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OHDSI / Eunomia

An R package that facilitates access to a variety of OMOP CDM sample data sets.
https://ohdsi.github.io/Eunomia/
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Error in extractLoadData #45

Open ginberg opened 1 year ago

ginberg commented 1 year ago

This happens when I have cleared my Eunomia data directory and I am using the develop branch

> library(Eunomia)
> connectionDetails <- getEunomiaConnectionDetails()
attempting to download GiBleed
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6863696 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

attempting to extract and load /Users/ginberg/Data/eunomia/GiBleed_5.3.zip
Unzipping /Users/ginberg/Data/eunomia/GiBleed_5.3.zip
Error in extractLoadData(from = archiveLocation, to = datasetLocation, :
Data file does not contain .CSV files to load into the database.

Apparently when unzipping, it adds the archive folder to the tempFileLocation, so the csv files are in a subdirectory of the tempFileLocation and the list.files can't find them. This is where the unzipping happens https://github.com/OHDSI/Eunomia/blob/develop/R/EunomiaData.R#L102 when adding junkpaths = TRUE, it does work for me. Have you seen this error before @fdefalco?

My sessionInfo

R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] Eunomia_2.0.0           DatabaseConnector_6.2.1

loaded via a namespace (and not attached):
 [1] fansi_1.0.4     tzdb_0.3.0      utf8_1.2.3      duckdb_0.6.1    R6_2.5.1        lifecycle_1.0.3 DBI_1.1.3       magrittr_2.0.3  RSQLite_2.3.1   pillar_1.9.0   
[11] rlang_1.1.0     cachem_1.0.7    cli_3.6.1       rstudioapi_0.14 blob_1.2.4      vctrs_0.6.1     tools_4.2.1     bit64_4.0.5     readr_2.1.4     glue_1.6.2     
[21] bit_4.0.5       hms_1.1.3       fastmap_1.1.1   compiler_4.2.1  pkgconfig_2.0.3 rJava_1.0-6     memoise_2.0.1   tibble_3.2.1
ginberg commented 1 year ago

this error now also shows up in the github actions build, see for example https://github.com/OHDSI/Eunomia/actions/runs/5119602037