From 4d5a0c8c08c77a3b6bedabec71c37ac7dfc526c0 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 30 Jul 2024 01:10:59 +0200
Subject: [PATCH] analyse missing args

---
 .../_process_cwl.R                            | 99 ++++++++++++++++++-
 1 file changed, 94 insertions(+), 5 deletions(-)

diff --git a/src/bd_rhapsody/bd_rhapsody_sequence_analysis/_process_cwl.R b/src/bd_rhapsody/bd_rhapsody_sequence_analysis/_process_cwl.R
index 60fb3f81..31d8f33b 100644
--- a/src/bd_rhapsody/bd_rhapsody_sequence_analysis/_process_cwl.R
+++ b/src/bd_rhapsody/bd_rhapsody_sequence_analysis/_process_cwl.R
@@ -1,8 +1,9 @@
 library(tidyverse)
 
+# fetch and read cwl file
 lines <- read_lines("https://bitbucket.org/CRSwDev/cwl/raw/8feeace1141b24749ea6003f8e6ad6d3ad5232de/v2.2.1/rhapsody_pipeline_2.2.1.cwl")
-
-js <- jsonlite::fromJSON(lines[-1], simplifyVector = FALSE)
+cwl_header <- lines[[1]]
+cwl_obj <- jsonlite::fromJSON(lines[-1], simplifyVector = FALSE)
 
 # recursively remove objects with `"class": "DockerRequirement"`
 remove_docker <- function(x) {
@@ -18,9 +19,97 @@ remove_docker <- function(x) {
     return(x)
   }
 }
-js2 <- remove_docker(js)
+cwl_obj_2 <- remove_docker(cwl_obj)
 # js2 <- js
 
-lines2 <- c(lines[[1]], jsonlite::toJSON(js2, auto_unbox = TRUE, pretty = TRUE))
+# write to file
+new_lines <- c(cwl_header, jsonlite::toJSON(cwl_obj_2, auto_unbox = TRUE, pretty = TRUE))
+
+write_lines(new_lines, "src/bd_rhapsody/bd_rhapsody_sequence_analysis/rhapsody_pipeline_2.2.1_nodocker.cwl")
+
+# detect main workflow arguments
+gr <- dynutils::list_as_tibble(cwl_obj_2$`$graph`)
+
+gr %>% print(n = 100)
+
+main <- gr %>% filter(gr$id == "#main")
+
+main_inputs <- main$inputs[[1]]
+
+input_ids <- main_inputs %>% map_chr("id") %>% gsub("^#main/", "", .)
+
+# check whether in config
+config <- yaml::read_yaml("src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml")
+config$all_arguments <- config$argument_groups %>% map("arguments") %>% list_flatten()
+arg_names <- config$all_arguments %>% map_chr("name") %>% gsub("^--", "", .)
+
+# arguments in cwl but not in config
+setdiff(tolower(input_ids), arg_names)
+
+# arguments in config but not in cwl
+setdiff(arg_names, tolower(input_ids))
+
+# create arguments from main_inputs
+arguments <- map(main_inputs, function(main_input) {
+  input_id <- main_input$id %>% gsub("^#main/", "", .)
+  input_type <- main_input$type[[2]]
+
+  if (is.list(input_type) && input_type$type == "array") {
+    multiple <- TRUE
+    input_type <- input_type$items
+  } else {
+    multiple <- FALSE
+  }
+
+  if (is.list(input_type) && input_type$type == "enum") {
+    choices <- input_type$symbols %>%
+      gsub(paste0(input_type$name, "/"), "", .)
+    input_type <- "enum"
+  } else {
+    choices <- NULL
+  }
+
+  description <-
+    if (is.null(main_input$label)) {
+      main_input$doc
+    } else if (is.null(main_input$doc)) {
+      main_input$label
+    } else {
+      paste0(main_input$label, ". ", main_input$doc)
+    }
+
+  type_map <- c(
+    "float" = "double",
+    "int" = "integer",
+    "string" = "string",
+    "boolean" = "boolean",
+    "File" = "file",
+    "enum" = "string"
+  )
+
+  out <- list(
+    name = paste0("--", tolower(input_id)),
+    type = type_map[input_type],
+    # TODO: use summary when viash 0.9 is released
+    # summary = main_input$doc,
+    # description = main_input$doc,
+    description = description,
+    multiple = multiple,
+    choices = choices,
+    info = list(
+      config_key = input_id
+    )
+  )
+
+  out[!sapply(out, is.null)]
+})
+
+
 
-write_lines(lines2, "src/mapping/bd_rhapsody_2/rhapsody_pipeline_2.2.1_nodocker.cwl")
+yaml::write_yaml(
+  arguments,
+  "src/bd_rhapsody/bd_rhapsody_sequence_analysis/arguments.yaml",
+  handlers = list(
+    logical = yaml::verbatim_logical
+  )
+)