Merge pull request #31 from pranavanba/main

Update progress statements and add total execution time timing
Sage-Bionetworks · Jul 12, 2024 · eac6b70 · eac6b70
2 parents 21f3e7a + 3adf936
commit eac6b70
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Showing 13 changed files with 14 additions and 12 deletions.
diff --git a/pipeline/run-pipeline.R b/pipeline/run-pipeline.R
@@ -1,3 +1,4 @@
+tictoc::tic(msg = "INFO: Total execution time")
 # Get config variables
 list2env(
   x = config::get(file = "config/config.yml", 
@@ -32,3 +33,4 @@ tictoc::toc()
 tictoc::tic(msg = "INFO: Store in Synapse")
 source("scripts/egress/egress.R")
 tictoc::toc()
+tictoc::toc()
diff --git a/scripts/egress/egress.R b/scripts/egress/egress.R
@@ -38,4 +38,4 @@ rm(latest_commit,
    file_name
 )
 
-cat("\n----Finished egress----\n")
+cat("----Finished----\n")
diff --git a/scripts/fetch-data/fetch_data.R b/scripts/fetch-data/fetch_data.R
@@ -61,5 +61,5 @@ if (!dir.exists(outputConceptsDir)) {
   dir.create(outputConceptsDir)
 }
 
-cat("\n----Finished----\n")
+cat("----Finished----\n")
 
diff --git a/scripts/process-data/fitbitactivitylogs.R b/scripts/process-data/fitbitactivitylogs.R
@@ -93,7 +93,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"),"\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(dataset,

diff --git a/scripts/process-data/fitbitdailydata.R b/scripts/process-data/fitbitdailydata.R
@@ -112,7 +112,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"), "\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(dataset,

diff --git a/scripts/process-data/fitbitecg.R b/scripts/process-data/fitbitecg.R
@@ -193,7 +193,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"), "\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(ecg_stat_summarize,

diff --git a/scripts/process-data/fitbitintradaycombined.R b/scripts/process-data/fitbitintradaycombined.R
@@ -126,7 +126,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"), "\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(dataset,

diff --git a/scripts/process-data/fitbitsleeplogs.R b/scripts/process-data/fitbitsleeplogs.R
@@ -432,7 +432,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"),"\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(sleeplogs_stat_summarize,

diff --git a/scripts/process-data/healthkitv2electrocardiogram.R b/scripts/process-data/healthkitv2electrocardiogram.R
@@ -196,7 +196,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"),"\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(ecg_stat_summarize,

diff --git a/scripts/process-data/healthkitv2samples.R b/scripts/process-data/healthkitv2samples.R
@@ -116,7 +116,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"),"\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(dataset,

diff --git a/scripts/process-data/healthkitv2statistics.R b/scripts/process-data/healthkitv2statistics.R
@@ -96,7 +96,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, glue::glue("{dataset}.csv")), row.names = F)
 cat(glue::glue("output_concepts written to {file.path(outputConceptsDir, paste0(dataset, '.csv'))}"),"\n")
 
-cat(paste0("\n----", glue::glue("Finished transforming data for {dataset}"),"\n"))
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(dataset,

diff --git a/scripts/process-data/participant_devices.R b/scripts/process-data/participant_devices.R
@@ -91,7 +91,7 @@ output_concepts %>%
   write.csv(file.path(outputConceptsDir, "participant_devices.csv"), row.names = F)
 cat(glue::glue("participant_devices written to {file.path(outputConceptsDir, 'participant_devices.csv')}"), "\n")
 
-cat(glue::glue("Finished tansforming device data for {dataset}"),"\n\n")
+cat("----Finished----\n")
 
 # Remove objects created here from the global environment
 rm(dataset,

diff --git a/scripts/write-output/final-output-concepts.R b/scripts/write-output/final-output-concepts.R
@@ -66,4 +66,4 @@ rm(datasets,
    valid_participants
 )
 
-cat("\n----Finished creating final output concepts----\n")
+cat("----Finished----\n")