Comments (5)
Never mind above error. It was a mistake on my end. I am using mysql 8.0.12 and it didn't allow to have root as a password. So, I chose some other password, but, forgot to update it in custom dictionary. Adding the credentials fixed above error.
After I updated the custom dictionary, I ran into multiple other issues all related to mysql version in pom.xml for ctakes-web-rest and ctakes-codebase-area.
Errors were:
-
Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup" failed. (Descriptor: )
-
java.sql.SQLException: Unable to load authentication plugin 'caching_sha2_password'.
I updated mysql version in both pom.xml to the one installed on my machine. But, I got another error:
com.mysql.cj.exceptions.InvalidConnectionAttributeException: The server time zone value 'PDT' is unrecognized or represents more than one time zone. You must configure either the server or JDBC driver (via the serverTimezone configuration property) to use a more specifc time zone value if you want to utilize time zone support.
which I fixed by adding "&serverTimezone=UTC" to the jdbc url in custom dictionary as below:
jdbc:mysql://127.0.0.1:3306/umls?useUnicode=true&characterEncoding=utf8&useSSL=false&serverTimezone=UTC
Hopefully this saves someone else from the headache of going through and figuring out what went wrong :)
Thanks!
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@legendactivated Glad you found help with the new README. Also glad that your problem was resolved.
@gandhirajan Should we add the &serverTimezone=UTC
by default?
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Thanks @legendactivated for your comment. I stumbled into the same problem when running MySQL 8.0.12. I tried the workarounds you mentioned, but still stumbled into more errors (such as: https://stackoverflow.com/questions/49984267/java-sql-sqlexception-unknown-system-variable-query-cache-size ).
Finally, if it would help anyone, in my case, the quickest solution was just to downgrade the MySQL to 5.7.24 (5.7 as specified in the README) and everything worked well without any modifications.
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@legendactivated I also meet the same problem as you,so i just ignore the MissingResourceException
?
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@lrog Assuming you're on Ubuntu 18.04, your switch from MySQL 8.0.12 to 5.7.24 should be fine because the default Ubuntu MySQL dist is very close: 5.7.27. Let us know if it's still not right, of course.
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Related Issues (20)
- JdbcRareWordDictionary Error HOT 8
- Question: Where to run custom dictionary creator tool after getting ctakes rest service up and running? HOT 8
- When running in web server, does it use "resources" folder from "ctakes-rest-service/ctakes-web-rest/src/main/" or from the SVN branch we download it from? HOT 2
- Question: Running Ctakes-rest-service on top of an existing ctakes user installation on windows HOT 1
- Another question HOT 2
- Inconsistent working of API HOT 2
- index.css:1 Failed to load resource: the server responded with a status of 404 () HOT 1
- Compilation error: ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java:[59,5] error: cannot find symbol HOT 4
- Question: How to update snowmed database?
- Exception: The server time zone value X is unrecognized
- Limited Results with Various Inputs HOT 1
- Could not resolve dependencies for project HOT 2
- If I just clone the ctakes-rest-service ignore the code-base-step HOT 1
- Dosage strength is not returned in the response HOT 2
- Project Status? HOT 3
- Having a hard time tracking down the source of this error / Building the Dockerized Solution HOT 4
- When hitting the running service, get sql error HOT 2
- Performance issues
- Guide to using a custom dictionary with this service?
- ctakes server picking terms which are not in custom dictionary
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