>>> | > > > 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).me
| >>>> | > > a
| >>>> | > > > 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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