Issue analyzing text after successful setup about ctakes-rest-service

[jbham]

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:

1. 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: )

2. 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!

[MatthewVita]

@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?

[lrog]

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.

[ileadall42]

@legendactivated I also meet the same problem as you,so i just ignore the MissingResourceException?

[MatthewVita]

@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.