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error_log3

Uthiru
Sep 27th, 2011
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  1.  ==========================================================================================
  2.  About this error_log:
  3.  ---------------------
  4.  1. Has two_variable_id exportable/importables both on EWAS and Pathway datasets.
  5.  2. Used new dataset (v38_mart).
  6.  3. Query of interest not working ("All modified proteins in a pathway" query throws error).
  7.  4. Uses FilterList.pm module that was altered by Damian.
  8.  ==========================================================================================
  9.  
  10.   (eval)  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:204
  11.   ModPerl::RegistryCooker::run  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:170
  12.   ModPerl::RegistryCooker::default_handler  /path/local/BioMart/apache/lib/ModPerl/Registry.pm:31
  13.   ModPerl::Registry::handler  -e:0
  14.   (eval)  -e:0
  15. 2011/09/27 06:45:25 BioMart.Web:260:DEBUG> Processing template error.tt
  16. 2011/09/27 06:45:25 BioMart.Web:264:INFO> START PROCESSING TEMPLATE error.tt
  17. 2011/09/27 06:45:25 BioMart.Web:271:INFO> !!!! 0 to get process template error.tt and print to string
  18. [Tue Sep 27 07:02:24 2011] [notice] caught SIGTERM, shutting down
  19. [Tue Sep 27 07:12:04 2011] [notice] Apache/2.2.15 (Unix) mod_perl/2.0.4 Perl/v5.10.1 configured -- resuming normal operations
  20. 2011/09/27 07:16:56 martview:65:DEBUG> initialized logger for martview
  21. 2011/09/27 07:16:56 BioMart.Web:176:DEBUG> Using existing registry passed to BioMart::Web constructor
  22. 2011/09/27 07:16:56 BioMart.Web:442:INFO> Creating new session and rewriting URL to http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8, then redirecting
  23. 2011/09/27 07:16:57 martview:65:DEBUG> initialized logger for martview
  24. 2011/09/27 07:16:57 BioMart.Web:176:DEBUG> Using existing registry passed to BioMart::Web constructor
  25. 2011/09/27 07:16:57 BioMart.Web:449:INFO> Restoring existing session 51bc417da0627f8600bfbf7a64a30fc8
  26. 2011/09/27 07:16:57 BioMart.Web:1450:INFO> Incoming CGI-params:
  27. $VAR1 = {};
  28. 2011/09/27 07:16:57 BioMart.Web:496:DEBUG> Saving parameters to session.
  29. 2011/09/27 07:16:57 BioMart.Web:260:DEBUG> Processing template main.tt
  30. 2011/09/27 07:16:57 BioMart.Web:264:INFO> START PROCESSING TEMPLATE main.tt
  31. 2011/09/27 07:16:57 BioMart.Web:271:INFO> !!!! 0.06 to get process template main.tt and print to SCALAR
  32. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[new_button_image], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  33. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[results_button_image], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  34. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[url_button_image], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  35. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[count_button_image], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  36. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[perl_button_image], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  37. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[xml_button_image], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  38. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[count_button_image_disabled], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  39. [Tue Sep 27 07:17:09 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[help_button_image], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  40. [Tue Sep 27 07:17:10 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[xml_button_image_disabled], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  41. [Tue Sep 27 07:17:10 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[url_button_image_disabled], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  42. [Tue Sep 27 07:17:10 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[results_button_image_disabled], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  43. [Tue Sep 27 07:17:13 2011] [error] [client 22.103.86.07] File does not exist: /path/local/BioMart0.7/biomart-perl/htdocs/biomart/[perl_button_image_disabled], referer: http://reactomedev.oicr.on.ca:5555/biomart/martview/51bc417da0627f8600bfbf7a64a30fc8
  44. 2011/09/27 07:17:24 martservice:89:DEBUG> initialized logger for martservice
  45. 2011/09/27 07:17:24 martservice:997:WARN> RECEIVED QUERY:<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query  virtualSchemaName = "default" header = "1" count = "" softwareVersion = "0.5" >      <Dataset name = "pathway" interface = "default" >               <Attribute name = "_displayname" />     </Dataset></Query>
  46. 2011/09/27 07:17:24 BioMart.QueryRunner:163:WARN> ATTRIBUTE: pathway    _displayname    main
  47. 2011/09/27 07:17:24 BioMart.QueryRunner:179:WARN> NO FILTERS
  48. 2011/09/27 07:17:24 BioMart.QueryRunner:415:DEBUG> Added attribute BioMart::Configuration::Attribute=HASH(0x426cdf0) to bottom dataset pathway
  49. 2011/09/27 07:17:24 BioMart.QueryRunner:437:DEBUG> Added dataset pathway interface default to bottom dataset pathway
  50. 2011/09/27 07:17:24 BioMart.QueryRunner:465:DEBUG> Bottom dataset pathway query params are: 22
  51. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 200
  52. 2011/09/27 07:17:24 BioMart.DatasetI:1174:DEBUG> Got results
  53. 2011/09/27 07:17:24 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  54. 2011/09/27 07:17:24 BioMart.QueryRunner:474:DEBUG> Bottom dataset pathway gave 200
  55. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 200,200
  56. 2011/09/27 07:17:24 BioMart.DatasetI:1174:DEBUG> Got results
  57. 2011/09/27 07:17:24 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  58. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 400,400
  59. 2011/09/27 07:17:24 BioMart.DatasetI:1174:DEBUG> Got results
  60. 2011/09/27 07:17:24 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  61. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 800,800
  62. 2011/09/27 07:17:24 BioMart.DatasetI:1174:DEBUG> Got results
  63. 2011/09/27 07:17:24 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  64. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 1600,1600
  65. 2011/09/27 07:17:24 BioMart.DatasetI:1174:DEBUG> Got results
  66. 2011/09/27 07:17:24 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  67. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 3200,3200
  68. 2011/09/27 07:17:24 BioMart.DatasetI:1174:DEBUG> Got results
  69. 2011/09/27 07:17:24 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  70. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 6400,6400
  71. 2011/09/27 07:17:24 BioMart.DatasetI:1174:DEBUG> Got results
  72. 2011/09/27 07:17:24 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  73. 2011/09/27 07:17:24 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 12800,12800
  74. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  75. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  76. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main._displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 13778,25600
  77. 2011/09/27 07:17:25 BioMart.DatasetI:1175:DEBUG> Got no results
  78. 2011/09/27 07:17:25 martservice:89:DEBUG> initialized logger for martservice
  79. 2011/09/27 07:17:25 martservice:997:WARN> RECEIVED QUERY:<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query  virtualSchemaName = "default" header = "1" count = "" softwareVersion = "0.5" >      <Dataset name = "pathway" interface = "default" >               <Attribute name = "species__displayname" />     </Dataset></Query>
  80. 2011/09/27 07:17:25 BioMart.QueryRunner:163:WARN> ATTRIBUTE: pathway    species__displayname    main
  81. 2011/09/27 07:17:25 BioMart.QueryRunner:179:WARN> NO FILTERS
  82. 2011/09/27 07:17:25 BioMart.QueryRunner:415:DEBUG> Added attribute BioMart::Configuration::Attribute=HASH(0x426d078) to bottom dataset pathway
  83. 2011/09/27 07:17:25 BioMart.QueryRunner:437:DEBUG> Added dataset pathway interface default to bottom dataset pathway
  84. 2011/09/27 07:17:25 BioMart.QueryRunner:465:DEBUG> Bottom dataset pathway query params are: 22
  85. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 200
  86. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  87. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  88. 2011/09/27 07:17:25 BioMart.QueryRunner:474:DEBUG> Bottom dataset pathway gave 200
  89. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 200,200
  90. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  91. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  92. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 400,400
  93. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  94. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  95. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 800,800
  96. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  97. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  98. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 1600,1600
  99. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  100. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  101. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 3200,3200
  102. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  103. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  104. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 6400,6400
  105. 2011/09/27 07:17:25 BioMart.DatasetI:1174:DEBUG> Got results
  106. 2011/09/27 07:17:25 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  107. 2011/09/27 07:17:25 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 12800,12800
  108. 2011/09/27 07:17:26 BioMart.DatasetI:1174:DEBUG> Got results
  109. 2011/09/27 07:17:26 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  110. 2011/09/27 07:17:26 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.species__displayname FROM test_reactome_mart.pathway__pathway__main main LIMIT 13778,25600
  111. 2011/09/27 07:17:26 BioMart.DatasetI:1175:DEBUG> Got no results
  112. 2011/09/27 07:17:44 martview:65:DEBUG> initialized logger for martview
  113. 2011/09/27 07:17:44 BioMart.Web:176:DEBUG> Using existing registry passed to BioMart::Web constructor
  114. 2011/09/27 07:17:44 BioMart.Web:442:INFO> Creating new session and rewriting URL to http://reactomedev.oicr.on.ca:5555/biomart/martview/b62659bca782eacb7446ae154c1d9610, then redirecting
  115. 2011/09/27 07:17:48 martview:68:DEBUG> Using existing logger Log::Log4perl::Logger=HASH(0xfcd43b0)
  116. 2011/09/27 07:17:48 martview:98:DEBUG> Using existing BioMart::Web object
  117. 2011/09/27 07:17:48 BioMart.Web:449:INFO> Restoring existing session b62659bca782eacb7446ae154c1d9610
  118. 2011/09/27 07:17:48 BioMart.Web:1450:INFO> Incoming CGI-params:
  119. $VAR1 = {};
  120. 2011/09/27 07:17:48 BioMart.Web:496:DEBUG> Saving parameters to session.
  121. 2011/09/27 07:17:48 BioMart.Web:1973:DEBUG> Need to query datasets pathway,entitywithaccessionedsequence for total entry counts for each
  122. 2011/09/27 07:17:48 BioMart.Web:1989:DEBUG> FILTERLIST_STRING IS ARRAY(0x10183438)
  123. 2011/09/27 07:17:48 BioMart.Web:1999:DEBUG> Enabled filters for dset pathway: pathway__filter.species_selection|pathway__filter._displayname
  124. 2011/09/27 07:17:48 BioMart.Web:2000:DEBUG> Enabled attributes for dset pathway: pathway__naive_attributes__attribute._displayname|pathway__naive_attributes__attribute.referencepeptidesequence__dm_identifier|pathway__naive_attributes__attribute.stableidentifier_identifier|pathway__naive_attributes__attribute.referencepeptidesequence__dm__displayname|pathway__naive_attributes__attribute.pathway_db_id
  125. 2011/09/27 07:17:48 BioMart.Web:546:DEBUG> #### STARTING extract_queryparams ####
  126. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute _displayname is an attributefilter
  127. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'pathway__naive_attributes__attributefilter._displayname', so is not an attributefilter
  128. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute _displayname instead
  129. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute referencepeptidesequence__dm_identifier is an attributefilter
  130. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'pathway__naive_attributes__attributefilter.referencepeptidesequence__dm_identifier', so is not an attributefilter
  131. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute referencepeptidesequence__dm_identifier instead
  132. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute stableidentifier_identifier is an attributefilter
  133. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'pathway__naive_attributes__attributefilter.stableidentifier_identifier', so is not an attributefilter
  134. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute stableidentifier_identifier instead
  135. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute referencepeptidesequence__dm__displayname is an attributefilter
  136. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'pathway__naive_attributes__attributefilter.referencepeptidesequence__dm__displayname', so is not an attributefilter
  137. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute referencepeptidesequence__dm__displayname instead
  138. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute pathway_db_id is an attributefilter
  139. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'pathway__naive_attributes__attributefilter.pathway_db_id', so is not an attributefilter
  140. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute pathway_db_id instead
  141. 2011/09/27 07:17:48 BioMart.Web:651:DEBUG> #### DEALING WITH pathway__filter.species_selection ####
  142. 2011/09/27 07:17:48 BioMart.Web:710:DEBUG> #### pathway__filter.species_selection HAS VALUE Homo sapiens####
  143. 2011/09/27 07:17:48 BioMart.Web:730:DEBUG> Adding values to filter species_selection: 'Homo sapiens'
  144. 2011/09/27 07:17:48 BioMart.Web:651:DEBUG> #### DEALING WITH pathway__filter._displayname ####
  145. 2011/09/27 07:17:48 BioMart.Web:710:DEBUG> #### pathway__filter._displayname HAS VALUE Degradation of beta-catenin by the destruction complex####
  146. 2011/09/27 07:17:48 BioMart.Web:730:DEBUG> Adding values to filter _displayname: 'Degradation of beta-catenin by the destruction complex'
  147. 2011/09/27 07:17:48 BioMart.Web:2037:DEBUG> Got outputformats html,txt,tsv,xls for attpage naive_attributes, in dataset pathway
  148. 2011/09/27 07:17:48 BioMart.Web:770:DEBUG> Getting dataset pathway in schema default from registry
  149. 2011/09/27 07:17:48 BioMart.Web:774:DEBUG> Using provided query object
  150. 2011/09/27 07:17:48 BioMart.Web:789:DEBUG> Processing attributes from dataset default.pathway
  151. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute _displayname
  152. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute referencepeptidesequence__dm_identifier
  153. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute stableidentifier_identifier
  154. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute referencepeptidesequence__dm__displayname
  155. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute pathway_db_id
  156. 2011/09/27 07:17:48 BioMart.Web:819:DEBUG> Processing filters from dataset default.pathway
  157. 2011/09/27 07:17:48 BioMart.Web:823:DEBUG> Enabling filter _displayname to query, setting values to Degradation of beta-catenin by the destruction complex
  158. 2011/09/27 07:17:48 BioMart.Web:823:DEBUG> Enabling filter species_selection to query, setting values to Homo sapiens
  159. 2011/09/27 07:17:48 BioMart.Web:1989:DEBUG> FILTERLIST_STRING IS ARRAY(0x100d82b0)
  160. 2011/09/27 07:17:48 BioMart.Web:1999:DEBUG> Enabled filters for dset entitywithaccessionedsequence:
  161. 2011/09/27 07:17:48 BioMart.Web:2000:DEBUG> Enabled attributes for dset entitywithaccessionedsequence: entitywithaccessionedsequence__naive_attributes__attribute.mod_hasmodifiedresidue_psimod_identifier|entitywithaccessionedsequence__naive_attributes__attribute.hasmodifiedresidue__displayname|entitywithaccessionedsequence__naive_attributes__attribute.hasmodifiedresidue_coordinate|entitywithaccessionedsequence__naive_attributes__attribute.hasmodifiedresidue_referencesequence_identifier
  162. 2011/09/27 07:17:48 BioMart.Web:546:DEBUG> #### STARTING extract_queryparams ####
  163. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute mod_hasmodifiedresidue_psimod_identifier is an attributefilter
  164. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'entitywithaccessionedsequence__naive_attributes__attributefilter.mod_hasmodifiedresidue_psimod_identifier', so is not an attributefilter
  165. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute mod_hasmodifiedresidue_psimod_identifier instead
  166. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute hasmodifiedresidue__displayname is an attributefilter
  167. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'entitywithaccessionedsequence__naive_attributes__attributefilter.hasmodifiedresidue__displayname', so is not an attributefilter
  168. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute hasmodifiedresidue__displayname instead
  169. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute hasmodifiedresidue_coordinate is an attributefilter
  170. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'entitywithaccessionedsequence__naive_attributes__attributefilter.hasmodifiedresidue_coordinate', so is not an attributefilter
  171. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute hasmodifiedresidue_coordinate instead
  172. 2011/09/27 07:17:48 BioMart.Web:569:DEBUG> Testing if attribute hasmodifiedresidue_referencesequence_identifier is an attributefilter
  173. 2011/09/27 07:17:48 BioMart.Web:613:DEBUG> Empty list of values for attributefilter 'entitywithaccessionedsequence__naive_attributes__attributefilter.hasmodifiedresidue_referencesequence_identifier', so is not an attributefilter
  174. 2011/09/27 07:17:48 BioMart.Web:615:DEBUG> Enabling attribute hasmodifiedresidue_referencesequence_identifier instead
  175. 2011/09/27 07:17:48 BioMart.Web:770:DEBUG> Getting dataset entitywithaccessionedsequence in schema default from registry
  176. 2011/09/27 07:17:48 BioMart.Web:774:DEBUG> Using provided query object
  177. 2011/09/27 07:17:48 BioMart.Web:789:DEBUG> Processing attributes from dataset default.entitywithaccessionedsequence
  178. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute mod_hasmodifiedresidue_psimod_identifier
  179. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute hasmodifiedresidue__displayname
  180. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute hasmodifiedresidue_coordinate
  181. 2011/09/27 07:17:48 BioMart.Web:793:DEBUG> Enabling attribute hasmodifiedresidue_referencesequence_identifier
  182. 2011/09/27 07:17:48 BioMart.Web:2137:DEBUG> Datasetcount added to query:   2
  183. 2011/09/27 07:17:48 BioMart.Web:2138:DEBUG> Datasetcount in session:       2
  184. 2011/09/27 07:17:48 BioMart.Web:2189:DEBUG> Query has both filters and attributes by now, let's go get some results!
  185. 2011/09/27 07:17:48 BioMart.Web:2212:DEBUG> Formatting data as HTML
  186. Use of uninitialized value in string eq at /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm line 2218.
  187. Use of uninitialized value in string eq at /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm line 2226.
  188. 2011/09/27 07:17:48 BioMart.Web:2412:DEBUG> Showing in browser.
  189. 2011/09/27 07:17:48 BioMart.Web:2426:DEBUG> Showing 10 entries in main panel
  190. 2011/09/27 07:17:48 BioMart.Web:2429:DEBUG> Sending query for execution to get full resultset
  191. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: pathway    _displayname    main
  192. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: pathway    referencepeptidesequence__dm_identifier pathway__referencepeptidesequence__dm
  193. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: pathway    stableidentifier_identifier main
  194. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: pathway    referencepeptidesequence__dm__displayname   pathway__referencepeptidesequence__dm
  195. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: pathway    pathway_db_id   main
  196. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: entitywithaccessionedsequence  mod_hasmodifiedresidue_psimod_identifier    main
  197. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: entitywithaccessionedsequence  hasmodifiedresidue__displayname main
  198. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: entitywithaccessionedsequence  hasmodifiedresidue_coordinate   main
  199. 2011/09/27 07:17:48 BioMart.QueryRunner:163:WARN> ATTRIBUTE: entitywithaccessionedsequence  hasmodifiedresidue_referencesequence_identifier main
  200. 2011/09/27 07:17:48 BioMart.QueryRunner:174:WARN> FILTER TABLE: pathway _displayname    main
  201. 2011/09/27 07:17:48 BioMart.QueryRunner:174:WARN> FILTER TABLE: pathway species_selection   main
  202. 2011/09/27 07:17:48 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT main.hasmodifiedresidue_referencesequence_identifier, main.referencednasequence_referencedatabase_ensembl_concat, main.mod_hasmodifiedresidue_psimod_identifier, main.hasmodifiedresidue__displayname, main.hasmodifiedresidue_coordinate, main.hasmodifiedresidue_referencesequence_identifier FROM test_reactome_mart.entitywithaccessionedsequence__itywithaccessionedsequence__main main LIMIT 200
  203. 2011/09/27 07:17:48 BioMart.DatasetI:1174:DEBUG> Got results
  204. 2011/09/27 07:17:48 BioMart.DatasetI:1261:DEBUG> Attribute hash
  205. 2011/09/27 07:17:48 BioMart.DatasetI:1262:DEBUG> Before hash: 200
  206. Use of uninitialized value $rowKey in hash element at /path/local/BioMart0.7/biomart-perl/lib/BioMart/DatasetI.pm line 1624.
  207. 2011/09/27 07:17:48 BioMart.DatasetI:1269:DEBUG> After hash: 200
  208. 2011/09/27 07:17:48 BioMart.DatasetI:1276:DEBUG> Returning defined has_data
  209. 2011/09/27 07:17:48 BioMart.QueryRunner:631:DEBUG> Non-bottom dataset entitywithaccessionedsequence gave 200
  210. 2011/09/27 07:17:48 BioMart.QueryRunner:415:DEBUG> Added attribute BioMart::Configuration::Attribute=HASH(0x426cdf0) to bottom dataset pathway
  211. 2011/09/27 07:17:48 BioMart.QueryRunner:415:DEBUG> Added attribute BioMart::Configuration::Attribute=HASH(0x4272148) to bottom dataset pathway
  212. 2011/09/27 07:17:48 BioMart.QueryRunner:415:DEBUG> Added attribute BioMart::Configuration::Attribute=HASH(0x426c658) to bottom dataset pathway
  213. 2011/09/27 07:17:48 BioMart.QueryRunner:415:DEBUG> Added attribute BioMart::Configuration::Attribute=HASH(0x4272658) to bottom dataset pathway
  214. 2011/09/27 07:17:48 BioMart.QueryRunner:415:DEBUG> Added attribute BioMart::Configuration::Attribute=HASH(0x426cb68) to bottom dataset pathway
  215. 2011/09/27 07:17:48 BioMart.QueryRunner:425:DEBUG> Added filter BioMart::Configuration::ValueFilter=HASH(0x427cc00) to bottom dataset pathway
  216. 2011/09/27 07:17:48 BioMart.QueryRunner:425:DEBUG> Added filter BioMart::Configuration::ValueFilter=HASH(0x427a128) to bottom dataset pathway
  217. 2011/09/27 07:17:48 BioMart.QueryRunner:425:DEBUG> Added filter BioMart::Configuration::FilterList=HASH(0x10521aa0) to bottom dataset pathway
  218. 2011/09/27 07:17:48 BioMart.QueryRunner:437:DEBUG> Added dataset pathway interface default to bottom dataset pathway
  219. 2011/09/27 07:17:48 BioMart.QueryRunner:465:DEBUG> Bottom dataset pathway query params are: 22
  220. 2011/09/27 07:17:48 BioMart.Dataset.TableSet:736:INFO> QUERY SQL:  SELECT pathway__referencepeptidesequence__dm.referencedatabase_uniprot, pathway__referencednasequence__dm.referencedatabase_ensembl, main._displayname, test_reactome_mart.pathway__referencepeptidesequence__dm.identifier, main.stableidentifier_identifier, test_reactome_mart.pathway__referencepeptidesequence__dm._displayname, main.pathway_DB_ID_key FROM test_reactome_mart.pathway__referencednasequence__dm, test_reactome_mart.pathway__referencepeptidesequence__dm, test_reactome_mart.pathway__pathway__main main WHERE (main._displayname = 'Degradation of beta-catenin by the destruction complex') AND (main.species__displayname = 'Homo sapiens') AND (( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000166913')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000103152')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000076685')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000135318')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000175899')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000142192')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000111701')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000115361')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000117054')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000122971')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000072778')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000018510')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000196839')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000156110')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000151729')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000005022')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000169100')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000105221')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000163631')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000116748')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000116337')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000133805')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000120868')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000100823')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000198931')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000173020')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000198899')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000198744')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000124172')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000169020')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000160916')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000167283')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000167863')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000002330')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000030110')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000171791')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000015475')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000153094')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000023445')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000110330')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000101966')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000089685')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000012048')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000139618')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000108821')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000164692')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000115953')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000160014, ENSG00000198668, ENSG00000143933')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000121691')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000114503')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000136937')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000129315')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000082258')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000135218')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000135404')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000010278')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000097046')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000136807')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000197766')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000003402')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000115252')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000123360')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000154678')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000065989')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000184588')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000105650')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000113448')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000185527')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000076555')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000140465')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000140505')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000160868')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000187048')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000213052')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000100197')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000130649')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000118260')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000049167')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000165474')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000164742')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000155897')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000172115')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000167969')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000116906')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000167986')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000134574')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000135829')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000104325')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000114956')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000185000, ENSG00000215711')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000126698')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000105486')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000005156')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000174405')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000070501')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000160710')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000088986')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000188985')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000127884')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000138798')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000105656')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000112759')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000174669')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000012061')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000032514')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000120705')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000185010')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000168040')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000158869')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000168496')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000115414')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000007933')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000146535')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000065135')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000127955')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000114353')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000156052')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000198814')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000173221')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000185245')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000203618')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000167588')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000169704')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000178732')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000100453')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSRNOG00000003990')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000163655')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000119125')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000188486')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000019991')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000134240')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000165704')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000113905')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000149131')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000164305')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000165806')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000064012')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000132906')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000003400')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000017427')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000017427')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000106348')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000178035')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000150995')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000123104')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000096433')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000185950')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000164171')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000005961')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000150093')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000056345')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000106992')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000004455')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000154027')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000108946')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000188191')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000114302')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000005249')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000072062')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000142875')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000165059')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000152495')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000143774')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000166548')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000113889')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000154229')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000166501')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000163932')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000171132')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000126583')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000163558')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000027075')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000184304')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000065675')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000067606')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000101911')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000147224')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000142208')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000165025')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000196419')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000079246')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000138385')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000174175')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000005893')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000181817')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000020426')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000116670')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000170430')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000100030')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000102882')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000107643')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000169032')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000126934')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000020922')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000167774')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000151366')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000184752')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000119013')) OR ( AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000184983')) OR ((pathway__referencepeptidesequence__dm.referencedatabase_uniprot = 'P49327') AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000169710'))) AND main.pathway_db_id_key=pathway__referencednasequence__dm.pathway_db_id_key AND main.pathway_db_id_key=test_reactome_mart.pathway__referencepeptidesequence__dm.pathway_db_id_key AND main.pathway_db_id_key=pathway__referencepeptidesequence__dm.pathway_db_id_key LIMIT 200
  221. DBD::mysql::st execute failed: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000166' at line 1 at /path/local/BioMart0.7/biomart-perl/lib/BioMart/Dataset/TableSet.pm line 236.
  222. 2011/09/27 07:17:48 BioMart.Web:2492:DEBUG> Serious error: Error during query execution: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000166' at line 1
  223.  
  224.  
  225. Trace begun at /path/local/BioMart0.7/biomart-perl/lib/BioMart/Dataset/TableSet.pm line 241
  226. BioMart::Dataset::TableSet::_fillAttributeTableWith('BioMart::Dataset::TableSet=HASH(0x426bb60)', 'BioMart::Query=HASH(0x10579e18)', 'BioMart::ResultTable=HASH(0x10544c20)', 0, 200) called at /path/local/BioMart0.7/biomart-perl/lib/BioMart/Dataset/TableSet.pm line 124
  227. BioMart::Dataset::TableSet::_getResultTable('BioMart::Dataset::TableSet=HASH(0x426bb60)', 'query', 'BioMart::Query=HASH(0x10579e18)', 'table', 'BioMart::ResultTable=HASH(0x10544c20)', 'batch_size', 200) called at /path/local/BioMart0.7/biomart-perl/lib/BioMart/DatasetI.pm line 1170
  228. BioMart::DatasetI::getResultTable('BioMart::Dataset::TableSet=HASH(0x426bb60)', 'query', 'BioMart::Query=HASH(0x10579e18)') called at /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm line 472
  229. BioMart::QueryRunner::_processPath('BioMart::QueryRunner=HASH(0x1057c420)', 'ARRAY(0x1051efe0)') called at /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm line 654
  230. BioMart::QueryRunner::_processPath('BioMart::QueryRunner=HASH(0x1057c420)', 'ARRAY(0x1051efe0)') called at /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm line 374
  231. BioMart::QueryRunner::_getResultTable('BioMart::QueryRunner=HASH(0x1057c420)', 'BioMart::Query=HASH(0x1057c180)') called at /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm line 194
  232. BioMart::QueryRunner::execute('BioMart::QueryRunner=HASH(0x1057c420)', 'BioMart::Query=HASH(0x1057c180)') called at /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm line 2433
  233. eval {...} at /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm line 2198
  234. BioMart::Web::handle_request('BioMart::Web=HASH(0x2478768)', 'CGI=HASH(0xfcd4590)') called at /path/local/BioMart0.7/biomart-perl/cgi-bin/martview line 105
  235. eval {...} at /path/local/BioMart0.7/biomart-perl/cgi-bin/martview line 104
  236. ModPerl::ROOT::ModPerl::Registry::usr_local_reactomes_Reactome_development_GKB_BioMart0_2e7_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x101e84f8)') called at /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm line 204
  237. eval {...} at /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm line 204
  238. ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0xfceac30)') called at /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm line 170
  239. ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0xfceac30)') called at /path/local/BioMart/apache/lib/ModPerl/Registry.pm line 31
  240. ModPerl::Registry::handler('ModPerl::Registry', 'Apache2::RequestRec=SCALAR(0x101e84f8)') called at -e line 0
  241. eval {...} at -e line 0
  242. 2011/09/27 07:17:48 martview:127:ERROR> ERROR: caught BioMart::Exception::Database: Error during query execution: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000166' at line 1
  243.  
  244. Stacktrace:
  245.   Exception::Class::Base::throw  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241
  246.   BioMart::Dataset::TableSet::_fillAttributeTableWith  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124
  247.   BioMart::Dataset::TableSet::_getResultTable  /path/local/BioMart0.7/biomart-perl/lib/BioMart/DatasetI.pm:1170
  248.   BioMart::DatasetI::getResultTable  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:472
  249.   BioMart::QueryRunner::_processPath  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:654
  250.   BioMart::QueryRunner::_processPath  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:374
  251.   BioMart::QueryRunner::_getResultTable  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:194
  252.   BioMart::QueryRunner::execute  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm:2433
  253.   (eval)  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm:2198
  254.   BioMart::Web::handle_request  /path/local/BioMart0.7/biomart-perl/cgi-bin/martview:105
  255.   (eval)  /path/local/BioMart0.7/biomart-perl/cgi-bin/martview:104
  256.   ModPerl::ROOT::ModPerl::Registry::usr_local_reactomes_Reactome_development_GKB_BioMart0_2e7_biomart_2dperl_cgi_2dbin_martview::handler  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:204
  257.   (eval)  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:204
  258.   ModPerl::RegistryCooker::run  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:170
  259.   ModPerl::RegistryCooker::default_handler  /path/local/BioMart/apache/lib/ModPerl/Registry.pm:31
  260.   ModPerl::Registry::handler  -e:0
  261.   (eval)  -e:0
  262. ERROR: caught BioMart::Exception::Database: Error during query execution: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000166' at line 1
  263.  
  264. Stacktrace:
  265.  Exception::Class::Base::throw  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241
  266.  BioMart::Dataset::TableSet::_fillAttributeTableWith  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124
  267.  BioMart::Dataset::TableSet::_getResultTable  /path/local/BioMart0.7/biomart-perl/lib/BioMart/DatasetI.pm:1170
  268.  BioMart::DatasetI::getResultTable  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:472
  269.  BioMart::QueryRunner::_processPath  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:654
  270.  BioMart::QueryRunner::_processPath  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:374
  271.  BioMart::QueryRunner::_getResultTable  /path/local/BioMart0.7/biomart-perl/lib/BioMart/QueryRunner.pm:194
  272.  BioMart::QueryRunner::execute  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm:2433
  273.  (eval)  /path/local/BioMart0.7/biomart-perl/lib/BioMart/Web.pm:2198
  274.  BioMart::Web::handle_request  /path/local/BioMart0.7/biomart-perl/cgi-bin/martview:105
  275.  (eval)  /path/local/BioMart0.7/biomart-perl/cgi-bin/martview:104
  276.  ModPerl::ROOT::ModPerl::Registry::usr_local_reactomes_Reactome_development_GKB_BioMart0_2e7_biomart_2dperl_cgi_2dbin_martview::handler  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:204
  277.  (eval)  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:204
  278.  ModPerl::RegistryCooker::run  /path/local/BioMart/apache/lib/ModPerl/RegistryCooker.pm:170
  279.  ModPerl::RegistryCooker::default_handler  /path/local/BioMart/apache/lib/ModPerl/Registry.pm:31
  280.  ModPerl::Registry::handler  -e:0
  281.  (eval)  -e:0
  282. 2011/09/27 07:17:48 BioMart.Web:260:DEBUG> Processing template error.tt
  283. 2011/09/27 07:17:48 BioMart.Web:264:INFO> START PROCESSING TEMPLATE error.tt
  284. 2011/09/27 07:17:48 BioMart.Web:271:INFO> !!!! 0 to get process template error.tt and print to string
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