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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/env perl | ||
| # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute | ||
| # Copyright [2016-2018] EMBL-European Bioinformatics Institute | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
|
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| use strict; | ||
| use warnings; | ||
|
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| use Data::Dumper; | ||
| use File::Temp qw{tempdir}; | ||
|
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| use Test::More tests => 18; | ||
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| use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor; | ||
| use Bio::EnsEMBL::Hive::ResourceClass; | ||
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| use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline); | ||
|
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| # eHive needs this to initialize the pipeline (and run db_cmd.pl) | ||
| use Cwd (); | ||
| use File::Basename (); | ||
| $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) ) ); | ||
|
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| my $dir = tempdir CLEANUP => 1; | ||
| chdir $dir; | ||
|
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| my $pipeline_url = 'sqlite:///ehive_test_pipeline_db'; | ||
|
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| my $hive_dba = init_pipeline('Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf', $pipeline_url, [-hive_force_init => 1]); | ||
|
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| my $job_a = $hive_dba->get_AnalysisJobAdaptor; | ||
| my $rcl_a = $hive_dba->get_ResourceClassAdaptor; | ||
| my $rde_a = $hive_dba->get_ResourceDescriptionAdaptor; | ||
| my $dfr_a = $hive_dba->get_DataflowRuleAdaptor; | ||
| my $ada_a = $hive_dba->get_AnalysisDataAdaptor; | ||
| my $acu_a = $hive_dba->get_AccumulatorAdaptor; | ||
| my $acr_a = $hive_dba->get_AnalysisCtrlRuleAdaptor; | ||
| my $ana_a = $hive_dba->get_AnalysisAdaptor; | ||
|
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| my $long_input_id = sprintf('{ "long_param" => "%s" }', 'tmp' x 1000); | ||
| my $new_job = Bio::EnsEMBL::Hive::AnalysisJob->new( | ||
| 'input_id' => $long_input_id, | ||
| 'analysis_id' => 1, | ||
| ); | ||
|
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| # Test the overflow into the analysis_data table | ||
| # Test overflow for input_id | ||
| is($ada_a->count_all(), 0, "Nothing in the analysis_data table (yet)"); | ||
|
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| $job_a->store($new_job); | ||
| is($ada_a->count_all(), 1, "1 entry in the analysis_data table"); | ||
|
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| is($ada_a->fetch_by_data_TO_analysis_data_id('unmatched input_id'), undef, 'fetch_by_data_to_analysis_data_id() returns undef when it cannot find the input_id'); | ||
| my $ext_data_id = $ada_a->fetch_by_data_TO_analysis_data_id($long_input_id); | ||
| is($ext_data_id, 1, 'analysis_data_id starts at 1'); | ||
|
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| my $fan_job = Bio::EnsEMBL::Hive::AnalysisJob->new( | ||
| 'input_id' => $long_input_id, | ||
| 'analysis_id' => 2, | ||
| ); | ||
|
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| $job_a->store($fan_job); | ||
| is($ada_a->count_all(), 1, "still 1 entry in the analysis_data table"); | ||
|
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| # Test overflow for resource description args | ||
|
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| Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->init_collections(); | ||
| my $new_rc = Bio::EnsEMBL::Hive::ResourceClass->add_new_or_update( | ||
| 'name' => 'testresourceclass', | ||
| ); | ||
|
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| my $long_sca = 'sc' x 129; | ||
| my $long_wca = 'wc' x 129; | ||
| my $new_rd = Bio::EnsEMBL::Hive::ResourceDescription->add_new_or_update( | ||
| 'resource_class' => $new_rc, | ||
| 'meadow_type' => 'test_meadow', | ||
| 'submission_cmd_args' => $long_sca, | ||
| 'worker_cmd_args' => $long_wca, | ||
| ); | ||
|
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| $rcl_a->store($new_rc); | ||
| $rde_a->store($new_rd); | ||
| is($ada_a->count_all(), 3, "New resource description overflowed two entries to analysis_data, total 3"); | ||
|
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| # Test overflow for to_analysis_urls | ||
|
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| my $long_struct_name = 'ta' x 129; | ||
| my $long_to_analysis_url = ':////accu?' . $long_struct_name; | ||
| my $new_dfr = Bio::EnsEMBL::Hive::DataflowRule->add_new_or_update( | ||
| 'from_analysis' => $ana_a->fetch_by_dbID(1), | ||
| 'to_analysis_url' => $long_to_analysis_url, | ||
| 'branch_code' => 3, | ||
| ); | ||
|
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| $dfr_a->store($new_dfr); | ||
| is($ada_a->count_all(), 4, "New to_analysis_url overflowed an entry to analysis_data, total 4"); | ||
|
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| # Test overflow for condition analysis urls | ||
|
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| my $long_cau = 'cau' x 86; | ||
| my $ctrled_analysis_id = 1; | ||
| my $new_acr = Bio::EnsEMBL::Hive::AnalysisCtrlRule->add_new_or_update( | ||
| 'condition_analysis_url' => $long_cau, | ||
| 'ctrled_analysis' => $ana_a->fetch_by_dbID($ctrled_analysis_id), | ||
| ); | ||
|
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| $acr_a->store($new_acr); | ||
| is($ada_a->count_all(), 5, "New condition_analysis_url overflowed an entry to analysis_data, total 5"); | ||
|
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| # Test overflow for accu key_signatures | ||
| # Note: AccumulatorAdaptor will complain if storing an accu without a proper fan job | ||
| # and semaphored funnel job | ||
|
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| my $accu_funnel_job = Bio::EnsEMBL::Hive::AnalysisJob->new( | ||
| 'input_id' => {}, | ||
| 'analysis_id' => 3, | ||
| ); | ||
| $job_a->store($accu_funnel_job); | ||
|
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| my $accu_fan_job = Bio::EnsEMBL::Hive::AnalysisJob->new( | ||
| 'input_id' => {}, | ||
| 'analysis_id' => 2, | ||
| 'semaphored_job_id' => $accu_funnel_job->dbID, | ||
| ); | ||
| $job_a->store($accu_fan_job); | ||
|
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| my $new_accu = Bio::EnsEMBL::Hive::Accumulator->new( | ||
| adaptor => $acu_a, | ||
| struct_name => $long_struct_name, | ||
| signature_template => '{key}', | ||
| ); | ||
|
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| my $long_key_signature = 'ks' x 129; | ||
| my $long_output_id = [ { 'key' => $long_key_signature, | ||
| $long_struct_name => 1, } ]; | ||
| $new_accu->dataflow( | ||
| $long_output_id, | ||
| $accu_fan_job, | ||
| ); | ||
|
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| is($ada_a->count_all(), 7, "Overflow for long struct_name and key_signature in accu"); | ||
|
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| # Test retrieval of overflow data | ||
|
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| my $fetched_rds = $rde_a->fetch_all(); | ||
| my $rd_with_long_args; | ||
| foreach my $fetched_rd (@$fetched_rds) { | ||
| if ($fetched_rd->resource_class_id() == $new_rc->dbID) { | ||
| $rd_with_long_args = $fetched_rd; | ||
| } | ||
| } | ||
|
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| is($rd_with_long_args->submission_cmd_args, $long_sca, "Retrieved long submission_cmd_args"); | ||
| is($rd_with_long_args->worker_cmd_args, $long_wca, "Retrieved long worker_cmd_args"); | ||
|
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| my $fetched_dfr = $dfr_a->fetch_by_dbID($new_dfr->dbID); | ||
| is ($fetched_dfr->to_analysis_url, $long_to_analysis_url, "Retrieved long to_analysis_url"); | ||
|
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| my $fetched_acr = $acr_a->fetch_by_ctrled_analysis_id($ctrled_analysis_id); | ||
| is ($fetched_acr->condition_analysis_url, $long_cau, "Retrieved long condition_analysis_url"); | ||
|
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| # $fetched_accu_structures->{$receiving_job_id}->{$struct_name}->{$key_signature} = value | ||
| my $fetched_accu_structures = $acu_a->fetch_structures_for_job_ids($accu_funnel_job->dbID); | ||
| my $fetched_accu_hash = $fetched_accu_structures->{$accu_funnel_job->dbID}; | ||
| my $fetched_struct_name = (keys(%$fetched_accu_hash))[0]; | ||
| my $fetched_key_signature = (keys(%$fetched_accu_hash->{$fetched_struct_name}))[0]; | ||
|
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| is ($fetched_struct_name, $long_struct_name, "fetched long struct_name from accu"); | ||
| is ($fetched_key_signature, $long_key_signature, "fetched long key_signature from accu"); | ||
|
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| done_testing(); |