@lee_evans
Thank you very much for your time to guide me during the platform’s installation process. Ιt is highly appreciated.
I have installed postgresql in my virtual machine hosting the docker image and created an empty database named OHDSI-CDMV5. I have also created a user ohdsi_stack_user with password ***, I have checked that the user has the right privileges to the specific database using phppgadmin and pgadmin. I have also created a schema called cdm under OHDSI-CDMV5 database where I created the CDMV5 tables using the respective DDL script. While I have not yet imported the CDMv5 vocabulary tables from OHDSI Athena web site and have not yet imported the 1k simulated patient CDM V5 dataset as you suggested (these need more time than I expected), I suppose that this should not be the problem since all the databases are there. I have also tried creating the ohdsi schema in the OHDSI-CDMV5 database manually. Still, I get the same error using ATLAS (“unable to connect to an instance of the webapi. please contact your administrator to resolve this issue.”) and I cannot see the expected table ohdsi.source_daimon.
Please note that when I start the docker container I get no error messages.
My docker-compose.yml is (interesting parts with bold)
version: ‘2’
services:
broadsea-methods-library:
image: ohdsi/broadsea-methodslibrary
ports:
- “8787:8787”
- “6311:6311”
broadsea-webtools:
image: ohdsi/broadsea-webtools
ports:
- “8080:8080”
volumes:
- .:/tmp/drivers/:ro
- .:/tmp/achilles-data-reports/:ro
environment:
- WEBAPI_URL=http://docker_IP:8080
- env=webapi-postgresql
- datasource.driverClassName=org.postgresql.Driver
- datasource.url=jdbc:postgresql://localhost/OHDSI-CDMV5
- datasource.cdm.schema=cdm
- datasource.ohdsi.schema=ohdsi
- datasource.username=ohdsi_stack_user
- datasource.password=****
- spring.jpa.properties.hibernate.default_schema=ohdsi
- spring.batch.repository.tableprefix=ohdsi.BATCH_
- flyway.datasource.driverClassName=org.postgresql.Driver
- flyway.datasource.url=jdbc:postgresql://localhost:5432/OHDSI-CDMV5
- flyway.schemas=ohdsi
- flyway.placeholders.ohdsiSchema=ohdsi
- flyway.datasource.username=ohdsi_stack_user
- flyway.datasource.password=***
- flyway.locations=classpath:db/migration/postgresql
I also thought that I should check atlas web application log files to search for errors that could provide for a hint.I tried searching in the atlas github repository for a logging mechanism but I can only find logging to the browser’s javascript console. In my browser’s console, I can see that the ATLAS application cannot contact the web api, as the error message suggests (console writes “http://docker_IP:8080/WebAPI/source/sources net::ERR_ADDRESS_UNREACHABLE”). Therefore, I am also wondering how can I be sure that I use the correct docker_IP. I have tested with “localhost” and the IPs shown using ifconfig (my server is ubuntu 16.04 and therefore there is nο docker toolbox available), with no luck.
Summarizing my questions:
- Do you see anything suspicious in my yml configuration? Do I miss anything?
- Is there any kind of log that I could check?
- Can I somehow confirm that I use the right IP address for the web API?
Thank you in advance,
Pantelis Natsiavas
