Source_source_daimon.sql configuration

Implementers
1

Hi all,

I am trying to install the Broadsea project according to https://github.com/OHDSI/Broadsea

I configured the PostgreSQL DB according to https://github.com/OHDSI/WebAPI/wiki/PostgreSQL-Installation-Guide

If I configured the DB exactly like that what should the “source_source_daimon.sql” look like? I configured it as:

-- remove any previously added database connection configuration data
truncate webapi.source;
truncate webapi.source_daimon;

-- OHDSI CDM source
INSERT INTO webapi.source( source_id, source_name, source_key, source_connection, source_dial$
 VALUES (1, 'OHDSI CDM V5 Database', 'OHDSI-CDMV5',
--  'jdbc:postgresql://192.168.99.100:5432/secret-database-name?user=secret-user-name&passwor$
  'jdbc:postgresql://localhost:5432/OHDSI?user=ohdsi_app_user&password=app1', 'postgresql');


-- CDM daimon
INSERT INTO webapi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, $

-- VOCABULARY daimon
INSERT INTO webapi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, $

-- RESULTS daimon
INSERT INTO webapi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, $

-- EVIDENCE daimon
INSERT INTO webapi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, $

but I get the following errors:

$ psql -f source_source_daimon.sql 
psql:postgresql/source_source_daimon.sql:2: ERROR:  relation "webapi.source" does not exist
psql:postgresql/source_source_daimon.sql:3: ERROR:  relation "webapi.source_daimon" does not exist
psql:postgresql/source_source_daimon.sql:9: ERROR:  relation "webapi.source" does not exist
LINE 1: INSERT INTO webapi.source( source_id, source_name, source_ke...
                    ^
psql:postgresql/source_source_daimon.sql:13: ERROR:  relation "webapi.source_daimon" does not exist
LINE 1: INSERT INTO webapi.source_daimon( source_daimon_id, source_i...
                    ^
psql:postgresql/source_source_daimon.sql:16: ERROR:  relation "webapi.source_daimon" does not exist
LINE 1: INSERT INTO webapi.source_daimon( source_daimon_id, source_i...
                    ^
psql:postgresql/source_source_daimon.sql:19: ERROR:  relation "webapi.source_daimon" does not exist
LINE 1: INSERT INTO webapi.source_daimon( source_daimon_id, source_i...
                    ^
psql:postgresql/source_source_daimon.sql:22: ERROR:  relation "webapi.source_daimon" does not exist
LINE 1: INSERT INTO webapi.source_daimon( source_daimon_id, source_i...

Any help would be greatly appreciated!

2

I am still stuck on this problem. Are there any suggestions?

Thank you.

3

There are 2 things I ran into recently that may help.

  1. Make sure you’ve run the WebAPI tomcat deployment. The source and source_daimon tables aren’t created until the first time the WebAPI code is launched. See “Installing WebAPI” section of https://github.com/OHDSI/WebAPI/wiki/WebAPI-Installation-Guide if you haven’t done that.

  2. When I followed the PostgresSQL-Installation-Guide it had me create a separate database called OHDSI. I found psql defaulted to a different database so I had to explicitly include the database name. For example, try

psql -f source_source_daimon.sql OHDSI

Hope one of these helps!

4

Andrew thanks a lot!

I have completed the steps that you mentioned. However, I am still getting some error when loading Atlas (see screenshot).
Any idea how this could be solved? Thanks again.

atlas
atlas1081×622 25.8 KB

5

The error seems to be within the WebAPI service. When I try to make a HTTP request from within the same container to this URL shown in the image above sometimes I get an 500 error and sometimes the request hangs (no response).

Is there some configuration missing from the WebAPI itself, or how could this error be solved?

6

I am still stuck on this problem. Are there any suggestions?

Thank you.

7

Any help would be appreciated. Thanks!