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k-joseph
Jun 3rd, 2014
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  1. 53099 [Thread-187] INFO org.apache.solr.handler.dataimport.DataImporter - Starting Full Import
  2. 53099 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  3. 53099 [Thread-187] INFO org.apache.solr.handler.dataimport.SimplePropertiesWriter - Read dataimport.properties
  4. 53099 [Thread-187] INFO org.apache.solr.core.SolrCore - [] REMOVING ALL DOCUMENTS FROM INDEX
  5. 53100 [Thread-187] INFO org.apache.solr.core.SolrCore - SolrDeletionPolicy.onInit: commits:num=1
  6. commit{dir=/home/k-joseph/.OpenMRS/solr/data/index,segFN=segments_3,version=1394192336380,generation=3,filenames=[segments_3]
  7. 53101 [Thread-187] INFO org.apache.solr.core.SolrCore - newest commit = 1394192336380
  8. 53101 [Thread-187] INFO org.apache.solr.handler.dataimport.JdbcDataSource - Creating a connection for entity patient_chart with URL: jdbc:mysql://localhost:3306/openmrs?autoReconnect=true&sessionVariables=storage_engine=InnoDB&useUnicode=true&characterEncoding=UTF-8
  9. 53540 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  10. 53843 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  11. 54034 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=1
  12. 54233 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  13. 54813 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  14. 54937 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  15. 55004 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  16. 55070 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  17. 55079 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  18. 55147 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  19. 55190 [btpool0-20] INFO org.apache.solr.core.SolrCore - [] webapp=/openmrs path=/dataimport params={command=full-import&clean=true} status=0 QTime=0
  20. 61115 [Thread-187] ERROR org.apache.solr.handler.dataimport.DocBuilder - Exception while processing: patient_chart document : SolrInputDocument[{}]:org.apache.solr.handler.dataimport.DataImportHandlerException: Unable to execute query: select person_id, obs_id, cc.concept_class_id, cn.name as concept_name, cd.description as concept_description, d.name as drug, obs_datetime, value_datetime, value_numeric, value_modifier, value_text, cc2.concept_class_id as value_coded_concept_class_id, cn2.name as value_coded_concept_name, cd2.description as value_coded_concept_description from obs o inner join concept c on c.concept_id = o.concept_id inner join concept_class cc on cc.concept_class_id = c.class_id inner join concept_name cn on cn.concept_id = o.concept_id left join concept_description cd on cd.concept_id = o.concept_id left join drug d on d.drug_id = o. value_drug left join concept c2 on c2.concept_id = value_coded left join concept_class cc2 on cc2.concept_class_id = c2.class_id left join concept_name cn2 on cn2.concept_id = o. value_coded left join concept_description cd2 on cd2.concept_id = o. value_coded Processing Document # 1
  21. at org.apache.solr.handler.dataimport.DataImportHandlerException.wrapAndThrow(DataImportHandlerException.java:72)
  22. at org.apache.solr.handler.dataimport.JdbcDataSource$ResultSetIterator.<init>(JdbcDataSource.java:253)
  23. at org.apache.solr.handler.dataimport.JdbcDataSource.getData(JdbcDataSource.java:210)
  24. at org.apache.solr.handler.dataimport.JdbcDataSource.getData(JdbcDataSource.java:39)
  25. at org.apache.solr.handler.dataimport.SqlEntityProcessor.initQuery(SqlEntityProcessor.java:59)
  26. at org.apache.solr.handler.dataimport.SqlEntityProcessor.nextRow(SqlEntityProcessor.java:73)
  27. at org.apache.solr.handler.dataimport.EntityProcessorWrapper.pullRow(EntityProcessorWrapper.java:330)
  28. at org.apache.solr.handler.dataimport.EntityProcessorWrapper.nextRow(EntityProcessorWrapper.java:296)
  29. at org.apache.solr.handler.dataimport.DocBuilder.buildDocument(DocBuilder.java:683)
  30. at org.apache.solr.handler.dataimport.DocBuilder.buildDocument(DocBuilder.java:619)
  31. at org.apache.solr.handler.dataimport.DocBuilder.doFullDump(DocBuilder.java:327)
  32. at org.apache.solr.handler.dataimport.DocBuilder.execute(DocBuilder.java:225)
  33. at org.apache.solr.handler.dataimport.DataImporter.doFullImport(DataImporter.java:375)
  34. at org.apache.solr.handler.dataimport.DataImporter.runCmd(DataImporter.java:445)
  35. at org.apache.solr.handler.dataimport.DataImporter$1.run(DataImporter.java:426)
  36. Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
  37. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  38. at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
  39. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  40. at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
  41. at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
  42. at com.mysql.jdbc.Util.getInstance(Util.java:386)
  43. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
  44. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
  45. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
  46. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:920)
  47. at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2395)
  48. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2316)
  49. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
  50. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
  51. at sun.reflect.GeneratedConstructorAccessor82.newInstance(Unknown Source)
  52. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  53. at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
  54. at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
  55. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
  56. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:347)
  57. at org.apache.solr.handler.dataimport.JdbcDataSource$1.call(JdbcDataSource.java:161)
  58. at org.apache.solr.handler.dataimport.JdbcDataSource$1.call(JdbcDataSource.java:129)
  59. at org.apache.solr.handler.dataimport.JdbcDataSource.getConnection(JdbcDataSource.java:363)
  60. at org.apache.solr.handler.dataimport.JdbcDataSource.access$200(JdbcDataSource.java:39)
  61. at org.apache.solr.handler.dataimport.JdbcDataSource$ResultSetIterator.<init>(JdbcDataSource.java:240)
  62. ... 13 more
  63. Caused by: java.sql.SQLException: Access denied for user 'openmrs_user'@'localhost' (using password: YES)
  64. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1086)
  65. at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4237)
  66. at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169)
  67. at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:928)
  68. at com.mysql.jdbc.MysqlIO.proceedHandshakeWithPluggableAuthentication(MysqlIO.java:1750)
  69. at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1290)
  70. at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2493)
  71. at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2334)
  72. ... 27 more
  73.  
  74. 61115 [Thread-187] INFO org.apache.solr.update.processor.LogUpdateProcessor - {deleteByQuery=*:*} 0 0
  75. 61116 [Thread-187] ERROR org.apache.solr.handler.dataimport.DataImporter - Full Import failed:java.lang.RuntimeException: java.lang.RuntimeException: org.apache.solr.handler.dataimport.DataImportHandlerException: Unable to execute query: select person_id, obs_id, cc.concept_class_id, cn.name as concept_name, cd.description as concept_description, d.name as drug, obs_datetime, value_datetime, value_numeric, value_modifier, value_text, cc2.concept_class_id as value_coded_concept_class_id, cn2.name as value_coded_concept_name, cd2.description as value_coded_concept_description from obs o inner join concept c on c.concept_id = o.concept_id inner join concept_class cc on cc.concept_class_id = c.class_id inner join concept_name cn on cn.concept_id = o.concept_id left join concept_description cd on cd.concept_id = o.concept_id left join drug d on d.drug_id = o. value_drug left join concept c2 on c2.concept_id = value_coded left join concept_class cc2 on cc2.concept_class_id = c2.class_id left join concept_name cn2 on cn2.concept_id = o. value_coded left join concept_description cd2 on cd2.concept_id = o. value_coded Processing Document # 1
  76. at org.apache.solr.handler.dataimport.DocBuilder.execute(DocBuilder.java:264)
  77. at org.apache.solr.handler.dataimport.DataImporter.doFullImport(DataImporter.java:375)
  78. at org.apache.solr.handler.dataimport.DataImporter.runCmd(DataImporter.java:445)
  79. at org.apache.solr.handler.dataimport.DataImporter$1.run(DataImporter.java:426)
  80. Caused by: java.lang.RuntimeException: org.apache.solr.handler.dataimport.DataImportHandlerException: Unable to execute query: select person_id, obs_id, cc.concept_class_id, cn.name as concept_name, cd.description as concept_description, d.name as drug, obs_datetime, value_datetime, value_numeric, value_modifier, value_text, cc2.concept_class_id as value_coded_concept_class_id, cn2.name as value_coded_concept_name, cd2.description as value_coded_concept_description from obs o inner join concept c on c.concept_id = o.concept_id inner join concept_class cc on cc.concept_class_id = c.class_id inner join concept_name cn on cn.concept_id = o.concept_id left join concept_description cd on cd.concept_id = o.concept_id left join drug d on d.drug_id = o. value_drug left join concept c2 on c2.concept_id = value_coded left join concept_class cc2 on cc2.concept_class_id = c2.class_id left join concept_name cn2 on cn2.concept_id = o. value_coded left join concept_description cd2 on cd2.concept_id = o. value_coded Processing Document # 1
  81. at org.apache.solr.handler.dataimport.DocBuilder.buildDocument(DocBuilder.java:621)
  82. at org.apache.solr.handler.dataimport.DocBuilder.doFullDump(DocBuilder.java:327)
  83. at org.apache.solr.handler.dataimport.DocBuilder.execute(DocBuilder.java:225)
  84. ... 3 more
  85. Caused by: org.apache.solr.handler.dataimport.DataImportHandlerException: Unable to execute query: select person_id, obs_id, cc.concept_class_id, cn.name as concept_name, cd.description as concept_description, d.name as drug, obs_datetime, value_datetime, value_numeric, value_modifier, value_text, cc2.concept_class_id as value_coded_concept_class_id, cn2.name as value_coded_concept_name, cd2.description as value_coded_concept_description from obs o inner join concept c on c.concept_id = o.concept_id inner join concept_class cc on cc.concept_class_id = c.class_id inner join concept_name cn on cn.concept_id = o.concept_id left join concept_description cd on cd.concept_id = o.concept_id left join drug d on d.drug_id = o. value_drug left join concept c2 on c2.concept_id = value_coded left join concept_class cc2 on cc2.concept_class_id = c2.class_id left join concept_name cn2 on cn2.concept_id = o. value_coded left join concept_description cd2 on cd2.concept_id = o. value_coded Processing Document # 1
  86. at org.apache.solr.handler.dataimport.DataImportHandlerException.wrapAndThrow(DataImportHandlerException.java:72)
  87. at org.apache.solr.handler.dataimport.JdbcDataSource$ResultSetIterator.<init>(JdbcDataSource.java:253)
  88. at org.apache.solr.handler.dataimport.JdbcDataSource.getData(JdbcDataSource.java:210)
  89. at org.apache.solr.handler.dataimport.JdbcDataSource.getData(JdbcDataSource.java:39)
  90. at org.apache.solr.handler.dataimport.SqlEntityProcessor.initQuery(SqlEntityProcessor.java:59)
  91. at org.apache.solr.handler.dataimport.SqlEntityProcessor.nextRow(SqlEntityProcessor.java:73)
  92. at org.apache.solr.handler.dataimport.EntityProcessorWrapper.pullRow(EntityProcessorWrapper.java:330)
  93. at org.apache.solr.handler.dataimport.EntityProcessorWrapper.nextRow(EntityProcessorWrapper.java:296)
  94. at org.apache.solr.handler.dataimport.DocBuilder.buildDocument(DocBuilder.java:683)
  95. at org.apache.solr.handler.dataimport.DocBuilder.buildDocument(DocBuilder.java:619)
  96. ... 5 more
  97. Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
  98. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  99. at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
  100. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  101. at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
  102. at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
  103. at com.mysql.jdbc.Util.getInstance(Util.java:386)
  104. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
  105. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
  106. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
  107. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:920)
  108. at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2395)
  109. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2316)
  110. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
  111. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
  112. at sun.reflect.GeneratedConstructorAccessor82.newInstance(Unknown Source)
  113. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  114. at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
  115. at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
  116. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
  117. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:347)
  118. at org.apache.solr.handler.dataimport.JdbcDataSource$1.call(JdbcDataSource.java:161)
  119. at org.apache.solr.handler.dataimport.JdbcDataSource$1.call(JdbcDataSource.java:129)
  120. at org.apache.solr.handler.dataimport.JdbcDataSource.getConnection(JdbcDataSource.java:363)
  121. at org.apache.solr.handler.dataimport.JdbcDataSource.access$200(JdbcDataSource.java:39)
  122. at org.apache.solr.handler.dataimport.JdbcDataSource$ResultSetIterator.<init>(JdbcDataSource.java:240)
  123. ... 13 more
  124. Caused by: java.sql.SQLException: Access denied for user 'openmrs_user'@'localhost' (using password: YES)
  125. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1086)
  126. at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4237)
  127. at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169)
  128. at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:928)
  129. at com.mysql.jdbc.MysqlIO.proceedHandshakeWithPluggableAuthentication(MysqlIO.java:1750)
  130. at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1290)
  131. at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2493)
  132. at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2334)
  133. ... 27 more
  134.  
  135. 61116 [Thread-187] INFO org.apache.solr.update.UpdateHandler - start rollback
  136. 61118 [Thread-187] INFO org.apache.solr.update.UpdateHandler - end_rollback
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