## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>"
)

## ----setup--------------------------------------------------------------------
library(tidyOhdsiSolutions)

# Disable ANSI colour codes so rendered HTML output is clean
options(pkg.no_color = TRUE)

## ----basic-messages-----------------------------------------------------------
msg_info("Loading configuration from disk")
msg_success("All 42 concept sets validated")
msg_warn("Column 'mappedSourceCode' is missing — using NA")
msg_danger("Connection pool exhausted (non-fatal, retrying)")
msg_process("Uploading results to the remote schema")
msg_bullet("concept_id 201826 — Type 2 Diabetes Mellitus")
msg_todo("Verify descendant flag for hypertension concept set")

## ----layout-------------------------------------------------------------------
msg_header("Step 1: Validate Input")
msg_info("Checking required columns")
msg_success("Validation passed")
msg_blank()
msg_header("Step 2: Build Cohort")
msg_process("Assembling concept set expressions")
msg_rule()
msg_info("Pipeline complete")

## ----msg-list-----------------------------------------------------------------
domains <- c(
  Condition   = "201826, 442793",
  Drug        = "1503297, 40163554",
  Measurement = "3004501"
)
msg_list(domains, header = "Concept set domains")

## ----msg-kv-------------------------------------------------------------------
run_info <- list(
  Package   = "tidyOhdsiSolutions",
  Version   = as.character(packageVersion("tidyOhdsiSolutions")),
  R_version = paste0(R.version$major, ".", R.version$minor),
  Date      = format(Sys.Date())
)
msg_kv(run_info)

## ----iteration-loop-----------------------------------------------------------
concept_sets <- list(
  diabetes     = c(201826L, 442793L),
  hypertension = c(320128L),
  obesity      = c(433736L, 4215968L)
)

for (nm in names(concept_sets)) {
  msg_header(nm)
  msg_info("Concepts: ", paste(concept_sets[[nm]], collapse = ", "))
  msg_success("Processed ", length(concept_sets[[nm]]), " concept(s)")
  msg_blank()
}

## ----iteration-safe-----------------------------------------------------------
sources <- list(
  schema_a = list(valid = TRUE,  rows = 1200L),
  schema_b = list(valid = FALSE, rows = 0L),
  schema_c = list(valid = TRUE,  rows = 850L)
)

results <- vector("list", length(sources))
names(results) <- names(sources)

for (nm in names(sources)) {
  results[[nm]] <- msg_try(
    on_error = "warn",
    expr = {
      src <- sources[[nm]]
      if (!src$valid) stop("Schema '", nm, "' failed validation")
      msg_success(nm, ": ", src$rows, " rows loaded")
      src$rows
    }
  )
}

## ----verbose-pattern----------------------------------------------------------
process_file <- function(path, verbose = TRUE) {
  msg_verbose("Opening: ", path, verbose = verbose)
  # ... processing ...
  msg_verbose("Done:    ", path, verbose = verbose)
  invisible(path)
}

# Verbose on (default)
process_file("data/concepts.csv")

# Verbose off
process_file("data/concepts.csv", verbose = FALSE)

## ----timing-simple------------------------------------------------------------
result <- msg_timed(
  expr  = Sys.sleep(0.05),
  msg   = "Sleeping"
)

## ----timing-iteration---------------------------------------------------------
concept_ids <- as.list(c(201826L, 442793L, 320128L, 433736L))

processed <- msg_timed(
  msg  = "Total batch time",
  expr = lapply(concept_ids, function(id) {
    msg_info("Processing concept_id ", id)
    id * 2L           # stand-in for real work
  })
)

## ----msg-abort----------------------------------------------------------------
validate_schema <- function(x) {
  if (!is.data.frame(x)) {
    msg_abort("Expected a data.frame, got: ", class(x)[1])
  }
  invisible(x)
}

# Catch the error and show its message
tryCatch(
  validate_schema("not a data frame"),
  error = function(e) msg_danger("Caught: ", conditionMessage(e))
)

## ----msg-warning--------------------------------------------------------------
withCallingHandlers(
  {
    msg_warning("Deprecated argument 'schema' — use 'cdm_schema' instead")
    msg_info("Continuing with default")
  },
  warning = function(w) {
    # Muffle so it does not print twice
    invokeRestart("muffleWarning")
  }
)

## ----msg-try-modes------------------------------------------------------------
# "warn"    — downgrade error to a styled warning
msg_try(stop("something went wrong"), on_error = "warn")

# "message" — emit as a styled danger message, no stop
msg_try(stop("non-critical failure"), on_error = "message")

# "ignore"  — silently swallow the error
msg_try(stop("ignored error"),        on_error = "ignore")
msg_info("Execution continued after all three")

## ----msg-debug-off------------------------------------------------------------
# Default: pkg.debug = FALSE, so nothing is printed
msg_debug("SQL query: SELECT * FROM concept WHERE ...")
msg_info("(no debug output above — pkg.debug is FALSE)")

## ----msg-debug-on-------------------------------------------------------------
options(pkg.debug = TRUE)
msg_debug("SQL query: SELECT * FROM concept WHERE ...")
options(pkg.debug = FALSE)   # reset

## ----progress-example, eval = FALSE-------------------------------------------
# files <- paste0("file_", seq_len(8), ".csv")
# pb    <- msg_progress(length(files), prefix = "Loading")
# 
# for (f in files) {
#   Sys.sleep(0.1)   # simulated I/O
#   pb$tick()
# }
# pb$done("All files loaded")

## ----spinner-example, eval = FALSE--------------------------------------------
# sp <- msg_spinner("Querying vocabulary server")
# 
# for (i in seq_len(30)) {
#   Sys.sleep(0.05)
#   sp$spin()
# }
# sp$done("Query complete")

## ----full-pipeline------------------------------------------------------------
run_pipeline <- function(concept_sets, verbose = TRUE) {

  msg_header("tidyOhdsiSolutions Pipeline")
  msg_kv(list(
    Steps       = as.character(length(concept_sets)),
    Verbose     = as.character(verbose)
  ))
  msg_blank()

  results <- vector("list", length(concept_sets))
  names(results) <- names(concept_sets)

  for (nm in names(concept_sets)) {
    msg_process("Processing: ", nm)

    results[[nm]] <- msg_try(on_error = "warn", expr = {
      ids <- concept_sets[[nm]]
      if (length(ids) == 0L) stop("'", nm, "' has no concept IDs")
      msg_verbose("  concept IDs: ", paste(ids, collapse = ", "),
                  verbose = verbose)
      ids
    })
  }

  msg_blank()
  msg_rule()

  succeeded <- sum(!vapply(results, is.null, logical(1L)))
  msg_success(succeeded, " / ", length(concept_sets), " concept sets processed")

  invisible(results)
}

concept_sets <- list(
  diabetes     = c(201826L, 442793L),
  hypertension = c(320128L),
  empty_set    = integer(0)      # will trigger a warning
)

out <- run_pipeline(concept_sets, verbose = TRUE)