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Fixes #657 #669

Merged
merged 1 commit into from
Jul 27, 2022
Merged

Fixes #657 #669

merged 1 commit into from
Jul 27, 2022

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AnthonyMolinaro
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To address this issue, the fix creates the achilles_analysis table from a pre-existing sql script, rather than generate it dynamically using CTAS and union-all. The table is populated using the data from the achilles_analysis_details.csv. This was successfully tested against cdm v5.3 on redshift. To test:

# Run achilles for all analyses
Achilles::achilles(connectionDetails = connectionDetails,
                   cdmDatabaseSchema = cdmDatabaseSchema,
                   resultsDatabaseSchema = resultsDatabaseSchema,
                   cdmVersion = "5.3")

# After deleting some analyses, runMissingAnalyses
Achilles::runMissingAnalyses(connectionDetails = connectionDetails,
                   cdmDatabaseSchema = cdmDatabaseSchema,
                   resultsDatabaseSchema = resultsDatabaseSchema)

# Update only
Achilles::achilles(connectionDetails = connectionDetails,
                   cdmDatabaseSchema = cdmDatabaseSchema,
                   resultsDatabaseSchema = resultsDatabaseSchema,
                   cdmVersion = "5.3",
                   updateGivenAnalysesOnly = T,
                   createTable = F,
                   analysisIds = c(402,702))

# Exclude certain analyses
Achilles::achilles(connectionDetails = connectionDetails,
                   cdmDatabaseSchema = cdmDatabaseSchema,
                   resultsDatabaseSchema = resultsDatabaseSchema,
                   cdmVersion = "5.3",
                   excludeAnalysisIds = c(402,702))

The above scenarios all ran without error.

@fdefalco fdefalco merged commit 65766e0 into main Jul 27, 2022
@fdefalco fdefalco deleted the issue-657 branch August 2, 2022 18:36
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2 participants