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Snowflake error on Achilles::exportToAres - "Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate" #775

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heschmidt04 opened this issue Nov 15, 2024 · 1 comment

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@heschmidt04
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@fdefalco I got this error as well that is mentioned in #676
"Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate"
So it means no output in the data directory for Ares.

I'm not well versed in R and not sure of the workflow/hand off for the process for Ares Export - so I'm not sure what I am not doing that might be missing or not.

My code I ran that I get that error consistently is included as a text file
Rscript-achilles-dqd-ares.txt

Context:

  1. Backing data store is Snowflake
  2. Using snowflake snowflake-jdbc-3.9.2.jar
  3. The R code will create the achilles.sql file to run in Snowflake.
  • Note achilles.sql doesn't include achilles_analysis table creation. Jared pointed out that I needed it so then I created the table with DDL and then this CSV was loaded

My library versions are

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] AresIndexer_0.2.0          DataQualityDashboard_2.6.1 Achilles_1.7.2             DatabaseConnector_6.3.2   

loaded via a namespace (and not attached):
 [1] bit_4.5.0            jsonlite_1.8.9       crayon_1.5.3         dplyr_1.1.4          compiler_4.4.1       tidyselect_1.2.1    
 [7] Rcpp_1.0.13-1        Andromeda_0.6.6      blob_1.2.4           stringr_1.5.1        urltools_1.7.3       fastmap_1.2.0       
[13] triebeard_0.4.1      readr_2.1.5          R6_2.5.1             generics_0.1.3       backports_1.5.0      checkmate_2.3.2     
[19] tibble_3.2.1         lubridate_1.9.3      DBI_1.2.3            pillar_1.9.0         tzdb_0.4.0           rlang_1.1.4         
[25] utf8_1.2.4           cachem_1.1.0         stringi_1.8.4        bit64_4.5.2          memoise_2.0.1        RSQLite_2.3.7       
[31] timechange_0.3.0     cli_3.6.3            withr_3.0.2          magrittr_2.0.3       rstudioapi_0.17.1    rJava_1.0-11        
[37] ParallelLogger_3.3.1 hms_1.1.3            lifecycle_1.0.4      vctrs_0.6.5          glue_1.8.0           data.table_1.16.2   
[43] SqlRender_1.19.0     fansi_1.0.6          tools_4.4.1          pkgconfig_2.0.3 

My traceback() output in R is

> traceback()
5: stop("no rows to aggregate")
4: aggregate.data.frame(as.data.frame(x), ...)
3: aggregate.default(totalRecordsData$records, by = list(domain = totalRecordsData$domain), 
       FUN = sum)
2: aggregate(totalRecordsData$records, by = list(domain = totalRecordsData$domain), 
       FUN = sum)
1: Achilles::exportToAres(connectionDetails = connectionDetails, 
       cdmDatabaseSchema = cdmDatabaseSchema, resultsDatabaseSchema = cdmDatabaseSchema, 
       vocabDatabaseSchema = cdmDatabaseSchema, outputPath = aresDataRoot)

The following tables are created with the R code and loaded in the same schema.

ACHILLES_ANALYSIS -- 294 records 
ACHILLES_RESULTS -- 790 records 
ACHILLES_RESULTS_DIST -- 1 record
DQDASHBOARD_RESULTS -- 2,344 records 

When I run the data density totalrecords SQL I get no results though so it makes me wonder what other gaps I might be missing.

@heschmidt04
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I also posted to OHDSI Developers forum in case someone would see it and give me feedback/guidance.
The OHDSI Dev Forum post - 22715

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