populate_config()

ref #10
OuhscBbmc · May 24, 2019 · 64e2a6c · 64e2a6c
1 parent a8f2dbf
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Showing 9 changed files with 317 additions and 16 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -24,6 +24,7 @@ Depends:
     stats
 Imports:
     dplyr,
+    glue,
     httr (>= 1.3.0),
     magrittr,
     purrr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(download_file_list)
+export(populate_config)
 export(retrieve_file_list)
 export(start_cdw_skeleton_1)
 export(start_r_analysis_skeleton)

diff --git a/R/populate-config.R b/R/populate-config.R
@@ -0,0 +1,46 @@
+#' @name populate_config
+#'
+#' @title Populated the configuration value with project-specific values.
+#'
+#' @description `populate_config()` starts with config file and replaces the
+#' template values with project-specific values.
+#'
+#' @param path_in [character] of the config file to populate.  Required.
+#' @param project_name [character] of the new project.  Required.
+#' @param path_out [character] of the config file to populate.  Required.
+#'
+#' @importFrom magrittr %>%
+#'
+#' @author Will Beasley
+#'
+#' @examples
+#' library(pluripotent)
+#'
+#' \dontrun{
+#' url_config <- "https://github.com/OuhscBbmc/cdw-skeleton-1/blob/master/config.yml?raw=true"
+#' path_in    <- "~/config.yml"
+#' path_out   <- "~/config-out.yml"
+#' utils::download.file(url=url_config, destfile=path_in)
+#' populate_config(
+#'   path_in        = path_in,
+#'   project_name   = "thumann-awesomeness-1",
+#'   path_out       = path_out
+#' )
+#' }
+
+#' @export
+populate_config <- function( path_in, project_name, path_out = path_in ) {
+
+  template  <- readr::read_file(path_in)
+
+  value <-
+    glue::glue(
+      paste0(template, "\n"),
+      project_name            = project_name,
+      schema_name             = gsub("-", "_", project_name),
+      path_directory          = "{path_directory}",
+      path_directory_output   = "{path_directory_output}"
+    )
+
+  readr::write_file(value, path_out)
+}
diff --git a/R/start-project.R b/R/start-project.R
@@ -2,7 +2,7 @@
 #' @aliases start_r_analysis_skeleton start_cdw_skeleton_1
 #'
 #'
-#' @title Start specific projects project
+#' @title Start specific projects
 #'
 #' @description `start_r_analysis_skeleton()` copies the files
 #' to the `destination_directory` on your local maachine.
@@ -95,5 +95,7 @@ start_skeleton <- function(
   directories[!dir.exists(directories)] %>%
     purrr::walk(~dir.create(., recursive = T))
 
+  #   browser()
+
   purrr::walk2(.x=d$source, .y=d$destination, .f=~utils::download.file(url=.x, destfile=.y))
 }
diff --git a/inst/tests/config-out.yml b/inst/tests/config-out.yml
@@ -0,0 +1,107 @@
+default:
+
+  project_name                                        : "thumann-awesomeness-1"
+  dsn_staging                                         :   "cdw_cache_staging"
+  # dsn_centricity                                      :   "cdw_outpost"
+  # dsn_idx                                             :   "cdw_waystation_idx"
+  schema_name                                         : "thumann_awesomeness_1"
+  path_directory                                      : "//pedsis/peds/data/BBMC/prairie-outpost/thumann-awesomeness-1"
+  path_directory_output                               : "{path_directory}/data/derived/%Y-%m-%d"
+  path_output_summary                                 : "{path_directory}/data/derived/%Y-%m-%d/_summary.csv"
+  path_output_description                             : "{path_directory}/data/derived/%Y-%m-%d/_description.md"
+  # path_output_summary                                 : "{path_directory_output}/_summary.csv"
+  # path_output_description                             : "{path_directory_output}/_description.md"
+
+  tables_to_scribe:
+    -
+      name: person
+      sql: "SELECT * FROM thumann_awesomeness_1.person"
+      columns_include: ""
+      #columns_exclude: ""
+      path_output: "{path_directory_output}/person.csv"
+      #path_output: "data-public/derived/%Y-%m-%d/person.csv"
+      row_unit: each row represents a distinct patient.
+    -
+      name: obs
+      sql: ""
+      columns_include: "mrn_flowcast, obs_date, obs_term, obs_value"
+      path_output: "{path_directory_output}/obs.csv"
+      #path_output: "data-public/derived/%Y-%m-%d/obs.csv"
+      row_unit: each row represents a distinct measurement
+    -
+      name: medicate
+      columns_include: "*"
+      #columns_exclude: "start_date, stop_date"
+      path_output: "{path_directory_output}/medicate.csv"
+      #path_output: "data-public/derived/%Y-%m-%d/medicate.csv"
+      row_unit: each row represents a distinct prescription
+
+ # #sweep and specify
+ # fs_input_review_required_centricity_diagnosis       : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-required/diagnosis"
+ # fs_input_review_required_centricity_location        : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-required/location"
+ # fs_input_review_required_centricity_medication      : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-required/medication"
+ # fs_input_review_required_centricity_obs             : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-required/obs"
+ # fs_input_review_required_idx_cpt                    : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-required/cpt"
+ # fs_input_review_required_idx_diagnosis              : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-required/diagnosis"
+ # fs_input_review_required_idx_location               : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-required/location"
+ # fs_input_review_required_idx_sched_location         : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-required/sched-location"
+ # fs_input_review_skip_centricity_diagnosis           : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-skip/diagnosis"
+ # fs_input_review_skip_centricity_location            : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-skip/location"
+ # fs_input_review_skip_centricity_medication          : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-skip/medication"
+ # fs_input_review_skip_centricity_obs                 : "{path_directory_output}/data-public/sweep-and-specify-centricity/input/review-skip/obs"
+ # fs_input_review_skip_idx_cpt                        : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-skip/cpt"
+ # fs_input_review_skip_idx_diagnosis                  : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-skip/diagnosis"
+ # fs_input_review_skip_idx_location                   : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-skip/location"
+ # fs_input_review_skip_idx_sched_location             : "{path_directory_output}/data-public/sweep-and-specify-idx/input/review-skip/sched-location"
+ # fs_review_centricity_diagnosis                      : "{path_directory_output}/data-public/sweep-and-specify-centricity/review/diagnosis"
+ # fs_review_centricity_location                       : "{path_directory_output}/data-public/sweep-and-specify-centricity/review/location"
+ # fs_review_centricity_medication                     : "{path_directory_output}/data-public/sweep-and-specify-centricity/review/medication"
+ # fs_review_centricity_obs                            : "{path_directory_output}/data-public/sweep-and-specify-centricity/review/obs"
+ # fs_review_idx_cpt                                   : "{path_directory_output}/data-public/sweep-and-specify-idx/review/cpt"
+ # fs_review_idx_diagnosis                             : "{path_directory_output}/data-public/sweep-and-specify-idx/review/diagnosis"
+ # fs_review_idx_location                              : "{path_directory_output}/data-public/sweep-and-specify-idx/review/location"
+ # fs_review_idx_sched_location                        : "{path_directory_output}/data-public/sweep-and-specify-idx/review/sched-location"
+ # fs_review_original_centricity_diagnosis             : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-original/diagnosis"
+ # fs_review_original_centricity_location              : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-original/location"
+ # fs_review_original_centricity_medication            : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-original/medication"
+ # fs_review_original_centricity_obs                   : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-original/obs"
+ # fs_review_original_idx_cpt                          : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-original/cpt"
+ # fs_review_original_idx_diagnosis                    : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-original/diagnosis"
+ # fs_review_original_idx_location                     : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-original/location"
+ # fs_review_original_idx_sched_location               : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-original/sched-location"
+ # fs_to_database_centricity_diagnosis                 : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-to-database/diagnosis"
+ # fs_to_database_centricity_location                  : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-to-database/location"
+ # fs_to_database_centricity_medication                : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-to-database/medication"
+ # fs_to_database_centricity_obs                       : "{path_directory_output}/data-public/sweep-and-specify-centricity/reviewed-to-database/obs"
+ # fs_to_database_idx_cpt                              : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-to-database/cpt"
+ # fs_to_database_idx_diagnosis                        : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-to-database/diagnosis"
+ # fs_to_database_idx_location                         : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-to-database/location"
+ # fs_to_database_idx_sched_location                   : "{path_directory_output}/data-public/sweep-and-specify-idx/reviewed-to-database/sched-location"
+
+ # gt_sql_review_required_centricity_diagnosis         : "manipulation/sweep-and-specify/sql/review-required-centricity-diagnosis.sql"
+ # gt_sql_review_required_centricity_location          : "manipulation/sweep-and-specify/sql/review-required-centricity-location.sql"
+ # gt_sql_review_required_centricity_medication        : "manipulation/sweep-and-specify/sql/review-required-centricity-medication.sql"
+ # gt_sql_review_required_centricity_obs               : "manipulation/sweep-and-specify/sql/review-required-centricity-obs.sql"
+ # gt_sql_review_required_idx_cpt                      : "manipulation/sweep-and-specify/sql/review-required-idx-cpt.sql"
+ # gt_sql_review_required_idx_diagnosis                : "manipulation/sweep-and-specify/sql/review-required-idx-diagnosis.sql"
+ # gt_sql_review_required_idx_location                 : "manipulation/sweep-and-specify/sql/review-required-idx-location.sql"
+ # gt_sql_review_required_idx_sched_location           : "manipulation/sweep-and-specify/sql/review-required-idx-sched-location.sql"
+ # gt_sql_review_skip_centricity_diagnosis             : "manipulation/sweep-and-specify/sql/review-skip-centricity-diagnosis.sql"
+ # gt_sql_review_skip_centricity_location              : "manipulation/sweep-and-specify/sql/review-skip-centricity-location.sql"
+ # gt_sql_review_skip_centricity_medication            : "manipulation/sweep-and-specify/sql/review-skip-centricity-medication.sql"
+ # gt_sql_review_skip_centricity_obs                   : "manipulation/sweep-and-specify/sql/review-skip-centricity-obs.sql"
+ # gt_sql_review_skip_idx_cpt                          : "manipulation/sweep-and-specify/sql/review-skip-idx-cpt.sql"
+ # gt_sql_review_skip_idx_diagnosis                    : "manipulation/sweep-and-specify/sql/review-skip-idx-diagnosis.sql"
+ # gt_sql_review_skip_idx_location                     : "manipulation/sweep-and-specify/sql/review-skip-idx-location.sql"
+ # gt_sql_review_skip_idx_sched_location               : "manipulation/sweep-and-specify/sql/review-skip-idx-sched-location.sql"
+
+ # fs_archive_centricity                               : "{path_directory_output}/data-public/sweep-and-specify-centricity/archive"
+ # fs_archive_idx                                      : "{path_directory_output}/data-public/sweep-and-specify-idx/archive"
+
+ # #csv report generator
+ # gt_sql_queries_to_csv                               : "manipulation/sql-queries-to-csv-report/sql-to-generate-csv"
+ # gt_sql_csv_report_generated                         : "manipulation/sql-queries-to-csv-report/sql-csv-report-generated"
+ # fs_csv_report                                       : "//pedsis/peds/data/BBMC/prairie-outpost/thumann-awesomeness-1/csv-report"
+
+  path_database                                        : "data-public/raw/emr-mock.sqlite"
+  # project_name                                        : !expr basename(getwd())