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The Genome Modeling System installer
https://github.com/genome/gms/wiki
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Missing column in schema (fragment_library.bisulfite_conversion) #108

Closed malachig closed 10 years ago

malachig commented 10 years ago

Testing the installer with the new merged versions of UR, workflow, and gms-core.

Getting the following error during metadata import:

DBD::Pg::st execute failed: ERROR:  column fragment_library.bisulfite_conversion does not exist
LINE 2: select instrument.fragment_library.bisulfite_conversion, ins...
               ^ at /opt/gms/TFLWB39/sw/ur/lib/UR/DBI.pm line 888.
ERROR: Failed to execute SQL 
select instrument.fragment_library.bisulfite_conversion, instrument.fragment_library.library_id, instrument.fragment_library.library_insert_size, instrument.fragment_library.FULL_NAME, instrument.fragment_library.original_insert_size, instrument.fragment_library.protocol, instrument.fragment_library.sample_id, instrument.fragment_library.transcript_strand
from instrument.fragment_library
where instrument.fragment_library.library_id in ('2891040499','2891040500','2891040501','2891040502','2891040503','2891040504','2891075264','2891229376','2891229400','2891242741','2891242742','2893186767')
order by instrument.fragment_library.library_id
ERROR:  column fragment_library.bisulfite_conversion does not exist
LINE 2: select instrument.fragment_library.bisulfite_conversion, ins...
               ^
$VAR1 = [];

ERROR: Failed to execute SQL 
select instrument.fragment_library.bisulfite_conversion, instrument.fragment_library.library_id, instrument.fragment_library.library_insert_size, instrument.fragment_library.FULL_NAME, instrument.fragment_library.original_insert_size, instrument.fragment_library.protocol, instrument.fragment_library.sample_id, instrument.fragment_library.transcript_strand
from instrument.fragment_library
where instrument.fragment_library.library_id in ('2891040499','2891040500','2891040501','2891040502','2891040503','2891040504','2891075264','2891229376','2891229400','2891242741','2891242742','2893186767')
order by instrument.fragment_library.library_id
ERROR:  column fragment_library.bisulfite_conversion does not exist
LINE 2: select instrument.fragment_library.bisulfite_conversion, ins...
               ^
$VAR1 = [];
 at /opt/gms/TFLWB39/sw/ur/lib/UR/DataSource/RDBMS.pm line 1602
    UR::DataSource::RDBMS::create_iterator_closure_for_rule('Genome::DataSource::GMSchema=HASH(0x3e92578)', 'UR::BoolExpr=HASH(0x82e65a0)') called at /opt/gms/TFLWB39/sw/ur/lib/UR/Context/ImportIterator.pm line 377
    UR::Context::_create_import_iterator_for_underlying_context('UR::Context::Process=HASH(0x2e13820)', 'UR::BoolExpr=HASH(0x82e65a0)', 'Genome::DataSource::GMSchema=HASH(0x3e92578)', 15042) called at /opt/gms/TFLWB39/sw/ur/lib/UR/Context/LoadingIterator.pm line 69
    UR::Context::LoadingIterator::_create('UR::Context::LoadingIterator', 'ARRAY(0x83263f8)', 'UR::Context::Process=HASH(0x2e13820)', 'UR::BoolExpr=HASH(0x82e65a0)', 'Genome::DataSource::GMSchema=HASH(0x3e92578)', 15042) called at /opt/gms/TFLWB39/sw/ur/lib/UR/Context.pm line 1812
    UR::Context::get_objects_for_class_and_rule('UR::Context::Process=HASH(0x2e13820)', 'Genome::Library', 'UR::BoolExpr=HASH(0x82e59e8)') called at /opt/gms/TFLWB39/sw/ur/lib/UR/Context.pm line 502
    UR::Context::query('UR::Context::Process=HASH(0x2e13820)', 'Genome::Library', 'id', 'ARRAY(0x58ae948)') called at /opt/gms/TFLWB39/sw/ur/lib/UR/Object.pm line 24
    UR::Object::get('Genome::Library', 'id', 'ARRAY(0x58ae948)') called at /opt/gms/TFLWB39/sw/genome/lib/perl/Genome/Model/Command/Import/Metadata.pm line 127
    Genome::Model::Command::Import::Metadata::execute('Genome::Model::Command::Import::Metadata=HASH(0x4158978)', 'HASH(0x572df20)') called at /opt/gms/TFLWB39/sw/ur/lib/Command/V2.pm line 214
    Command::V2::execute('Genome::Model::Command::Import::Metadata=HASH(0x4158978)', 'HASH(0x572df20)') called at /opt/gms/TFLWB39/sw/ur/lib/Command/Dispatch/Shell.pm line 136
    Command::V2::_execute_delegate_class_with_params('Genome::Command', 'Genome::Model::Command::Import::Metadata', 'HASH(0x572df20)', '/opt/gms/TFLWB39/sw/genome/bin/genome\x{0}model\x{0}import\x{0}metadata\x{0}1...') called at /opt/gms/TFLWB39/sw/ur/lib/Command/Dispatch/Shell.pm line 74
    Command::V2::_execute_with_shell_params_and_return_exit_code('Genome::Command', 'model', 'import', 'metadata', '18177dd5eca44514a47f367d9804e17a-2014.1.16.dat') called at /opt/gms/TFLWB39/sw/ur/lib/Command/Dispatch/Shell.pm line 42
    eval {...} called at /opt/gms/TFLWB39/sw/ur/lib/Command/Dispatch/Shell.pm line 41
    Command::V2::_cmdline_run('Genome::Command', 'model', 'import', 'metadata', '18177dd5eca44514a47f367d9804e17a-2014.1.16.dat') called at /opt/gms/TFLWB39/sw/ur/lib/Command/Dispatch/Shell.pm line 19
    Command::V2::execute_with_shell_params_and_exit('Genome::Command') called at /opt/gms/TFLWB39/sw/genome/bin/genome line 25

This issue is awaiting a sync of the postgres schema.

sakoht commented 10 years ago

This is something you can run to get the schema for a table in postgres whenever a problem like this occurs:

psql -h gms-postgres -d genome -U gms-user -c '\d instrument.fragment_library'

Then update setup/schema.sql, as has already been done for this issue.

https://github.com/genome/gms/commit/6b445ac5e333c02351a86260de3458d0d05b278b

malachig commented 10 years ago

The schema differences are being systematically examined in issue #109. There are some questions/concerns there that may be blocking progress for now.

malachig commented 10 years ago

Updates to the schema have been incorporated. Closing this issue now.