Closed stkleinbaum closed 5 years ago
Are you still having this issue? We have not been able to reproduce it. Will need all of your configuration data to assess.
I am getting a similar error, but since nobody added to this thread, I do not know how to proceed:
Error creating bean with name 'referenceCCDAValidationController': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: org.sitenv.referenceccda.services.ReferenceCCDAValidationService org.sitenv.referenceccda.controllers.ReferenceCCDAValidationController.referenceCcdaValidationService; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException:
Error creating bean with name 'referenceCCDAValidationService' defined in file [/opt/tomcat/webapps/referenceccdaservice/WEB-INF/classes/org/sitenv/referenceccda/services/ReferenceCCDAValidationService.class]: Unsatisfied dependency expressed through constructor argument with index 1 of type [org.sitenv.referenceccda.validators.vocabulary.VocabularyCCDAValidator]: :
Error creating bean with name 'vocabularyCCDAValidator' defined in file [/opt/tomcat/webapps/referenceccdaservice/WEB-INF/classes/org/sitenv/referenceccda/validators/vocabulary/VocabularyCCDAValidator.class]: Unsatisfied dependency expressed through constructor argument with index 0 of type [org.sitenv.vocabularies.validation.services.VocabularyValidationService]: :
Error creating bean with name 'vocabularyValidationService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException:
Error creating bean with name 'vocabularyValidationConfigurations' defined in org.sitenv.vocabularies.configuration.CodeValidatorApiConfiguration: Unsatisfied dependency expressed through constructor argument with index 0 of type [org.sitenv.vocabularies.configuration.ValidationConfigurationLoader]: :
Error creating bean with name 'validationConfigurationLoader' defined in org.sitenv.vocabularies.configuration.CodeValidatorApiConfiguration: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.sitenv.vocabularies.configuration.ValidationConfigurationLoader]: Factory method 'validationConfigurationLoader' threw exception; nested exception is java.lang.NoClassDefFound
Error: javax/xml/bind/JAXBException; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'validationConfigurationLoader' defined in org.sitenv.vocabularies.configuration.CodeValidatorApiConfiguration: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.sitenv.vocabularies.configuration.ValidationConfigurationLoader]: Factory method 'validationConfigurationLoader' threw exception; nested exception is java.lang.NoClassDefFound
Error: javax/xml/bind/JAXBException; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'vocabularyValidationService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException:
Error creating bean with name 'vocabularyValidationConfigurations' defined in org.sitenv.vocabularies.configuration.CodeValidatorApiConfiguration: Unsatisfied dependency expressed through constructor argument with index 0 of type [org.sitenv.vocabularies.configuration.ValidationConfigurationLoader]: :
Error creating bean with name 'validationConfigurationLoader' defined in org.sitenv.vocabularies.configuration.CodeValidatorApiConfiguration: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.sitenv.vocabularies.configuration.ValidationConfigurationLoader]: Factory method 'validationConfigurationLoader' threw exception; nested exception is java.lang.NoClassDefFound
Error: javax/xml/bind/JAXBException; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'validationConfigurationLoader' defined in org.sitenv.vocabularies.configuration.CodeValidatorApiConfiguration: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.sitenv.vocabularies.configuration.ValidationConfigurationLoader]: Factory method 'validationConfigurationLoader' threw exception; nested exception is java.lang.NoClassDefFound
Error: javax/xml/bind/JAXBException; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException:
Error creating bean with name 'vocabularyCCDAValidator' defined in file [/opt/tomcat/webapps/referenceccdaservice/WEB-INF/classes/org/sitenv/referenceccda/validators/vocabulary/VocabularyCCDAValidator.class]: Unsatisfied dependency expressed through constructor argument with index 0 of type [org.sitenv.vocabularies.validation.services.VocabularyValidationService]: :
Error creating bean with name 'vocabularyValidationService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException:
PLEASE NOTE:
Everything is installed per the instructions supplied via this GitHub project, but:
1) I am a systems engineer. I am not a Java developer. So, these Java related errors are completely foreign to me.
2) As it relates to this project, I have NO idea which value sets to download, as the value set names mean nothing to me. Any assistance in identifying value sets to be downloaded, would also be greatly appreciated.
Do you have the code-validator dependency/did you also follow the instructions here https://github.com/siteadmin/code-validator-api and here https://github.com/siteadmin/code-validator-api/tree/master/codevalidator-api/docs ?
@drbgfc I just encountered something similar.
Error occurred during deployment: Exception while loading the app : java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'vocabularyCCDAValidator' defined in file [/opt/glassfish4/glassfish/domains/domain1/applications/referenceccdaservice/WEB-INF/classes/org/sitenv/referenceccda/validators/vocabulary/VocabularyCCDAValidator.class]: Unsatisfied dependency expressed through constructor argument with index 0 of type [org.sitenv.vocabularies.validation.services.VocabularyValidationService]: : Error creating bean with name 'vocabularyValidationService': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'vocabularyValidationConfigurations' defined in org.sitenv.vocabularies.configuration.CodeValidatorApiConfiguration: Unsatisfied dependenc .... msg.seeServerLog
java version "1.8.0_181" Java(TM) SE Runtime Environment (build 1.8.0_181-b13) Java HotSpot(TM) 64-Bit Server VM (build 25.181-b13, mixed mode)
Deploying on Glassfish 4.12
Ubuntu 18
@forgotpw1 what version are you using of the ref val? Did you update recently? Was it successful ever before for you with the exact same setup (machine/server/etc.)? If so, what version? Thanks.
@drbgfc Thank you for your quick reply. This is the first crack on running it.
I am using the most recent release
It might be missing the configuration with https://github.com/siteadmin/code-validator-api
Looking into how to include these extra params and code sets with glassfish.
@forgotpw1 No Problem. Unfortunately we've never run it on anything other than Tomcat so I can't really help in that regard. Maybe you can get it running on Tomcat first and then you can try configuring on glassfish knowing there are no issues unrelated to glassfish itself.
@drbgfc Thank you for bringing that up. Yes. I am going to try on tomcat8
@drbgfc I gave this a try on tomcat 8 and after some tinkering get the following output... referenceccdaservice.2018-08-03.log
Thanks for posting the log. I will try to reproduce locally so that I can address the issue.
I have been trying to repro this for the last couple of hours with no luck. The latest version of the war works for me both locally and works in the SITE test server as well as the SITE prod server. I tried different value sets as well locally. I will keep looking into it but maybe one of you can try the prior WAR to see if it has anything to do with the version? Thanks.
*Did either of you try tomcat 7?
@drbgfc Thank you for looking into the war. It could be the contents of the code_repository and valueset_repository folders we have to set up differently. The directions aren't exactly clear what go in there. After digging around it seems like the valueset_repository should be XLS files (?), and the codeset_repository? no idea. this file? https://raw.githubusercontent.com/siteadmin/reference-ccda-validator/develop/configuration/codesystems.txt
Is there a minimum set of code_repository data and valueset data we can use so the app loads that could be included in the repository in the correct location
I will try a earlier version of the war and reading the source more to see why this fails
I have seen your responses in google groups. I seems like the explanation of the dependency of the code-validator-api (https://github.com/siteadmin/code-validator-api) on might need a better example.
Should we be moving the source of https://github.com/siteadmin/code-validator-api someplace?
No problem.
The valueset_repository should be '.xlsx' files. They used to be .xls files but we have since updated to support the '.xlsx' and the newer format must be used. Sorry for any confusion. These formats are standardized to the VSAC formatting. Any value sets which are not in VSAC we hand-created and provided in the same format. A user can do the same with any set they want to support.
The code_repository should contain folders such as CDT, CPT, LOINC, SNOMED-CT, etc. Within each folder the file types can vary from .xlsx, to .csv, to .txt. The formats can vary as well. The reason for this is that there is no standard for these. Each licensee has their own format and there is little to no coordination between code systems. In addition, there is no standard for even the same code system as when they are updated they often change the formatting, if only slightly. But it can be a breaking change. We can't control how they provide the data, and we can't supply the data in a controlled manner since it is licensed. This makes it it unfortuante and hard to manage. I don't think there is a minimum set of code systems that must be supplied in order for the application to load. For testing purposes, I would start with 1, such as SNOMED-CT.
To solve the issues I would need to take a close look at your file structure and at a minimum your referenceccdaservice.xml file and its location.
The code-validator dependency is injected in the WAR so one should not need to handle that on their own. I'm sure we could improve the documentation. We are currently working on updating all of the value sets and thus related documentation. If you look in https://github.com/siteadmin/code-validator-api/tree/master/codevalidator-api/docs in the develop branch, some of that work has already been done, and will be merged to master end of month.
Also - This information will help resolve if you are still having issues: --Log files: ---What you see on startup and the log for that date in tomcat/logs/ e.g. referenceccdaservice.2018-08-XX.log --File structure and configuration: ---file structure of value set repo and code repo ---referenceccdaservice.xml (located tomcat/conf/Catalina/localhost) ---Is ccdaReferenceValidatorConfig.xml located in the path configured in referenceccdaservice.xml?
localhost.2018-08-10.log catalina.2018-08-10.log referenceccdaservice.2018-08-10.log I have configured but getting error attached is log file.
Below is directory configuration:
There are many, many, many reasons the error "Error creating bean with name 'vocabularyCCDAValidator'" can be triggered. As such, @rabindra0388 can you create a new issue if you are still having the issue? Closing this for now to keep th issues separated. Sorry for the inconvenience.
Hi,
I followed the readme to run referenceccdaservice.war locally on tomcat 8 but it fails with an exception
How can I fix this?
Best