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OHDSI / Achilles

Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM database
https://ohdsi.github.io/Achilles/
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cdm_v6 sql error in analysis 500 #422

Closed robchallen closed 3 years ago

robchallen commented 5 years ago

Expected behavior

Achilles analysis runs on cdm_v6

Actual behavior

SQL error generated due to incorrect column name in 500.sql

left join @cdmDatabaseSchema.concept CN on C.condition_type_concept_id = CN.concept_id and CN.concept_class = 'Death Type'

shoudl be

left join @cdmDatabaseSchema.concept CN on C.condition_type_concept_id = CN.concept_id and CN.concept_class_id = 'Death Type'

Steps to reproduce behavior

achilles(connectionDetails, cdmDatabaseSchema = "omop.dbo", resultsDatabaseSchema="omopResults.dbo", vocabDatabaseSchema = "omop.dbo", numThreads = 1, sourceName = "My Source Name", cdmVersion = "6.0", runHeel = TRUE, runCostAnalysis = FALSE,

sqlOnly = TRUE,

     outputFolder = "~/Dropbox/tmp/achilles/sql"
     analysisIds = c(500)
     )
alondhe commented 5 years ago

As commented in the other issue, CDMv6 support is due out in Achilles v1.8.0: https://github.com/OHDSI/Achilles/milestone/13

robchallen commented 5 years ago

Fair enough.

For completeness I found the following other errors in this branch:

Analysis 501 -- ERROR Error: Error executing SQL: com.microsoft.sqlserver.jdbc.SQLServerException: Invalid column name 'concept_class'. An error report has been created at /home/robchallen/Dropbox/tmp/achilles/errorReport.txt

Analysis 504 -- ERROR Error: Error executing SQL: com.microsoft.sqlserver.jdbc.SQLServerException: The multi-part identifier "p1.gender_concept_id" could not be bound. An error report has been created at /home/robchallen/Dropbox/tmp/achilles/errorReport.txt

Analysis 505 -- ERROR Error: Error executing SQL: com.microsoft.sqlserver.jdbc.SQLServerException: Invalid column name 'concept_class'. An error report has been created at /home/robchallen/Dropbox/tmp/achilles/errorReport.txt

Analysis 506 -- ERROR Error: Error executing SQL: com.microsoft.sqlserver.jdbc.SQLServerException: Column 'omop.dbo.person.person_id' is invalid in the select list because it is not contained in either an aggregate function or the GROUP BY clause. An error report has been created at /home/robchallen/Dropbox/tmp/achilles/errorReport.txt

rpeys commented 5 years ago

@alondhe I see that v6 updates are planned to be completed this november, but I am wondering when they are planned to get underway? I want to know when others will be actively committing code & responding to pull requests, issues, etc. I'm happy to help contribute but want to schedule myself to overlap with others so it doesn't turn into a one person project... thanks!

alondhe commented 5 years ago

Hi @rpeys -- I think after the Symposium is when we'll start developing the v6 support. None of the analytic tools (Atlas, CohortMethod, etc) will be on v6 until end of year. Thanks for helping push this along!

fdefalco commented 3 years ago

Achilles only supports CDM v5.x at this time. CDM 6 will not be supported as the specification has gone unutilized in the community. Expect next version support with updated CDM v7 specification.