standardizing column name case

This should resolve errors with case sensitive platforms such as DuckDb where within the achilles package both upper case and lower case were used, standardized now on lower case.

R/Achilles.R

@@ -218,16 +218,16 @@ achilles <- function(connectionDetails,
   if (!missing(analysisIds)) {
     # If specific analysis_ids are given, run only those
     analysisDetails <-
-      analysisDetails[analysisDetails$ANALYSIS_ID %in% analysisIds,]
+      analysisDetails[analysisDetails$analysis_id %in% analysisIds,]
   } else if (defaultAnalysesOnly) {
     # If specific analyses are not given, determine whether or not to run only default analyses
     analysisDetails <-
       analysisDetails[analysisDetails$IS_DEFAULT == 1,]
   }
 
   # Remove unwanted analyses that have not already been excluded, if any are specified
-  if (!missing(excludeAnalysisIds) && any(analysisDetails$ANALYSIS_ID %in% excludeAnalysisIds)) {
-    analysisDetails <- analysisDetails[-which(analysisDetails$ANALYSIS_ID %in% excludeAnalysisIds),]
+  if (!missing(excludeAnalysisIds) && any(analysisDetails$analysis_id %in% excludeAnalysisIds)) {
+    analysisDetails <- analysisDetails[-which(analysisDetails$analysis_id %in% excludeAnalysisIds),]
   }
 
   resultsTables <- list(
@@ -238,7 +238,7 @@ achilles <- function(connectionDetails,
         file = system.file("csv", "schemas", "schema_achilles_results.csv", package = "Achilles"),
         header = TRUE
       ),
-      analysisIds = analysisDetails[analysisDetails$DISTRIBUTION <=0, ]$ANALYSIS_ID
+      analysisIds = analysisDetails[analysisDetails$distribution <=0, ]$analysis_id
     ),
     list(
       detailType = "results_dist",
@@ -247,7 +247,7 @@ achilles <- function(connectionDetails,
         file = system.file("csv","schemas","schema_achilles_results_dist.csv",package = "Achilles"),
         header = TRUE
       ),
-      analysisIds = analysisDetails[abs(analysisDetails$DISTRIBUTION) == 1, ]$ANALYSIS_ID
+      analysisIds = analysisDetails[abs(analysisDetails$distribution) == 1, ]$analysis_id
     )
   )
 
@@ -376,7 +376,7 @@ achilles <- function(connectionDetails,
   }
 
   # Generate Main Analyses
-  mainAnalysisIds <- analysisDetails$ANALYSIS_ID
+  mainAnalysisIds <- analysisDetails$analysis_id
 
   mainSqls <- lapply(mainAnalysisIds, function(analysisId) {
     list(
@@ -409,7 +409,7 @@ achilles <- function(connectionDetails,
         start <- Sys.time()
         ParallelLogger::logInfo(sprintf("Analysis %d (%s) -- START",
                                         mainSql$analysisId,
-                                        analysisDetails$ANALYSIS_NAME[analysisDetails$ANALYSIS_ID ==
+                                        analysisDetails$analysis_name[analysisDetails$analysis_id ==
           mainSql$analysisId]))
         tryCatch({
           DatabaseConnector::executeSql(connection = connection,
@@ -435,7 +435,7 @@ achilles <- function(connectionDetails,
         ParallelLogger::logInfo(sprintf("[Main Analysis] [START] %d (%s)",
                                         as.integer(mainSql$analysisId),
 
-          analysisDetails$ANALYSIS_NAME[analysisDetails$ANALYSIS_ID == mainSql$analysisId]))
+          analysisDetails$ANALYSIS_NAME[analysisDetails$analysis_id == mainSql$analysisId]))
         tryCatch({
           DatabaseConnector::executeSql(connection = connection,
                                         sql = mainSql$sql,
@@ -460,15 +460,15 @@ achilles <- function(connectionDetails,
 
   # Merge scratch tables into final analysis tables
   include <- sapply(resultsTables, function(d) {
-    any(d$analysisIds %in% analysisDetails$ANALYSIS_ID)
+    any(d$analysisIds %in% analysisDetails$analysis_id)
   })
   resultsTablesToMerge <- resultsTables[include]
 
   mergeSqls <- lapply(resultsTablesToMerge, function(table) {
     .mergeAchillesScratchTables(
       resultsTable = table,
       connectionDetails = connectionDetails,
-      analysisIds = analysisDetails$ANALYSIS_ID,
+      analysisIds = analysisDetails$analysis_id,
       createTable = createTable,
       schemaDelim = schemaDelim,
       scratchDatabaseSchema = scratchDatabaseSchema,
@@ -581,7 +581,7 @@ achilles <- function(connectionDetails,
   indicesSql <- "/* INDEX CREATION SKIPPED PER USER REQUEST */"
 
   if (createIndices) {
-    achillesTables <- lapply(unique(analysisDetails$DISTRIBUTION), function(a) {
+    achillesTables <- lapply(unique(analysisDetails$distribution), function(a) {
       if (a == 0) {
         "achilles_results"
       } else {
@@ -619,7 +619,7 @@ achilles <- function(connectionDetails,
                           resultsTable = "achilles_results",
 
     resultsDistributionTable = "achilles_results_dist", analysis_table = "achilles_analysis", sourceName = sourceName,
-    analysisIds = analysisDetails$ANALYSIS_ID, achillesSql = paste(achillesSql, collapse = "\n\n"),
+    analysisIds = analysisDetails$analysis_id, achillesSql = paste(achillesSql, collapse = "\n\n"),
     indicesSql = indicesSql, call = match.call())
 
   class(achillesResults) <- "achillesResults"
@@ -807,18 +807,18 @@ dropAllScratchTables <- function(connectionDetails,
     analysisDetails <- getAnalysisDetails()
 
     if (defaultAnalysesOnly) {
-      resultsTables <- lapply(analysisDetails$ANALYSIS_ID[analysisDetails$DISTRIBUTION <= 0 & analysisDetails$IS_DEFAULT ==
+      resultsTables <- lapply(analysisDetails$analysis_id[analysisDetails$distribution <= 0 & analysisDetails$IS_DEFAULT ==
         1], function(id) {
         sprintf("%s_%d", tempAchillesPrefix, id)
       })
     } else {
-      resultsTables <- lapply(analysisDetails$ANALYSIS_ID[analysisDetails$DISTRIBUTION <= 0],
+      resultsTables <- lapply(analysisDetails$analysis_id[analysisDetails$distribution <= 0],
                               function(id) {
         sprintf("%s_%d", tempAchillesPrefix, id)
       })
     }
 
-    resultsDistTables <- lapply(analysisDetails$ANALYSIS_ID[abs(analysisDetails$DISTRIBUTION) ==
+    resultsDistTables <- lapply(analysisDetails$analysis_id[abs(analysisDetails$distribution) ==
       1], function(id) {
       sprintf("%s_dist_%d", tempAchillesPrefix, id)
     })
@@ -1059,8 +1059,8 @@ optimizeAtlasCache <- function(connectionDetails,
 }
 
 .deleteExistingResults <- function(connectionDetails, resultsDatabaseSchema, analysisDetails) {
-  resultIds <- analysisDetails$ANALYSIS_ID[analysisDetails$DISTRIBUTION == 0]
-  distIds <- analysisDetails$ANALYSIS_ID[analysisDetails$DISTRIBUTION == 1]
+  resultIds <- analysisDetails$analysis_id[analysisDetails$distribution == 0]
+  distIds <- analysisDetails$analysis_id[analysisDetails$distribution == 1]
 
   if (length(resultIds) > 0) {
     sql <- SqlRender::render(sql = "delete from @resultsDatabaseSchema.achilles_results where analysis_id in (@analysisIds);",

R/listMissingAnalyses.r

@@ -73,11 +73,7 @@ listMissingAnalyses <- function(connectionDetails, resultsDatabaseSchema) {
 
   missingAnalysisIds <- setdiff(allAnalysisIds, existingAnalysisIds)
 
-  colsToDisplay <- c("ANALYSIS_ID",
-                     "DISTRIBUTION",
-                     "CATEGORY",
-                     "IS_DEFAULT",
-                     "ANALYSIS_NAME")
+  colsToDisplay <- c("analysis_id","distribution","category","is_default","analysis_name")
   retVal <- analysisDetails[analysisDetails$ANALYSIS_ID %in% missingAnalysisIds, colsToDisplay]
   retVal <- retVal[order(retVal$ANALYSIS_ID), ]
 

inst/csv/achilles/achilles_analysis_details.csv

@@ -1,4 +1,4 @@
-ANALYSIS_ID,DISTRIBUTION,DISTRIBUTED_FIELD,ANALYSIS_NAME,STRATUM_1_NAME,STRATUM_2_NAME,STRATUM_3_NAME,STRATUM_4_NAME,STRATUM_5_NAME,IS_DEFAULT,CATEGORY
+analysis_id,distribution,distributed_field,analysis_name,stratum_1_name,stratum_2_name,stratum_3_name,stratum_4_name,stratum_5_name,is_default,category
 0,-1,,Source name,,,,,,1,General
 1,0,,Number of persons,,,,,,1,Person
 2,0,,Number of persons by gender,gender_concept_id,,,,,1,Person

inst/csv/schemas/schema_achilles_results.csv

@@ -1,4 +1,4 @@
-FIELD_NAME,FIELD_TYPE
+field_name,field_type
 analysis_id,int
 stratum_1,varchar(255)
 stratum_2,varchar(255)

inst/csv/schemas/schema_achilles_results_concept_count.csv

@@ -1,4 +1,4 @@
-FIELD_NAME,FIELD_TYPE
+field_name,field_type
 concept_id,int
 record_count,bigint
 descendant_record_count,bigint

inst/csv/schemas/schema_achilles_results_dist.csv

@@ -1,4 +1,4 @@
-FIELD_NAME,FIELD_TYPE
+field_name,field_type
 analysis_id,int
 stratum_1,varchar(255)
 stratum_2,varchar(255)