prepare task result processors for viash 0.9 (#455)

* prepare task result processors for viash 0.9 * remove assertion
openproblems-bio · May 31, 2024 · 2a8390c · 2a8390c
1 parent 907447b
commit 2a8390c
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Showing 2 changed files with 34 additions and 19 deletions.
diff --git a/src/common/process_task_results/get_method_info/script.R b/src/common/process_task_results/get_method_info/script.R
@@ -16,20 +16,28 @@ outputs <- map(configs, function(config) {
   if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") {
     return(NULL)
   }
-  info <- config$functionality$info
+
+  # prep for viash 0.9.0
+  build_info <- config$build_info %||% config$info
+  if ("functionality" %in% names(config)) {
+    config[names(config$functionality)] <- config$functionality
+    config[["functionality"]] <- NULL
+  }
+
+  info <- config$info
 
   # add extra info
-  info$config_path <- gsub(".*openproblems-v2/src/", "src/", config$info$config)
-  info$task_id <- gsub("/.*", "", config$functionality$namespace)
-  info$id <- config$functionality$name
-  info$namespace <- config$functionality$namespace
-  info$commit_sha <- config$info$git_commit %||% "missing-sha"
+  info$config_path <- gsub(".*/src/", "src/", build_info$config)
+  info$task_id <- gsub("/.*", "", config$namespace)
+  info$id <- config$name
+  info$namespace <- config$namespace
+  info$commit_sha <- build_info$git_commit %||% "missing-sha"
   info$code_version <- "missing-version"
-  info$implementation_url <- paste0(
-    "https://github.com/openproblems-bio/openproblems-v2/tree/",
-    info$commit_sha, "/",
-    info$config_path
-  )
+    info$implementation_url <- paste0(
+      build_info$git_remote, "/blob/",
+      build_info$git_commit, "/",
+      info$config_path
+    )
 
   # ↑ this could be used as the new format
 

diff --git a/src/common/process_task_results/get_metric_info/script.R b/src/common/process_task_results/get_metric_info/script.R
@@ -17,20 +17,27 @@ outputs <- map(configs, function(config) {
     return(NULL)
   }
 
+  # prep for viash 0.9.0
+  build_info <- config$build_info %||% config$info
+  if ("functionality" %in% names(config)) {
+    config[names(config$functionality)] <- config$functionality
+    config[["functionality"]] <- NULL
+  }
+
   map(
-    config$functionality$info$metrics,
+    config$info$metrics,
     function(info) {
       # add extra info
-      info$config_path <- gsub(".*openproblems-v2/src/", "src/", config$info$config)
-      info$task_id <- gsub("/.*", "", config$functionality$namespace)
+      info$config_path <- gsub(".*/src/", "src/", build_info$config)
+      info$task_id <- gsub("/.*", "", config$namespace)
       info$id <- info$name
-      info$component_id <- config$functionality$name
-      info$namespace <- config$functionality$namespace
-      info$commit_sha <- config$info$git_commit %||% "missing-sha"
+      info$component_id <- config$name
+      info$namespace <- config$namespace
+      info$commit_sha <- build_info$git_commit %||% "missing-sha"
       info$code_version <- "missing-version"
       info$implementation_url <- paste0(
-        "https://github.com/openproblems-bio/openproblems-v2/tree/",
-        info$commit_sha, "/",
+        build_info$git_remote, "/blob/",
+        build_info$git_commit, "/",
         info$config_path
       )