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jerome24

Openmrs upgrade is hanging on Tomcat7 on Ubuntu server

jerome24
Nov 17th, 2020
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  1. Nov 17, 2020 3:12:42 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
  2. WARNING: Problem with directory [/usr/share/tomcat7/common/classes], exists: [false], isDirectory: [false], canRead: [false]
  3. Nov 17, 2020 3:12:43 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
  4. WARNING: Problem with directory [/usr/share/tomcat7/common], exists: [false], isDirectory: [false], canRead: [false]
  5. Nov 17, 2020 3:12:44 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
  6. WARNING: Problem with directory [/usr/share/tomcat7/server/classes], exists: [false], isDirectory: [false], canRead: [false]
  7. Nov 17, 2020 3:12:44 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
  8. WARNING: Problem with directory [/usr/share/tomcat7/server], exists: [false], isDirectory: [false], canRead: [false]
  9. Nov 17, 2020 3:12:44 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
  10. WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
  11. Nov 17, 2020 3:12:44 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
  12. WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
  13. Nov 17, 2020 3:12:49 PM org.apache.coyote.AbstractProtocol init
  14. INFO: Initializing ProtocolHandler ["http-bio-8080"]
  15. Nov 17, 2020 3:12:49 PM org.apache.catalina.startup.Catalina load
  16. INFO: Initialization processed in 4503 ms
  17. Nov 17, 2020 3:12:49 PM org.apache.catalina.core.StandardService startInternal
  18. INFO: Starting service Catalina
  19. Nov 17, 2020 3:12:49 PM org.apache.catalina.core.StandardEngine startInternal
  20. INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
  21. Nov 17, 2020 3:12:49 PM org.apache.catalina.startup.HostConfig deployDescriptor
  22. INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/manager.xml
  23. Nov 17, 2020 3:12:51 PM org.apache.catalina.util.SessionIdGenerator createSecureRandom
  24. INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [117] milliseconds.
  25. Nov 17, 2020 3:12:51 PM org.apache.catalina.startup.HostConfig deployDescriptor
  26. INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
  27. Nov 17, 2020 3:12:51 PM org.apache.catalina.startup.HostConfig deployWAR
  28. INFO: Deploying web application archive /var/lib/tomcat7/webapps/openmrs.war
  29. WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2078) |2020-11-17 15:13:12,407| Unable to find a runtime properties file at /var/lib/tomcat7/openmrs-runtime.properties
  30. WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2078) |2020-11-17 15:13:12,467| Unable to find a runtime properties file at /var/lib/tomcat7/openmrs-runtime.properties
  31. INFO - Listener.contextInitialized(173) |2020-11-17 15:13:12,473| Using runtime properties file: /usr/share/tomcat7/.OpenMRS/openmrs-runtime.properties
  32. INFO 11/17/20 3:13 PM:liquibase: Reading from `liquibasechangelog`
  33. WARNING 11/17/20 3:13 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  34. WARNING 11/17/20 3:13 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  35. WARNING 11/17/20 3:13 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  36. INFO 11/17/20 3:13 PM:liquibase: Reading from `liquibasechangelog`
  37. WARNING 11/17/20 3:13 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  38. WARNING 11/17/20 3:13 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  39. WARNING 11/17/20 3:13 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  40. WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2078) |2020-11-17 15:13:20,512| Unable to find a runtime properties file at /var/lib/tomcat7/openmrs-runtime.properties
  41. Nov 17, 2020 3:13:20 PM org.apache.catalina.startup.HostConfig deployDirectory
  42. INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
  43. Nov 17, 2020 3:13:21 PM org.apache.coyote.AbstractProtocol start
  44. INFO: Starting ProtocolHandler ["http-bio-8080"]
  45. Nov 17, 2020 3:13:21 PM org.apache.catalina.startup.Catalina start
  46. INFO: Server startup in 31698 ms
  47. ERROR - CommonsLogLogChute.log(96) |2020-11-17 15:15:43,591| #parse() null argument
  48. ERROR - CommonsLogLogChute.log(96) |2020-11-17 15:15:44,581| #parse() null argument
  49. ERROR - CommonsLogLogChute.log(96) |2020-11-17 15:15:53,956| #parse() null argument
  50. ERROR - CommonsLogLogChute.log(96) |2020-11-17 15:15:53,976| #parse() null argument
  51. ERROR - CommonsLogLogChute.log(96) |2020-11-17 15:15:57,935| #parse() null argument
  52. ERROR - CommonsLogLogChute.log(96) |2020-11-17 15:15:57,939| #parse() null argument
  53. INFO 11/17/20 3:15 PM:liquibase: Reading from `liquibasechangelog`
  54. WARNING 11/17/20 3:15 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  55. WARNING 11/17/20 3:15 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  56. WARNING 11/17/20 3:15 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  57. ERROR - DatabaseUpdater.executeChangelog(230) |2020-11-17 15:15:59,198| Could not release lock
  58. liquibase.exception.LockException: liquibase.exception.LockException: Did not update change log lock correctly.
  59.  
  60. 0 rows were updated instead of the expected 1 row using executor liquibase.executor.jvm.JdbcExecutor there are 0 rows in the table
  61. at liquibase.lockservice.LockService.releaseLock(LockService.java:152)
  62. at org.openmrs.util.DatabaseUpdater.executeChangelog(DatabaseUpdater.java:227)
  63. at org.openmrs.util.DatabaseUpdater.executeChangelog(DatabaseUpdater.java:150)
  64. at org.openmrs.web.filter.update.UpdateFilter$UpdateFilterCompletion$1.run(UpdateFilter.java:726)
  65. at java.lang.Thread.run(Thread.java:748)
  66. Caused by: liquibase.exception.LockException: Did not update change log lock correctly.
  67.  
  68. 0 rows were updated instead of the expected 1 row using executor liquibase.executor.jvm.JdbcExecutor there are 0 rows in the table
  69. at liquibase.lockservice.LockService.releaseLock(LockService.java:140)
  70. ... 4 more
  71. ERROR - UpdateFilter$UpdateFilterCompletion$1.run(742) |2020-11-17 15:15:59,215| Unable to update the database
  72. org.openmrs.util.DatabaseUpdateException: There was an error while updating the database to the latest. file: liquibase-update-to-latest.xml. Error: liquibase.exception.DatabaseException: Empty result set, expected one row
  73. at org.openmrs.util.DatabaseUpdater.executeChangelog(DatabaseUpdater.java:154)
  74. at org.openmrs.web.filter.update.UpdateFilter$UpdateFilterCompletion$1.run(UpdateFilter.java:726)
  75. at java.lang.Thread.run(Thread.java:748)
  76. Caused by: liquibase.exception.LockException: liquibase.exception.DatabaseException: Empty result set, expected one row
  77. at liquibase.lockservice.LockService.acquireLock(LockService.java:121)
  78. at liquibase.lockservice.LockService.waitForLock(LockService.java:61)
  79. at org.openmrs.util.DatabaseUpdater.executeChangelog(DatabaseUpdater.java:208)
  80. at org.openmrs.util.DatabaseUpdater.executeChangelog(DatabaseUpdater.java:150)
  81. ... 2 more
  82. Caused by: liquibase.exception.DatabaseException: Empty result set, expected one row
  83. at liquibase.util.JdbcUtils.requiredSingleResult(JdbcUtils.java:124)
  84. at liquibase.executor.jvm.JdbcExecutor.queryForObject(JdbcExecutor.java:159)
  85. at liquibase.executor.jvm.JdbcExecutor.queryForObject(JdbcExecutor.java:167)
  86. at liquibase.executor.jvm.JdbcExecutor.queryForObject(JdbcExecutor.java:163)
  87. at liquibase.lockservice.LockService.acquireLock(LockService.java:96)
  88. ... 5 more
  89. INFO 11/17/20 3:15 PM:liquibase: Reading from `liquibasechangelog`
  90. WARNING 11/17/20 3:16 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  91. WARNING 11/17/20 3:16 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  92. WARNING 11/17/20 3:16 PM:liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use <sql> and re-specify all configuration if this is the case
  93.  
  94.  
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