Merge pull request #13 from OHDSI/develop

update to v0.0.4

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Ulysses
 Title: Automate OHDSI Study Setup
-Version: 0.0.3
+Version: 0.0.4
 Authors@R: 
     person("Martin", "Lavallee", , "[email protected]", role = c("aut", "cre"))
 Description: Automates setup of OHDSI study and provides functions to assist on improving organization

NAMESPACE

@@ -2,37 +2,54 @@
 
 export("%>%")
 export(addConfig)
+export(addDataSources)
+export(addLinks)
+export(addStudyMember)
+export(addTags)
 export(buildStudyHub)
 export(checkConfig)
 export(checkDatabaseCredential)
 export(cohortManifest)
 export(defaultCredentials)
+export(importCredentialsToConfig)
+export(importImages)
+export(initConfig)
 export(isOhdsiStudy)
 export(makeAnalysisPlan)
 export(makeAnalysisScript)
 export(makeCaprScript)
 export(makeCohortDetails)
-export(makeConfig)
 export(makeContributionGuidelines)
 export(makeHowToRun)
 export(makeInternals)
 export(makeKeyringSetup)
-export(makeMeetingMinutes)
+export(makeMigrationScript)
 export(makeNews)
-export(makeOhdsiProtocol)
 export(makeReadMe)
 export(makeResultsReport)
-export(makeStudySettings)
-export(makeTechSpecs)
 export(makeWebApiScript)
 export(moduleTable)
 export(newOhdsiStudy)
 export(previewStudyHub)
 export(publishStudyToRepository)
-export(requestStudyRepository)
+export(retrieveStudySettings)
 export(setCredential)
 export(setMultipleCredentials)
+export(setStudyAuthors)
+export(setStudyDescription)
+export(setStudyInfo)
 export(setStudyKeyring)
+export(setStudyLinks)
+export(setStudyTags)
+export(setStudyTimeline)
+export(updateDeveloperInfo)
+export(updateLeadInfo)
+export(updateStudyDescription)
+export(updateStudyEndDate)
+export(updateStudyStatus)
+export(updateStudyTitle)
+export(updateStudyVersion)
+export(updateTherapeuticArea)
 export(zipResults)
 import(fs)
 import(rlang)

NEWS.md

@@ -1,3 +1,15 @@
+Ulysses 0.0.4
+=============
+* Finalize Directory
+* Finalize meta fields for _study.yml
+* Reconfigure `newOhdsiStudy()` with better meta inputs
+* Add functions to interface with _study.yml
+* Reroute makeFiles to directory and meta fields
+* Add `makeMigrationsScript()` template
+* Update study hub website format
+* Update vignette
+
+
 Ulysses 0.0.3
 =============
 

R/config.R

@@ -31,7 +31,7 @@ checkConfig <- function() {
                     bullet = "warning", bullet_col = "yellow")
 
     txt <- glue::glue(
-      "`Ulysses::makeConfig(block = '[block_name]', database = '[database_name]')` "
+      "`Ulysses::initConfig()` "
     )
     cli::cat_line("To create config.yml edit and run function:\n\n  ", crayon::red(txt), "\n")
     cli::cat_line()
@@ -40,6 +40,148 @@ checkConfig <- function() {
 
 }
 
+#TODO keep this list up to date
+knownDataSourceTable <- function() {
+
+  dt <- tibble::tibble(
+    databaseName = c("Optum Clinformatics", "Optum Market Clarity", "Merative MarketScan",
+                     "German DA", "CPRD Gold", "CPRD Aurum", "THIN Belgium", "JMDC", "MDV"),
+    blockId = c("optumClaims", "optumEHR", "mktscan", "da", "gold", "aurum", "thin", "jmdc", "mdv")
+  )
+  return(dt)
+}
+
+
+
+config_block_text <- function(block, database, title, dbms, user,
+                              password, connectionString, cdmDatabaseSchema, resultsDatabaseSchema,
+                              workDatabaseSchema, tempEmulationSchema, cohortTable) {
+
+  txt <- glue::glue(
+    "\n\n# {title} Credentials\n
+{block}:
+  databaseName: {database}
+  dbms: {dbms}
+  user: {user}
+  password: {password}
+  connectionString: {connectionString}
+  cdmDatabaseSchema: {cdmDatabaseSchema}
+  resultsDatabaseSchema: {resultsDatabaseSchema}
+  vocabDatabaseSchema: {cdmDatabaseSchema}
+  workDatabaseSchema: {workDatabaseSchema}
+  tempEmulationSchema: {tempEmulationSchema}
+  cohortTable: {cohortTable}
+  \n\n")
+  return(txt)
+}
+#' Function to import credentials in stored csv to study config.yml
+#' @param credFile a credential.csv file stored in a secure location
+#' @param projectPath the path to the project
+#' @param open toggle on whether the file should be opened
+#' @export
+importCredentialsToConfig <- function(credFile, projectPath = here::here(), open = TRUE) {
+
+  # import credentials
+  creds <- readr::read_csv(file = credFile, show_col_types = FALSE)
+
+  # check _study.yml for loaded databases
+  studyMeta <- retrieveStudySettings(projectPath)$study
+  dataSources <- studyMeta$about$`data-sources`
+
+  # subset creds with loaded Data Sources
+  dt <- creds %>%
+    dplyr::filter(
+      db_title %in% dataSources
+    )
+  # make cred text for config file
+  config_txt <- purrr::pmap_chr(
+    dt,
+    ~config_block_text(
+      block = ..1,
+      database = ..2,
+      title = ..3,
+      dbms = ..4,
+      user = ..9,
+      password = ..10,
+      connectionString = ..5,
+      cdmDatabaseSchema = ..6,
+      resultsDatabaseSchema = ..8,
+      workDatabaseSchema = ..7,
+      tempEmulationSchema = ..7,
+      cohortTable = paste0("cohort_", ..1)
+    )
+  )
+
+  header <- glue::glue(" # Config File for {studyMeta$title}\n
+default:
+  projectName: {studyMeta$id}
+  ")
+
+  full_txt <- c(header, config_txt)
+  readr::write_lines(full_txt, file = fs::path(projectPath, "config.yml"))
+
+  cli::cat_bullet("Initializing config.yml using imported credentials",
+                  bullet = "tick", bullet_col = "green")
+
+
+  if (open) {
+
+    cli::cat_bullet("Check config.yml",
+                    bullet = "bullet", bullet_col = "red")
+
+    rstudioapi::navigateToFile(file = fs::path(projectPath, "config.yml"))
+  }
+
+  invisible(full_txt)
+
+}
+
+
+#' Function to create a config.yml file
+#' @param block the name of the config block, defaults to BlockName
+#' @param database the name of the database for the block, default to DatabaseName
+#' @param withKeyring should the config file use keyring, default FALSE
+#' @param projectPath the path to the project
+#' @param open toggle on whether the file should be opened
+#' @export
+initConfig <- function(block = "BlockName",
+                       database = "DatabaseName",
+                       withKeyring = FALSE,
+                       projectPath = here::here(),
+                       open = TRUE) {
+
+  # retrieve study meta
+  studyMeta <- retrieveStudySettings(projectPath = projectPath)$study
+
+
+  data <- rlang::list2(
+    'Title' = studyMeta$title,
+    'ID' = studyMeta$id,
+    'Cohort' = paste(studyMeta$id, database, sep = "_"),
+    'Block' = block,
+    'Database' = database
+  )
+
+  if (withKeyring) {
+    template_file <- "config_keyring.yml"
+  } else {
+    template_file <- "config_raw.yml"
+  }
+
+  usethis::use_template(
+    template = template_file,
+    save_as = fs::path("config.yml"),
+    data = data,
+    open = open,
+    package = "Ulysses")
+
+  usethis::use_git_ignore(ignores = "config.yml")
+
+  invisible(data)
+}
+
+
+
 #' Add a line to the config file
 #' @param block the name of the config block
 #' @param database the name of the database for the block, default to block name