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OHDSI / WhiteRabbit

WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.
http://ohdsi.github.io/WhiteRabbit
Apache License 2.0
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While accesing mysql database from whiterabbit for scan getting the below Error #174

Open abhishekverma2601 opened 5 years ago

abhishekverma2601 commented 5 years ago

Error is cannot connect to db server , could not open a connection with DB server while connecting to mysql database using whiterabbit . Please help .From the windows command prompt i can connect to the mysql database using same credentials .

abhishekverma2601 commented 5 years ago

I have mysql database on my system and i am able to connect it using same credentials on the command prompt .Do i need to install any driver for the whiterabbit to connect to mysql database present in my system ?

MaximMoinat commented 5 years ago

Installation of the mysql driver should not be needed. It seems like the connection settings are wrong. Could you share what command and settings you are using to connect with the command prompt and what you are entering into WR?

abhishekverma2601 commented 5 years ago

`Please find the doc file containing the command entered at command prompt and the whiterabbit gui attached .Please let me know if you have any other questions ,thanks .

whiterabbit_issue.docx `

abhishekverma2601 commented 5 years ago

Can you please confirm how white rabbit executable knows the where the MYSQL binary and how it will use the which driver to use to connect to MySQLDB? As with other connect tools like SQL workbench we do provide the drivers but there is no options here .

MaximMoinat commented 5 years ago

The MySql driver is included. See repo/mysql in the downloaded zip, it should include a file like mysql-connector-java-5.1.37-bin.jar.

abhishekverma2601 commented 5 years ago

My MySQL version is 8.0.17 MySQL Community Server and the connector version is 5.1.3.7 for the whiterabbit , I have copied the MySQL java connector from the repo to the MySQL program files but still I have the same connection issue .

abhishekverma2601 commented 5 years ago

MaximMoinat commented 5 years ago

I was not able to replicate the problem on MariaDB MySQL, version 10.0.17. Worked fine for me. The MySql connector version should not matter.

I will test with Community Server 8.0.17 as well in the coming week.

abhishekverma2601 commented 5 years ago

Thanks Maxim for response . Also do I need to import all the concept related table to our mysql CDM database (currently no vocalbulary is created ), is any utility available for this .I tries importing MySQL using CSV but it is failing for some records due to data truncation .

MaximMoinat commented 5 years ago

This is not needed for WhiteRabbit. For further help setting up your OMOP CDM database, please refer to the Common Data Model repo.