Initial dataset definition

analysis/create_project_actions.R

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+#### load required packages ####
+library("tidyverse")
+library("yaml")
+library("here")
+library("glue")
+
+
+#### create defaults list ####
+defaults_list <- list(
+  version = "3.0",
+  expectations = list(population_size = 1000L)
+)
+
+
+#### create comment and generic action functions ####
+# create comment function
+comment <- function(...){
+  list_comments <- list(...)
+  comments <- map(list_comments, ~paste0("## ", ., " ##"))
+  comments
+}
+
+# create function to convert comment "actions" in a yaml string into proper comments
+convert_comment_actions <- function(yaml.txt){
+  yaml.txt %>%
+    str_replace_all("\\\n(\\s*)\\'\\'\\:(\\s*)\\'", "\n\\1")  %>%
+    str_replace_all("([^\\'])\\\n(\\s*)\\#\\#", "\\1\n\n\\2\\#\\#") %>%
+    str_replace_all("\\#\\#\\'\\\n", "\n")
+}
+
+# create generic action function
+action <- function(
+    name,
+    run,
+    dummy_data_file = NULL,
+    arguments = NULL,
+    needs = NULL,
+    highly_sensitive = NULL,
+    moderately_sensitive = NULL
+){
+
+  outputs <- list(
+    moderately_sensitive = moderately_sensitive,
+    highly_sensitive = highly_sensitive
+  )
+  outputs[sapply(outputs, is.null)] <- NULL
+
+  action <- list(
+    run = paste(c(run, arguments), collapse = " "),
+    dummy_data_file = dummy_data_file,
+    needs = needs,
+    outputs = outputs
+  )
+  action[sapply(action, is.null)] <- NULL
+
+  action_list <- list(name = action)
+  names(action_list) <- name
+
+  action_list
+}
+
+
+#### combine all actions into a list ####
+# create list of actions
+actions_list <- splice(
+
+  # Post YAML disclaimer
+  comment("# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #",
+          "DO NOT EDIT project.yaml DIRECTLY",
+          "This file is created by create_project_actions.R",
+          "Edit and run create_project_actions.R to update the project.yaml",
+          "# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #"
+  ),
+
+  action(
+    name = "generate_study_population",
+    run = "ehrql:v1 generate-dataset analysis/dataset_definition.py 
+    --output output/study_data.csv",
+    needs = NULL,
+    highly_sensitive = list(
+      cohort = glue("output/study_data.csv")
+    )
+  )
+)
+
+
+#### combine actions_list and defaults_list ####
+# combine everything
+project_list <- splice(
+  defaults_list,
+  list(actions = actions_list)
+)
+
+
+#### convert list to yaml and output yaml file ####
+# convert list to yaml and output yaml file
+as.yaml(project_list, indent = 2) %>%
+  # convert comment actions to comments
+  convert_comment_actions() %>%
+  # add one blank line before level 1 and level 2 keys
+  str_replace_all("\\\n(\\w)", "\n\n\\1") %>%
+  str_replace_all("\\\n\\s\\s(\\w)", "\n\n  \\1") %>%
+  writeLines("project.yaml")
+print("YAML file printed!")
+
+# return number of actions
+print(paste0("YAML created with ", length(actions_list), " actions."))