Getting an error inside of a freshly minted PLE package from Atlas around the Redshift syntax for CreateAllCohorts at Line 73.
Error looks like this:
DBMS:
redshiftError:
java.sql.SQLException: Amazon Invalid operation: syntax error at or near “)”
Position: 182;SQL:
INSERT INTO #Codesets (ancestor_concept_id, concept_id)
SELECT ancestor_concept_id, descendant_concept_id
FROM full_201907_omop_v5.CONCEPT_ANCESTOR
WHERE ancestor_concept_id IN ()
My traceback is:
R version:
R version 3.5.1 (2018-07-02)
Platform:
x86_64-pc-linux-gnu
Attached base packages:
- stats
- graphics
- grDevices
- utils
- datasets
- methods
- base
Other attached packages:
- stringr (1.4.0)
- plyr (1.8.4)
- survival (2.44-1.1)
- ParallelLogger (1.1.0)
- OhdsiSharing (0.1.3)
- MethodEvaluation (1.0.1)
- ffbase (0.12.7)
- ff (2.2-14)
- bit (1.1-14)
- ggplot2 (3.2.1)
- CohortMethod (3.0.2)
- FeatureExtraction (2.2.3)
- Cyclops (2.0.2)
- EmpiricalCalibration (2.0.0)
- SqlRender (1.6.3)
- devtools (2.2.1)
- usethis (1.5.1)
- TOFA20200128 (0.0.1)
- DatabaseConnector (2.4.1)
It looks like the package is upset with syntax around this point:
DatabaseConnector::executeSql(conn, sql)
Coming out of:
sql <- SqlRender::loadRenderTranslateSql(“NegativeControlOutcomes.sql”,
“TOFA20200128”,
dbms = connectionDetails$dbms,
oracleTempSchema = oracleTempSchema,
cdm_database_schema = cdmDatabaseSchema,
target_database_schema = cohortDatabaseSchema,
target_cohort_table = cohortTable,
outcome_ids = unique(negativeControlOutcomes$outcomeId))
According to GitHub, it’s been about 28 days since I’ve tried to run a full PLE so wondering what’s new and different. I think my packages are up to date but maybe that’s my problem. Is there something I’m missing re: SqlRender? I’ve only seen this kind of syntax issue when I was working with @cukarthik’s custom code. Usually this doesn’t come up in an out of Atlas PLE.
