[ome-users] OME install woes

august august at develop.ment.org
Wed Apr 5 23:41:26 BST 2006 

Some install woes.

I have two machines that are identicle in hardware and are running the
same Ubuntu Linux OS version.   One machine has installed successfully.
The other machine is having more problems, and I don't know what it is
exactly.

The install script stopped the first time at:

ERROR LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/OMEIS/Experiment.ome" -- OUTPUT:
"500 EOF when chunk header expected

I drop the ome database and run the install sript again, but get a
Success in loading the Experiment.ome file.  The next one after that,
Plate.ome, fails however.  And so on.  The next run through.  Plate.ome
is successfully uploaded, but the one after it fails.

any I deas why this is?

Seems the problem is in OME::Image::Server::__callOMEIS

below is the tailend of the insall script output and of the
CoreDatabase.log file


thanks -august.
 


------------------------------------------------------------
[SUCCESS].
  \__ /home/swaroop/OME/src/xml/OME/Core/Experimenter.ome [SUCCESS].
  \__ /home/swaroop/OME/src/xml/OME/Core/Group.ome [SUCCESS].
  \__ /home/swaroop/OME/src/xml/OME/Core/Instrument.ome NOTICE:  CREATE
TABLE / PRIMARY KEY will create implicit index "instruments_pkey" for table
"instruments"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"light_sources_pkey" for table "light_sources"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index "lasers_pkey"
for table "lasers"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"filaments_pkey" for table "filaments"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index "arcs_pkey"
for table "arcs"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"detectors_pkey" for table "detectors"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"objectives_pkey" for table "objectives"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index "filter_pkey"
for table "filter"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"excitation_filters_pkey" for table "excitation_filters"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"dichroics_pkey" for table "dichroics"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"emission_filters_pkey" for table "emission_filters"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"filter_sets_pkey" for table "filter_sets"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index "otfs_pkey"
for table "otfs"
[SUCCESS].
  \__ /home/swaroop/OME/src/xml/OME/Core/Image.ome NOTICE:  CREATE TABLE /
PRIMARY KEY will create implicit index "image_info_pkey" for table
"image_info"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"imaging_environments_pkey" for table "imaging_environments"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"thumbnails_pkey" for table "thumbnails"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"logical_channels_pkey" for table "logical_channels"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"channel_components_pkey" for table "channel_components"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"display_channels_pkey" for table "display_channels"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"display_options_pkey" for table "display_options"NOTICE:  CREATE TABLE /
PRIMARY KEY will create implicit index "display_roi_pkey" for table
"display_roi"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"stage_labels_pkey" for table "stage_labels"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"image_plates_pkey" for table "image_plates"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"image_pixels_pkey" for table "image_pixels"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"image_dimensions_pkey" for table "image_dimensions"
[SUCCESS].
  \__ /home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome [FAILURE].


--------------------------------------------------------------------
Creating OME PostgreSQL SUPERUSER (ome)
SUCCESS LOADING CLASS "OME::LookupTable"
SUCCESS LOADING CLASS "OME::LookupTable::Entry"
SUCCESS LOADING CLASS "OME::DataTable"
SUCCESS LOADING CLASS "OME::DataTable::Column"
SUCCESS LOADING CLASS "OME::SemanticType"
SUCCESS LOADING CLASS "OME::SemanticType::Element"
SUCCESS LOADING CLASS "OME::SemanticType::BootstrapExperimenter"
SUCCESS LOADING CLASS "OME::SemanticType::BootstrapGroup"
SUCCESS LOADING CLASS "OME::SemanticType::BootstrapExperimenterGroup"
SUCCESS LOADING CLASS "OME::SemanticType::BootstrapRepository"
SUCCESS LOADING CLASS "OME::Dataset"
SUCCESS LOADING CLASS "OME::Project"
SUCCESS LOADING CLASS "OME::Project::DatasetMap"
SUCCESS LOADING CLASS "OME::Image"
SUCCESS LOADING CLASS "OME::Image::DatasetMap"
SUCCESS LOADING CLASS "OME::Feature"
SUCCESS LOADING CLASS "OME::UserState"
SUCCESS LOADING CLASS "OME::ViewerPreferences"
SUCCESS LOADING CLASS "OME::LSID"
SUCCESS LOADING CLASS "OME::Module::Category"
SUCCESS LOADING CLASS "OME::Module"
SUCCESS LOADING CLASS "OME::Module::FormalInput"
SUCCESS LOADING CLASS "OME::Module::FormalOutput"
SUCCESS LOADING CLASS "OME::AnalysisChain"
SUCCESS LOADING CLASS "OME::AnalysisChain::Node"
SUCCESS LOADING CLASS "OME::AnalysisChain::Link"
SUCCESS LOADING CLASS "OME::AnalysisPath"
SUCCESS LOADING CLASS "OME::AnalysisPath::Map"
SUCCESS LOADING CLASS "OME::ModuleExecution"
SUCCESS LOADING CLASS "OME::ModuleExecution::ActualInput"
SUCCESS LOADING CLASS "OME::ModuleExecution::SemanticTypeOutput"
SUCCESS LOADING CLASS "OME::ModuleExecution::ParentalOutput"
SUCCESS LOADING CLASS "OME::ModuleExecution::VirtualMEXMap"
SUCCESS LOADING CLASS "OME::AnalysisChainExecution"
SUCCESS LOADING CLASS "OME::AnalysisChainExecution::NodeExecution"
SUCCESS LOADING CLASS "OME::Task"
SUCCESS LOADING CLASS "OME::Analysis::Engine::Worker"
SUCCESS LOADING CLASS "OME::Configuration::Variable"
Checking repository
Repository URL: http://fiddler/cgi-bin/omeis
ENVIRONMENT->omeis_url(): http://fiddler/cgi-bin/omeis
Getting an LWP user agent
Generating request for http://fiddler/cgi-bin/omeis
Getting response from http://fiddler/cgi-bin/omeis
Parsing response from http://fiddler/cgi-bin/omeis
Repository is configured correctly
SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/Experiment.ome"
SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/Plate.ome"
SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/Screen.ome"
SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/Experimenter.ome"
SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/Group.ome"
SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/Instrument.ome"
SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/Image.ome"
ERROR LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome" -- OUTPUT: "500 EOF when chunk header expected
 at /home/swaroop/OME/src/perl2/OME/Image/Server.pm line 474
	OME::Image::Server::__callOMEIS('OME::Image::Server', 'Method', 'UploadFile', 'File', '/home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome') called at /home/swaroop/OME/src/perl2/OME/Image/Server.pm line 1061
	OME::Image::Server::uploadFile('OME::Image::Server', '/home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome') called at /home/swaroop/OME/src/perl2/OME/Image/Server/File.pm line 117
	OME::Image::Server::File::upload('OME::Image::Server::File', '/home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome') called at /home/swaroop/OME/src/perl2/OME/Tasks/OMEImport.pm line 138
	OME::Tasks::OMEImport::importFile('OME::Tasks::OMEImport=HASH(0x94ca160)', '/home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome', 'NoDuplicates', 1, 'IgnoreAlterTableErrors', 1) called at /home/swaroop/OME/src/perl2/OME/Install/CoreDatabaseTablesTask.pm line 768
	eval {...} called at /home/swaroop/OME/src/perl2/OME/Install/CoreDatabaseTablesTask.pm line 767
	OME::Install::CoreDatabaseTablesTask::load_xml_core('OME::Session=HASH(0x94c164c)', 'GLOB(0x843575c)') called at /home/swaroop/OME/src/perl2/OME/Install/CoreDatabaseTablesTask.pm line 1113
	OME::Install::CoreDatabaseTablesTask::execute() called at (eval 169) line 1
	eval 'OME::Install::CoreDatabaseTablesTask::execute()
;' called at ./install.pl line 79
	main::run_tasks() called at ./install.pl line 249
"

More information about the ome-users mailing list