Atlas setup

[Gupr1989]

Hi Team,

I have followed the below steps. with few changes to pom.xml I was able to generate WebAPI.war file.

https://github.com/OHDSI/WebAPI/wiki/WebAPI-Installation-Guide

when I try to deploy the war file in tomcat, server crashes without error.

Can you please help me with this.

[anthonysena]

@Gupr1989 - can you obtain any information from the tomcat log files (in your CATALINA_HOME/logs directory)?

[Gupr1989]

@anthonysena

Thanks for response, I got Atlas and Achilles running now with few data. Can you please help me get the sample data that you are using in demo Atlas. https://atlas-demo.ohdsi.org/#/datasources/SYNPUF1K/drugera.

I have downloaded the data from the below link, achilles>data>SAMPLE json files has no data for drugera and data in many other reports are missing after running Achilles exportToJson. http://www.ltscomputingllc.com/downloads/

[anthonysena]

@Gupr1989 - a few thoughts: if you have the SYNPUF data downloaded and ready, you may be able to build out the derived tables (i.e. drug_era) using the information on https://ohdsi.github.io/CommonDataModel/cdm53.html#Standardized_Derived_Elements. There are SQL scripts you can run such as https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras that will build the drug eras for you. You may then need to re-run Achilles to have that information for the ATLAS data sources.

Another option is to try and use the data from the OHDSI on AWS project:

https://github.com/OHDSI/OHDSIonAWS/tree/master/datasources

I have not tried to use this myself but I know that those scripts are used when deploying the OHDSI stack on AWS.

[Gupr1989]

@anthonysena I am on CDM v5.4 Got the DDL from here - https://github.com/OHDSI/CommonDataModel/tree/main/inst/ddl/5.4/postgresql and using the below data https://caruscloud.uniklinikum-dresden.de/index.php/s/Qog8B5WCTHFHmjW/download

with the above data I can just see person , data density and observation period in both Achilles and Atlas I see all the csv data that I got online does not have data for concept table, is it something we have to create in atlas ? I am looking to see records in drug era, and add new concepts in atlas (I created sample records in concepts tables and added all constraints, no luck)

I have gone through the link - https://ohdsi.github.io/CommonDataModel/sqlScripts.html#drug_eras Tried executing sql query in my postgres, sql does not return any record because of where clause concept.vocabulary_id = 'RxNorm', and concept_class_id = 'Ingredient'

when I try to copy --https://github.com/OHDSI/OHDSIonAWS/blob/master/datasources/CMSDESynPUF1kpostgres.sql --COPY OMOP.CONCEPT FROM '/tmp/tempdata/CONCEPT.csv' WITH DELIMITER E'\t' CSV HEADER QUOTE E'\b'; I get error - No such file or directory.

It will be helpful if I get data in csv for all the tables including concept as we see in atlas demo.

[anthonysena]

with the above data I can just see person , data density and observation period in both Achilles and Atlas I see all the csv data that I got online does not have data for concept table, is it something we have to create in atlas ? I am looking to see records in drug era, and add new concepts in atlas (I created sample records in concepts tables and added all constraints, no luck)

Looking at the data you shared, it lacks the vocabulary tables which is by design; you must obtain these files from Athena. If you include the vocabulary tables from Athena in conjunction with the tables you downloaded, you should have a fully formed CDM. I'd also recommend that you re-create the results schema tables per https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration#results-schema-setup since you'll need to create the concept_hierarchy table which is built from the vocabulary tables.

On a related note, you may also want to explore the OHDSI ETL-Synthea project: https://github.com/OHDSI/ETL-Synthea which is a great resource for creating synthetic data in the CDM format.

Hope this helps!

[chrisknoll]

Will close this issue since it's related to setup and configuration. Feel free to continue here, but the forums are a great resource for asking these questions.