hello,
now I compared an older working version of my program (a few days old)
with the current version which shows the bug, using show_sql=true
and the log4j-debug-mode.
What strikes me is that the query for loading a Project produces 1 row in
the working version, and 8 in the broken one (Tested with the
HSQLDB-frontend). And there are exactly 8 GibbsSamplingResults-objects (broken)
instead of one (working) underneath the SequenceList.
The resultset output looks like this in the broken version:
Code:
13:14:05,522 DEBUG Loader:1877 - loading entity: [de.bhc.pepa.Project#1]
[...]
13:14:05,546 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Sequence#1], EntityKey[de.bhc.pepa.Project#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResults#1], EntityKey[de.bhc.gibbssampler.GlobalPWM#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResult#1], EntityKey[de.bhc.gibbssampler.Alignment#1], EntityKey[de.bhc.gibbssampler.Dictionary#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], null, null, null, null, null, null, null, null, EntityKey[de.bhc.gibbssampler.PWM#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.GibbsSamplerParameters#1], EntityKey[de.bhc.gibbssampler.Background#1], EntityKey[de.bhc.pepa.Project#1]
13:14:05,567 DEBUG Loader:1008 - found row of collection: [de.bhc.pepa.Project.hitlists#1]
13:14:05,576 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._list#1]
13:14:05,579 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:14:05,583 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
13:14:05,584 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Sequence#1], EntityKey[de.bhc.pepa.Project#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResults#1], EntityKey[de.bhc.gibbssampler.GlobalPWM#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResult#2], EntityKey[de.bhc.gibbssampler.Alignment#2], EntityKey[de.bhc.gibbssampler.Dictionary#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], null, null, null, null, null, null, null, null, EntityKey[de.bhc.gibbssampler.PWM#2], EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.GibbsSamplerParameters#1], EntityKey[de.bhc.gibbssampler.Background#1], EntityKey[de.bhc.pepa.Project#1]
13:14:05,586 DEBUG Loader:1008 - found row of collection: [de.bhc.pepa.Project.hitlists#1]
13:14:05,587 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._list#1]
13:14:05,587 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:14:05,588 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
13:14:05,591 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Sequence#2], EntityKey[de.bhc.pepa.Project#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResults#1], EntityKey[de.bhc.gibbssampler.GlobalPWM#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResult#1], EntityKey[de.bhc.gibbssampler.Alignment#1], EntityKey[de.bhc.gibbssampler.Dictionary#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], null, null, null, null, null, null, null, null, EntityKey[de.bhc.gibbssampler.PWM#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.GibbsSamplerParameters#1], EntityKey[de.bhc.gibbssampler.Background#1], EntityKey[de.bhc.pepa.Project#1]
13:14:05,591 DEBUG Loader:1008 - found row of collection: [de.bhc.pepa.Project.hitlists#1]
13:14:05,592 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._list#1]
13:14:05,593 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:14:05,594 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
13:14:05,594 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Sequence#2], EntityKey[de.bhc.pepa.Project#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResults#1], EntityKey[de.bhc.gibbssampler.GlobalPWM#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResult#2], EntityKey[de.bhc.gibbssampler.Alignment#2], EntityKey[de.bhc.gibbssampler.Dictionary#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], null, null, null, null, null, null, null, null, EntityKey[de.bhc.gibbssampler.PWM#2], EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.GibbsSamplerParameters#1], EntityKey[de.bhc.gibbssampler.Background#1], EntityKey[de.bhc.pepa.Project#1]
13:14:05,595 DEBUG Loader:1008 - found row of collection: [de.bhc.pepa.Project.hitlists#1]
13:14:05,595 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._list#1]
13:14:05,595 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:14:05,596 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
13:14:05,596 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Sequence#3], EntityKey[de.bhc.pepa.Project#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResults#1], EntityKey[de.bhc.gibbssampler.GlobalPWM#1], EntityKey[de.bhc.gibbssampler.GibbsSamplingResult#1], EntityKey[de.bhc.gibbssampler.Alignment#1], EntityKey[de.bhc.gibbssampler.Dictionary#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], null, null, null, null, null, null, null, null, EntityKey[de.bhc.gibbssampler.PWM#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.GibbsSamplerParameters#1], EntityKey[de.bhc.gibbssampler.Background#1], EntityKey[de.bhc.pepa.Project#1]
13:14:05,597 DEBUG Loader:1008 - found row of collection: [de.bhc.pepa.Project.hitlists#1]
13:14:05,597 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._list#1]
13:14:05,597 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:14:05,600 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
=> the pattern repeats 8 times
In the correct case it looks like this:
Code:
13:17:31,112 DEBUG AbstractBatcher:426 - about to open ResultSet (open ResultSets: 0, globally: 0)
13:17:31,112 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Background#1], null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, EntityKey[de.bhc.pepa.Project#1]
13:17:31,134 DEBUG Loader:1008 - found row of collection: [de.bhc.pepa.Project.hitlists#1]
13:17:31,143 DEBUG AbstractBatcher:433 - about to close ResultSet (open ResultSets: 1, globally: 1)
13:17:31,143 DEBUG AbstractBatcher:418 - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
13:17:31,144 DEBUG TwoPhaseLoad:130 - resolving associations for [de.bhc.gibbssampler.SequenceList#1]
13:17:31,156 DEBUG TwoPhaseLoad:226 - done materializing entity [de.bhc.gibbssampler.SequenceList#1]
13:17:31,157 DEBUG TwoPhaseLoad:130 - resolving associations for [de.bhc.gibbssampler.Background#1]
13:17:31,161 DEBUG TwoPhaseLoad:226 - done materializing entity [de.bhc.gibbssampler.Background#1]
13:17:31,162 DEBUG TwoPhaseLoad:130 - resolving associations for [de.bhc.pepa.Project#1]
13:17:31,163 DEBUG TwoPhaseLoad:226 - done materializing entity [de.bhc.pepa.Project#1]
13:17:31,163 DEBUG CollectionLoadContext:240 - 1 collections were found in result set for role: de.bhc.pepa.Project.hitlists
13:17:31,164 DEBUG CollectionLoadContext:283 - collection fully initialized: [de.bhc.pepa.Project.hitlists#1]
13:17:31,164 DEBUG CollectionLoadContext:249 - 1 collections initialized for role: de.bhc.pepa.Project.hitlists
13:17:31,164 DEBUG CollectionLoadContext:233 - no collections were found in result set for role: de.bhc.gibbssampler.SequenceList._list
13:17:31,165 DEBUG CollectionLoadContext:233 - no collections were found in result set for role: de.bhc.gibbssampler.SequenceList._results
13:17:31,167 DEBUG CollectionLoadContext:233 - no collections were found in result set for role: de.bhc.gibbssampler.GibbsSamplingResults.results
13:17:31,167 DEBUG CollectionLoadContext:233 - no collections were found in result set for role: de.bhc.gibbssampler.GibbsSamplingResults.splits
13:17:31,168 DEBUG StatefulPersistenceContext:860 - initializing non-lazy collections
13:17:31,169 DEBUG Loader:2011 - loading collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:17:31,170 DEBUG AbstractBatcher:410 - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
13:17:31,170 DEBUG SQL:111 - select results0_.sequencelists_id as sequence1_3_, results0_._results_id as column2_3_, gibbssampl1_.id as id8_0_, gibbssampl1_.globalpwm_id as globalpwm6_8_0_, gibbssampl1_.maximum_fitness as maximum2_8_0_, gibbssampl1_.params_id as params7_8_0_, gibbssampl1_.runid as runid8_0_, gibbssampl1_.sorted as sorted8_0_, gibbssampl1_.version as version8_0_, globalpwm2_.id as id9_1_, globalpwm2_.class_counts as class2_9_1_, globalpwm2_.class_counts_log as class3_9_1_, globalpwm2_.class_relfreq as class4_9_1_, globalpwm2_.class_relfreq_log as class5_9_1_, globalpwm2_.class_width as class6_9_1_, globalpwm2_.class_widths_log as class7_9_1_, globalpwm2_.log as log9_1_, globalpwm2_.max_ax as max9_9_1_, globalpwm2_.max_ax_log as max10_9_1_, globalpwm2_.min_ax as min11_9_1_, globalpwm2_.min_ax_log as min12_9_1_, globalpwm2_.number_classes as number13_9_1_, globalpwm2_.total_global_counts as total14_9_1_, globalpwm2_.version as version9_1_, gibbssampl3_.id as id6_2_, gibbssampl3_.W as W6_2_, gibbssampl3_.alphabet as alphabet6_2_, gibbssampl3_.convergenceThreshold as converge4_6_2_, gibbssampl3_.deterministicSeeds as determin5_6_2_, gibbssampl3_.deterministicSeqOrder as determin6_6_2_, gibbssampl3_.lawrence93Algorithm as lawrence7_6_2_, gibbssampl3_.lawrencePseudocounts as lawrence8_6_2_, gibbssampl3_.maxInnerIter as maxInner9_6_2_, gibbssampl3_.pseudocountsLinearFactor as pseudoc10_6_2_ from sequencelists_gibbs_result_set results0_ left outer join gibbs_result_set gibbssampl1_ on results0_._results_id=gibbssampl1_.id left outer join globalpwms globalpwm2_ on gibbssampl1_.globalpwm_id=globalpwm2_.id left outer join gibbs_params gibbssampl3_ on gibbssampl1_.params_id=gibbssampl3_.id where results0_.sequencelists_id=?
Hibernate: select results0_.sequencelists_id as sequence1_3_, results0_._results_id as column2_3_, gibbssampl1_.id as id8_0_, gibbssampl1_.globalpwm_id as globalpwm6_8_0_, gibbssampl1_.maximum_fitness as maximum2_8_0_, gibbssampl1_.params_id as params7_8_0_, gibbssampl1_.runid as runid8_0_, gibbssampl1_.sorted as sorted8_0_, gibbssampl1_.version as version8_0_, globalpwm2_.id as id9_1_, globalpwm2_.class_counts as class2_9_1_, globalpwm2_.class_counts_log as class3_9_1_, globalpwm2_.class_relfreq as class4_9_1_, globalpwm2_.class_relfreq_log as class5_9_1_, globalpwm2_.class_width as class6_9_1_, globalpwm2_.class_widths_log as class7_9_1_, globalpwm2_.log as log9_1_, globalpwm2_.max_ax as max9_9_1_, globalpwm2_.max_ax_log as max10_9_1_, globalpwm2_.min_ax as min11_9_1_, globalpwm2_.min_ax_log as min12_9_1_, globalpwm2_.number_classes as number13_9_1_, globalpwm2_.total_global_counts as total14_9_1_, globalpwm2_.version as version9_1_, gibbssampl3_.id as id6_2_, gibbssampl3_.W as W6_2_, gibbssampl3_.alphabet as alphabet6_2_, gibbssampl3_.convergenceThreshold as converge4_6_2_, gibbssampl3_.deterministicSeeds as determin5_6_2_, gibbssampl3_.deterministicSeqOrder as determin6_6_2_, gibbssampl3_.lawrence93Algorithm as lawrence7_6_2_, gibbssampl3_.lawrencePseudocounts as lawrence8_6_2_, gibbssampl3_.maxInnerIter as maxInner9_6_2_, gibbssampl3_.pseudocountsLinearFactor as pseudoc10_6_2_ from sequencelists_gibbs_result_set results0_ left outer join gibbs_result_set gibbssampl1_ on results0_._results_id=gibbssampl1_.id left outer join globalpwms globalpwm2_ on gibbssampl1_.globalpwm_id=globalpwm2_.id left outer join gibbs_params gibbssampl3_ on gibbssampl1_.params_id=gibbssampl3_.id where results0_.sequencelists_id=?
13:17:31,175 DEBUG AbstractBatcher:426 - about to open ResultSet (open ResultSets: 0, globally: 0)
13:17:31,176 DEBUG Loader:1078 - result set contains (possibly empty) collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:17:31,176 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.GibbsSamplingResults#1], EntityKey[de.bhc.gibbssampler.GlobalPWM#1], EntityKey[de.bhc.gibbssampler.GibbsSamplerParameters#1]
13:17:31,181 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.SequenceList._results#1]
13:17:31,181 DEBUG AbstractBatcher:433 - about to close ResultSet (open ResultSets: 1, globally: 1)
13:17:31,182 DEBUG AbstractBatcher:418 - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
13:17:31,182 DEBUG TwoPhaseLoad:130 - resolving associations for [de.bhc.gibbssampler.GibbsSamplingResults#1]
13:17:31,183 DEBUG TwoPhaseLoad:226 - done materializing entity [de.bhc.gibbssampler.GibbsSamplingResults#1]
13:17:31,183 DEBUG TwoPhaseLoad:130 - resolving associations for [de.bhc.gibbssampler.GlobalPWM#1]
13:17:31,185 DEBUG TwoPhaseLoad:226 - done materializing entity [de.bhc.gibbssampler.GlobalPWM#1]
13:17:31,185 DEBUG TwoPhaseLoad:130 - resolving associations for [de.bhc.gibbssampler.GibbsSamplerParameters#1]
13:17:31,186 DEBUG TwoPhaseLoad:226 - done materializing entity [de.bhc.gibbssampler.GibbsSamplerParameters#1]
13:17:31,186 DEBUG CollectionLoadContext:240 - 1 collections were found in result set for role: de.bhc.gibbssampler.SequenceList._results
13:17:31,188 DEBUG CollectionLoadContext:283 - collection fully initialized: [de.bhc.gibbssampler.SequenceList._results#1]
13:17:31,188 DEBUG CollectionLoadContext:249 - 1 collections initialized for role: de.bhc.gibbssampler.SequenceList._results
13:17:31,189 DEBUG Loader:2035 - done loading collection
13:17:31,189 DEBUG Loader:2011 - loading collection: [de.bhc.gibbssampler.GibbsSamplingResults.splits#1]
13:17:31,190 DEBUG AbstractBatcher:410 - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
13:17:31,190 DEBUG SQL:111 - select splits0_.gibbs_result_set_id as gibbs1_17_, splits0_.splits_id as splits2_17_, splits0_.indexcol as indexcol17_, gsresultsp1_.id as id10_0_, gsresultsp1_.GSR_id as GSR4_10_0_, gsresultsp1_.ax_threshold as ax2_10_0_, gsresultsp1_.lower_id as lower5_10_0_, gsresultsp1_.pwm_index as pwm3_10_0_, gsresultsp1_.upper_id as upper6_10_0_, gibbssampl2_.id as id7_1_, gibbssampl2_.alignment_id as alignment6_7_1_, gibbssampl2_.fitness as fitness7_1_, gibbssampl2_.most_probable_pattern as most3_7_1_, gibbssampl2_.num_copies as num4_7_1_, gibbssampl2_.pwm_id as pwm7_7_1_, gibbssampl2_.result_set_id as result8_7_1_, gibbssampl2_.version as version7_1_, alignment3_.id as id5_2_, alignment3_._Ax as column2_5_2_, alignment3_._W as column3_5_2_, alignment3_._a_k as column4_5_2_, alignment3_._input_dictionary_id as column6_5_2_, alignment3_._pwm_id as column7_5_2_, alignment3_._sl_id as column8_5_2_, alignment3_.version as version5_2_, dictionary4_.id as id4_3_, dictionary4_._dict as colum2_4_3_, dictionary4_._sl_id as column4_4_3_, dictionary4_.version as version4_3_, sequenceli5_.id as id3_4_, sequenceli5_._bg_id as column6_3_4_, sequenceli5_._patterns as column2_3_4_, sequenceli5_._project_id as column7_3_4_, sequenceli5_.containing_split_id as containing8_3_4_, sequenceli5_.idInProject as idInProj3_3_4_, sequenceli5_.name as name3_4_, sequenceli5_.version as version3_4_, background6_.id as id2_5_, background6_._alphabet as column2_2_5_, background6_._from_file as column3_2_5_, background6_._map as column4_2_5_, background6_._poolname as column5_2_5_, background6_._seq_elt_counts as column6_2_5_, background6_._sl_id as column9_2_5_, background6_._total_num_seq_elements as column7_2_5_, background6_.version as version2_5_, sequenceli7_.id as id3_6_, sequenceli7_._bg_id as column6_3_6_, sequenceli7_._patterns as column2_3_6_, sequenceli7_._project_id as column7_3_6_, sequenceli7_.containing_split_id as containing8_3_6_, sequenceli7_.idInProject as idInProj3_3_6_, sequenceli7_.name as name3_6_, sequenceli7_.version as version3_6_, project8_.id as id11_7_, project8_.creation_date as creation2_11_7_, project8_.description as descript3_11_7_, project8_.dirname as dirname11_7_, project8_.hitlist_count as hitlist5_11_7_, project8_.lastHitsetDirectory as lastHits6_11_7_, project8_.lastPWMViewDirectory as lastPWMV7_11_7_, project8_.modification_date as modifica8_11_7_, project8_.name as name11_7_, project8_.owner as owner11_7_, project8_.run_count as run11_11_7_, project8_.test_run_count as test12_11_7_, project8_.version as version11_7_, gsresultsp9_.id as id10_8_, gsresultsp9_.GSR_id as GSR4_10_8_, gsresultsp9_.ax_threshold as ax2_10_8_, gsresultsp9_.lower_id as lower5_10_8_, gsresultsp9_.pwm_index as pwm3_10_8_, gsresultsp9_.upper_id as upper6_10_8_, sequenceli10_.id as id3_9_, sequenceli10_._bg_id as column6_3_9_, sequenceli10_._patterns as column2_3_9_, sequenceli10_._project_id as column7_3_9_, sequenceli10_.containing_split_id as containing8_3_9_, sequenceli10_.idInProject as idInProj3_3_9_, sequenceli10_.name as name3_9_, sequenceli10_.version as version3_9_, sequenceli11_.id as id3_10_, sequenceli11_._bg_id as column6_3_10_, sequenceli11_._patterns as column2_3_10_, sequenceli11_._project_id as column7_3_10_, sequenceli11_.containing_split_id as containing8_3_10_, sequenceli11_.idInProject as idInProj3_3_10_, sequenceli11_.name as name3_10_, sequenceli11_.version as version3_10_, pwm12_.id as id1_11_, pwm12_._counts as column2_1_11_, pwm12_._p_j as column3_1_11_, pwm12_._q_ij as column4_1_11_, pwm12_.version as version1_11_, sequenceli13_.id as id3_12_, sequenceli13_._bg_id as column6_3_12_, sequenceli13_._patterns as column2_3_12_, sequenceli13_._project_id as column7_3_12_, sequenceli13_.containing_split_id as containing8_3_12_, sequenceli13_.idInProject as idInProj3_3_12_, sequenceli13_.name as name3_12_, sequenceli13_.version as version3_12_, pwm14_.id as id1_13_, pwm14_._counts as column2_1_13_, pwm14_._p_j as column3_1_13_, pwm14_._q_ij as column4_1_13_, pwm14_.version as version1_13_, gibbssampl15_.id as id8_14_, gibbssampl15_.globalpwm_id as globalpwm6_8_14_, gibbssampl15_.maximum_fitness as maximum2_8_14_, gibbssampl15_.params_id as params7_8_14_, gibbssampl15_.runid as runid8_14_, gibbssampl15_.sorted as sorted8_14_, gibbssampl15_.version as version8_14_, globalpwm16_.id as id9_15_, globalpwm16_.class_counts as class2_9_15_, globalpwm16_.class_counts_log as class3_9_15_, globalpwm16_.class_relfreq as class4_9_15_, globalpwm16_.class_relfreq_log as class5_9_15_, globalpwm16_.class_width as class6_9_15_, globalpwm16_.class_widths_log as class7_9_15_, globalpwm16_.log as log9_15_, globalpwm16_.max_ax as max9_9_15_, globalpwm16_.max_ax_log as max10_9_15_, globalpwm16_.min_ax as min11_9_15_, globalpwm16_.min_ax_log as min12_9_15_, globalpwm16_.number_classes as number13_9_15_, globalpwm16_.total_global_counts as total14_9_15_, globalpwm16_.version as version9_15_, gibbssampl17_.id as id6_16_, gibbssampl17_.W as W6_16_, gibbssampl17_.alphabet as alphabet6_16_, gibbssampl17_.convergenceThreshold as converge4_6_16_, gibbssampl17_.deterministicSeeds as determin5_6_16_, gibbssampl17_.deterministicSeqOrder as determin6_6_16_, gibbssampl17_.lawrence93Algorithm as lawrence7_6_16_, gibbssampl17_.lawrencePseudocounts as lawrence8_6_16_, gibbssampl17_.maxInnerIter as maxInner9_6_16_, gibbssampl17_.pseudocountsLinearFactor as pseudoc10_6_16_ from gibbs_result_set_gsresultsplit splits0_ left outer join gsresultsplit gsresultsp1_ on splits0_.splits_id=gsresultsp1_.id left outer join gibbs_results gibbssampl2_ on gsresultsp1_.GSR_id=gibbssampl2_.id left outer join alignments alignment3_ on gibbssampl2_.alignment_id=alignment3_.id left outer join dicts dictionary4_ on alignment3_._input_dictionary_id=dictionary4_.id left outer join sequencelists sequenceli5_ on dictionary4_._sl_id=sequenceli5_.id left outer join bgs background6_ on sequenceli5_._bg_id=background6_.id left outer join sequencelists sequenceli7_ on background6_._sl_id=sequenceli7_.id left outer join projects project8_ on sequenceli7_._project_id=project8_.id left outer join gsresultsplit gsresultsp9_ on sequenceli7_.containing_split_id=gsresultsp9_.id left outer join sequencelists sequenceli10_ on gsresultsp9_.lower_id=sequenceli10_.id left outer join sequencelists sequenceli11_ on gsresultsp9_.upper_id=sequenceli11_.id left outer join pwms pwm12_ on alignment3_._pwm_id=pwm12_.id left outer join sequencelists sequenceli13_ on alignment3_._sl_id=sequenceli13_.id left outer join pwms pwm14_ on gibbssampl2_.pwm_id=pwm14_.id left outer join gibbs_result_set gibbssampl15_ on gibbssampl2_.result_set_id=gibbssampl15_.id left outer join globalpwms globalpwm16_ on gibbssampl15_.globalpwm_id=globalpwm16_.id left outer join gibbs_params gibbssampl17_ on gibbssampl15_.params_id=gibbssampl17_.id where splits0_.gibbs_result_set_id=?
13:17:31,199 DEBUG AbstractBatcher:426 - about to open ResultSet (open ResultSets: 0, globally: 0)
13:17:31,201 DEBUG Loader:1078 - result set contains (possibly empty) collection: [de.bhc.gibbssampler.GibbsSamplingResults.splits#1]
13:17:31,202 DEBUG AbstractBatcher:433 - about to close ResultSet (open ResultSets: 1, globally: 1)
13:17:31,202 DEBUG AbstractBatcher:418 - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
13:17:31,202 DEBUG CollectionLoadContext:240 - 1 collections were found in result set for role: de.bhc.gibbssampler.GibbsSamplingResults.splits
13:17:31,203 DEBUG CollectionLoadContext:283 - collection fully initialized: [de.bhc.gibbssampler.GibbsSamplingResults.splits#1]
13:17:31,203 DEBUG CollectionLoadContext:249 - 1 collections initialized for role: de.bhc.gibbssampler.GibbsSamplingResults.splits
13:17:31,203 DEBUG Loader:2035 - done loading collection
13:17:31,204 DEBUG Loader:2011 - loading collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
13:17:31,204 DEBUG AbstractBatcher:410 - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
13:17:31,204 DEBUG SQL:111 - select results0_.gibbs_result_set_id as gibbs1_17_, results0_.results_id as results2_17_, results0_.indexcol as indexcol17_, gibbssampl1_.id as id7_0_, gibbssampl1_.alignment_id as alignment6_7_0_, gibbssampl1_.fitness as fitness7_0_, gibbssampl1_.most_probable_pattern as most3_7_0_, gibbssampl1_.num_copies as num4_7_0_, gibbssampl1_.pwm_id as pwm7_7_0_, gibbssampl1_.result_set_id as result8_7_0_, gibbssampl1_.version as version7_0_, alignment2_.id as id5_1_, alignment2_._Ax as column2_5_1_, alignment2_._W as column3_5_1_, alignment2_._a_k as column4_5_1_, alignment2_._input_dictionary_id as column6_5_1_, alignment2_._pwm_id as column7_5_1_, alignment2_._sl_id as column8_5_1_, alignment2_.version as version5_1_, dictionary3_.id as id4_2_, dictionary3_._dict as column2_4_2_, dictionary3_._sl_id as column4_4_2_, dictionary3_.version as version4_2_, sequenceli4_.id as id3_3_, sequenceli4_._bg_id as column6_3_3_, sequenceli4_._patterns as column2_3_3_, sequenceli4_._project_id as column7_3_3_, sequenceli4_.containing_split_id as containing8_3_3_, sequenceli4_.idInProject as idInProj3_3_3_, sequenceli4_.name as name3_3_, sequenceli4_.version as version3_3_, background5_.id as id2_4_, background5_._alphabet as column2_2_4_, background5_._from_file as column3_2_4_, background5_._map as column4_2_4_, background5_._poolname as column5_2_4_, background5_._seq_elt_counts as column6_2_4_, background5_._sl_id as column9_2_4_, background5_._total_num_seq_elements as column7_2_4_, background5_.version as version2_4_, sequenceli6_.id as id3_5_, sequenceli6_._bg_id as column6_3_5_, sequenceli6_._patterns as column2_3_5_, sequenceli6_._project_id as column7_3_5_, sequenceli6_.containing_split_id as containing8_3_5_, sequenceli6_.idInProject as idInProj3_3_5_, sequenceli6_.name as name3_5_, sequenceli6_.version as version3_5_, project7_.id as id11_6_, project7_.creation_date as creation2_11_6_, project7_.description as descript3_11_6_, project7_.dirname as dirname11_6_, project7_.hitlist_count as hitlist5_11_6_, project7_.lastHitsetDirectory as lastHits6_11_6_, project7_.lastPWMViewDirectory as lastPWMV7_11_6_, project7_.modification_date as modifica8_11_6_, project7_.name as name11_6_, project7_.owner as owner11_6_, project7_.run_count as run11_11_6_, project7_.test_run_count as test12_11_6_, project7_.version as version11_6_, gsresultsp8_.id as id10_7_, gsresultsp8_.GSR_id as GSR4_10_7_, gsresultsp8_.ax_threshold as ax2_10_7_, gsresultsp8_.lower_id as lower5_10_7_, gsresultsp8_.pwm_index as pwm3_10_7_, gsresultsp8_.upper_id as upper6_10_7_, gibbssampl9_.id as id7_8_, gibbssampl9_.alignment_id as alignment6_7_8_, gibbssampl9_.fitness as fitness7_8_, gibbssampl9_.most_probable_pattern as most3_7_8_, gibbssampl9_.num_copies as num4_7_8_, gibbssampl9_.pwm_id as pwm7_7_8_, gibbssampl9_.result_set_id as result8_7_8_, gibbssampl9_.version as version7_8_, pwm10_.id as id1_9_, pwm10_._counts as column2_1_9_, pwm10_._p_j as column3_1_9_, pwm10_._q_ij as column4_1_9_, pwm10_.version as version1_9_, gibbssampl11_.id as id8_10_, gibbssampl11_.globalpwm_id as globalpwm6_8_10_, gibbssampl11_.maximum_fitness as maximum2_8_10_, gibbssampl11_.params_id as params7_8_10_, gibbssampl11_.runid as runid8_10_, gibbssampl11_.sorted as sorted8_10_, gibbssampl11_.version as version8_10_, globalpwm12_.id as id9_11_, globalpwm12_.class_counts as class2_9_11_, globalpwm12_.class_counts_log as class3_9_11_, globalpwm12_.class_relfreq as class4_9_11_, globalpwm12_.class_relfreq_log as class5_9_11_, globalpwm12_.class_width as class6_9_11_, globalpwm12_.class_widths_log as class7_9_11_, globalpwm12_.log as log9_11_, globalpwm12_.max_ax as max9_9_11_, globalpwm12_.max_ax_log as max10_9_11_, globalpwm12_.min_ax as min11_9_11_, globalpwm12_.min_ax_log as min12_9_11_, globalpwm12_.number_classes as number13_9_11_, globalpwm12_.total_global_counts as total14_9_11_, globalpwm12_.version as version9_11_, gibbssampl13_.id as id6_12_, gibbssampl13_.W as W6_12_, gibbssampl13_.alphabet as alphabet6_12_, gibbssampl13_.convergenceThreshold as converge4_6_12_, gibbssampl13_.deterministicSeeds as determin5_6_12_, gibbssampl13_.deterministicSeqOrder as determin6_6_12_, gibbssampl13_.lawrence93Algorithm as lawrence7_6_12_, gibbssampl13_.lawrencePseudocounts as lawrence8_6_12_, gibbssampl13_.maxInnerIter as maxInner9_6_12_, gibbssampl13_.pseudocountsLinearFactor as pseudoc10_6_12_, sequenceli14_.id as id3_13_, sequenceli14_._bg_id as column6_3_13_, sequenceli14_._patterns as column2_3_13_, sequenceli14_._project_id as column7_3_13_, sequenceli14_.containing_split_id as containing8_3_13_, sequenceli14_.idInProject as idInProj3_3_13_, sequenceli14_.name as name3_13_, sequenceli14_.version as version3_13_, sequenceli15_.id as id3_14_, sequenceli15_._bg_id as column6_3_14_, sequenceli15_._patterns as column2_3_14_, sequenceli15_._project_id as column7_3_14_, sequenceli15_.containing_split_id as containing8_3_14_, sequenceli15_.idInProject as idInProj3_3_14_, sequenceli15_.name as name3_14_, sequenceli15_.version as version3_14_, pwm16_.id as id1_15_, pwm16_._counts as column2_1_15_, pwm16_._p_j as column3_1_15_, pwm16_._q_ij as column4_1_15_, pwm16_.version as version1_15_, sequenceli17_.id as id3_16_, sequenceli17_._bg_id as column6_3_16_, sequenceli17_._patterns as column2_3_16_, sequenceli17_._project_id as column7_3_16_, sequenceli17_.containing_split_id as containing8_3_16_, sequenceli17_.idInProject as idInProj3_3_16_, sequenceli17_.name as name3_16_, sequenceli17_.version as version3_16_ from gibbs_result_set_gibbs_results results0_ left outer join gibbs_results gibbssampl1_ on results0_.results_id=gibbssampl1_.id left outer join alignments alignment2_ on gibbssampl1_.alignment_id=alignment2_.id left outer join dicts dictionary3_ on alignment2_._input_dictionary_id=dictionary3_.id left outer join sequencelists sequenceli4_ on dictionary3_._sl_id=sequenceli4_.id left outer join bgs background5_ on sequenceli4_._bg_id=background5_.id left outer join sequencelists sequenceli6_ on background5_._sl_id=sequenceli6_.id left outer join projects project7_ on sequenceli6_._project_id=project7_.id left outer join gsresultsplit gsresultsp8_ on sequenceli6_.containing_split_id=gsresultsp8_.id left outer join gibbs_results gibbssampl9_ on gsresultsp8_.GSR_id=gibbssampl9_.id left outer join pwms pwm10_ on gibbssampl9_.pwm_id=pwm10_.id left outer join gibbs_result_set gibbssampl11_ on gibbssampl9_.result_set_id=gibbssampl11_.id left outer join globalpwms globalpwm12_ on gibbssampl11_.globalpwm_id=globalpwm12_.id left outer join gibbs_params gibbssampl13_ on gibbssampl11_.params_id=gibbssampl13_.id left outer join sequencelists sequenceli14_ on gsresultsp8_.lower_id=sequenceli14_.id left outer join sequencelists sequenceli15_ on gsresultsp8_.upper_id=sequenceli15_.id left outer join pwms pwm16_ on alignment2_._pwm_id=pwm16_.id left outer join sequencelists sequenceli17_ on alignment2_._sl_id=sequenceli17_.id where results0_.gibbs_result_set_id=?
Hibernate: select results0_.gibbs_result_set_id as gibbs1_17_, results0_.results_id as results2_17_, results0_.indexcol as indexcol17_, gibbssampl1_.id as id7_0_, gibbssampl1_.alignment_id as alignment6_7_0_, gibbssampl1_.fitness as fitness7_0_, gibbssampl1_.most_probable_pattern as most3_7_0_, gibbssampl1_.num_copies as num4_7_0_, gibbssampl1_.pwm_id as pwm7_7_0_, gibbssampl1_.result_set_id as result8_7_0_, gibbssampl1_.version as version7_0_, alignment2_.id as id5_1_, alignment2_._Ax as column2_5_1_, alignment2_._W as column3_5_1_, alignment2_._a_k as column4_5_1_, alignment2_._input_dictionary_id as column6_5_1_, alignment2_._pwm_id as column7_5_1_, alignment2_._sl_id as column8_5_1_, alignment2_.version as version5_1_, dictionary3_.id as id4_2_, dictionary3_._dict as column2_4_2_, dictionary3_._sl_id as column4_4_2_, dictionary3_.version as version4_2_, sequenceli4_.id as id3_3_, sequenceli4_._bg_id as column6_3_3_, sequenceli4_._patterns as column2_3_3_, sequenceli4_._project_id as column7_3_3_, sequenceli4_.containing_split_id as containing8_3_3_, sequenceli4_.idInProject as idInProj3_3_3_, sequenceli4_.name as name3_3_, sequenceli4_.version as version3_3_, background5_.id as id2_4_, background5_._alphabet as column2_2_4_, background5_._from_file as column3_2_4_, background5_._map as column4_2_4_, background5_._poolname as column5_2_4_, background5_._seq_elt_counts as column6_2_4_, background5_._sl_id as column9_2_4_, background5_._total_num_seq_elements as column7_2_4_, background5_.version as version2_4_, sequenceli6_.id as id3_5_, sequenceli6_._bg_id as column6_3_5_, sequenceli6_._patterns as column2_3_5_, sequenceli6_._project_id as column7_3_5_, sequenceli6_.containing_split_id as containing8_3_5_, sequenceli6_.idInProject as idInProj3_3_5_, sequenceli6_.name as name3_5_, sequenceli6_.version as version3_5_, project7_.id as id11_6_, project7_.creation_date as creation2_11_6_, project7_.description as descript3_11_6_, project7_.dirname as dirname11_6_, project7_.hitlist_count as hitlist5_11_6_, project7_.lastHitsetDirectory as lastHits6_11_6_, project7_.lastPWMViewDirectory as lastPWMV7_11_6_, project7_.modification_date as modifica8_11_6_, project7_.name as name11_6_, project7_.owner as owner11_6_, project7_.run_count as run11_11_6_, project7_.test_run_count as test12_11_6_, project7_.version as version11_6_, gsresultsp8_.id as id10_7_, gsresultsp8_.GSR_id as GSR4_10_7_, gsresultsp8_.ax_threshold as ax2_10_7_, gsresultsp8_.lower_id as lower5_10_7_, gsresultsp8_.pwm_index as pwm3_10_7_, gsresultsp8_.upper_id as upper6_10_7_, gibbssampl9_.id as id7_8_, gibbssampl9_.alignment_id as alignment6_7_8_, gibbssampl9_.fitness as fitness7_8_, gibbssampl9_.most_probable_pattern as most3_7_8_, gibbssampl9_.num_copies as num4_7_8_, gibbssampl9_.pwm_id as pwm7_7_8_, gibbssampl9_.result_set_id as result8_7_8_, gibbssampl9_.version as version7_8_, pwm10_.id as id1_9_, pwm10_._counts as column2_1_9_, pwm10_._p_j as column3_1_9_, pwm10_._q_ij as column4_1_9_, pwm10_.version as version1_9_, gibbssampl11_.id as id8_10_, gibbssampl11_.globalpwm_id as globalpwm6_8_10_, gibbssampl11_.maximum_fitness as maximum2_8_10_, gibbssampl11_.params_id as params7_8_10_, gibbssampl11_.runid as runid8_10_, gibbssampl11_.sorted as sorted8_10_, gibbssampl11_.version as version8_10_, globalpwm12_.id as id9_11_, globalpwm12_.class_counts as class2_9_11_, globalpwm12_.class_counts_log as class3_9_11_, globalpwm12_.class_relfreq as class4_9_11_, globalpwm12_.class_relfreq_log as class5_9_11_, globalpwm12_.class_width as class6_9_11_, globalpwm12_.class_widths_log as class7_9_11_, globalpwm12_.log as log9_11_, globalpwm12_.max_ax as max9_9_11_, globalpwm12_.max_ax_log as max10_9_11_, globalpwm12_.min_ax as min11_9_11_, globalpwm12_.min_ax_log as min12_9_11_, globalpwm12_.number_classes as number13_9_11_, globalpwm12_.total_global_counts as total14_9_11_, globalpwm12_.version as version9_11_, gibbssampl13_.id as id6_12_, gibbssampl13_.W as W6_12_, gibbssampl13_.alphabet as alphabet6_12_, gibbssampl13_.convergenceThreshold as converge4_6_12_, gibbssampl13_.deterministicSeeds as determin5_6_12_, gibbssampl13_.deterministicSeqOrder as determin6_6_12_, gibbssampl13_.lawrence93Algorithm as lawrence7_6_12_, gibbssampl13_.lawrencePseudocounts as lawrence8_6_12_, gibbssampl13_.maxInnerIter as maxInner9_6_12_, gibbssampl13_.pseudocountsLinearFactor as pseudoc10_6_12_, sequenceli14_.id as id3_13_, sequenceli14_._bg_id as column6_3_13_, sequenceli14_._patterns as column2_3_13_, sequenceli14_._project_id as column7_3_13_, sequenceli14_.containing_split_id as containing8_3_13_, sequenceli14_.idInProject as idInProj3_3_13_, sequenceli14_.name as name3_13_, sequenceli14_.version as version3_13_, sequenceli15_.id as id3_14_, sequenceli15_._bg_id as column6_3_14_, sequenceli15_._patterns as column2_3_14_, sequenceli15_._project_id as column7_3_14_, sequenceli15_.containing_split_id as containing8_3_14_, sequenceli15_.idInProject as idInProj3_3_14_, sequenceli15_.name as name3_14_, sequenceli15_.version as version3_14_, pwm16_.id as id1_15_, pwm16_._counts as column2_1_15_, pwm16_._p_j as column3_1_15_, pwm16_._q_ij as column4_1_15_, pwm16_.version as version1_15_, sequenceli17_.id as id3_16_, sequenceli17_._bg_id as column6_3_16_, sequenceli17_._patterns as column2_3_16_, sequenceli17_._project_id as column7_3_16_, sequenceli17_.containing_split_id as containing8_3_16_, sequenceli17_.idInProject as idInProj3_3_16_, sequenceli17_.name as name3_16_, sequenceli17_.version as version3_16_ from gibbs_result_set_gibbs_results results0_ left outer join gibbs_results gibbssampl1_ on results0_.results_id=gibbssampl1_.id left outer join alignments alignment2_ on gibbssampl1_.alignment_id=alignment2_.id left outer join dicts dictionary3_ on alignment2_._input_dictionary_id=dictionary3_.id left outer join sequencelists sequenceli4_ on dictionary3_._sl_id=sequenceli4_.id left outer join bgs background5_ on sequenceli4_._bg_id=background5_.id left outer join sequencelists sequenceli6_ on background5_._sl_id=sequenceli6_.id left outer join projects project7_ on sequenceli6_._project_id=project7_.id left outer join gsresultsplit gsresultsp8_ on sequenceli6_.containing_split_id=gsresultsp8_.id left outer join gibbs_results gibbssampl9_ on gsresultsp8_.GSR_id=gibbssampl9_.id left outer join pwms pwm10_ on gibbssampl9_.pwm_id=pwm10_.id left outer join gibbs_result_set gibbssampl11_ on gibbssampl9_.result_set_id=gibbssampl11_.id left outer join globalpwms globalpwm12_ on gibbssampl11_.globalpwm_id=globalpwm12_.id left outer join gibbs_params gibbssampl13_ on gibbssampl11_.params_id=gibbssampl13_.id left outer join sequencelists sequenceli14_ on gsresultsp8_.lower_id=sequenceli14_.id left outer join sequencelists sequenceli15_ on gsresultsp8_.upper_id=sequenceli15_.id left outer join pwms pwm16_ on alignment2_._pwm_id=pwm16_.id left outer join sequencelists sequenceli17_ on alignment2_._sl_id=sequenceli17_.id where results0_.gibbs_result_set_id=?
13:17:31,210 DEBUG AbstractBatcher:426 - about to open ResultSet (open ResultSets: 0, globally: 0)
13:17:31,210 DEBUG Loader:1078 - result set contains (possibly empty) collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
13:17:31,211 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.GibbsSamplingResult#1], EntityKey[de.bhc.gibbssampler.Alignment#1], EntityKey[de.bhc.gibbssampler.Dictionary#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Background#1], null, null, null, null, null, null, null, null, null, null, EntityKey[de.bhc.gibbssampler.PWM#1], EntityKey[de.bhc.gibbssampler.SequenceList#1]
13:17:31,213 DEBUG Loader:1008 - found row of collection: [de.bhc.gibbssampler.GibbsSamplingResults.results#1]
13:17:31,214 DEBUG Loader:1197 - result row: EntityKey[de.bhc.gibbssampler.GibbsSamplingResult#2], EntityKey[de.bhc.gibbssampler.Alignment#2], EntityKey[de.bhc.gibbssampler.Dictionary#1], EntityKey[de.bhc.gibbssampler.SequenceList#1], EntityKey[de.bhc.gibbssampler.Background#1], null, null, null, null, null, null, null, null, null, null, EntityKey[de.bhc.gibbssampler.PWM#2], EntityKey[de.bhc.gibbssampler.SequenceList#1]
[...]
Could someone please tell me whether my Mappings contain errors?
If not, could I file a bugreport?
Here is the SQL in the broken version:
http://www.pastey.net/133502Here is the SQL in the working version:
http://www.pastey.net/133503But how can I debug this 20k SQL?
Thanks a lot!
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