Merge pull request #15 from CNAG-Biomedical-Informatics/fix_rank_base…

…d_on_converted_data

Fix rank based on converted data

data/.gitignore

@@ -2,6 +2,7 @@
 uploads/rankInput/*.json
 uploads/ontologies/*.yaml
 uploads/weights/*.yaml
+uploads/config/*.yaml
 
 output/simulatedData/*.json
 output/tmp/*.json
@@ -15,3 +16,4 @@ output/rankedCohortMatrixes/*
 output/convertedData/*
 !output/convertedData/README.md
 
+

data/temp/conversionConfig.yaml

@@ -0,0 +1,12 @@
+allowed_terms:
+- Bar
+- Baz
+- Foo
+- id
+array_terms: Bar
+format: CSV
+id_correspondence:
+  CSV:
+  - Bar: Bar
+primary_key: id
+

data/temp/conversionOutput.json

@@ -0,0 +1 @@
+[{"Bar":[["bar1a"],["bar1b"]],"Baz":["baz1"],"Foo":["foo1"],"id":["PR_00000001"]},{"Bar":[["bar2a"],["bar2b"]],"Baz":["baz2"],"Foo":["foo2"],"id":["PR_00000002"]}]

phenoRankeR/R/fct_helpers.R

@@ -120,10 +120,15 @@ validateYAML <- function(yaml_input) {
 outputDownloadHandler <- function(data_sources, file_names, zip_download = FALSE) {
   downloadHandler(
     filename = function() {
+      ext <- ".json"
+      if (length(file_names) == 1 && grepl("conversionConfig", file_names)) {
+        ext <- ".yaml"
+      }
+
       if (zip_download) {
         "phenoRankerSim.zip"
       } else {
-        paste0(file_names, ".json")
+        paste0(file_names, ext)
       }
     },
     content = function(file) {
@@ -135,17 +140,53 @@ outputDownloadHandler <- function(data_sources, file_names, zip_download = FALSE
         # Need to set wd otherwise the files will be inside nested folders
         setwd(temp_dir)
 
+        # Initialize a vector to hold the full filenames with extensions
+        full_file_names <- c()
+
         for (i in seq_along(data_sources)) {
-          content_file <- file.path(paste0(file_names[i], ".json"))
-          writeLines(as.character(toJSON(data_sources[[i]])), content_file)
+
+          # check if the file is a yaml file
+          fn <- file_names[[i]]
+          print("fn")
+          print(fn)
+          if (fn == "conversionConfig") {
+            print("inside conversionConfig")
+            content_file <- file.path(paste0(fn, ".yaml"))
+            print("content_file")
+            print(content_file)
+            writeLines(data_sources[[i]], content_file)
+
+            # Add the yaml file to the vector
+            full_file_names <- c(full_file_names, paste0(fn, ".yaml"))
+
+          } else {
+            content_file <- file.path(paste0(file_names[i], ".json"))
+            writeLines(as.character(toJSON(data_sources[[i]])), content_file)
+
+            # Add the json file to the vector
+            full_file_names <- c(full_file_names, paste0(file_names[i], ".json"))
+          }
+          # content_file <- file.path(paste0(file_names[i], ".json"))
+          # writeLines(as.character(toJSON(data_sources[[i]])), content_file)
         }
         zip(
           file,
-          files = paste0(file_names, ".json")
+          # files = paste0(file_names, ".json")
+          files = full_file_names
         )
         unlink(temp_dir, recursive = TRUE)
       } else {
-        writeLines(as.character(toJSON(data_sources)), file)
+        if (grepl("conversionConfig", file_names)) {
+          print("data_sources")
+          print(data_sources)
+
+          print("file")
+          print(file)
+
+          writeLines(data_sources, file)
+        } else {
+          writeLines(as.character(toJSON(data_sources)), file)
+        }
       }
     }
   )

phenoRankeR/R/mod_conv_mode.R

@@ -142,8 +142,6 @@ mod_conv_output_viewer_server <- function(id, conv_out, cfg_out) {
     print("cfg_out")
     print(cfg_out)
 
-    # data arives here but there is nothing rendered
-
     output$conv_output_viewer <- renderUI({
       fluidRow(
         generateJsonView(conv_out, "JSON output", 6),

phenoRankeR/R/mod_patient_mode.R

@@ -874,6 +874,9 @@ mod_patient_mode_server <- function(
           paste0(timestamp,"_config.yaml")
         )
 
+        print("input$yamlEditor_config")
+        print(input$yamlEditor_config)
+
         writeLines(
           input$yamlEditor_config,
           extra_config_file_path