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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

Hi,

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!

-Alice


(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?

image


(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


(Chris Knoll) #12

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


(alice) #13

My apologies for the late reply…thank you so much

Oh no…we did not create the results schema tables by using the /results/ddl service. After running the Achilles analysis, we already had results schema in our cdm database, containing 5 tables: results.ACHILLES_analysis, results.achilles_heel_results, results.achilles_results, results.achilles_results_derived, results.achilles_results_dist, and results.concept_hierarchy… We assumed they were the same

Some points for clarification

  1. The ddl at localhost:8080/WebAPI/ddl/results is in mssql dialect?
  2. in the script, ‘@results_schema’ to be replaced with ‘results’ ?
  3. what to replace ‘@results_database_schema’ —>?
  4. what to replace ‘@vocab_schema’ —>?
  5. Do we need run the section ‘Create hierarchy lookup table for the treemap hierarchies’ and ‘Populate the hierarchy lookup table per treemap’ as ‘concept_hierarchy’ table was generated in Achilles call.

I am very sorry, it appeared when I clicked on ‘cohort definitions’, but now when I clicked it, it is not showing the error anymore…

Thank you for your help


(Chris Knoll) #14

You’ll need to create the other tables using the ddl service.

It defaults to the mssql dialect, but you can use dialect=postgresql for postgresql. You can also add &schema=yourSchema and it will replace all @results_schema tokens with the value you provide, however you still need to manually replace @results_database_schema and @vocab_schema. This is a bug which will be addressed in a future release.

Replace it with the same value as your @results_schema.

Use the schema that contain your CDM tables.

No, if you already generated this as part of achilles, you don’t need to do it again here.


(alice) #15

@Chris_Knoll

Thank you for the advice. I have created the other tables using the ddl service.

Data sources and profiles section, and search seem to be working:

But I am not sure how to test if the rest of the sections (concept Sets, cohort Definitions, characterisations, cohort pathways, incidence rates, estimation, prediction) are correctly set up and would be grateful for advice on how to go about checking.

Further, I have some questions/issues which i encountered during set up

  1. Am using WebAPI 2.5.0 and Atlas 2.6.0. I did not use the latest version of WebAPI 2.6.0 due to a build error

  2. Under the Data Sources > Death, some of the charts are not showing

Lastly, I would like to share the list of tables I used in the cdm, results and webapi schema. Hope that this will help other users who are setting up Atlas too


(Chris Knoll) #16

You’ll need webAPI 2.6 to access the features like Chracterization and Pathways. You can run Atlas 2.5 against WebAPI 2.6 (WebAPI is backwards compatable) but atlas 2.6 will look for services in webAPI that will not be available. So you may consider downgrading your Atlas to 2.5, or if you can post the problems you had with the build on 2.6, we’d like to help you resolve those.


(alice) #17

Thank you, that’s very helpful

Here is the issue with the build on 2.6. I attache the settings.xml file too



I see… having issues with loading the characterizations, cohort pathways, estimation and predictions section. Could it be incompatibility issues too

cdm schema(database: cdm, schema: dbo)


results schema(database: cdm, schema: results)
image
webapi schema(database: OHDSI, schema: dbo)


(Chris Knoll) #18

Your tables look good (from a v2.5 perspective). When you upgrade to 2.6, you can pull the /ddl/results service again and you’ll find new tables to add/modify.

The maven error seems to indicate that the sourcecode you are compiling is not finding the ‘windowed criteria’ class in one of the dependent libraries. Interestingly I thought that class was introduced post 2.6 but I need to check with @pavgra.

I’ll refer him to this issue and get his perspective on this.

-Chris


(alice) #19

Okay, thank you.


(Pavel Grafkin) #20

@alicesaw, may I ask if you are trying to build latest master branch or the 2.6.0 release commit?


t