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Snowflake numeric type issue with Ares Exporter - Achilles::exportToAres - for CDM version 5.4 #366

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heschmidt04 opened this issue Mar 15, 2024 · 0 comments

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@heschmidt04
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Describe the bug
Ares Exporter fails on numeric type because temp table in memory has autosensing data type conversion issue. A search on github Ares issues didn't yield anything for me if this has happened before in export.

To Reproduce
Steps to reproduce the behavior:

  1. Run Achilles generated SQL in Snowflake with sqlonly = T to create Achilles tables
  2. Run DQD in RStudio - authentication via external browser to Snowflake
  3. Run Ares Exporter in RStudio - authentication via external browser to Snowflake
  4. Run modified SQL from RStudio Ares Exporter error errorReportSql.txt in Snowflake

Expected behavior
Ares Exporter to write files to output folder.
Is there a possible work around for this part?

Screenshots
DBMS: snowflake

Error: net.snowflake.client.jdbc.SnowflakeSQLException: Numeric value '' is not recognized

Stackoverflow: https://stackoverflow.com/questions/70176093/numeric-value-is-not-recognized

-- SQL modified to debug 
CREATE TABLE AO_export_error AS 
select    t1.table_name as SERIES_NAME
        , t1.stratum_1 as X_CALENDAR_MONTH
        , round(1.0*t1.count_value/denom.count_value,5) as Y_RECORD_COUNT
from
(
        select 'Visit occurrence' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 220 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Condition occurrence' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 420 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Death' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 502 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Procedure occurrence' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 620 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Drug exposure' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 720 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Observation' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 820 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Drug era' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 920 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Condition era' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 1020 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Observation period' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 111 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Measurement' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 1820 GROUP BY analysis_id, stratum_1, count_value
) t1
inner join
(select CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 117 GROUP BY analysis_id, stratum_1, count_value) denom -- WORKS  
on t1.stratum_1 = denom.stratum_1
ORDER BY SERIES_NAME, t1.stratum_1

-- Debugging work 
CREATE OR REPLACE TABLE AO_export_denom AS
SELECT 
    CAST(stratum_1 as bigint) stratum_1
    , count_value 
FROM achilles_results 
WHERE analysis_id = 117 
GROUP BY analysis_id
        , stratum_1
        , count_value

-- Debugging work 
CREATE OR REPLACE TABLE AO_export_t1 AS 
        select 'Visit occurrence' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 220 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Condition occurrence' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 420 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Death' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 502 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Procedure occurrence' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 620 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Drug exposure' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 720 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Observation' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 820 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Drug era' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 920 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Condition era' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 1020 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Observation period' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 111 GROUP BY analysis_id, stratum_1, count_value
        union all
        select 'Measurement' as table_name, CAST(stratum_1 as bigint) stratum_1, count_value from achilles_results where analysis_id = 1820 GROUP BY analysis_id, stratum_1, count_value
-- Putting debug together 

SELECT   
      t1.table_name as SERIES_NAME
    , t1.stratum_1 as X_CALENDAR_MONTH
    , round(1.0*t1.count_value/denom.count_value,5) as Y_RECORD_COUNT
FROM AO_export_t1 AS t1 
JOIN AO_export_denom AS denom 
  ON t1.stratum_1 = denom.stratum_1
ORDER BY SERIES_NAME, t1.stratum_1

The work around works because the datatype is auto sensed

-- AO_EXPORT_DENOM

name	type	kind
STRATUM_1	NUMBER(38,0)	COLUMN
COUNT_VALUE	NUMBER(38,0)	COLUMN

-- AO_EXPORT_T1

name	type	kind
TABLE_NAME	VARCHAR(20)	COLUMN
STRATUM_1	NUMBER(38,0)	COLUMN
COUNT_VALUE	NUMBER(38,0)	COLUMN

Desktop (please complete the following information):
R version: R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20

Attached base packages:

  • stats
  • graphics
  • grDevices
  • utils
  • datasets
  • methods
  • base

Other attached packages:

  • AresIndexer (0.2.0)
  • DataQualityDashboard (2.5.0)
  • Achilles (1.7.2)
  • DatabaseConnector (6.3.2)

Additional context
Files that were created from the process are these. No error.txt file in the errors directory.

Mar 15 17:06 dq-result_camel.json
Mar 15 17:06 log_DqDashboard_Snowflake-MGB-OMOP.txt -- binary file??? Not sure why.
Mar 15 17:06 dq-result.json
Mar 15 17:06 datadensity-total.csv
Mar 15 17:06 records-by-domain.csv

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