Merge pull request #24 from OHDSI/develop

Develop v007

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Ulysses
 Title: Automate OHDSI Study Setup
-Version: 0.0.6
+Version: 0.0.7
 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
@@ -28,7 +28,8 @@ Imports:
     usethis,
     whisker,
     withr,
-    yaml
+    yaml,
+    RJSONIO
 Suggests: 
     knitr,
     rmarkdown,

NEWS.md

@@ -1,65 +1,69 @@
-Ulysses 0.0.6
+Ulysses 0.0.7
 =============
 
-* correct start_study vignette
-* add fix in initConfig
+* fix importAtlasCohorts => use RJSONIO with digits
+* change all keyring fns to use only db. 
+* update function to review credentials
+* fix and simplify cohortManifest function #26
+* fix migration bug #25
 
-Ulysses 0.0.5
-=============
-* Add functions to import credentials
-* Add functions to import ATLAS assets
-* Write vignettes to creds and ATLAS 
-* add folder cohorts/conceptSets/json
+# Ulysses 0.0.6
 
-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
+-   correct start_study vignette
+-   add fix in initConfig
 
+# Ulysses 0.0.5
 
-Ulysses 0.0.3
-=============
+-   Add functions to import credentials
+-   Add functions to import ATLAS assets
+-   Write vignettes to creds and ATLAS
+-   add folder cohorts/conceptSets/json
 
-* add study hub builder
-* convert all documents to qmd
-* add functions to define study settings prior to build
-* add cohort functions
-    - `cohortManifest` lists cohorts used in study
-    - `makeCohortDetails` renders human-readable file to convey cohort definitions
-    - add versioning to cohort definitions
+# Ulysses 0.0.4
 
-Ulysses 0.0.2
-=============
+-   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
 
-* Add keyring functions and update SetupKeyring.R template
-* Update repository request email template
-* Add git function to publish repo to remote
-* Fix bugs in HowToRun and KeyringSetup template
+# Ulysses 0.0.3
 
-Ulysses 0.0.1
-=============
+-   add study hub builder
+-   convert all documents to qmd
+-   add functions to define study settings prior to build
+-   add cohort functions
+    -   `cohortManifest` lists cohorts used in study
+    -   `makeCohortDetails` renders human-readable file to convey cohort definitions
+    -   add versioning to cohort definitions
+
+# Ulysses 0.0.2
+
+-   Add keyring functions and update SetupKeyring.R template
+-   Update repository request email template
+-   Add git function to publish repo to remote
+-   Fix bugs in HowToRun and KeyringSetup template
+
+# Ulysses 0.0.1
 
-* Add initial functionality
-    * file templates for:
-        - Analysis script
-        - Cohort Details
-        - Contribution Guidelines
-        - Example Script
-        - How to run
-        - Internal function file
-        - Meeting minutes
-        - News
-        - Email templates
-        - Readme
-        - Results report
-        - Study Protocol
-        - Study SAP
-        - Config.yml
-    * initialize ohdsi study in R
-* Added a `NEWS.md` file to track changes to the package.
+-   Add initial functionality
+    -   file templates for:
+        -   Analysis script
+        -   Cohort Details
+        -   Contribution Guidelines
+        -   Example Script
+        -   How to run
+        -   Internal function file
+        -   Meeting minutes
+        -   News
+        -   Email templates
+        -   Readme
+        -   Results report
+        -   Study Protocol
+        -   Study SAP
+        -   Config.yml
+    -   initialize ohdsi study in R
+-   Added a `NEWS.md` file to track changes to the package.

R/atlas.R

@@ -8,7 +8,7 @@
 #' @export
 setAtlasCredentials <- function(keyringName = "atlas",
                                 keyringPassword = "ohdsi") {
-  creds <- c("baseurl", "authMethod", "user", "password")
+  creds <- c("baseUrl", "authMethod", "user", "password")
 
   keyringFn <- purrr::safely(maybeUnlockKeyring)
   tt <- keyringFn(keyringName = keyringName, keyringPassword)
@@ -24,18 +24,16 @@ setAtlasCredentials <- function(keyringName = "atlas",
   # set credentials
   purrr::walk(
     creds,
-    ~set_cred(
+    ~set_cred2(
       cred = .x,
-      db = db,
-      keyringName = keyringName)
+      db = keyringName)
   )
 
   # check credentials
   purrr::walk(
     creds,
     ~checkDatabaseCredential(
       cred = .x,
-      db = db,
       keyringName = keyringName,
       verbose = FALSE)
   )
@@ -67,20 +65,12 @@ format_cohort_expression <- function(expression) {
     circe$EndStrategy <- NULL
   }
 
-  circeJson <- jsonlite::toJSON(circe, pretty = TRUE, auto_unbox = TRUE) |>
-    as.character()
-  return(circeJson)
-}
-
-
-format_cs_expression <- function(expression) {
-
-  circeJson <- jsonlite::toJSON(expression, pretty = TRUE, auto_unbox = TRUE) |>
-    as.character()
+  circeJson <- RJSONIO::toJSON(circe, digits = 23)
 
   return(circeJson)
 }
 
+
 # Function to get a cohort from atlas by Id
 get_cohort_from_atlas <- function(cohortId,
                                authFirst = FALSE,
@@ -89,7 +79,8 @@ get_cohort_from_atlas <- function(cohortId,
   # check to unlock keyring
   maybeUnlockKeyring(keyringName = keyringName, keyringPassword = keyringPassword)
 
-  baseUrl <- keyring::key_get("atlas_baseurl", keyring = "atlas")
+  baseUrl <- keyring::key_get("baseUrl", keyring = keyringName)
+
 
   if (authFirst) {
 
@@ -101,9 +92,9 @@ get_cohort_from_atlas <- function(cohortId,
 
     ROhdsiWebApi::authorizeWebApi(
       baseUrl = baseUrl,
-      authMethod = keyring::key_get("atlas_authMethod", keyring = "atlas"),
-      webApiUsername = keyring::key_get("atlas_user", keyring = "atlas"),
-      webApiPassword = keyring::key_get("atlas_password", keyring = "atlas")
+      authMethod = keyring::key_get("authMethod", keyring = keyringName),
+      webApiUsername = keyring::key_get("user", keyring = keyringName),
+      webApiPassword = keyring::key_get("password", keyring = keyringName)
     )
   }
 
@@ -127,7 +118,10 @@ get_cs_from_atlas <- function(id,
   # check to unlock keyring
   maybeUnlockKeyring(keyringName = keyringName, keyringPassword = keyringPassword)
 
-  baseUrl <- keyring::key_get("atlas_baseurl", keyring = "atlas")
+  baseUrl <- keyring::key_get(
+    service = "baseUrl",
+    keyring = keyringName
+  )
 
   if (authFirst) {
 
@@ -139,9 +133,9 @@ get_cs_from_atlas <- function(id,
 
     ROhdsiWebApi::authorizeWebApi(
       baseUrl = baseUrl,
-      authMethod = keyring::key_get("atlas_authMethod", keyring = "atlas"),
-      webApiUsername = keyring::key_get("atlas_user", keyring = "atlas"),
-      webApiPassword = keyring::key_get("atlas_password", keyring = "atlas")
+      authMethod = keyring::key_get("authMethod", keyring = keyringName),
+      webApiUsername = keyring::key_get("user", keyring = keyringName),
+      webApiPassword = keyring::key_get("password", keyring = keyringName)
     )
   }
 
@@ -151,7 +145,7 @@ get_cs_from_atlas <- function(id,
   tb <- tibble::tibble(
     id = cs$id,
     name = cs$name,
-    expression = format_cs_expression(cs$expression),
+    expression = RJSONIO::toJSON(cs$expression, digits = 23),
     saveName = glue::glue("{id}_{name}") |> snakecase::to_snake_case()
   )