Merge branch 'develop' into dev-fix-table

R/synapse_rest_api.R

@@ -146,7 +146,7 @@ synapse_entity_children <- function(url = "https://repo-prod.prod.sagebase.org/r
     resp <- httr::content(req)
     output <- c(output, resp$page)
   }
-  bind_rows(output)
+  dplyr::bind_rows(output)
 
 }
 
@@ -157,6 +157,9 @@ synapse_entity_children <- function(url = "https://repo-prod.prod.sagebase.org/r
 #' @param nextPageToken Synapse next page token
 synapse_projects_user <- function(url = "https://repo-prod.prod.sagebase.org/repo/v1/projects/user", auth, nextPageToken=NULL) {
   principalId <- synapse_user_profile(auth = auth)[["ownerId"]]
+
+  if (is.null(principalId)) stop("Synapse token not valid")
+
   hreq <- httr::GET(url = file.path(url, principalId),
                     query = list(nextPageToken=nextPageToken))
   output <- list()
@@ -174,7 +177,7 @@ synapse_projects_user <- function(url = "https://repo-prod.prod.sagebase.org/rep
 #' @title Get projects within scope of Synapse project
 #' 
 #' @param url Synapse api endpoint
-#' @param id Synapse ID
+#' @param id Synapse project ID
 #' @param auth Synapse token
 synapse_get_project_scope <- function(url = "https://repo-prod.prod.sagebase.org/repo/v1/entity/",
                                       id, auth) {

tests/testthat/test_synapse_rest_api.R

@@ -24,13 +24,152 @@ test_that("is_certified returns TRUE or FALSE", {
 
 })
 
-test_that("get returns a tibble or error", {
+test_that("synapse_get returns a tibble", {
 
-  good_req <- synapse_get(id="syn23643255", auth=Sys.getenv("SYNAPSE_PAT"))
+  good_req <- synapse_get(id="syn61941085", auth=Sys.getenv("SYNAPSE_PAT"))
   expect_true(length(good_req) > 1)
+})
+
+test_that("synapse_get errors as expected", {
 
+  # nonexistant id
   expect_error(synapse_get(id="bad", auth=Sys.getenv("SYNAPSE_PAT")))
+
+  # NULL id
   expect_error(synapse_get(id=NULL, auth=Sys.getenv("SYNAPSE_PAT")))
+
+  # nonexistant id and auth
   expect_error(synapse_get(id="bad", auth="bad"))
 
 })
+
+test_that("synapse_access returns TRUE/FALSE", {
+
+  # has DOWNLOAD access
+  expect_true(
+    synapse_access(id="syn62147982", access = "DOWNLOAD", auth=Sys.getenv("SYNAPSE_PAT"))
+    )
+
+  # doesn not have DOWNLOAD access
+  expect_false(
+    synapse_access(id="syn23643255", access = "DOWNLOAD", auth=Sys.getenv("SYNAPSE_PAT"))
+  )
+
+  # Bad PAT ("")
+  expect_false(
+    synapse_access(id="syn23643255", access = "DOWNLOAD", auth="")
+  )
+})
+
+test_that("synapse_access returns errors as expected", {
+
+  # non existent access argument
+  expect_error(
+    synapse_access(id="syn23643255", access = "TYPO", auth=Sys.getenv("SYNAPSE_PAT"))
+  )
+
+  # non existent id argument
+  expect_error(
+    synapse_access(id="not an id", access = "DOWNLOAD", auth=Sys.getenv("SYNAPSE_PAT"))
+  )
+
+  # bad PAT (string) 
+  expect_error(
+    synapse_access(id="syn23643255", access = "DOWNLOAD", auth="adfadsf")
+  )
+})
+
+test_that("synapse_entity_children returns a tibble", {
+
+  # all arguments valid
+  req <- synapse_entity_children(
+    parentId="syn35187716", includeTypes = list("file", "folder"), auth=Sys.getenv("SYNAPSE_PAT")
+    )
+
+  expect_true(
+    all(c("tbl_df", "data.frame") %in% class(req))
+  )
+
+  # no children to return
+  req_no_children <- synapse_entity_children(
+    parentId="syn35187716", includeTypes = "projects", auth=Sys.getenv("SYNAPSE_PAT")
+    )
+
+  expect_true(
+    all(c("tbl_df", "data.frame") %in% class(req_no_children))
+  )
+
+  # typo in parentId
+  req_parentId_typo <- synapse_entity_children(
+    parentId="not an id", includeTypes = "projects", auth=Sys.getenv("SYNAPSE_PAT")
+  )
+
+  expect_true(
+    all(c("tbl_df", "data.frame") %in% class(req_parentId_typo))
+  )
+
+  # typo in auth
+  req_auth_typo <- synapse_entity_children(
+    parentId="syn35187716", includeTypes = "projects", auth="not an auth"
+  )
+
+  expect_true(
+    all(c("tbl_df", "data.frame") %in% class(req_auth_typo))
+  )
+})
+
+test_that("synapse_projects_user returns expected tibble", {
+  req <- synapse_projects_user(auth=Sys.getenv("SYNAPSE_PAT"))
+  expect_identical(names(req), c("name", "id", "lastActivity", "modifiedOn", "modifiedBy"))
+})
+
+test_that("synapse_projects_user errors when auth token is not valid", {
+  expect_error(
+    req <- synapse_projects_user(auth="ABC")
+  )
+})
+
+test_that("synapse_table_query", {
+
+  # Return token
+  id <- "syn61941085"
+  query <- sprintf("select id from %s limit 1", id)
+  token <- synapse_table_query(id = id, auth = Sys.getenv("SYNAPSE_PAT"), query = query, partMask = 0x10)
+
+  expect_identical(names(token), "token")
+
+  # not a table (returns error message but does not error)
+  id <- "syn52578158"
+  query <- sprintf("select id from %s limit 1", id)
+  project_resp <- synapse_table_query(id = id, query = query, partMask = 0x10, auth = Sys.getenv("SYNAPSE_PAT"))
+
+  expect_identical(project_resp$reason, "syn52578158 is not a table or view")
+
+  # invalid access token (returns error message but does not error)
+  id <- "syn52578158"
+  query <- sprintf("select id from %s limit 1", id)
+  invalid_auth_resp <- synapse_table_query(id = id, query = query, partMask = 0x10, auth = "auth")
+
+  expect_identical(invalid_auth_resp$reason, "Invalid access token")
+})
+
+# TODO: Add tests for functions used in DCA dashboard modules
+# test_that("synapse_table_get success", {
+# 
+# })
+# 
+# test_that("get_synapse_table_names success", {
+#
+# })
+
+# test_that("synapse_storage_projects success", {
+# 
+# })
+# 
+# test_that("synapse_download_file_handle success", {
+#   
+# })
+# 
+# test_that("synapse_get_manifests_in_asset_view success", {
+#   
+# })