Connecting Olympus to Oracle

Emanuel_Villa · August 28, 2015, 2:28pm

Dear all, I am trying to connect Olympus to my Oracle OMOP CDM V5, first I got an error about not being able to create a schema mentioning the “cohort_definition” table, since I had it blank I decided to drop it and let the script re-run to see if it will re-create it on its own.

I think it worked, because now I have another error:
“WebAPI was not able to start up successfully, please check your configuration. (org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘flyway’ defined in class path resource [org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration$FlywayConfiguration.class]: Invocation of init method failed; nested exception is org.flywaydb.core.api.FlywayException: Schema “OMOP” contains a failed migration to version 1.0.0.3 !)”

Any ideas?

Thanks in advance.

Emanuel_Villa · August 28, 2015, 2:31pm

Forgot to ask about this:

The configuration asks for 3 schemas, one for the CDM, another for results, and one more for cohort database, in all these 3 I have the same, can that be the problem?

Do I need different schemas for each thing?

Thanks

alfranke · August 28, 2015, 3:18pm

I don’t believe you need to have separate schemas. With that said, Flyway will fail if an object already exists that it is supposed to manage (cohort_definition_sequence, cohort_definition, cohort_definition_details). Looks like the Flyway migration failed at 1.0.0.3. You should have more detail in the log file (e.g. what part of the script failed, etc.). Can you include a more complete log?

github.com

OHDSI/WebAPI/blob/master/src/main/resources/db/migration/oracle/V1.0.0.3__cohort_definition_persistence.sql

CREATE TABLE ${ohdsiSchema}.cohort_definition(
	id Number(10) NOT NULL ,
	name Varchar2(255) NOT NULL,
	description Varchar2(1000) NULL,
	expression_type Varchar2(50) NULL,
	created_by Varchar2(255) NULL,
	created_date Timestamp(3) NULL,
	modified_by Varchar2(255) NULL,
	modified_date Timestamp(3) NULL,
	CONSTRAINT PK_cohort_definition PRIMARY KEY (id) 
);

CREATE TABLE ${ohdsiSchema}.cohort_definition_details(
	id Number(10),
	expression CLOB NOT NULL,
	CONSTRAINT PK_cohort_def_details PRIMARY KEY (id),
	CONSTRAINT FK_cdd_cd 
          FOREIGN KEY (id)
          REFERENCES cohort_definition(id)
);

Emanuel_Villa · August 28, 2015, 3:46pm

Thanks for you prompt reply,

I am running in a mac, only “log” I can see comes from the console out, unless you point me in the right direction to where to find it.

About more databases, the cohort_definition table you sent doesn’t look at all like the cohort_definition on the model, I wonder if that will create a problem:

    CREATE TABLE cohort_definition (
  cohort_definition_id				INTEGER			NOT NULL,
  cohort_definition_name			VARCHAR(255)	NOT NULL,
  cohort_definition_description		CLOB	NULL,
  definition_type_concept_id		INTEGER			NOT NULL,
  cohort_definition_syntax			CLOB	NULL,
  subject_concept_id				INTEGER			NOT NULL,
  cohort_initiation_date			DATE			NULL
);

Here is the last lines from the console:

WebAPI was not able to start up successfully, please check your configuration. (org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'flyway' defined in class path resource [org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration$FlywayConfiguration.class]: Invocation of init method failed; nested exception is org.flywaydb.core.api.FlywayException: Schema "OMOP" contains a failed migration to version 1.0.0.3 !)

Emanuel_Villa · August 28, 2015, 3:47pm

Ok…

I just quickly made a local PostgreSQL server in my machine and created different schemas for each thing:
OMOPCDM, RESULTS and COHORT

And it worked, however, I don’t have any data in there yet, I am going to give it a try and post later.

Thanks.

alfranke · August 28, 2015, 3:58pm

I’ll defer to @Chris_Knoll & @Frank regarding the cohort_definition model and naming. The object managed by Flyway (“results or OHDSI schema”) is intended to be different than the model. Not sure why it’s named the same.

The last lines of your log are not enough. The error would be indicated above these lines. You could increase the buffer of the console/terminal, or “pipe” the log output to a file (e.g. java > Olympus.log) and then tail it in another terminal OR you could launch Olympus using nohup and that should create a nohup.out file you can review (on Mac it appears to be ‘screen’ instead of nohup). You then would have to kill the process).