[ome-users] Error during install: ImportModule.ome

Sat Jun 24 01:31:14 BST 2006

Hi,

I am trying to install OME using the following configuration:

OME-2.4.0 stable release
RHLinux 9 with lots of updates...
Perl 5.8.8
Postgres 8.0.8
Apache 2.0.55
DBI: 1.51
DBD::Pg 1.49
(generally most up-to-date version of all perl modules)

I am running into the following problem during the database bootstrap.
The tables are created, configuration is initialized, and the install
script proceeds to the "Finalize Database" step.

Has anybody seen similar errors?
Any help would be greatly appreciated.

THX!
Ralph

---------------------
 Finalizing Database
---------------------

  \__ Creating repository object

What is the URL of the OME Image server (omeis) ?
[http://bava.geron.com/cgi-bin/omeis]: http://10.1.2.28/cgi-bin/omeis
Checking OMEIS repository [SUCCESS].
Importing core XML
  \__ /u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Experiment.ome
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"experiments_pkey" for table "experiments"
[SUCCESS].
  \__ /u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Plate.ome
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"plates_pkey" for table "plates"
[SUCCESS].
  \__ /u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Screen.ome
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"screens_pkey" for table "screens"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"plate_screen_map_pkey" for table "plate_screen_map"
[SUCCESS].
  \__
/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Experimenter.ome
[SUCCESS].
  \__ /u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Group.ome
[SUCCESS].
  \__ /u01/bioinformatics/geron/OME/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].
  \__ /u01/bioinformatics/geron/OME/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].
  \__
/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/OMEIS/Repository.ome
[SUCCESS].
  \__
/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/OMEIS/OriginalFile.om
e NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"original_files_pkey" for table "original_files"
[SUCCESS].
  \__
/u01/bioinformatics/geron/OME/OME/src/xml/OME/Import/ImportModule.ome
DBD::Pg::st execute failed: ERROR:  syntax error at or near "$1" at
character 172
[FAILURE].

Errors executing task: Error loading XML file
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Import/ImportModule.ome",
see CoreDatabaseTablesTask.log details. at (eval 181) line 1

 at install.pl line 80
        main::run_tasks() called at install.pl line 249
# Looks like your test died before it could output anything.

Here's the CoreDatabaseTablesTask.log section:

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://10.1.2.28/cgi-bin/omeis
ENVIRONMENT->omeis_url(): http://10.1.2.28/cgi-bin/omeis
Getting an LWP user agent
Generating request for http://10.1.2.28/cgi-bin/omeis
Getting response from http://10.1.2.28/cgi-bin/omeis
Parsing response from http://10.1.2.28/cgi-bin/omeis
Repository is configured correctly
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Experiment.ome"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Plate.ome"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Screen.ome"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Experimenter.ome"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Group.ome"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Instrument.ome"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/Image.ome"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/OMEIS/Repository.ome
"
SUCCESS LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Core/OMEIS/OriginalFile.o
me"
ERROR LOADING XML FILE
"/u01/bioinformatics/geron/OME/OME/src/xml/OME/Import/ImportModule.ome"
-- OUTPUT: "DBD::Pg::st execute failed: ERROR:  syntax error at or near
"$1" at character 172"