CohortMethod & SelfControlledCaseSeries produce a Results*.zip file at the end of execution which then required when uploading results. These modules currently have some code that attempts to create a Results.zip if one is not present since the CM/SCCS upload methods require this as input:
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# TODO: This is something CM does differently. |
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# Find the results zip file in the results sub folder |
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resultsFolder <- private$jobContext$moduleExecutionSettings$resultsSubFolder |
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zipFiles <- list.files( |
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path = resultsFolder, |
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pattern = "\\.zip$", |
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full.names = TRUE |
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) |
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|
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if (length(zipFiles) > 0) { |
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zipFileName <- zipFiles[1] |
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} else { |
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# Create a zip file from the results in the directory |
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DatabaseConnector::createZipFile( |
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zipFile = "results.zip", |
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files = list.files(resultsFolder, pattern = ".*\\.csv$"), |
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rootFolder = resultsFolder |
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) |
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zipFileName <- file.path(resultsFolder, "results.zip") |
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} |
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# TODO: This function does not expose |
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# a way to specify the database identifier file |
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# which makes the purge problematic since I'm |
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# not sure how it will know what to purge... |
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CohortMethod::uploadResults( |
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connectionDetails = resultsConnectionDetails, |
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schema = resultsDataModelSettings$resultsDatabaseSchema, |
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zipFileName = zipFileName, |
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purgeSiteDataBeforeUploading = FALSE |
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) |
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}, |
Specifically, "results.zip" gets written to the current directory (getwd()) while CohortMethod then tries to read it from resultsFolder which is a bug.
A separate, but related issue: should CM/SCCS produce a .zip file as part of execution that is then required for upload when running through Strategus?
Tagging @msuchard (thanks for reporting this) and @schuemie
