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  3. 2011-03-10 15:37:54,314 []: Working with 'i_Investigation.txt' investigation file from '/vol/bioinvindex/Submissions/E305-2'
  4. 2011-03-10 15:37:54,318 [[fmt:investigation file:i_Investigation.txt]]: TabLoader, loading format: investigation from /vol/bioinvindex/Submissions/E305-2/i_Investigation.txt
  5. 2011-03-10 15:37:54,478 [[fmt:study_samples file:s_Biological Variation.txt]]: TabLoader, loading format: study_samples from /vol/bioinvindex/Submissions/E305-2/s_Biological Variation.txt
  6. 2011-03-10 15:37:54,529 []: WARNING: the ontology source 'NEWT' is declared in the investigation file but never used
  7. 2011-03-10 15:37:54,529 []: WARNING: the ontology source 'TO' is declared in the investigation file but never used
  8. 2011-03-10 15:37:54,529 []: WARNING: the ontology source 'MS' is declared in the investigation file but never used
  9. 2011-03-10 15:37:54,530 []: WARNING: the protocol 'identification' is declared in the investigation file for the study 'Biological Variation' but is never used
  10. 2011-03-10 15:37:54,530 []: WARNING: the protocol 'Growthcondition' is declared in the investigation file for the study 'Biological Variation' but is never used
  11. 2011-03-10 15:37:54,530 []: WARNING: the protocol 'UPLC-Run1' is declared in the investigation file for the study 'Biological Variation' but is never used
  12. 2011-03-10 15:37:54,530 []: WARNING: the protocol 'mass spectrometry' is declared in the investigation file for the study 'Biological Variation' but is never used
  13. 2011-03-10 15:37:54,530 []: WARNING: the protocol 'Grinding-robot1' is declared in the investigation file for the study 'Biological Variation' but is never used
  14. 2011-03-10 15:37:54,531 []: WARNING: the protocol 'extraction' is declared in the investigation file for the study 'Biological Variation' but is never used
  15. 2011-03-10 15:37:54,531 []: WARNING: the protocol 'MS-measurement-20-1000-pos' is declared in the investigation file for the study 'Biological Variation' but is never used
  16. 2011-03-10 15:37:54,531 []: WARNING: the protocol 'labeling' is declared in the investigation file for the study 'Biological Variation' but is never used
  17. 2011-03-10 15:37:54,531 []: WARNING: the protocol 'data transformation' is declared in the investigation file for the study 'Biological Variation' but is never used
  18. 2011-03-10 15:37:54,531 []: WARNING: the protocol 'Extraction-schmidt1' is declared in the investigation file for the study 'Biological Variation' but is never used
  19. 2011-03-10 15:37:54,818 []: Persisting 21 object(s)
  20. 2011-03-10 15:37:57,732 []: Mapping package com.google.common.collect
  21. 2011-03-10 15:37:57,736 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Annotation
  22. 2011-03-10 15:37:57,737 []: Bind entity uk.ac.ebi.bioinvindex.model.Annotation on table annotation
  23. 2011-03-10 15:37:57,738 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.AssayResult
  24. 2011-03-10 15:37:57,739 []: Bind entity uk.ac.ebi.bioinvindex.model.AssayResult on table ASSAYRESULT
  25. 2011-03-10 15:37:57,742 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Contact
  26. 2011-03-10 15:37:57,742 []: Bind entity uk.ac.ebi.bioinvindex.model.Contact on table contact
  27. 2011-03-10 15:37:57,746 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Data
  28. 2011-03-10 15:37:57,746 []: Bind entity uk.ac.ebi.bioinvindex.model.Data on table data
  29. 2011-03-10 15:37:57,749 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Investigation
  30. 2011-03-10 15:37:57,749 []: Bind entity uk.ac.ebi.bioinvindex.model.Investigation on table INVESTIGATION
  31. 2011-03-10 15:37:57,753 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Material
  32. 2011-03-10 15:37:57,754 []: Bind entity uk.ac.ebi.bioinvindex.model.Material on table material
  33. 2011-03-10 15:37:57,756 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Protocol
  34. 2011-03-10 15:37:57,757 []: Bind entity uk.ac.ebi.bioinvindex.model.Protocol on table PROTOCOL
  35. 2011-03-10 15:37:57,760 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Publication
  36. 2011-03-10 15:37:57,760 []: Bind entity uk.ac.ebi.bioinvindex.model.Publication on table publication
  37. 2011-03-10 15:37:57,763 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.Study
  38. 2011-03-10 15:37:57,763 []: Bind entity uk.ac.ebi.bioinvindex.model.Study on table study
  39. 2011-03-10 15:37:57,771 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.Assay
  40. 2011-03-10 15:37:57,771 []: Bind entity uk.ac.ebi.bioinvindex.model.processing.Assay on table ASSAY
  41. 2011-03-10 15:37:57,774 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.Processing
  42. 2011-03-10 15:37:57,775 []: Bind entity uk.ac.ebi.bioinvindex.model.processing.Processing on table PROCESSING
  43. 2011-03-10 15:37:57,779 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.DataAcquisition
  44. 2011-03-10 15:37:57,780 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.Node
  45. 2011-03-10 15:37:57,780 []: Bind entity uk.ac.ebi.bioinvindex.model.processing.Node on table NODE
  46. 2011-03-10 15:37:57,783 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.DataNode
  47. 2011-03-10 15:37:57,784 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.DataProcessing
  48. 2011-03-10 15:37:57,785 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.MaterialNode
  49. 2011-03-10 15:37:57,786 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.MaterialProcessing
  50. 2011-03-10 15:37:57,786 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.processing.ProtocolApplication
  51. 2011-03-10 15:37:57,787 []: Bind entity uk.ac.ebi.bioinvindex.model.processing.ProtocolApplication on table PROTOCOLAPPLICATION
  52. 2011-03-10 15:37:57,789 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.AnnotationType
  53. 2011-03-10 15:37:57,789 []: Bind entity uk.ac.ebi.bioinvindex.model.term.AnnotationType on table annotation_type
  54. 2011-03-10 15:37:57,791 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.OntologyEntry
  55. 2011-03-10 15:37:57,792 []: Bind entity uk.ac.ebi.bioinvindex.model.term.OntologyEntry on table ontology_entry
  56. 2011-03-10 15:37:57,793 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.AssayTechnology
  57. 2011-03-10 15:37:57,794 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.Property
  58. 2011-03-10 15:37:57,794 []: Bind entity uk.ac.ebi.bioinvindex.model.term.Property on table PROPERTY
  59. 2011-03-10 15:37:57,798 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.Characteristic
  60. 2011-03-10 15:37:57,798 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.PropertyValue
  61. 2011-03-10 15:37:57,799 []: Bind entity uk.ac.ebi.bioinvindex.model.term.PropertyValue on table property_value
  62. 2011-03-10 15:37:57,802 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.CharacteristicValue
  63. 2011-03-10 15:37:57,803 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.ContactRole
  64. 2011-03-10 15:37:57,803 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.DataType
  65. 2011-03-10 15:37:57,804 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.Design
  66. 2011-03-10 15:37:57,804 []: Bind entity uk.ac.ebi.bioinvindex.model.term.Design on table design
  67. 2011-03-10 15:37:57,806 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.Measurement
  68. 2011-03-10 15:37:57,806 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.Factor
  69. 2011-03-10 15:37:57,807 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.FactorValue
  70. 2011-03-10 15:37:57,807 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.MaterialRole
  71. 2011-03-10 15:37:57,808 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.mibbi.MIProject
  72. 2011-03-10 15:37:57,808 []: Bind entity uk.ac.ebi.bioinvindex.mibbi.MIProject on table miproject
  73. 2011-03-10 15:37:57,809 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.OntologyTerm
  74. 2011-03-10 15:37:57,809 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.Parameter
  75. 2011-03-10 15:37:57,810 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.ParameterValue
  76. 2011-03-10 15:37:57,811 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.ProtocolComponent
  77. 2011-03-10 15:37:57,811 []: Bind entity uk.ac.ebi.bioinvindex.model.term.ProtocolComponent on table protocol_component
  78. 2011-03-10 15:37:57,813 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.ProtocolType
  79. 2011-03-10 15:37:57,813 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.PublicationStatus
  80. 2011-03-10 15:37:57,814 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.Unit
  81. 2011-03-10 15:37:57,814 []: Bind entity uk.ac.ebi.bioinvindex.model.term.Unit on table unit
  82. 2011-03-10 15:37:57,816 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.term.UnitValue
  83. 2011-03-10 15:37:57,816 []: Bind entity uk.ac.ebi.bioinvindex.model.term.UnitValue on table unit_value
  84. 2011-03-10 15:37:57,818 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.security.User
  85. 2011-03-10 15:37:57,819 []: Bind entity uk.ac.ebi.bioinvindex.model.security.User on table user_detail
  86. 2011-03-10 15:37:57,820 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.security.Person
  87. 2011-03-10 15:37:57,821 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.xref.AssayTypeDataLocation
  88. 2011-03-10 15:37:57,822 []: Bind entity uk.ac.ebi.bioinvindex.model.xref.AssayTypeDataLocation on table AssayType2REFERENCE_SOURCE
  89. 2011-03-10 15:37:57,823 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.xref.ReferenceSource
  90. 2011-03-10 15:37:57,823 []: Bind entity uk.ac.ebi.bioinvindex.model.xref.ReferenceSource on table REFERENCE_SOURCE
  91. 2011-03-10 15:37:57,825 []: Binding entity from annotated class: uk.ac.ebi.bioinvindex.model.xref.Xref
  92. 2011-03-10 15:37:57,825 []: Bind entity uk.ac.ebi.bioinvindex.model.xref.Xref on table xref
  93. 2011-03-10 15:37:57,831 []: Mapping collection: uk.ac.ebi.bioinvindex.model.processing.Processing.protocolApplications -> PROTOCOLAPPLICATION
  94. 2011-03-10 15:37:57,832 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Study.designs -> design
  95. 2011-03-10 15:37:57,833 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Protocol.parameters -> PROPERTY
  96. 2011-03-10 15:37:57,833 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Protocol.components -> protocol_component
  97. 2011-03-10 15:37:57,835 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Investigation.contacts -> contact
  98. 2011-03-10 15:37:57,836 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Investigation.publications -> publication
  99. 2011-03-10 15:37:57,836 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Material.characteristicValues -> property_value
  100. 2011-03-10 15:37:57,836 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Study.assayResults -> ASSAYRESULT
  101. 2011-03-10 15:37:57,837 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Study.assays -> ASSAY
  102. 2011-03-10 15:37:57,837 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Study.contacts -> contact
  103. 2011-03-10 15:37:57,837 []: Mapping collection: uk.ac.ebi.bioinvindex.model.Study.publications -> publication
  104. 2011-03-10 15:37:57,838 []: Mapping collection: uk.ac.ebi.bioinvindex.model.processing.ProtocolApplication.parameterValues -> property_value
  105. 2011-03-10 15:37:57,838 []: Mapping collection: uk.ac.ebi.bioinvindex.model.term.Property.propertyValues -> property_value
  106. 2011-03-10 15:37:57,963 []: Using Hibernate built-in connection pool (not for production use!)
  107. 2011-03-10 15:37:57,963 []: Hibernate connection pool size: 20
  108. 2011-03-10 15:37:57,963 []: autocommit mode: true
  109. 2011-03-10 15:37:57,964 []: using driver: org.postgresql.Driver at URL: jdbc:postgresql://rdbms.ipb-sub.ipb-halle.de/bioinvindex
  110. 2011-03-10 15:37:57,964 []: connection properties: {user=neumanns, password=****, autocommit=true, release_mode=auto}
  111. 2011-03-10 15:37:57,970 []: RDBMS: PostgreSQL, version: 8.3.3
  112. 2011-03-10 15:37:57,970 []: JDBC driver: PostgreSQL Native Driver, version: PostgreSQL 8.4 JDBC3 (build 701)
  113. 2011-03-10 15:37:57,971 []: Using dialect: org.hibernate.dialect.PostgreSQLDialect
  114. 2011-03-10 15:37:57,972 []: Transaction strategy: org.hibernate.transaction.JDBCTransactionFactory
  115. 2011-03-10 15:37:57,973 []: No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
  116. 2011-03-10 15:37:57,973 []: Automatic flush during beforeCompletion(): disabled
  117. 2011-03-10 15:37:57,974 []: Automatic session close at end of transaction: disabled
  118. 2011-03-10 15:37:57,974 []: JDBC batch size: 15
  119. 2011-03-10 15:37:57,975 []: JDBC batch updates for versioned data: disabled
  120. 2011-03-10 15:37:57,975 []: Scrollable result sets: enabled
  121. 2011-03-10 15:37:57,976 []: JDBC3 getGeneratedKeys(): enabled
  122. 2011-03-10 15:37:57,976 []: Connection release mode: auto
  123. 2011-03-10 15:37:57,977 []: Default batch fetch size: 1
  124. 2011-03-10 15:37:57,977 []: Generate SQL with comments: disabled
  125. 2011-03-10 15:37:57,978 []: Order SQL updates by primary key: disabled
  126. 2011-03-10 15:37:57,978 []: Order SQL inserts for batching: disabled
  127. 2011-03-10 15:37:57,979 []: Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
  128. 2011-03-10 15:37:57,980 []: Using ASTQueryTranslatorFactory
  129. 2011-03-10 15:37:57,980 []: Query language substitutions: {}
  130. 2011-03-10 15:37:57,981 []: JPA-QL strict compliance: enabled
  131. 2011-03-10 15:37:57,981 []: Second-level cache: enabled
  132. 2011-03-10 15:37:57,982 []: Query cache: disabled
  133. 2011-03-10 15:37:57,982 []: Cache region factory : org.hibernate.cache.impl.NoCachingRegionFactory
  134. 2011-03-10 15:37:57,983 []: Optimize cache for minimal puts: disabled
  135. 2011-03-10 15:37:57,983 []: Structured second-level cache entries: disabled
  136. 2011-03-10 15:37:57,984 []: Statistics: disabled
  137. 2011-03-10 15:37:57,984 []: Deleted entity synthetic identifier rollback: disabled
  138. 2011-03-10 15:37:57,984 []: Default entity-mode: pojo
  139. 2011-03-10 15:37:57,985 []: Named query checking : enabled
  140. 2011-03-10 15:37:58,011 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  141. 2011-03-10 15:37:58,015 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  142. 2011-03-10 15:37:58,018 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  143. 2011-03-10 15:37:58,020 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  144. 2011-03-10 15:37:58,022 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  145. 2011-03-10 15:37:58,030 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  146. 2011-03-10 15:37:58,031 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  147. 2011-03-10 15:37:58,036 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  148. 2011-03-10 15:37:58,038 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  149. 2011-03-10 15:37:58,043 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  150. 2011-03-10 15:37:58,045 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  151. 2011-03-10 15:37:58,046 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  152. 2011-03-10 15:37:58,048 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  153. 2011-03-10 15:37:58,052 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  154. 2011-03-10 15:37:58,059 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  155. 2011-03-10 15:37:58,064 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  156. 2011-03-10 15:37:58,065 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  157. 2011-03-10 15:37:58,068 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  158. 2011-03-10 15:37:58,070 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  159. 2011-03-10 15:37:58,071 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  160. 2011-03-10 15:37:58,072 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  161. 2011-03-10 15:37:58,074 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  162. 2011-03-10 15:37:58,080 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  163. 2011-03-10 15:37:58,085 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  164. 2011-03-10 15:37:58,087 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  165. 2011-03-10 15:37:58,089 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  166. 2011-03-10 15:37:58,092 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  167. 2011-03-10 15:37:58,094 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  168. 2011-03-10 15:37:58,097 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  169. 2011-03-10 15:37:58,098 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  170. 2011-03-10 15:37:58,101 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  171. 2011-03-10 15:37:58,107 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  172. 2011-03-10 15:37:58,111 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  173. 2011-03-10 15:37:58,113 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  174. 2011-03-10 15:37:58,116 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  175. 2011-03-10 15:37:58,119 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  176. 2011-03-10 15:37:58,121 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  177. 2011-03-10 15:37:58,123 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  178. 2011-03-10 15:37:58,124 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  179. 2011-03-10 15:37:58,125 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  180. 2011-03-10 15:37:58,126 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  181. 2011-03-10 15:37:58,127 []: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  182. 2011-03-10 15:37:58,207 []: building session factory
  183. 2011-03-10 15:37:58,375 []: Not binding factory to JNDI, no JNDI name configured
  184. 2011-03-10 15:37:58,376 []: Running hbm2ddl schema update
  185. 2011-03-10 15:37:58,376 []: fetching database metadata
  186. 2011-03-10 15:37:58,378 []: updating schema
  187. 2011-03-10 15:37:58,447 []: table found: public.assay
  188. 2011-03-10 15:37:58,447 []: columns: [id, platform, technology, study_id, submission_ts, material_id, endpoint, acc]
  189. 2011-03-10 15:37:58,448 []: foreign keys: [fk3baf2597400b98f, fk3baf259fbeeaf5a, fk3baf2593eaeee1a, fk3baf2591afa3eaf]
  190. 2011-03-10 15:37:58,448 []: indexes: [assay_acc_key, assay_pkey]
  191. 2011-03-10 15:37:58,472 []: table found: public.assayresult
  192. 2011-03-10 15:37:58,472 []: columns: [id, data_id, study_id, submission_ts]
  193. 2011-03-10 15:37:58,472 []: foreign keys: [fk6828c7b6f14f7c7a, fk6828c7b63eaeee1a]
  194. 2011-03-10 15:37:58,473 []: indexes: [assayresult_pkey]
  195. 2011-03-10 15:37:58,495 []: table found: public.assay_annotation
  196. 2011-03-10 15:37:58,495 []: columns: [assay_id, annotations_id]
  197. 2011-03-10 15:37:58,495 []: foreign keys: [fkc34a8cd5662fe33f, fkc34a8cd5e734245]
  198. 2011-03-10 15:37:58,496 []: indexes: [assay_annotation_annotations_id_key]
  199. 2011-03-10 15:37:58,518 []: table found: public.annotationtype2ontologyentry
  200. 2011-03-10 15:37:58,518 []: columns: [at_id, oe_id]
  201. 2011-03-10 15:37:58,518 []: foreign keys: [fkfd2868bad0b42b2, fkfd2868ba5b825601]
  202. 2011-03-10 15:37:58,518 []: indexes: []
  203. 2011-03-10 15:37:58,541 []: table found: public.assayresult2assay
  204. 2011-03-10 15:37:58,541 []: columns: [ar_id, assay_id]
  205. 2011-03-10 15:37:58,541 []: foreign keys: [fk580458bd662fe33f, fk580458bd406dc8df]
  206. 2011-03-10 15:37:58,542 []: indexes: []
  207. 2011-03-10 15:37:58,564 []: table found: public.assayresult2propertyvalue
  208. 2011-03-10 15:37:58,564 []: columns: [ar_id, pv_id]
  209. 2011-03-10 15:37:58,564 []: foreign keys: [fk780d0ae04aaf274e, fk780d0ae0406dc8df]
  210. 2011-03-10 15:37:58,564 []: indexes: []
  211. 2011-03-10 15:37:58,587 []: table found: public.assaytype2reference_source
  212. 2011-03-10 15:37:58,588 []: columns: [id, source, technologytype, submission_ts, measurementtype]
  213. 2011-03-10 15:37:58,588 []: foreign keys: [fk3475130e599a4b4e]
  214. 2011-03-10 15:37:58,589 []: indexes: [assaytype2reference_source_pkey]
  215. 2011-03-10 15:37:58,613 []: table found: public.design2ot
  216. 2011-03-10 15:37:58,613 []: columns: [design_id, ot_id]
  217. 2011-03-10 15:37:58,614 []: foreign keys: [fkda7be2f99e69c1fc, fkda7be2f95b892792]
  218. 2011-03-10 15:37:58,614 []: indexes: []
  219. 2011-03-10 15:37:58,638 []: table found: public.investigation
  220. 2011-03-10 15:37:58,639 []: columns: [id, title, submissiondate, description, submission_ts, releasedate, acc]
  221. 2011-03-10 15:37:58,639 []: foreign keys: []
  222. 2011-03-10 15:37:58,639 []: indexes: [investigation_pkey, investigation_acc_key]
  223. 2011-03-10 15:37:58,664 []: table found: public.investigation_annotation
  224. 2011-03-10 15:37:58,664 []: columns: [investigation_id, annotations_id]
  225. 2011-03-10 15:37:58,665 []: foreign keys: [fk10d044ace734245, fk10d044ac21f7b77a]
  226. 2011-03-10 15:37:58,665 []: indexes: [investigation_annotation_annotations_id_key]
  227. 2011-03-10 15:37:58,692 []: table found: public.node
  228. 2011-03-10 15:37:58,693 []: columns: [id, data_id, study_id, submission_ts, material_id, acc, obj_type]
  229. 2011-03-10 15:37:58,693 []: foreign keys: [fk24a602fbeeaf5a, fk24a6023eaeee1a, fk24a602f14f7c7a]
  230. 2011-03-10 15:37:58,693 []: indexes: [node_pkey, node_acc_key]
  231. 2011-03-10 15:37:58,717 []: table found: public.node_annotation
  232. 2011-03-10 15:37:58,718 []: columns: [annotations_id, node_id]
  233. 2011-03-10 15:37:58,718 []: foreign keys: [fk6629258c610ad1b5, fk6629258ce734245]
  234. 2011-03-10 15:37:58,718 []: indexes: [node_annotation_annotations_id_key]
  235. 2011-03-10 15:37:58,743 []: table found: public.processing
  236. 2011-03-10 15:37:58,744 []: columns: [id, study_id, submission_ts, acc, obj_type]
  237. 2011-03-10 15:37:58,744 []: foreign keys: [fk36141b133eaeee1a]
  238. 2011-03-10 15:37:58,745 []: indexes: [processing_acc_key, processing_pkey]
  239. 2011-03-10 15:37:58,768 []: table found: public.processing_annotation
  240. 2011-03-10 15:37:58,769 []: columns: [processing_id, annotations_id]
  241. 2011-03-10 15:37:58,770 []: foreign keys: [fk283a8bdb808153d5, fk283a8bdbe734245]
  242. 2011-03-10 15:37:58,770 []: indexes: [processing_annotation_annotations_id_key]
  243. 2011-03-10 15:37:58,795 []: table found: public.property
  244. 2011-03-10 15:37:58,795 []: columns: [protocol_id, position, id, value, submission_ts, role, obj_type]
  245. 2011-03-10 15:37:58,796 []: foreign keys: [fkf373cdd52f656dba]
  246. 2011-03-10 15:37:58,796 []: indexes: [property_pkey]
  247. 2011-03-10 15:37:58,822 []: table found: public.property_annotation
  248. 2011-03-10 15:37:58,823 []: columns: [property_id, annotations_id]
  249. 2011-03-10 15:37:58,823 []: foreign keys: [fk316ebd9e734245, fk316ebd9b98e7e1c]
  250. 2011-03-10 15:37:58,824 []: indexes: [property_annotation_annotations_id_key]
  251. 2011-03-10 15:37:58,852 []: table found: public.protocol
  252. 2011-03-10 15:37:58,853 []: columns: [id, description, name, submission_ts, type, uri, acc, version]
  253. 2011-03-10 15:37:58,854 []: foreign keys: [fkf3b07e989a615cae]
  254. 2011-03-10 15:37:58,854 []: indexes: [protocol_pkey, protocol_acc_key]
  255. 2011-03-10 15:37:58,883 []: table found: public.protocolapplication
  256. 2011-03-10 15:37:58,884 []: columns: [protocol_id, position, id, submission_ts, proto_app_id, acc]
  257. 2011-03-10 15:37:58,884 []: foreign keys: [fkbc268b982ae5443e, fkbc268b982f656dba]
  258. 2011-03-10 15:37:58,885 []: indexes: [protocolapplication_pkey, protocolapplication_acc_key]
  259. 2011-03-10 15:37:58,912 []: table found: public.protocolapplication_annotation
  260. 2011-03-10 15:37:58,913 []: columns: [protocolapplication_id, annotations_id]
  261. 2011-03-10 15:37:58,913 []: foreign keys: [fk3a8d0636f29b69ff, fk3a8d0636e734245]
  262. 2011-03-10 15:37:58,914 []: indexes: [protocolapplication_annotation_annotations_id_key]
  263. 2011-03-10 15:37:58,942 []: table found: public.protocol_annotation
  264. 2011-03-10 15:37:58,943 []: columns: [protocol_id, annotations_id]
  265. 2011-03-10 15:37:58,943 []: foreign keys: [fkc35d33362f656dba, fkc35d3336e734245]
  266. 2011-03-10 15:37:58,944 []: indexes: [protocol_annotation_annotations_id_key]
  267. 2011-03-10 15:37:58,985 []: table found: public.property2oe
  268. 2011-03-10 15:37:58,986 []: columns: [property_id, oe_id]
  269. 2011-03-10 15:37:58,986 []: foreign keys: [fkb4544373b98e7e1c, fkb45443735b825601]
  270. 2011-03-10 15:37:58,986 []: indexes: []
  271. 2011-03-10 15:37:59,026 []: table found: public.propertyvalue2ot
  272. 2011-03-10 15:37:59,027 []: columns: [oe_id, pv_id]
  273. 2011-03-10 15:37:59,027 []: foreign keys: [fk9621d39b5b825601, fk9621d39b4aaf274e]
  274. 2011-03-10 15:37:59,028 []: indexes: []
  275. 2011-03-10 15:37:59,067 []: table found: public.reference_source
  276. 2011-03-10 15:37:59,067 []: columns: [id, description, name, submission_ts, url, acc, version]
  277. 2011-03-10 15:37:59,068 []: foreign keys: []
  278. 2011-03-10 15:37:59,068 []: indexes: [reference_source_pkey, reference_source_acc_key]
  279. 2011-03-10 15:37:59,094 []: table found: public.reference_source_annotation
  280. 2011-03-10 15:37:59,095 []: columns: [reference_source_id, annotations_id]
  281. 2011-03-10 15:37:59,095 []: foreign keys: [fk1f74b9bfe734245, fk1f74b9bf6b280afe]
  282. 2011-03-10 15:37:59,095 []: indexes: [reference_source_annotation_annotations_id_key]
  283. 2011-03-10 15:37:59,119 []: table found: public.study2investigation
  284. 2011-03-10 15:37:59,119 []: columns: [study_id, investigation_id]
  285. 2011-03-10 15:37:59,120 []: foreign keys: [fk2e9495d93eaeee1a, fk2e9495d921f7b77a]
  286. 2011-03-10 15:37:59,120 []: indexes: []
  287. 2011-03-10 15:37:59,144 []: table found: public.study2miproject
  288. 2011-03-10 15:37:59,144 []: columns: [miproject_id, study_id]
  289. 2011-03-10 15:37:59,145 []: foreign keys: [fk1cee08543eaeee1a, fk1cee0854cd8e3e7e]
  290. 2011-03-10 15:37:59,145 []: indexes: []
  291. 2011-03-10 15:37:59,169 []: table found: public.study2protocol
  292. 2011-03-10 15:37:59,170 []: columns: [protocol_id, study_id]
  293. 2011-03-10 15:37:59,170 []: foreign keys: [fk30c6d1613eaeee1a, fk30c6d1612f656dba]
  294. 2011-03-10 15:37:59,171 []: indexes: [study2protocol_protocol_id_key]
  295. 2011-03-10 15:37:59,194 []: table found: public.study2user
  296. 2011-03-10 15:37:59,195 []: columns: [study_id, user_id]
  297. 2011-03-10 15:37:59,195 []: foreign keys: [fk580dfb14589ea508, fk580dfb143eaeee1a]
  298. 2011-03-10 15:37:59,196 []: indexes: []
  299. 2011-03-10 15:37:59,219 []: table found: public.unit2oe
  300. 2011-03-10 15:37:59,220 []: columns: [oe_id, unit_id]
  301. 2011-03-10 15:37:59,220 []: foreign keys: [fk5223e5645b825601, fk5223e564c4ecbcbc]
  302. 2011-03-10 15:37:59,220 []: indexes: []
  303. 2011-03-10 15:37:59,243 []: table found: public.unitvalue2ot
  304. 2011-03-10 15:37:59,244 []: columns: [uv_id, ot_id]
  305. 2011-03-10 15:37:59,245 []: foreign keys: [fk992ec04ac0cfa584, fk992ec04a5b892792]
  306. 2011-03-10 15:37:59,245 []: indexes: []
  307. 2011-03-10 15:37:59,268 []: table found: public.annotation
  308. 2011-03-10 15:37:59,269 []: columns: [id, text, submission_ts, type_id]
  309. 2011-03-10 15:37:59,269 []: foreign keys: [fka34feb2fd4a50e4b]
  310. 2011-03-10 15:37:59,269 []: indexes: [annotation_pkey]
  311. 2011-03-10 15:37:59,292 []: table found: public.annotation_type
  312. 2011-03-10 15:37:59,293 []: columns: [id, value, submission_ts]
  313. 2011-03-10 15:37:59,293 []: foreign keys: []
  314. 2011-03-10 15:37:59,294 []: indexes: [annotation_type_pkey]
  315. 2011-03-10 15:37:59,318 []: table found: public.annotation_type_annotation
  316. 2011-03-10 15:37:59,318 []: columns: [annotation_type_id, annotations_id]
  317. 2011-03-10 15:37:59,319 []: foreign keys: [fk5842cc44e734245, fk5842cc444ffa013b]
  318. 2011-03-10 15:37:59,319 []: indexes: [annotation_type_annotation_annotations_id_key]
  319. 2011-03-10 15:37:59,343 []: table found: public.assay2xref
  320. 2011-03-10 15:37:59,343 []: columns: [xref_id, assay_id]
  321. 2011-03-10 15:37:59,344 []: foreign keys: [fkb16895744613960d, fkb1689574662fe33f]
  322. 2011-03-10 15:37:59,344 []: indexes: [assay2xref_xref_id_key]
  323. 2011-03-10 15:37:59,375 []: table found: public.contact
  324. 2011-03-10 15:37:59,376 []: columns: [phone, fax, lastname, firstname, url, id, address, email, study_id, submission_ts, midinitials, investigation_id, affiliation]
  325. 2011-03-10 15:37:59,376 []: foreign keys: [fk38b7242021f7b77a, fk38b724203eaeee1a]
  326. 2011-03-10 15:37:59,377 []: indexes: [contact_pkey]
  327. 2011-03-10 15:37:59,405 []: table found: public.contact_annotation
  328. 2011-03-10 15:37:59,406 []: columns: [contact_id, annotations_id]
  329. 2011-03-10 15:37:59,406 []: foreign keys: [fkd48d48ae1bfb7aba, fkd48d48aee734245]
  330. 2011-03-10 15:37:59,407 []: indexes: [contact_annotation_annotations_id_key]
  331. 2011-03-10 15:37:59,436 []: table found: public.data
  332. 2011-03-10 15:37:59,437 []: columns: [id, name, submission_ts, datamatrixurl, type, url, acc, node_id]
  333. 2011-03-10 15:37:59,438 []: foreign keys: [fk2eefaad6433aff, fk2eefaaeaef5c0]
  334. 2011-03-10 15:37:59,438 []: indexes: [data_pkey, data_acc_key]
  335. 2011-03-10 15:37:59,466 []: table found: public.data2fv
  336. 2011-03-10 15:37:59,467 []: columns: [data_id, factorvalues_id]
  337. 2011-03-10 15:37:59,467 []: foreign keys: [fk5604c098c0e71a89, fk5604c098f14f7c7a]
  338. 2011-03-10 15:37:59,468 []: indexes: [data2fv_factorvalues_id_key]
  339. 2011-03-10 15:37:59,495 []: table found: public.data_annotation
  340. 2011-03-10 15:37:59,495 []: columns: [data_id, annotations_id]
  341. 2011-03-10 15:37:59,496 []: foreign keys: [fk909bc2e4e734245, fk909bc2e4f14f7c7a]
  342. 2011-03-10 15:37:59,496 []: indexes: [data_annotation_annotations_id_key]
  343. 2011-03-10 15:37:59,520 []: table found: public.design
  344. 2011-03-10 15:37:59,521 []: columns: [id, study_id, value, submission_ts]
  345. 2011-03-10 15:37:59,521 []: foreign keys: [fkb069c1be3eaeee1a]
  346. 2011-03-10 15:37:59,522 []: indexes: [design_pkey]
  347. 2011-03-10 15:37:59,545 []: table found: public.design_annotation
  348. 2011-03-10 15:37:59,546 []: columns: [design_id, annotations_id]
  349. 2011-03-10 15:37:59,547 []: foreign keys: [fkabaa9c509e69c1fc, fkabaa9c50e734245]
  350. 2011-03-10 15:37:59,547 []: indexes: [design_annotation_annotations_id_key]
  351. 2011-03-10 15:37:59,570 []: table found: public.investigation2xref
  352. 2011-03-10 15:37:59,571 []: columns: [xref_id, investigation_id]
  353. 2011-03-10 15:37:59,571 []: foreign keys: [fk5834ca8b21f7b77a, fk5834ca8b4613960d]
  354. 2011-03-10 15:37:59,572 []: indexes: [investigation2xref_xref_id_key]
  355. 2011-03-10 15:37:59,596 []: table found: public.material
  356. 2011-03-10 15:37:59,597 []: columns: [id, name, submission_ts, type, acc, node_id]
  357. 2011-03-10 15:37:59,598 []: foreign keys: [fk11d3652712ad44f9, fk11d365278359547c]
  358. 2011-03-10 15:37:59,598 []: indexes: [material_pkey, material_acc_key]
  359. 2011-03-10 15:37:59,621 []: table found: public.material2fv
  360. 2011-03-10 15:37:59,622 []: columns: [factorvalues_id, material_id]
  361. 2011-03-10 15:37:59,622 []: foreign keys: [fk6748fdfbfbeeaf5a, fk6748fdfbc0e71a89]
  362. 2011-03-10 15:37:59,623 []: indexes: [material2fv_factorvalues_id_key]
  363. 2011-03-10 15:37:59,646 []: table found: public.material_annotation
  364. 2011-03-10 15:37:59,647 []: columns: [material_id, annotations_id]
  365. 2011-03-10 15:37:59,647 []: foreign keys: [fkc2c9ed47fbeeaf5a, fkc2c9ed47e734245]
  366. 2011-03-10 15:37:59,647 []: indexes: [material_annotation_annotations_id_key]
  367. 2011-03-10 15:37:59,671 []: table found: public.miproject
  368. 2011-03-10 15:37:59,672 []: columns: [id, acronym, submission_ts, url, fullname]
  369. 2011-03-10 15:37:59,672 []: foreign keys: []
  370. 2011-03-10 15:37:59,673 []: indexes: [miproject_pkey]
  371. 2011-03-10 15:37:59,697 []: table found: public.ontology_entry
  372. 2011-03-10 15:37:59,698 []: columns: [id, source, name, submission_ts, acc, obj_type]
  373. 2011-03-10 15:37:59,698 []: foreign keys: [fk4411fd82599a4b4e]
  374. 2011-03-10 15:37:59,698 []: indexes: [ontology_entry_pkey]
  375. 2011-03-10 15:37:59,722 []: table found: public.ontology_entry_annotation
  376. 2011-03-10 15:37:59,722 []: columns: [ontology_entry_id, annotations_id]
  377. 2011-03-10 15:37:59,723 []: foreign keys: [fk94221e0ce734245, fk94221e0cba609e19]
  378. 2011-03-10 15:37:59,723 []: indexes: [ontology_entry_annotation_annotations_id_key]
  379. 2011-03-10 15:37:59,746 []: table found: public.processing_inputs
  380. 2011-03-10 15:37:59,747 []: columns: [proc_id, node_id]
  381. 2011-03-10 15:37:59,747 []: foreign keys: [fk8b68e495fa10d4b2, fk8b68e495610ad1b5]
  382. 2011-03-10 15:37:59,748 []: indexes: []
  383. 2011-03-10 15:37:59,771 []: table found: public.processing_outputs
  384. 2011-03-10 15:37:59,772 []: columns: [proc_id, node_id]
  385. 2011-03-10 15:37:59,772 []: foreign keys: [fk2b411a66610ad1b5, fk2b411a66fa10d4b2]
  386. 2011-03-10 15:37:59,773 []: indexes: []
  387. 2011-03-10 15:37:59,800 []: table found: public.property_value
  388. 2011-03-10 15:37:59,801 []: columns: [property_id, id, unit, ar_id, value, submission_ts, protocol_app_id, material_id, obj_type]
  389. 2011-03-10 15:37:59,801 []: foreign keys: [fka48c5e87ba5eab8f, fka48c5e87fbeeaf5a, fka48c5e87b98e7e1c, fka48c5e87406dc8df, fka48c5e874233a67d]
  390. 2011-03-10 15:37:59,802 []: indexes: [property_value_pkey]
  391. 2011-03-10 15:37:59,825 []: table found: public.property_value_annotation
  392. 2011-03-10 15:37:59,826 []: columns: [property_value_id, annotations_id]
  393. 2011-03-10 15:37:59,826 []: foreign keys: [fk798957e7ef3b7b2d, fk798957e7e734245]
  394. 2011-03-10 15:37:59,827 []: indexes: [property_value_annotation_annotations_id_key]
  395. 2011-03-10 15:37:59,850 []: table found: public.protocol_component
  396. 2011-03-10 15:37:59,851 []: columns: [protocol_id, id, value, submission_ts]
  397. 2011-03-10 15:37:59,851 []: foreign keys: [fk174b48162f656dba]
  398. 2011-03-10 15:37:59,851 []: indexes: [protocol_component_pkey]
  399. 2011-03-10 15:37:59,875 []: table found: public.protocol_component_2_term
  400. 2011-03-10 15:37:59,875 []: columns: [component_id, ontology_term_id]
  401. 2011-03-10 15:37:59,876 []: foreign keys: [fk6c80dca2e6c280bb, fk6c80dca23cca8aa0]
  402. 2011-03-10 15:37:59,876 []: indexes: []
  403. 2011-03-10 15:37:59,907 []: table found: public.protocol_component_annotation
  404. 2011-03-10 15:37:59,908 []: columns: [protocol_component_id, annotations_id]
  405. 2011-03-10 15:37:59,909 []: foreign keys: [fk7fca2ef8e734245, fk7fca2ef81c25dce7]
  406. 2011-03-10 15:37:59,909 []: indexes: [protocol_component_annotation_annotations_id_key]
  407. 2011-03-10 15:37:59,947 []: table found: public.publication
  408. 2011-03-10 15:37:59,948 []: columns: [id, title, pmid, study_id, status_id, submission_ts, investigation_id, doi, authorlist]
  409. 2011-03-10 15:37:59,949 []: foreign keys: [fkbfbba22c3eaeee1a, fkbfbba22cd1536b84, fkbfbba22c21f7b77a]
  410. 2011-03-10 15:37:59,949 []: indexes: [publication_pkey]
  411. 2011-03-10 15:37:59,984 []: table found: public.publication_annotation
  412. 2011-03-10 15:37:59,985 []: columns: [publication_id, annotations_id]
  413. 2011-03-10 15:37:59,985 []: foreign keys: [fk4ec1cb227581af3a, fk4ec1cb22e734245]
  414. 2011-03-10 15:37:59,986 []: indexes: [publication_annotation_annotations_id_key]
  415. 2011-03-10 15:38:00,021 []: table found: public.role2contact
  416. 2011-03-10 15:38:00,022 []: columns: [role_id, contact_id]
  417. 2011-03-10 15:38:00,022 []: foreign keys: [fkcf29224ccc75e78, fkcf292241bfb7aba]
  418. 2011-03-10 15:38:00,022 []: indexes: []
  419. 2011-03-10 15:38:00,057 []: table found: public.study
  420. 2011-03-10 15:38:00,057 []: columns: [id, title, submissiondate, objective, obfuscationcode, status, description, submission_ts, releasedate, acc]
  421. 2011-03-10 15:38:00,058 []: foreign keys: []
  422. 2011-03-10 15:38:00,058 []: indexes: [study_pkey, study_acc_key]
  423. 2011-03-10 15:38:00,093 []: table found: public.study2xref
  424. 2011-03-10 15:38:00,093 []: columns: [xref_id, study_id]
  425. 2011-03-10 15:38:00,094 []: foreign keys: [fke14c04243eaeee1a, fke14c04244613960d]
  426. 2011-03-10 15:38:00,094 []: indexes: [study2xref_xref_id_key]
  427. 2011-03-10 15:38:00,128 []: table found: public.study_annotation
  428. 2011-03-10 15:38:00,129 []: columns: [study_id, annotations_id]
  429. 2011-03-10 15:38:00,129 []: foreign keys: [fkf8a3eb653eaeee1a, fkf8a3eb65e734245]
  430. 2011-03-10 15:38:00,130 []: indexes: [study_annotation_annotations_id_key]
  431. 2011-03-10 15:38:00,163 []: table found: public.unit
  432. 2011-03-10 15:38:00,163 []: columns: [id, value, submission_ts]
  433. 2011-03-10 15:38:00,164 []: foreign keys: []
  434. 2011-03-10 15:38:00,164 []: indexes: [unit_pkey]
  435. 2011-03-10 15:38:00,198 []: table found: public.unit_annotation
  436. 2011-03-10 15:38:00,199 []: columns: [unit_id, annotations_id]
  437. 2011-03-10 15:38:00,199 []: foreign keys: [fk52ff0ccae734245, fk52ff0ccac4ecbcbc]
  438. 2011-03-10 15:38:00,200 []: indexes: [unit_annotation_annotations_id_key]
  439. 2011-03-10 15:38:00,234 []: table found: public.unit_value
  440. 2011-03-10 15:38:00,234 []: columns: [id, value, submission_ts, unit_id]
  441. 2011-03-10 15:38:00,235 []: foreign keys: [fk976f9af6c4ecbcbc]
  442. 2011-03-10 15:38:00,235 []: indexes: [unit_value_pkey]
  443. 2011-03-10 15:38:00,269 []: table found: public.unit_value_annotation
  444. 2011-03-10 15:38:00,270 []: columns: [unit_value_id, annotations_id]
  445. 2011-03-10 15:38:00,271 []: foreign keys: [fke38f5018e734245, fke38f50187ecb3d0f]
  446. 2011-03-10 15:38:00,271 []: indexes: [unit_value_annotation_annotations_id_key]
  447. 2011-03-10 15:38:00,301 []: table found: public.user_detail
  448. 2011-03-10 15:38:00,301 []: columns: [id, username, joindate, email, address, submission_ts, lastname, role, affiliation, firstname, password, obj_type]
  449. 2011-03-10 15:38:00,302 []: foreign keys: []
  450. 2011-03-10 15:38:00,302 []: indexes: [user_detail_pkey, user_detail_username_key]
  451. 2011-03-10 15:38:00,325 []: table found: public.xref
  452. 2011-03-10 15:38:00,326 []: columns: [id, source_id, submission_ts, acc]
  453. 2011-03-10 15:38:00,326 []: foreign keys: [fk38451b29ce32f2]
  454. 2011-03-10 15:38:00,327 []: indexes: [xref_pkey]
  455. 2011-03-10 15:38:00,353 []: table found: public.hibernate_sequences
  456. 2011-03-10 15:38:00,354 []: columns: [sequence_next_hi_value, sequence_name]
  457. 2011-03-10 15:38:00,354 []: foreign keys: []
  458. 2011-03-10 15:38:00,355 []: indexes: []
  459. 2011-03-10 15:38:00,355 []: schema update complete
  460. 2011-03-10 15:38:01,389 []: Data Location Manager, Total no of data locations: 26
  461. 2011-03-10 15:38:01,416 []:
  462. java.lang.NullPointerException
  463. at uk.ac.ebi.bioinvindex.unloading.UnloadManager.queueSimple(UnloadManager.java:275)
  464. at uk.ac.ebi.bioinvindex.unloading.AbstractUnloader.queue(AbstractUnloader.java:131)
  465. at uk.ac.ebi.bioinvindex.unloading.DataLocationUnloader.queue(DataLocationUnloader.java:72)
  466. at uk.ac.ebi.bioinvindex.unloading.DataLocationUnloader.queue(DataLocationUnloader.java:59)
  467. at uk.ac.ebi.bioinvindex.unloading.UnloadManager.queue(UnloadManager.java:320)
  468. at uk.ac.ebi.bioinvindex.unloading.UnloadManager.queue(UnloadManager.java:331)
  469. at uk.ac.ebi.bioinvindex.utils.datasourceload.DataSourceLoader.persistLocations(DataSourceLoader.java:144)
  470. at uk.ac.ebi.bioinvindex.utils.datasourceload.DataSourceLoader.loadAll(DataSourceLoader.java:118)
  471. at org.isatools.isatab.commandline.AbstractImportLayerShellCommand.createDataLocationManager(AbstractImportLayerShellCommand.java:385)
  472. at org.isatools.isatab.export.DataFilesDispatcher.<init>(DataFilesDispatcher.java:115)
  473. at org.isatools.isatab.ISATABPersister.persist(ISATABPersister.java:94)
  474. at org.isatools.isatab.gui_invokers.GUIISATABLoader.persist(GUIISATABLoader.java:101)
  475. at org.isatools.gui.datamanager.DataManagerToolUI.loadToDatabase(DataManagerToolUI.java:706)
  476. at org.isatools.gui.CommonUI$3.run(CommonUI.java:239)
  477. at java.lang.Thread.run(Thread.java:662)
  478. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  479. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  480. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  481. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  482. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  483. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  484. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  485. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  486. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  487. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  488. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  489. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  490. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  491. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  492. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  493. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  494. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  495. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  496. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  497. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  498. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  499. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  500. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  501. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  502. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  503. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  504. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  505. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  506. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  507. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  508. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  509. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  510. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  511. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  512. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  513. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  514. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  515. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  516. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  517. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  518. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
  519. Message: @DocumentId specified on an entity which is not indexed by itself. Annotation gets ignored. Use @Field instead.
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