[ome-devel] Help loading data...

[Malone, Scott]

Tom,
	I have downloaded and installed the cvs code, I think.  On the
web page it is still showing 2.4.1, is this correct?  I did not specifiy
that I was importing the images through the web interface and not with
the ome commandline tool.  

	I'm not sure I understand how the image loading through the
commandline works.  I believe that I have successfully loaded an image
with the commandline tool, but I don't know how to associate the image
with a user in OME.  I don't seem to be able to find the image once I
log into OME.

	That begin said, I have changed the Engine.pm that you modified
with the one in the distribution.  I'm still seeing the same error
messages, but were should I look for the debug output from Engine.pm?


I have attached the screen output and the httpd error log files for the
import errors...

Thanks,

Scott Malone
System Integration Engineer - LINUX
Hartwell Center for Bioinformatics and Biotechnology
St. Jude Children's Research Hospital
901.495.4947
scott.malone at stjude.org
 
> -----Original Message-----
> From: T. J. Macura [mailto:tm289 at hermes.cam.ac.uk] On Behalf Of Tomasz
> Macura
> Sent: Saturday, November 26, 2005 6:11 AM
> To: Malone, Scott
> Cc: ome-devel at lists.openmicroscopy.org.uk
> Subject: Re: [ome-devel] Help loading data...
> 
> Hi Scott,
> 
> Sorry for the delay getting back to you. I was sick last week and had
my
> laptop (on which I work) stolen. I needed a few days to get back up to
> speed.
> 
> It sounds like you are having a serious problem. Could you please try
> OME from CVS? http://cvs.openmicroscopy.org.uk/ We are preparing to
> rollout release candidates for 2.5.0 so the codebase is currently
pretty
> stable.
> 
> Once you get OME from CVS please replace
> OME/src/perl2/OME/Analysis/Engine.pm with the attached Engine.pm . I
> added a debug statement in an attempt to triage your problem.
> 
> Thanks for your feedback. Have a great Thanksgiving Weekend!
> 
> Tom
> 
> P.S.: next time please run the ome commandline tool (omeadmin) with
the
> environmental variable OME_DEBUG set to 1. Also please email me back
the
> full output to the screen from the ome import command.
> 
> On Fri, 2005-11-18 at 14:50 -0600, Malone, Scott wrote:
> > I'm currently having a problem uploading file in to OME.  I can
upload
> > them has the user omeadmin, but once I created a separate user I get
> > the following error...
> >
> >
> >
> > Can't call method "attribute_sort_time" on an undefined value
> > at /usr/lib/perl5/site_perl/5.8.0/OME/Analysis/Engine.pm line 853.
> >
> >
> >
> > Any suggestion on why I might be getting this and what I can do to
> > stop it?  We are currently running version 2.4.1
> >
> >
> >
> >
> >
> > Scott Malone
> >
> > System Integration Engineer - LINUX
> >
> > Hartwell Center for Bioinformatics and Biotechnology
> >
> > St. Jude Children's Research Hospital
> >
> > 901.495.4947
> >
> > scott.malone at stjude.org
> 

-------------- next part --------------
A non-text attachment was scrubbed...
Name: output.jpg
Type: image/jpeg
Size: 35777 bytes
Desc: output.jpg
Url : http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20051130/4e2ca38e/output-0001.jpg
-------------- next part --------------
05/11/30 12:39:41 serve.pl[15927]: Serving package - OME::Web::ImportImages.
05/11/30 12:39:41 serve.pl[15927]: getOMESession: found existing userState(s)
05/11/30 12:39:42 serve.pl[15927]: createWithKey: updating userState
05/11/30 12:39:42 serve.pl[15927]: createWithKey: returning session
*DEBUG* PARAM[Path]: /ome/user_data/smalone
*DEBUG* PARAM[action]: Add to Queue
*DEBUG* PARAM[new_or_existing]: existing
*DEBUG* PARAM[existing_dataset]: Test
*DEBUG* PARAM[name]:
*DEBUG* PARAM[description]:
*DEBUG* PARAM[add_selected]: /ome/user_data/smalone/WT-1_Series02_z010_ch00.tif
[Wed Nov 30 12:39:42 2005] [error] [client 199.76.2.157] File does not exist: /ome/web/html/favicon.ico
05/11/30 12:39:44 serve.pl[15928]: Serving package - OME::Web::ImportImages.
05/11/30 12:39:44 serve.pl[15928]: getOMESession: found existing userState(s)
05/11/30 12:39:44 serve.pl[15928]: createWithKey: updating userState
05/11/30 12:39:44 serve.pl[15928]: createWithKey: returning session
*DEBUG* PARAM[import_queue]: /ome/user_data/smalone/WT-1_Series02_z010_ch00.tif
*DEBUG* PARAM[Path]: /ome/user_data/smalone
*DEBUG* PARAM[action]: import
*DEBUG* PARAM[new_or_existing]: existing
*DEBUG* PARAM[existing_dataset]: Test
*DEBUG* PARAM[name]:
*DEBUG* PARAM[description]:
05/11/30 12:39:44 serve.pl[16109]: Serving package - OME::Web::TaskProgress.
05/11/30 12:39:44 serve.pl[15928]: Loading attribute type package OME::SemanticType::__Repository
05/11/30 12:39:44 serve.pl[15928]: Loading data table package OME::DataTable::__REPOSITORIES
05/11/30 12:39:44 serve.pl[16109]: getOMESession: found existing userState(s)
05/11/30 12:39:44 serve.pl[16109]: createWithKey: updating userState
05/11/30 12:39:45 serve.pl[16109]: createWithKey: returning session
[Wed Nov 30 12:39:46 2005] [error] [client 199.76.2.157] File does not exist: /ome/web/html/favicon.ico
05/11/30 12:39:47 serve.pl[15928]: Loading attribute type package OME::SemanticType::__FilenamePattern
05/11/30 12:39:47 serve.pl[15928]: Loading data table package OME::DataTable::__FILENAME_PATTERN
05/11/30 12:39:47 serve.pl[15928]: Checking WT-1_Series02_z010_ch00.tif for ^(.+)(_w)(\d+)(.*)

05/11/30 12:39:47 serve.pl[15928]: deleting WT-1_Series02_z010_ch00.tif in singleton group WT-1_Series02_z010_ch00
05/11/30 12:39:47 serve.pl[15928]: Loading attribute type package OME::SemanticType::__OriginalFile
05/11/30 12:39:47 serve.pl[15928]: Loading data table package OME::DataTable::__ORIGINAL_FILES
05/11/30 12:39:47 serve.pl[15928]: Loading attribute type package OME::SemanticType::__Pixels
05/11/30 12:39:47 serve.pl[15928]: Loading data table package OME::DataTable::__IMAGE_PIXELS
05/11/30 12:39:47 serve.pl[15928]: shifted WT-1_Series02_z010_ch00.tif
[Wed Nov 30 12:39:48 2005] [error] [client 199.76.2.147] Files/145: Warning, unknown field with tag 33923 (0x8483) ignored.
[Wed Nov 30 12:39:48 2005] [error] [client 199.76.2.147] Files/145: Warning, unknown field with tag 33923 (0x8483) ignored.
05/11/30 12:39:48 serve.pl[15928]: Touch 'TIFF' WT-1_Series02_z010_ch00.tif

05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__LogicalChannel
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__LOGICAL_CHANNELS
05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__LightSource
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__LIGHT_SOURCES
05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__Instrument
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__INSTRUMENTS
05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__Detector
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__DETECTORS
05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__OTF
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__OTFS
05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__Filter
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__FILTER
05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__Objective
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__OBJECTIVES
05/11/30 12:39:48 serve.pl[15928]: Loading attribute type package OME::SemanticType::__PixelChannelComponent
05/11/30 12:39:48 serve.pl[15928]: Loading data table package OME::DataTable::__CHANNEL_COMPONENTS
05/11/30 12:39:48 serve.pl[16109]: Serving package - OME::Web::TaskProgress.
05/11/30 12:39:49 serve.pl[16109]: getOMESession: found existing userState(s)
05/11/30 12:39:49 serve.pl[16109]: createWithKey: updating userState
05/11/30 12:39:49 serve.pl[16109]: createWithKey: returning session
05/11/30 12:39:49 serve.pl[15928]: Loading attribute type package OME::SemanticType::__DisplayChannel
05/11/30 12:39:49 serve.pl[15928]: Loading data table package OME::DataTable::__DISPLAY_CHANNELS
05/11/30 12:39:49 serve.pl[15928]: Loading attribute type package OME::SemanticType::__DisplayOptions
05/11/30 12:39:49 serve.pl[15928]: Loading data table package OME::DataTable::__DISPLAY_OPTIONS
05/11/30 12:39:49 serve.pl[15928]: OME::ImportEngine::ImportEngine->importFiles: imported WT-1_Series02_z010_ch00
[Wed Nov 30 12:39:49 2005] [error] [client 199.76.2.157] File does not exist: /ome/web/html/favicon.ico
05/11/30 12:39:49 serve.pl[15928]: Round 1...
05/11/30 12:39:49 serve.pl[15928]:   isNodeReady(Original files,0)
05/11/30 12:39:49 serve.pl[15928]:   executeNodeWithTarget(Original files,0)
05/11/30 12:39:49 serve.pl[15928]:   getUniversalExecution(
05/11/30 12:39:50 serve.pl[16109]: Serving package - OME::Web::TaskProgress.
05/11/30 12:39:50 serve.pl[16109]: getOMESession: found existing userState(s)
05/11/30 12:39:50 serve.pl[16109]: createWithKey: updating userState
05/11/30 12:39:50 serve.pl[16109]: createWithKey: returning session