My fellow OHDSIans, I am having troubling running the cpt4.jar command to append CPT4 records to the CONCEPT.csv file
when I run this command in my Bash prompt in AWS Cloud9:
travis-admin:~/environment/cms-synpuf-files/vocabulary $ java -Dumls-apikey=XXXXXX -jar cpt4.jar 5
I get this big error message:
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2024-05-02 02:59:05,194 main ERROR FileManager (logs/logfile.log) java.io.FileNotFoundException: logs/logfile.log (Invalid argument) java.io.FileNotFoundException: logs/logfile.log (Invalid argument)
at java.base/java.io.FileOutputStream.open0(Native Method)
at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293)
at java.base/java.io.FileOutputStream.(FileOutputStream.java:235)
at org.apache.logging.log4j.core.appender.FileManager$FileManagerFactory.createManager(FileManager.java:438)
at org.apache.logging.log4j.core.appender.FileManager$FileManagerFactory.createManager(FileManager.java:422)
at org.apache.logging.log4j.core.appender.AbstractManager.getManager(AbstractManager.java:114)
at org.apache.logging.log4j.core.appender.OutputStreamManager.getManager(OutputStreamManager.java:100)
at org.apache.logging.log4j.core.appender.FileManager.getFileManager(FileManager.java:182)
at org.apache.logging.log4j.core.appender.FileAppender$Builder.build(FileAppender.java:96)
at org.apache.logging.log4j.core.appender.FileAppender$Builder.build(FileAppender.java:52)
at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.build(PluginBuilder.java:122)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createPluginObject(AbstractConfiguration.java:1120)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:1045)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:1037)
at org.apache.logging.log4j.core.config.AbstractConfiguration.doConfigure(AbstractConfiguration.java:651)
at org.apache.logging.log4j.core.config.AbstractConfiguration.initialize(AbstractConfiguration.java:247)
at org.apache.logging.log4j.core.config.AbstractConfiguration.start(AbstractConfiguration.java:293)
at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:626)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:699)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:716)
at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:270)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:245)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:47)
at org.apache.logging.log4j.LogManager.getContext(LogManager.java:176)
at org.apache.logging.slf4j.Log4jLoggerFactory.getContext(Log4jLoggerFactory.java:54)
at org.apache.logging.log4j.spi.AbstractLoggerAdapter.getLogger(AbstractLoggerAdapter.java:47)
at org.apache.logging.slf4j.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:33)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:358)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:383)
at org.odhsi.utils.cpt.Application.(Application.java:17)
2024-05-02 02:59:05,237 main ERROR Could not create plugin of type class org.apache.logging.log4j.core.appender.FileAppender for element File: java.lang.IllegalStateException: ManagerFactory [org.apache.logging.log4j.core.appender.FileManager$FileManagerFactory@942a29c] unable to create manager for [logs/logfile.log] with data [org.apache.logging.log4j.core.appender.FileManager$FactoryData@1ed6388a] java.lang.IllegalStateException: ManagerFactory [org.apache.logging.log4j.core.appender.FileManager$FileManagerFactory@942a29c] unable to create manager for [logs/logfile.log] with data [org.apache.logging.log4j.core.appender.FileManager$FactoryData@1ed6388a]
at org.apache.logging.log4j.core.appender.AbstractManager.getManager(AbstractManager.java:116)
at org.apache.logging.log4j.core.appender.OutputStreamManager.getManager(OutputStreamManager.java:100)
at org.apache.logging.log4j.core.appender.FileManager.getFileManager(FileManager.java:182)
at org.apache.logging.log4j.core.appender.FileAppender$Builder.build(FileAppender.java:96)
at org.apache.logging.log4j.core.appender.FileAppender$Builder.build(FileAppender.java:52)
at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.build(PluginBuilder.java:122)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createPluginObject(AbstractConfiguration.java:1120)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:1045)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:1037)
at org.apache.logging.log4j.core.config.AbstractConfiguration.doConfigure(AbstractConfiguration.java:651)
at org.apache.logging.log4j.core.config.AbstractConfiguration.initialize(AbstractConfiguration.java:247)
at org.apache.logging.log4j.core.config.AbstractConfiguration.start(AbstractConfiguration.java:293)
at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:626)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:699)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:716)
at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:270)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:245)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:47)
at org.apache.logging.log4j.LogManager.getContext(LogManager.java:176)
at org.apache.logging.slf4j.Log4jLoggerFactory.getContext(Log4jLoggerFactory.java:54)
at org.apache.logging.log4j.spi.AbstractLoggerAdapter.getLogger(AbstractLoggerAdapter.java:47)
at org.apache.logging.slf4j.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:33)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:358)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:383)
at org.odhsi.utils.cpt.Application.(Application.java:17)
2024-05-02 02:59:05,244 main ERROR Unable to invoke factory method in class org.apache.logging.log4j.core.appender.FileAppender for element File: java.lang.IllegalStateException: No factory method found for class org.apache.logging.log4j.core.appender.FileAppender java.lang.IllegalStateException: No factory method found for class org.apache.logging.log4j.core.appender.FileAppender
at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.findFactoryMethod(PluginBuilder.java:236)
at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.build(PluginBuilder.java:134)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createPluginObject(AbstractConfiguration.java:1120)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:1045)
at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:1037)
at org.apache.logging.log4j.core.config.AbstractConfiguration.doConfigure(AbstractConfiguration.java:651)
at org.apache.logging.log4j.core.config.AbstractConfiguration.initialize(AbstractConfiguration.java:247)
at org.apache.logging.log4j.core.config.AbstractConfiguration.start(AbstractConfiguration.java:293)
at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:626)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:699)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:716)
at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:270)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:245)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:47)
at org.apache.logging.log4j.LogManager.getContext(LogManager.java:176)
at org.apache.logging.slf4j.Log4jLoggerFactory.getContext(Log4jLoggerFactory.java:54)
at org.apache.logging.log4j.spi.AbstractLoggerAdapter.getLogger(AbstractLoggerAdapter.java:47)
at org.apache.logging.slf4j.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:33)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:358)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:383)
at org.odhsi.utils.cpt.Application.(Application.java:17)
2024-05-02 02:59:05,246 main ERROR Null object returned for File in Appenders.
2024-05-02 02:59:05,322 main ERROR Unable to locate appender “File_Appender” for logger config “root”
[INFO ] 2024-05-02 02:59:07.748 [main] ConceptService - Writing updated data to CONCEPT.csv
A couple other points:
-
When the error message says “logs/logfile.log” not found above, I know for a fact that the logs sub-directory is in the vocabulary directory and the logfile.log file is present.
-
After the error messages above, the program does go through updating the over 17K records, but then does not complete the task of appending to CONCEPT.csv
Any help would be much appreciated! Travis