stargin 97 metadata and import

See #3

dal/flow-97.R

@@ -0,0 +1,52 @@
+# This is a hack of https://github.com/OuhscBbmc/miechv-3/blob/master/manipulation/osdh/osdh-flow.R
+#   That file runs everything (those dozens of files) dynamically.
+#   This one is hard-coded, and requires one manual stop (to run the C#).
+#   But since there are so few files, I think it's an acceptable compromise.
+
+rm(list=ls(all=TRUE)) #Clear the memory for any variables set from any previous runs.
+
+# ---- load-sources ------------------------------------------------------------
+
+
+# ---- load-packages -----------------------------------------------------------
+library(magrittr)
+requireNamespace("testit")
+
+# ---- declare-globals ---------------------------------------------------------
+path_sources <- c(
+  # 97
+  "dal/import-97-metadata.R",
+  "dal/import-97-raw.R",
+  "dal/outcomes/outcomes-97.R"
+)
+
+file.exists(path_sources)
+all_sources_exist <- path_sources %>%
+  purrr::map_lgl(file.exists) %>%
+  all()
+if( !all_sources_exist ) stop("All source files to be run should exist.")
+
+
+# ---- load-data ---------------------------------------------------------------
+
+# ---- tweak-data --------------------------------------------------------------
+
+# ---- run-sources -------------------------------------------------------------
+
+message("Preparing to run\n\t", paste(path_sources, collapse="\n\t"))
+
+(start_time <- Sys.time())
+
+
+# dir.create(output="./stitched-output/dal/", recursive=T)
+knitr::stitch_rmd(script="./dal/import-97-metadata.R", output="./stitched-output/dal/import-97-metadata.md")
+knitr::stitch_rmd(script="./dal/import-97-raw.R", output="./stitched-output/dal/import-97-raw.md")
+
+stop("Now run the C# program, then come back to run the rest of the R scripts.")
+
+knitr::stitch_rmd(script="./dal/outcomes/outcomes-97.R", output="./stitched-output/dal/outcomes/outcomes-97.md") # dir.create("./stitched-output/dal/outcomes/", recursive=T)
+
+
+message("Completed flow-97 at ", Sys.time(), " (in ", round(elapsed_duration, 2), " mins.)")
+
+# ---- verify-values -----------------------------------------------------------

dal/import-79-metadata.R

@@ -43,15 +43,6 @@ lst_col_types <- list(
     Active                              = readr::col_logical(),
     Notes                               = readr::col_character()
   ),
-  # item_97 = readr::cols_only(
-  #   ID                                  = readr::col_integer(),
-  #   Label                               = readr::col_character(),
-  #   MinValue                            = readr::col_integer(),
-  #   MinNonnegative                      = readr::col_integer(),
-  #   MaxValue                            = readr::col_integer(),
-  #   Active                              = readr::col_logical(),
-  #   Notes                               = readr::col_character()
-  # ),
   LUExtractSource = col_types_minimal,
   LUMarkerEvidence = col_types_minimal,
   LUGender = col_types_minimal,
@@ -138,19 +129,6 @@ lst_col_types <- list(
     Active                              = readr::col_integer(),
     Notes                               = readr::col_character()
   )
-  # variable_97 = readr::cols_only(
-  #   # ID                                  = readr::col_integer(),
-  #   VariableCode                        = readr::col_character(),
-  #   Item                                = readr::col_integer(),
-  #   Generation                          = readr::col_integer(),
-  #   ExtractSource                       = readr::col_integer(),
-  #   SurveySource                        = readr::col_integer(),
-  #   SurveyYear                          = readr::col_integer(),
-  #   LoopIndex                           = readr::col_integer(),
-  #   Translate                           = readr::col_integer(),
-  #   Active                              = readr::col_integer(),
-  #   Notes                               = readr::col_character()
-  # )
 )
 
 col_types_mapping <- readr::cols_only(
@@ -199,7 +177,7 @@ ds_table
 rm(directory_in) # rm(col_types_tulsa)
 
 # ---- tweak-data --------------------------------------------------------------
-# OuhscMunge::column_rename_headstart(ds_county) #Spit out columns to help write call ato `dplyr::rename()`.
+# OuhscMunge::column_rename_headstart(ds_county) #Spit out columns to help write call to `dplyr::rename()`.
 
 ds_file <- ds_file %>%
   dplyr::left_join( ds_mapping, by=c("name"="table_name")) %>%
@@ -416,4 +394,4 @@ DBI::dbDisconnect(channel); rm(channel)
 RODBC::odbcClose(channel_rodbc); rm(channel_rodbc)
 
 duration_in_seconds <- round(as.numeric(difftime(Sys.time(), start_time, units="secs")))
-cat("File completed by `", Sys.info()["user"], "` at ", strftime(Sys.time(), "%Y-%m-%d, %H:%M %z"), " in ",  duration_in_seconds, " seconds.", sep="")
+cat("`import-79-metadata.R` file completed by `", Sys.info()["user"], "` at ", strftime(Sys.time(), "%Y-%m-%d, %H:%M %z"), " in ",  duration_in_seconds, " seconds.", sep="")