#Story: Reports in Atlas Data Sources for MU CDM data

[shossain-mizzou]

• [x] https://github.com/Missouri-BMI/OMOP_ON_P_CDM/issues/30
• [x] #38
• [ ] Error with Visit report
• [ ] Error with Condition report
• [ ] Error with Procedure report
• [ ] Error with Measurement report
• [ ] Error with Death report
• [ ] Error with Observation report

[shossain-mizzou]

@vasanthi014, would you look into that error? I re-run the Achilles and found the error

errorReportSql.txt

[shossain-mizzou]

@vasanthi014 I have shared all the missing and not populated tables

table missing:

all_visits assign_all_visit_ids final_visit_ids cohort source_to_standard_vocab_map source_to_source_vocab_map

not populated: cost DEVICE_EXPOSURE DRUG_ERA OBSERVATION (all null) PROVIDER (all null) VISIT_DETAIL

[shossain-mizzou]

I dont see any errors in achilles or in webapi. We atleast need to populate the observation, provider, and visit_detail table in SNOWFLAKE. Other reports should work if we have the data.

[shossain-mizzou]

@vasanthi014, Could you share the source code for converting the PCORNET to OMOP CDM?

[vasanthi014]

https://github.com/Missouri-BMI/OMOP_ON_P_CDM/tree/pcornet-to-omop-cdm

[vasanthi014]

Fyi, this is what we using as a base for our OMOP conversion https://github.com/National-COVID-Cohort-Collaborative/Data-Ingestion-and-Harmonization

[shossain-mizzou]

closing the ticket. We are now able to see all the analysis from the Atlast

[shossain-mizzou]

https://forums.ohdsi.org/t/how-to-force-the-update-of-reports-in-atlas/14282

[shossain-mizzou]

Comment from the post :

If you are updating the underlying report data (like you re-ran Achilles with new CDM data), your WebAPI may have already cached results. So, to clear this cache, you need to delete records from the WebAPI database. The two tables are:

achilles_cache: this stores the Data Sources reports (like Condition Occurence reports). cdm_cache: this stores the record counts that are displayed when you search the vocabulary or look at the ‘included concepts’ of a concept set. Those columns are RC/DRC and PC/PRC (record count, descendant record count, and person count, descendent person count).

We don’t have a button in the Atlas UI that can clear this cache. So, you should run a TRUNCATE on those two tables in your WebAPI database if you want the new results to be fetched from the results schema on your SOURCE.