Merge pull request PecanProject#10 from ashiklom/custom-list

Pass additional customization list to `submit.workflow`

Author: mdietze

R/submit.workflow.R

@@ -14,6 +14,8 @@
 ##' @param sensitivity.analysis Whether or not to perform a sensitivity analysis. Can also take
 ##' a sensitivity setting object as input. Default: FALSE (logical or list)
 ##' @param notes Additional notes that the user need to specify for the submitted workflow. Default: NULL
+##' @param workflow_list_mods List of additional changes to be applied to the
+##'   workflow list. Passed to [utils::modifyList()]. Default = `list() (no changes)`.
 ##' @return Response obtained from the `POST /api/workflows/` endpoint
 ##' @author Tezan Sahu, Alexey Shiklomanov
 ##' @export
@@ -27,7 +29,8 @@
 ##'   end_date="2003-12-31", inputs=list(met=list(id=99000000003)))
 
 submit.workflow <- function(server, model_id, site_id, pfts, start_date, end_date, inputs, meta.analysis = list(),
-                            ensemble_size=1, sensitivity_variable = "NPP", sensitivity.analysis = FALSE, notes = NULL) {
+                            ensemble_size=1, sensitivity_variable = "NPP", sensitivity.analysis = FALSE, notes = NULL,
+                            workflow_list_mods = list()) {
   # Prepare the workflow based on the parameters set by user
   workflow <- list()
   workflow$pfts <- lapply(pfts, function(x) list(name = x))
@@ -80,6 +83,9 @@ submit.workflow <- function(server, model_id, site_id, pfts, start_date, end_dat
     workflow$info$notes <- notes
   }
 
+  # Apply any additional user changes (if any)
+  workflow <- modifyList(workflow, workflow_list_mods)
+
   # Submit the prepared workflow to the PEcAn API in XML format
   # NOTE: Use XML here because JSON doesn't like duplicate tags (which we use
   # for PFTs, among other things).

inst/run-test-list.R

@@ -41,11 +41,21 @@ test_list <- read.csv("inst/integration-test-list.csv", comment.char = "#") %>%
   as_tibble() %>%
   # Only test models that are available on the target machine
   inner_join(models, c("model_name", "revision")) %>%
-  mutate(start_date = if_else(is.na(start_date), default_start_date, as.character(start_date)),
-         end_date = if_else(is.na(end_date), default_end_date, as.character(end_date)),
-         # TODO: Add more inputs here
-         inputs = pmap(., configure_inputs),
-         pfts = strsplit(pfts, "|", fixed = TRUE))
+  mutate(
+    start_date = if_else(is.na(start_date), default_start_date, as.character(start_date)),
+    end_date = if_else(is.na(end_date), default_end_date, as.character(end_date)),
+    # TODO: Add more inputs here
+    inputs = pmap(., configure_inputs),
+    pfts = strsplit(pfts, "|", fixed = TRUE),
+    # ED2-specific customizations
+    workflow_list_mods = if_else(
+      model_name == "ED2.2",
+      list(list(model = list(phenol.scheme = 0,
+                             ed_misc = list(output_month = 12),
+                             edin = "ED2IN.r2.2.0"))),
+      list(list())
+    )
+  )
 
 test_runs <- test_list %>%
   select_if(colnames(.) %in% names(formals(submit.workflow))) %>%