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Some errors using Atlas after installation

(alice) #1

I successfully installed atlas but the features apart from data sources and search don’t seem to be working. I’m wondering if there was anything that went wrong with the installation or was it the data used. Please advise
Below are some of the issues

when typing http://localhost:8080/Atlas

(alice) #2

when click on ‘cohort definitions’

(alice) #3

When click on ‘new concept set’

(alice) #4

when try to find person_id 10 under ‘profiles’

(alice) #5

Please advise, thank you

(alice) #6

I just want to add that regarding the 500 errors, the messages show the DaimonType (CDM) not found in source. For example:

{"methodName":"run","fileName":"Thread.java","lineNumber":748,"className":"java.lang.Thread","nativeMethod":false}],"localizedMessage":"DaimonType (CDM) not found in Source","message":"DaimonType (CDM) not found in Source","suppressed":[]},"headers":{"id":"1e633487-d2f0-7246-2b05-57c085bf7439","timestamp":1541553533321}}

Have looked at various discussions with the same problems, advice is check the records in the Source and Source Daimon tables to make sure that the database and schemas are correct. But have checked many times and still can’t find the cause of the error

webapi schema is called ‘dbo’ and stored under database ‘ohdsi’
cdm schema is called ‘dbo’ and stored under database ‘CDM’
results schema is called ‘results’ and stored under database ‘results’

You can see the insert statements I wrote here, it is pointing to the correct schemas:

Also, there are other messages, e.g. bad SQL grammar when loading profile,

[]},“localizedMessage”:“PreparedStatementCallback; bad SQL grammar [select subject_id, cohort_definition_id, cohort_start_date, cohort_end_date\nfrom results.cohort\nwhere subject_id = ?\n]; nested exception is com.microsoft.sqlserver.jdbc.SQLServerException: Invalid object name ‘results.cohort’.”,“suppressed”:[]},“headers”:{“id”:“6349d8f7-5134-46da-233d-56f04d59601a”,“timestamp”:1541554585095}}

Is this an issue with the configuration, or are we missing some tables/data from our cdm/results/webapi schemas?

(alice) #7


We are still facing the above issue but so close to getting it to work. Any advice would be another step to success. Please help, thanks and very much appreciated!


(Taha Abdul-Basser) #8

Hi @alicesaw. Your Default Vocabulary data source may be misconfigured. Try choosing the My CDM vocbulary as the default, clearing the cache and reloading.

(alice) #9

Thank you @t_abdul_basser. Nope, still does not work.

(alice) #10

@t_abdul_basser can view data sources, do vocabulary search with the current configuration, but the rest have error. Is this information sufficient help you to narrow down the source of the error?


(Chris Knoll) #11

It does look like your source with source_id = 1 has 3 daimons set up on it, 0,1,2 which should correspond to vocab, cdm, results. So, it’s confusing that it says the CDM daimon type is not found in the source. Can you please expand the ‘stack trace’ property, it says the exception ended in ‘getTableQualifier’ but we’d like to know what was the call that led into that (so expand the stackTrace).

In addition, if you can tell us the URL that was requested that resulted in this error, that would also help.


(Chris Knoll) #12

Have you created the results schema tables by using the /results/ddl service (/WebAPI/results/ddl)?