[ome-users] OMERO 5 Flex Import Problem
Christophe TREFOIS
christophe.trefois at uni.lu
Wed Nov 20 18:06:43 GMT 2013
Hi Melissa,
Now the error log reads the following:
2013-11-20 15:43:10,034 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Raw Flex reader map values: \\cia-273\images;\\10.79.2.101\hcs\OperaArchiveCol
2013-11-20 15:43:10,034 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Raw Flex reader map values: \\cia-273\images;\\10.79.2.101\hcs\OperaArchiveCol
2013-11-20 15:43:10,034 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Raw Flex reader map values: \\cia-273\images;\\10.79.2.101\hcs\OperaArchiveCol
2013-11-20 15:43:10,034 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Raw Flex reader map values: \\cia-273\images;\\10.79.2.101\hcs\OperaArchiveCol
2013-11-20 15:43:10,035 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-3' = '\\cia-273\images'.
2013-11-20 15:43:10,037 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-3' = '\\10.79.2.101\hcs\OperaArchiveCol'.
2013-11-20 15:43:10,037 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-1' = '\\cia-273\images'.
2013-11-20 15:43:10,039 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-1' = '\\10.79.2.101\hcs\OperaArchiveCol'.
2013-11-20 15:43:10,039 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-2' = '\\cia-273\images'.
2013-11-20 15:43:10,041 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-2' = '\\10.79.2.101\hcs\OperaArchiveCol'.
2013-11-20 15:43:10,042 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-4' = '\\cia-273\images'.
2013-11-20 15:43:10,043 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-17) Added Flex reader server map 'CIA-4' = '\\10.79.2.101\hcs\OperaArchiveCol'.
2013-11-20 15:43:10,043 INFO [ ome.formats.importer.ImportConfig] ( Thread-17) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June 2013
2013-11-20 15:46:02,254 DEBUG [ ome.scifio.io.Location] ( Thread-17) Location.mapFile: embedded-stream.raw -> null
2013-11-20 15:46:02,702 DEBUG [penmicroscopy.shoola.util.NetworkChecker] ( Thread-17) Network status: true (in 448 ms.)
2013-11-20 15:46:13,750 DEBUG [penmicroscopy.shoola.util.NetworkChecker] ( Thread-19) Network status: true (in 533 ms.)
2013-11-20 15:46:13,785 DEBUG [.shoola.env.ui.DownloadAndLaunchActivity] (entQueue-0) C:\Users\Megatron\omero\filesOmero\importLog_730
2013-11-20 15:46:13,788 DEBUG [penmicroscopy.shoola.util.NetworkChecker] ( Thread-20) Cached networkup: true
2013-11-20 15:46:13,802 ERROR [.openmicroscopy.shoola.env.ui.FileLoader] (entQueue-0) Data Retrieval Failure: java.lang.NullPointerException
at org.openmicroscopy.shoola.env.data.OMEROGateway.download(OMEROGateway.java:3766)
at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:3744)
at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.downloadFile(OmeroMetadataServiceImpl.java:1357)
at org.openmicroscopy.shoola.env.data.views.calls.FilesLoader$1.doCall(FilesLoader.java:100)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)
Data Retrieval Failure: java.lang.NullPointerException
at org.openmicroscopy.shoola.env.data.OMEROGateway.download(OMEROGateway.java:3766)
at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:3744)
at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.downloadFile(OmeroMetadataServiceImpl.java:1357)
at org.openmicroscopy.shoola.env.data.views.calls.FilesLoader$1.doCall(FilesLoader.java:100)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)
Exception in thread "AWT-EventQueue-0"
Is it possible to see the details of the variables at this step?
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)?
Thank you for your feedback on this,
--
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 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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