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

Tue Jun 27 20:58:57 BST 2006

Hi Ralph,

Every time I have seen the 'DBD::Pg::st execute failed: ERROR:  syntax error
at or near "$1"' error, it's been due to a buggy version of DBD::Pg. So I
second Ilya's advice to downgrade DBD::Pg (as the website's install notes
explain, many versions of it cause problems with OME). One easy way to make
things work is to uninstall DBD::Pg, then rerun the OME installer. It will
detect that DBD::Pg is not installed and offer to download and install a
known working version from the OME repository.

-Curtis

On 6/23/06, Brandenberger, Ralph <RBrandenberger at geron.com> wrote:
>
> 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"
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