From 708a6c29df2039665d5e4084fa53f7005c9b92ea Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 26 Oct 2023 11:30:51 -0700
Subject: [PATCH 01/41] Read in dcc config as json instead of csv. Move
 template menu config to server.R

---
 global.R | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/global.R b/global.R
index 585042df..62a303f7 100644
--- a/global.R
+++ b/global.R
@@ -35,8 +35,10 @@ plan(multicore, workers = ncores)
 source_files <- list.files(c("functions", "modules"), pattern = "*\\.R$", recursive = TRUE, full.names = TRUE)
 sapply(source_files, FUN = source)
 
-dcc_config_file <- Sys.getenv("DCA_DCC_CONFIG")
-dcc_config <- read_csv(dcc_config_file, show_col_types = FALSE)
+if (Sys.getenv("DCA_DCC_CONFIG") == "") stop("missing DCA_DCC_CONFIG environment variable")
+dca_dcc_config <- read_json(Sys.getenv("DCA_DCC_CONFIG"), simplifyVector = TRUE)
+tenants_config <- dca_dcc_config$tenants
+
 
 ## Set Up OAuth
 client_id <- Sys.getenv("DCA_CLIENT_ID")
@@ -125,11 +127,6 @@ api <- oauth_endpoint(
 # The 'openid' scope is required by the protocol for retrieving user information.
 scope <- "openid view download modify"
 
-template_config_files <- setNames(dcc_config$template_menu_config_file,
-dcc_config$synapse_asset_view)
-if (dca_schematic_api == "offline") template_config_files <- setNames("www/template_config/config_offline.json",
-  "synXXXXXX")
-
 ## Set Up Virtual Environment
 # ShinyAppys has a limit of 7000 files which this app' grossly exceeds
 # due to its Python dependencies.  To get around the limit we zip up

From 7b19f592aee7cd241373d8232817f9b25e4adec2 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 26 Oct 2023 11:31:44 -0700
Subject: [PATCH 02/41] Refactor asset view dropdown to be consistent with new
 config in global.R

---
 ui.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ui.R b/ui.R
index bcc3a80a..d39afd82 100644
--- a/ui.R
+++ b/ui.R
@@ -138,8 +138,8 @@ ui <- shinydashboardPlus::dashboardPage(
         selectInput(
           inputId = "dropdown_asset_view",
           label = NULL,
-          choices = setNames(dcc_config$synapse_asset_view,
-                 dcc_config$project_name)
+          choices = setNames(tenants_config$synapse_asset_view,
+                             tenants_config$name)
         ),
         actionButton("btn_asset_view", "Next",
         class = "btn-primary-color"

From 759bc1319ff5549ffefd450724bf7b0d2d2d6185 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 26 Oct 2023 11:32:45 -0700
Subject: [PATCH 03/41] WIP: first pass at refactoring server code to handle
 the new dcc config json file

---
 server.R | 60 ++++++++++++++++++++------------------------------------
 1 file changed, 21 insertions(+), 39 deletions(-)

diff --git a/server.R b/server.R
index c05bd399..4015ffab 100644
--- a/server.R
+++ b/server.R
@@ -34,25 +34,18 @@ shinyServer(function(input, output, session) {
   
   ######## session global variables ########
   # read config in
-  if (grepl("dev", dcc_config_file)) {
-    def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev/demo/dca-template-config.json")
-  } else if (grepl("staging", dcc_config_file)) {
-    def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/staging/demo/dca-template-config.json")
-  } else def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/dca-template-config.json")
-  
   config <- reactiveVal()
-  config_schema <- reactiveVal(def_config)
-  model_ops <- setNames(dcc_config$data_model_url,
-  dcc_config$synapse_asset_view)
+  config_schema <- reactiveVal()
   
   # mapping from display name to schema name
   template_namedList <- reactiveVal()
   
-  all_asset_views <- setNames(dcc_config$synapse_asset_view,
-  dcc_config$project_name)
+  all_asset_views <- setNames(tenants_config$synapse_asset_view,
+                              tenants_config$name)
   asset_views <- reactiveVal(c("mock dca fileview"="syn33715412"))
   
-  dcc_config_react <- reactiveVal(dcc_config)
+  dcc_config_react <- reactiveVal()
+  tenant_config_react <- reactiveVal()
   
   manifest_data <- reactiveVal()
   validation_res <- reactiveVal()
@@ -60,7 +53,7 @@ shinyServer(function(input, output, session) {
   
   data_list <- list(
     projects = reactiveVal(NA), folders = reactiveVal(NULL),
-    template = reactiveVal(setNames(def_config$schema_name, def_config$display_name)),
+    template = reactiveVal(NULL),
     files = reactiveVal(NULL),
     master_asset_view = reactiveVal(NULL)
   )
@@ -74,10 +67,11 @@ shinyServer(function(input, output, session) {
   
   isUpdateFolder <- reactiveVal(FALSE)
   
-  data_model_options <- setNames(dcc_config$data_model_url,
-    dcc_config$synapse_asset_view)
   data_model = reactiveVal(NULL)
   
+  if (dca_schematic_api == "offline") template_config_files <- setNames("www/template_config/config_offline.json",
+                                                                        "synXXXXXX")
+  
   # data available to the user
   syn_store <- NULL # gets list of projects they have access to
   
@@ -169,10 +163,18 @@ shinyServer(function(input, output, session) {
     av_names <- names(asset_views()[asset_views() %in% selected$master_asset_view()])
     selected$master_asset_view_label(av_names)
     
-    dcc_config_react(dcc_config[dcc_config$synapse_asset_view == selected$master_asset_view(), ])
-    if (dca_schematic_api == "offline") dcc_config_react(dcc_config[dcc_config$project_name == "DCA Demo", ])
+    tenant_config_react(tenants_config[tenants_config$synapse_asset_view == selected$master_asset_view(), ])
+    if (dca_schematic_api == "offline") tenant_config_react(tenants_config[tenants_config$name == "DCA Demo", ])
+    
+    dcc_config_react(read_json(tenant_config_react()$config_location))
+    
+    model_ops <- reactive(setNames(dcc_config_react()$data_model_url,
+                          dcc_config_react()$synapse_asset_view))
     
-    data_model(data_model_options[selected$master_asset_view()])
+    data_model(model_ops())
+    
+    template_config_files <- setNames(dcc_config_react()$template_menu_config_file,
+                                      dcc_config_react()$synapse_asset_view)
     
     output$sass <- renderUI({
     tags$head(tags$style(css()))
@@ -232,27 +234,7 @@ shinyServer(function(input, output, session) {
     # Use the template dropdown config file from the appropriate branch of
     # data_curator_config
     conf_file <- reactiveVal(template_config_files[input$dropdown_asset_view])
-    if (!file.exists(conf_file())){
-      if (grepl("dev", dcc_config_file)) {
-        conf_file(
-          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev",
-                    conf_file()
-          )
-        )
-      } else if (grepl("staging", dcc_config_file)) {
-        conf_file(
-          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/staging",
-                    conf_file()
-          )
-        )
-      } else {
-        conf_file(
-          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main",
-                    conf_file()
-          )
-        )
-      }
-    }
+
     config_df <- jsonlite::fromJSON(conf_file())
     
     conf_template <- setNames(config_df[[1]]$schema_name, config_df[[1]]$display_name)

From 9788024941ee401aadeacb3639357e87f4f71380 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 26 Oct 2023 12:15:22 -0700
Subject: [PATCH 04/41] update logo location for new config structure

---
 server.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/server.R b/server.R
index 4015ffab..56b69911 100644
--- a/server.R
+++ b/server.R
@@ -192,8 +192,7 @@ shinyServer(function(input, output, session) {
       color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
     
     logo_img <- ifelse(!is.na(dcc_config_react()$logo_location),
-      paste0("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/",
-        dcc_config_react()$logo_location),
+        dcc_config_react()$logo_location,
       "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/Logo_Sage_Logomark.png")
     
     logo_link <- ifelse(!is.na(dcc_config_react()$logo_link),

From 0576e86007bb49ac31b828f55c49ac0a9195e509 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 26 Oct 2023 12:23:58 -0700
Subject: [PATCH 05/41] Fix color on initial waiter screen after selecting
 asset view.

---
 server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server.R b/server.R
index 56b69911..d5641065 100644
--- a/server.R
+++ b/server.R
@@ -156,7 +156,7 @@ shinyServer(function(input, output, session) {
   # within the selected asset view.
   observeEvent(input$btn_asset_view, {
     dcWaiter("show", msg = paste0("Getting data. This may take a minute."),
-      color=col2rgba(col2rgb("#CD0BBC01")))
+      color="#2a668d")
     shinyjs::disable("btn_asset_view")
     
     selected$master_asset_view(input$dropdown_asset_view)

From 4bc9b3b796293988eb8596df48cf5a6f0801f2f1 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Fri, 27 Oct 2023 09:10:25 -0700
Subject: [PATCH 06/41] Create a variable for the root directory of the config
 file

---
 global.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/global.R b/global.R
index 62a303f7..7a91d30a 100644
--- a/global.R
+++ b/global.R
@@ -38,7 +38,7 @@ sapply(source_files, FUN = source)
 if (Sys.getenv("DCA_DCC_CONFIG") == "") stop("missing DCA_DCC_CONFIG environment variable")
 dca_dcc_config <- read_json(Sys.getenv("DCA_DCC_CONFIG"), simplifyVector = TRUE)
 tenants_config <- dca_dcc_config$tenants
-
+config_dir <- dirname(Sys.getenv("DCA_DCC_CONFIG"))
 
 ## Set Up OAuth
 client_id <- Sys.getenv("DCA_CLIENT_ID")

From 9356ecb3f1413f765dca596956c0bd696efdc2e0 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Fri, 27 Oct 2023 09:11:04 -0700
Subject: [PATCH 07/41] Combine config root dir and config filepath to read
 files.

---
 server.R | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/server.R b/server.R
index d5641065..83297e28 100644
--- a/server.R
+++ b/server.R
@@ -166,7 +166,9 @@ shinyServer(function(input, output, session) {
     tenant_config_react(tenants_config[tenants_config$synapse_asset_view == selected$master_asset_view(), ])
     if (dca_schematic_api == "offline") tenant_config_react(tenants_config[tenants_config$name == "DCA Demo", ])
     
-    dcc_config_react(read_json(tenant_config_react()$config_location))
+    dcc_config_react(read_json(
+      file.path(config_dir, tenant_config_react()$config_location))
+    )
     
     model_ops <- reactive(setNames(dcc_config_react()$data_model_url,
                           dcc_config_react()$synapse_asset_view))
@@ -192,7 +194,7 @@ shinyServer(function(input, output, session) {
       color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
     
     logo_img <- ifelse(!is.na(dcc_config_react()$logo_location),
-        dcc_config_react()$logo_location,
+        file.path(config_dir, dcc_config_react()$logo_location),
       "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/Logo_Sage_Logomark.png")
     
     logo_link <- ifelse(!is.na(dcc_config_react()$logo_link),
@@ -232,7 +234,9 @@ shinyServer(function(input, output, session) {
     }
     # Use the template dropdown config file from the appropriate branch of
     # data_curator_config
-    conf_file <- reactiveVal(template_config_files[input$dropdown_asset_view])
+    conf_file <- reactiveVal(
+      file.path(config_dir, template_config_files[input$dropdown_asset_view])
+      )
 
     config_df <- jsonlite::fromJSON(conf_file())
     

From 02958635736b592da03d64a209fa70ff35382719 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 13:35:05 -0700
Subject: [PATCH 08/41] Add functions to generate template config

---
 DESCRIPTION         |  2 +-
 NAMESPACE           |  6 +++++
 R/template_config.R | 57 +++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 64 insertions(+), 1 deletion(-)
 create mode 100644 R/template_config.R

diff --git a/DESCRIPTION b/DESCRIPTION
index b1c50b7e..01dbb94b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -6,6 +6,6 @@ Authors: Rongrong Chai, Xengie Doan, Milen Nikolov, Sujay Patil, Robert Allaway,
 License: file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Suggests: 
     covr
diff --git a/NAMESPACE b/NAMESPACE
index 69ce606e..e2614d54 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+export(create_json_template_config)
+export(create_template_config)
+export(format_edge_type)
 export(get_asset_view_table)
+export(get_display_names)
+export(graph_by_edge_type)
 export(manifest_download)
 export(manifest_generate)
 export(manifest_populate)
@@ -14,3 +19,4 @@ export(synapse_access)
 export(synapse_get)
 export(synapse_is_certified)
 export(synapse_user_profile)
+export(write_template_config)
diff --git a/R/template_config.R b/R/template_config.R
new file mode 100644
index 00000000..420b9c00
--- /dev/null
+++ b/R/template_config.R
@@ -0,0 +1,57 @@
+#' @export
+graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
+                               schema_url, relationship = "requiresDependency") {
+  req <- httr::GET(url = url,
+                   query = list(
+                     schema_url = schema_url,
+                     relationship = relationship
+                   ))
+  httr::content(req)
+}
+
+#' @export
+format_edge_type <- function(edge_types) {
+  et <- dplyr::bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], schema_name=x[[1]])))
+  et |> dplyr::filter(value %in% c("Component", "Filename")) |> 
+    dplyr::group_by(schema_name) |> 
+    dplyr::summarise(file_based = "Filename" %in% value)
+}
+
+#' @export
+get_display_names <- function(qlist) {
+  if (!"schema_url" %in% names(qlist)) stop("qlist needs element named `schema_url`")
+  if (!"node_list" %in% names(qlist)) stop("qlist needs at least one element named `node_list`")
+  httr::GET(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get_nodes_display_names",
+            query = qlist
+  )
+}
+
+#' @export
+create_template_config <- function(data_model) {
+  edges <- graph_by_edge_type(schema_url = data_model)
+  schema_names <- format_edge_type(edges)
+  nl <- setNames(as.list(schema_names$schema_name), rep("node_list", length(schema_names$schema_name)))
+  dnames <- get_display_names(c(schema_url = data_model, nl)) |> httr::content()
+  data.frame(display_name = unlist(dnames), schema_name = unlist(nl)) |>
+    dplyr::left_join(schema_names, by = "schema_name") |>
+    dplyr::mutate(type = ifelse(file_based, "file", "record")) |>
+    dplyr::select(-file_based)
+}
+
+#' @export
+create_json_template_config <- function(data_model) {
+  df <- create_template_config(data_model)
+  schematic_version <- httr::GET("https://schematic-dev.api.sagebionetworks.org/v1/version") |>
+    httr::content()
+  list(
+    manifest_schemas = df,
+    service_version = schematic_version,
+    schema_version = ""
+  )
+}
+
+#' @export
+write_template_config <- function(data_model, file) {
+  df <- create_json_template_config(data_model)
+  jsonlite::write_json(data_model, file)
+}

From 1787935846e0f9b637db1bfca72f58a69259fc0d Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 14:13:53 -0700
Subject: [PATCH 09/41] add httr to imports

---
 DESCRIPTION | 1 +
 NAMESPACE   | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 01dbb94b..8187773d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,5 +7,6 @@ License: file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+Imports: httr
 Suggests: 
     covr
diff --git a/NAMESPACE b/NAMESPACE
index e2614d54..ec428efc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -20,3 +20,5 @@ export(synapse_get)
 export(synapse_is_certified)
 export(synapse_user_profile)
 export(write_template_config)
+importFrom(httr,GET)
+importFrom(httr,content)

From 14188c88c9ebc51b932bbb1a057efcdac90b83ff Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 14:16:42 -0700
Subject: [PATCH 10/41] add dplyr and jsonlite to imports

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8187773d..e4c778ef 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,6 +7,6 @@ License: file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Imports: httr
+Imports: httr, dplyr, jsonlite
 Suggests: 
     covr

From afe02176d8bf9b0f9946a168d1767fe6d634b08d Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 14:26:19 -0700
Subject: [PATCH 11/41] use df not argument

---
 R/template_config.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index 420b9c00..5aff82da 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -1,4 +1,5 @@
 #' @export
+#' @importFrom httr GET content
 graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
                                schema_url, relationship = "requiresDependency") {
   req <- httr::GET(url = url,
@@ -53,5 +54,5 @@ create_json_template_config <- function(data_model) {
 #' @export
 write_template_config <- function(data_model, file) {
   df <- create_json_template_config(data_model)
-  jsonlite::write_json(data_model, file)
+  jsonlite::write_json(df, file)
 }

From db1827af0eb9cc5cf6ff02cd916353e23f76662b Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 14:29:22 -0700
Subject: [PATCH 12/41] add pretty and flatten argument to write json

---
 R/template_config.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index 5aff82da..03ad2423 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -54,5 +54,5 @@ create_json_template_config <- function(data_model) {
 #' @export
 write_template_config <- function(data_model, file) {
   df <- create_json_template_config(data_model)
-  jsonlite::write_json(df, file)
+  jsonlite::write_json(df, file, pretty = TRUE, flatten = TRUE)
 }

From 2c97e9ffd8615beccb82fdcfcd7107fc30a53661 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 14:34:27 -0700
Subject: [PATCH 13/41] use autounbox to write config

---
 R/template_config.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index 03ad2423..b0548147 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -54,5 +54,5 @@ create_json_template_config <- function(data_model) {
 #' @export
 write_template_config <- function(data_model, file) {
   df <- create_json_template_config(data_model)
-  jsonlite::write_json(df, file, pretty = TRUE, flatten = TRUE)
+  jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)
 }

From c903aed863c2d0e3f2216a4dc50c5a5d2c63b18f Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:10:50 -0800
Subject: [PATCH 14/41] put graph_by_edge_type in schematic rest api file

---
 R/schematic_rest_api.R | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/R/schematic_rest_api.R b/R/schematic_rest_api.R
index c2db54ad..6e293987 100644
--- a/R/schematic_rest_api.R
+++ b/R/schematic_rest_api.R
@@ -317,3 +317,17 @@ get_asset_view_table <- function(url="http://localhost:3001/v1/storage/assets/ta
   
 }
 
+#' @param url URL of schematic API endpoint
+#' @param schema_url URL of data model
+#' @param relationship Argument to schematic graph_by_edge_type
+#' @export
+#' @importFrom httr GET content
+graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
+                               schema_url, relationship = "requiresDependency") {
+  req <- httr::GET(url = url,
+                   query = list(
+                     schema_url = schema_url,
+                     relationship = relationship
+                   ))
+  httr::content(req)
+}

From 11c164d034377ce4f40dc4878430ce14c1ef6605 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:11:19 -0800
Subject: [PATCH 15/41] Clarify function names

---
 R/template_config.R | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

diff --git a/R/template_config.R b/R/template_config.R
index b0548147..060da0e3 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -1,15 +1,3 @@
-#' @export
-#' @importFrom httr GET content
-graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
-                               schema_url, relationship = "requiresDependency") {
-  req <- httr::GET(url = url,
-                   query = list(
-                     schema_url = schema_url,
-                     relationship = relationship
-                   ))
-  httr::content(req)
-}
-
 #' @export
 format_edge_type <- function(edge_types) {
   et <- dplyr::bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], schema_name=x[[1]])))
@@ -40,7 +28,7 @@ create_template_config <- function(data_model) {
 }
 
 #' @export
-create_json_template_config <- function(data_model) {
+create_dca_template_config <- function(data_model) {
   df <- create_template_config(data_model)
   schematic_version <- httr::GET("https://schematic-dev.api.sagebionetworks.org/v1/version") |>
     httr::content()
@@ -51,8 +39,8 @@ create_json_template_config <- function(data_model) {
   )
 }
 
-#' @export
-write_template_config <- function(data_model, file) {
+# Create a DCA-specific template generation function
+write_dca_template_config <- function(data_model, file) {
   df <- create_json_template_config(data_model)
   jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)
 }

From 9da3090219a9921e1684e591286da97296cd1637 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:13:06 -0800
Subject: [PATCH 16/41] export write_dca_template_config

---
 R/template_config.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index 060da0e3..52370104 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -39,7 +39,8 @@ create_dca_template_config <- function(data_model) {
   )
 }
 
-# Create a DCA-specific template generation function
+#' @export
+#' @description Create a DCA-specific template generation function
 write_dca_template_config <- function(data_model, file) {
   df <- create_json_template_config(data_model)
   jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)

From 0c76c2ae43e7b426b07d0f774aa6cfac168ffe58 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:19:26 -0800
Subject: [PATCH 17/41] export write_dca_template_config

---
 NAMESPACE | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index ec428efc..61256a54 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(create_json_template_config)
+export(create_dca_template_config)
 export(create_template_config)
 export(format_edge_type)
 export(get_asset_view_table)
@@ -19,6 +19,5 @@ export(synapse_access)
 export(synapse_get)
 export(synapse_is_certified)
 export(synapse_user_profile)
-export(write_template_config)
 importFrom(httr,GET)
 importFrom(httr,content)

From 59c714bd9bf2d883fda6a6dacca54a1c247dbabc Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:24:04 -0800
Subject: [PATCH 18/41] export write_dca_template_config for real

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index 61256a54..f36e80b2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -19,5 +19,6 @@ export(synapse_access)
 export(synapse_get)
 export(synapse_is_certified)
 export(synapse_user_profile)
+export(write_dca_template_config)
 importFrom(httr,GET)
 importFrom(httr,content)

From b285343ea756a1621e1b964a280189c845f966d4 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:26:34 -0800
Subject: [PATCH 19/41] fix function name in write_dca_template_config

---
 R/template_config.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index 52370104..51272b45 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -42,6 +42,6 @@ create_dca_template_config <- function(data_model) {
 #' @export
 #' @description Create a DCA-specific template generation function
 write_dca_template_config <- function(data_model, file) {
-  df <- create_json_template_config(data_model)
+  df <- create_dca_json_template_config(data_model)
   jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)
 }

From 05dc6577a2f5bfb1b2e3e954c55118d7355a1ec9 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:30:09 -0800
Subject: [PATCH 20/41] fix function name in write_dca_template_config again

---
 R/template_config.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index 51272b45..d341a767 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -42,6 +42,6 @@ create_dca_template_config <- function(data_model) {
 #' @export
 #' @description Create a DCA-specific template generation function
 write_dca_template_config <- function(data_model, file) {
-  df <- create_dca_json_template_config(data_model)
+  df <- create_dca_template_config(data_model)
   jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)
 }

From d583b95afdf4d2d5f3fc2ee9a88b41ac027a1331 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 10:14:54 -0800
Subject: [PATCH 21/41] remove dca and schematic version from footer

---
 ui.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/ui.R b/ui.R
index 60070479..532bb9f7 100644
--- a/ui.R
+++ b/ui.R
@@ -124,7 +124,7 @@ ui <- shinydashboardPlus::dashboardPage(
   ),
   uiOutput("sass"),
   # load dependencies
-  use_notiflix_report(width = "400px"),
+  use_notiflix_report(width = "500px", messageMaxLength = 10000),
   use_waiter(),
   tabItems(
   # second tab content
@@ -298,9 +298,6 @@ ui <- shinydashboardPlus::dashboardPage(
   ),
   # waiter loading screen
   dcWaiter("show", landing = TRUE)
-  ),
-  footer = dashboardFooter(
-    left = sprintf("DCA %s - Schematic %s", dca_version, schematic_version)
   )
 )
 

From 403e10c5ddcc9885571123b185e22bcf88854381 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 10:15:24 -0800
Subject: [PATCH 22/41] display dcc and portal help links if set

---
 server.R | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/server.R b/server.R
index abc7a345..8cab7d20 100644
--- a/server.R
+++ b/server.R
@@ -309,13 +309,21 @@ shinyServer(function(input, output, session) {
   })
   
   observeEvent(input$info_box, {
+    
+    data_model_link <- ifelse(dcc_config_react()$data_model_info == "",
+                              dcc_config_react()$data_model_url,
+                              dcc_config_react()$data_model_info)
+    dca_help_link <- ifelse(is.null(dcc_config_react()$dca_help_link), "", dcc_config_react()$dca_help_link)
+    portal_help_link <- ifelse(is.null(dcc_config_react()$portal_help_link), "", dcc_config_react()$portal_help_link)
+    
     nx_report_info(
-      title = "App Info",
+      title = "About Data Curator",
       tags$ul(
-        tags$li("DCA Help Docs: ", "todo"),
-        tags$li("Portal Help Docs: ", "todo"),
-        tags$li("Data model: ", data_model()),
-        tags$li("Asset view: ", selected$master_asset_view()),
+        #tags$li(tags$a(href = "https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/2732818485/Data+Curator+App+Setup+for+DCCs+and+Science+Teams+at+Sage", "DCA Help Docs", target = "_blank")),
+        if (dca_help_link != "") tags$li(tags$a(href = dca_help_link, "DCA Help Docs", target = "_blank")),
+        if (portal_help_link != "") tags$li(tags$a(href = portal_help_link, "Portal Help Docs", target = "_blank")),
+        if (data_model_link != "") tags$li(tags$a(href = data_model_link, "Data Model Info", target = "_blank")),
+        tags$li(tags$a(href = paste0("https://www.synapse.org/#!Synapse:", selected$master_asset_view()), paste("Asset View:", selected$master_asset_view()), target = "_blank")),
         tags$li("DCA version: ", dca_version),
         tags$li("Schematic version: ", schematic_version),
       )

From 6549cda9be47b080ef262bb863d382c565b136a5 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 15:28:54 -0800
Subject: [PATCH 23/41] Use nested structure for dca_config and only reference
 primary_col in once place

---
 server.R | 84 +++++++++++++++++++++++++++++---------------------------
 1 file changed, 43 insertions(+), 41 deletions(-)

diff --git a/server.R b/server.R
index 8cab7d20..0d4bdfe8 100644
--- a/server.R
+++ b/server.R
@@ -170,35 +170,37 @@ shinyServer(function(input, output, session) {
       file.path(config_dir, tenant_config_react()$config_location))
     )
     
-    model_ops <- reactive(setNames(dcc_config_react()$data_model_url,
-                          dcc_config_react()$synapse_asset_view))
+    model_ops <- reactive(setNames(dcc_config_react()$dcc$data_model_url,
+                          dcc_config_react()$dcc$synapse_asset_view))
     
     data_model(model_ops())
     
-    template_config_files <- setNames(dcc_config_react()$template_menu_config_file,
-                                      dcc_config_react()$synapse_asset_view)
+    template_config_files <- setNames(dcc_config_react()$dcc$template_menu_config_file,
+                                      dcc_config_react()$dcc$synapse_asset_view)
     
     output$sass <- renderUI({
     tags$head(tags$style(css()))
     })
+    
+    primary_col <- reactive(col2rgba(dcc_config_react()$dca$primary_col, 255*0.9))
     css <- reactive({
     # Don't change theme for default projects
-    sass(input = list(primary_col=dcc_config_react()$primary_col,
-      htan_col=dcc_config_react()$secondary_col,
-      sidebar_col=dcc_config_react()$sidebar_col,
+    sass(input = list(primary_col=dcc_config_react()$dca$primary_col,
+      htan_col=dcc_config_react()$dca$secondary_col,
+      sidebar_col=dcc_config_react()$dca$sidebar_col,
       sass_file("www/scss/main.scss")))
     })
     
     dcWaiter("hide")
     dcWaiter("show", msg = paste0("Getting data. This may take a minute."),
-      color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
+      color = primary_col())
     
-    logo_img <- ifelse(!is.na(dcc_config_react()$logo_location),
-        file.path(config_dir, dcc_config_react()$logo_location),
+    logo_img <- ifelse(!is.na(dcc_config_react()$dcc$logo_location),
+        file.path(config_dir, dcc_config_react()$dcc$logo_location),
       "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/Logo_Sage_Logomark.png")
     
-    logo_link <- ifelse(!is.na(dcc_config_react()$logo_link),
-      dcc_config_react()$logo_link,
+    logo_link <- ifelse(!is.na(dcc_config_react()$dcc$logo_link),
+      dcc_config_react()$dcc$logo_link,
       "https://synapse.org"
     )
     
@@ -310,11 +312,11 @@ shinyServer(function(input, output, session) {
   
   observeEvent(input$info_box, {
     
-    data_model_link <- ifelse(dcc_config_react()$data_model_info == "",
-                              dcc_config_react()$data_model_url,
-                              dcc_config_react()$data_model_info)
-    dca_help_link <- ifelse(is.null(dcc_config_react()$dca_help_link), "", dcc_config_react()$dca_help_link)
-    portal_help_link <- ifelse(is.null(dcc_config_react()$portal_help_link), "", dcc_config_react()$portal_help_link)
+    data_model_link <- ifelse(dcc_config_react()$dcc$data_model_info == "",
+                              dcc_config_react()$dcc$data_model_url,
+                              dcc_config_react()$dcc$data_model_info)
+    dca_help_link <- ifelse(is.null(dcc_config_react()$dcc$dca_help_link), "", dcc_config_react()$dcc$dca_help_link)
+    portal_help_link <- ifelse(is.null(dcc_config_react()$dcc$portal_help_link), "", dcc_config_react()$dcc$portal_help_link)
     
     nx_report_info(
       title = "About Data Curator",
@@ -335,7 +337,7 @@ shinyServer(function(input, output, session) {
   observeEvent(input$btn_project, {
     ######## Update Folder List ########
     dcWaiter("show", msg = paste0("Getting data"),
-    color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
+    color = primary_col())
     shinyjs::disable("btn_project")
     selected$project(data_list$projects()[names(data_list$projects()) == input$dropdown_project])
     
@@ -407,7 +409,7 @@ shinyServer(function(input, output, session) {
   # Goal of this button is to updpate the template reactive object
   # with the template the user chooses
   observeEvent(input$btn_template_select, {
-    dcWaiter("show", msg = "Please wait", color = col2rgba(dcc_config_react()$primary_col, 255*0.9), sleep=0)
+    dcWaiter("show", msg = "Please wait", color = primary_col(), sleep=0)
     shinyjs::disable("btn_template_select")
     selected$schema(data_list$template()[input$dropdown_template])
     shinyjs::show(select = "li:nth-child(5)")
@@ -427,7 +429,7 @@ shinyServer(function(input, output, session) {
   # Goal of this button is to get the files within a folder the user selects
   observeEvent(input$btn_folder, {
   
-    dcWaiter("show", msg = paste0("Getting data"), color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
+    dcWaiter("show", msg = paste0("Getting data"), color = primary_col())
     shinyjs::disable("btn_folder")
     shinyjs::show(select = "li:nth-child(4)")
 
@@ -586,7 +588,7 @@ shinyServer(function(input, output, session) {
   observeEvent(c(input$`switchTab4-Next`, input$tabs), {
   
     req(input$tabs == "tab_template")
-    dcWaiter("show", msg = "Getting template. This may take a minute.", color = dcc_config_react()$primary_col)
+    dcWaiter("show", msg = "Getting template. This may take a minute.", color = dcc_config_react()$dca$primary_col)
     
     ### This doesn't work - try moving manifest_generate outside of downloadButton
     .schema <- selected$schema()
@@ -594,15 +596,15 @@ shinyServer(function(input, output, session) {
     .schema_url <- data_model()
     .asset_view <- selected$master_asset_view()
     .template <- paste(
-      dcc_config_react()$project_name,
+      dcc_config_react()$dcc$project_name,
       "-",
       input$dropdown_template
     )
     .url <- ifelse(dca_schematic_api != "offline",
     file.path(api_uri, "v1/manifest/generate"),
     NA)
-    .output_format <- dcc_config_react()$manifest_output_format
-    .use_annotations <- dcc_config_react()$manifest_use_annotations
+    .output_format <- dcc_config_react()$schematic$manifest_generate$output_format
+    .use_annotations <- dcc_config_react()$schematic$manifest_generate$use_annotations
     
     promises::future_promise({
       try({
@@ -642,7 +644,7 @@ shinyServer(function(input, output, session) {
       shinyjs::enable("btn_template_select")
       updateTabsetPanel(session, "tab_template_select")
     } else {
-      if (dcc_config_react()$manifest_output_format == "google_sheet") {
+      if (dcc_config_react()$schematic$manifest_generate$output_format == "google_sheet") {
         shinyjs::show("div_template")
       } else shinyjs::show("div_download_data")
     }
@@ -660,7 +662,7 @@ shinyServer(function(input, output, session) {
     filename = function() sprintf("%s.xlsx", input$dropdown_template),
     #filename = function() sprintf("%s.csv", input$dropdown_template),
     content = function(file) {
-    dcWaiter("show", msg = "Downloading data", color = dcc_config_react()$primary_col)
+    dcWaiter("show", msg = "Downloading data", color = dcc_config_react()$dca$primary_col)
     dcWaiter("hide", sleep = 0)
     writeBin(manifest_data(), file)
     }
@@ -705,7 +707,7 @@ shinyServer(function(input, output, session) {
   ######## Validation Section #######
   observeEvent(input$btn_validate, {
   
-    dcWaiter("show", msg = "Validating manifest. This may take a minute.", color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
+    dcWaiter("show", msg = "Validating manifest. This may take a minute.", color = primary_col())
     
     # Reset validation_result in case user reuploads the same file. This makes
     # the validation_res observer trigger any time this button is pressed.
@@ -718,7 +720,7 @@ shinyServer(function(input, output, session) {
     .data_model <- data_model()
     .infile_data <- inFile$data()
     .dd_template <- input$dropdown_template
-    .restrict_rules <- dcc_config_react()$validate_restrict_rules
+    .restrict_rules <- dcc_config_react()$schematic$model_validate$restrict_rules
     
     promises::future_promise({
       annotation_status <- switch(dca_schematic_api,
@@ -774,7 +776,7 @@ shinyServer(function(input, output, session) {
         dcWaiter("update", msg = paste0(validation_res()$error_type, " Found !!! "), spin = spin_inner_circles(), sleep = 2.5)
         shinyjs::show("box_submit")
       } else {
-          if (dca_schematic_api != "offline" & dcc_config_react()$manifest_output_format == "google_sheet") {
+          if (dca_schematic_api != "offline" & dcc_config_react()$schematic$manifest_generate$output_format == "google_sheet") {
           #output$val_gsheet <- renderUI(
           #actionButton("btn_val_gsheet", "  Generate Google Sheet Link", icon = icon("table"), class = "btn-primary-color")
           #)
@@ -796,7 +798,7 @@ shinyServer(function(input, output, session) {
   # if user click gsheet_btn, generating gsheet
   observeEvent(input$btn_val_gsheet, {
     # loading screen for Google link generation
-    dcWaiter("show", msg = "Generating link...", color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
+    dcWaiter("show", msg = "Generating link...", color = primary_col())
     filled_manifest <- switch(dca_schematic_api,
       reticulate = manifest_populate_py(paste0(config$community, " ", input$dropdown_template),
         inFile$raw()$datapath,
@@ -832,7 +834,7 @@ shinyServer(function(input, output, session) {
   ######## Submission Section ########
   observeEvent(input$btn_submit, {
     # loading screen for submitting data
-    dcWaiter("show", msg = "Submitting data. This may take a minute.", color = col2rgba(dcc_config_react()$primary_col, 255*0.9))
+    dcWaiter("show", msg = "Submitting data. This may take a minute.", color = primary_col())
     
     
     if (is.null(selected$folder())) {
@@ -896,11 +898,11 @@ shinyServer(function(input, output, session) {
       .data_model <- data_model()
       .schema <- selected$schema()
       .asset_view <- selected$master_asset_view()
-      .submit_use_schema_labels <- dcc_config_react()$submit_use_schema_labels
-      .table_manipulation <- dcc_config_react()$submit_table_manipulation
-      .submit_manifest_record_type <- dcc_config_react()$submit_manifest_record_type
-      .restrict_rules <- dcc_config_react()$validate_restrict_rules
-      .hide_blanks <- dcc_config_react()$submit_hide_blanks
+      .submit_use_schema_labels <- dcc_config_react()$schematic$model_submit$use_schema_labels
+      .table_manipulation <- dcc_config_react()$schematic$model_submit$table_manipulation
+      .submit_manifest_record_type <- dcc_config_react()$schematic$model_submit$manifest_record_type
+      .restrict_rules <- dcc_config_react()$schematic$model_validate$restrict_rules
+      .hide_blanks <- dcc_config_react()$schematic$model_submit$hide_blanks
       
       # associates metadata with data and returns manifest id
       promises::future_promise({
@@ -941,11 +943,11 @@ shinyServer(function(input, output, session) {
     .data_model <- data_model()
     .schema <- selected$schema()
     .asset_view <- selected$master_asset_view()
-    .submit_use_schema_labels <- dcc_config_react()$submit_use_schema_labels
-    .table_manipulation <- dcc_config_react()$submit_table_manipulation
-    .submit_manifest_record_type <- dcc_config_react()$submit_manifest_record_type
-    .restrict_rules <- dcc_config_react()$validate_restrict_rules
-    .hide_blanks <- dcc_config_react()$submit_hide_blanks
+    .submit_use_schema_labels <- dcc_config_react()$schematic$model_submit$use_schema_labels
+    .table_manipulation <- dcc_config_react()$schematic$model_submit$table_manipulation
+    .submit_manifest_record_type <- dcc_config_react()$schematic$model_submit$manifest_record_type
+    .restrict_rules <- dcc_config_react()$schematic$model_validate$restrict_rules
+    .hide_blanks <- dcc_config_react()$schematic$model_submit$hide_blanks
     # associates metadata with data and returns manifest id
     promises::future_promise({
       try({

From fe1e76ad5909eae54b74e9561f173875e337f729 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 8 Nov 2023 16:05:45 -0800
Subject: [PATCH 24/41] When determining which components are file- or
 record-based, filter to all components first, then use this to filter against
 attributes that depend on component and filename

---
 R/template_config.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index d341a767..6d2b47b6 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -1,9 +1,13 @@
 #' @export
 format_edge_type <- function(edge_types) {
   et <- dplyr::bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], schema_name=x[[1]])))
+  components <- et |>
+    dplyr::filter(, tolower(value) == "component") |>
+    dplyr::pull(schema_name)
   et |> dplyr::filter(value %in% c("Component", "Filename")) |> 
     dplyr::group_by(schema_name) |> 
-    dplyr::summarise(file_based = "Filename" %in% value)
+    dplyr::summarise(file_based = "Filename" %in% value) %>%
+    dplyr::filter(schema_name %in% components)
 }
 
 #' @export

From 0a7cc6c98c5191cbfbd73afadc895f9f2f324635 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 8 Nov 2023 17:02:02 -0800
Subject: [PATCH 25/41] Add options to include or exclude schemas from template
 config

---
 R/template_config.R | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/R/template_config.R b/R/template_config.R
index 6d2b47b6..59da14c7 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -20,20 +20,24 @@ get_display_names <- function(qlist) {
 }
 
 #' @export
-create_template_config <- function(data_model) {
+create_template_config <- function(data_model, include_schemas=NULL, exclude_schemas=NULL) {
+  if (!is.null(include_schemas) & !is.null(exclude_schemas)) stop("include_schemas and exclude_schemas cannot both have values")
   edges <- graph_by_edge_type(schema_url = data_model)
   schema_names <- format_edge_type(edges)
   nl <- setNames(as.list(schema_names$schema_name), rep("node_list", length(schema_names$schema_name)))
   dnames <- get_display_names(c(schema_url = data_model, nl)) |> httr::content()
-  data.frame(display_name = unlist(dnames), schema_name = unlist(nl)) |>
+  config <- data.frame(display_name = unlist(dnames), schema_name = unlist(nl)) |>
     dplyr::left_join(schema_names, by = "schema_name") |>
     dplyr::mutate(type = ifelse(file_based, "file", "record")) |>
     dplyr::select(-file_based)
+  if (!is.null(include_schemas)) config <- dplyr::filter(config, schema_name %in% include_schemas)
+  if (!is.null(exclude_schemas)) config <- dplyr::filter(config, !schema_name %in% exclude_schemas)
+  config
 }
 
 #' @export
-create_dca_template_config <- function(data_model) {
-  df <- create_template_config(data_model)
+create_dca_template_config <- function(data_model, include_schemas=NULL, exclude_schemas=NULL) {
+  df <- create_template_config(data_model, include_schemas, exclude_schemas)
   schematic_version <- httr::GET("https://schematic-dev.api.sagebionetworks.org/v1/version") |>
     httr::content()
   list(
@@ -45,7 +49,7 @@ create_dca_template_config <- function(data_model) {
 
 #' @export
 #' @description Create a DCA-specific template generation function
-write_dca_template_config <- function(data_model, file) {
-  df <- create_dca_template_config(data_model)
+write_dca_template_config <- function(data_model, file, include_schemas, exclude_schemas) {
+  df <- create_dca_template_config(data_model, include_schemas, exclude_schemas)
   jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)
 }

From 491f6d951225e7dd9f36ee88ddc673d3edd8c8d5 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 9 Nov 2023 13:44:00 -0800
Subject: [PATCH 26/41] default include_schemas and exclude_schemas to NULL.
 Check if values are in the data model

---
 R/template_config.R | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/R/template_config.R b/R/template_config.R
index 59da14c7..f322b940 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -21,7 +21,7 @@ get_display_names <- function(qlist) {
 
 #' @export
 create_template_config <- function(data_model, include_schemas=NULL, exclude_schemas=NULL) {
-  if (!is.null(include_schemas) & !is.null(exclude_schemas)) stop("include_schemas and exclude_schemas cannot both have values")
+  if (!is.null(include_schemas) && !is.null(exclude_schemas)) stop("include_schemas and exclude_schemas cannot both have values")
   edges <- graph_by_edge_type(schema_url = data_model)
   schema_names <- format_edge_type(edges)
   nl <- setNames(as.list(schema_names$schema_name), rep("node_list", length(schema_names$schema_name)))
@@ -30,8 +30,14 @@ create_template_config <- function(data_model, include_schemas=NULL, exclude_sch
     dplyr::left_join(schema_names, by = "schema_name") |>
     dplyr::mutate(type = ifelse(file_based, "file", "record")) |>
     dplyr::select(-file_based)
-  if (!is.null(include_schemas)) config <- dplyr::filter(config, schema_name %in% include_schemas)
-  if (!is.null(exclude_schemas)) config <- dplyr::filter(config, !schema_name %in% exclude_schemas)
+  if (!is.null(include_schemas)) {
+    if (any(length(x <- setdiff(include_schemas, config$schema_name)))) stop(sprintf("%s is not a schema name in the data model", x))
+    config <- dplyr::filter(config, schema_name %in% include_schemas)
+  }
+  if (!is.null(exclude_schemas)) {
+    if (any(length(y <- setdiff(exclude_schemas, config$schema_name)))) stop(sprintf("%s is not a schema name in the data model", y))
+    config <- dplyr::filter(config, !schema_name %in% exclude_schemas)
+  }
   config
 }
 

From c0e749e6474fa9968d3973077ce4c4591a2d871f Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 9 Nov 2023 14:09:32 -0800
Subject: [PATCH 27/41] set include_schemas and exclude_schemas to NULL

---
 R/template_config.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index f322b940..1cbb891d 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -55,7 +55,7 @@ create_dca_template_config <- function(data_model, include_schemas=NULL, exclude
 
 #' @export
 #' @description Create a DCA-specific template generation function
-write_dca_template_config <- function(data_model, file, include_schemas, exclude_schemas) {
+write_dca_template_config <- function(data_model, file, include_schemas=NULL, exclude_schemas=NULL) {
   df <- create_dca_template_config(data_model, include_schemas, exclude_schemas)
   jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)
 }

From e4bbc21364c7ad4043bf973188ea7b698546ddd0 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 9 Nov 2023 14:13:07 -0800
Subject: [PATCH 28/41] use base pipe operator

---
 R/template_config.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/template_config.R b/R/template_config.R
index 1cbb891d..2844d9a3 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -6,7 +6,7 @@ format_edge_type <- function(edge_types) {
     dplyr::pull(schema_name)
   et |> dplyr::filter(value %in% c("Component", "Filename")) |> 
     dplyr::group_by(schema_name) |> 
-    dplyr::summarise(file_based = "Filename" %in% value) %>%
+    dplyr::summarise(file_based = "Filename" %in% value) |>
     dplyr::filter(schema_name %in% components)
 }
 

From ebe4ed39e72b9c151d319e8f92cd20aad49fe017 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 9 Nov 2023 14:26:07 -0800
Subject: [PATCH 29/41] remove empty argument from filter

---
 R/template_config.R | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/R/template_config.R b/R/template_config.R
index 2844d9a3..f421bd8c 100644
--- a/R/template_config.R
+++ b/R/template_config.R
@@ -1,11 +1,12 @@
 #' @export
 format_edge_type <- function(edge_types) {
-  et <- dplyr::bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], schema_name=x[[1]])))
+  et <- dplyr::bind_rows(lapply(edge_types, function(x) data.frame(value = x[[2]], schema_name = x[[1]])))
   components <- et |>
-    dplyr::filter(, tolower(value) == "component") |>
+    dplyr::filter(tolower(value) == "component") |>
     dplyr::pull(schema_name)
-  et |> dplyr::filter(value %in% c("Component", "Filename")) |> 
-    dplyr::group_by(schema_name) |> 
+  et |>
+    dplyr::filter(value %in% c("Component", "Filename")) |>
+    dplyr::group_by(schema_name) |>
     dplyr::summarise(file_based = "Filename" %in% value) |>
     dplyr::filter(schema_name %in% components)
 }
@@ -14,13 +15,14 @@ format_edge_type <- function(edge_types) {
 get_display_names <- function(qlist) {
   if (!"schema_url" %in% names(qlist)) stop("qlist needs element named `schema_url`")
   if (!"node_list" %in% names(qlist)) stop("qlist needs at least one element named `node_list`")
-  httr::GET(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get_nodes_display_names",
-            query = qlist
+  httr::GET(
+    url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get_nodes_display_names",
+    query = qlist
   )
 }
 
 #' @export
-create_template_config <- function(data_model, include_schemas=NULL, exclude_schemas=NULL) {
+create_template_config <- function(data_model, include_schemas = NULL, exclude_schemas = NULL) {
   if (!is.null(include_schemas) && !is.null(exclude_schemas)) stop("include_schemas and exclude_schemas cannot both have values")
   edges <- graph_by_edge_type(schema_url = data_model)
   schema_names <- format_edge_type(edges)
@@ -42,7 +44,7 @@ create_template_config <- function(data_model, include_schemas=NULL, exclude_sch
 }
 
 #' @export
-create_dca_template_config <- function(data_model, include_schemas=NULL, exclude_schemas=NULL) {
+create_dca_template_config <- function(data_model, include_schemas = NULL, exclude_schemas = NULL) {
   df <- create_template_config(data_model, include_schemas, exclude_schemas)
   schematic_version <- httr::GET("https://schematic-dev.api.sagebionetworks.org/v1/version") |>
     httr::content()
@@ -55,7 +57,7 @@ create_dca_template_config <- function(data_model, include_schemas=NULL, exclude
 
 #' @export
 #' @description Create a DCA-specific template generation function
-write_dca_template_config <- function(data_model, file, include_schemas=NULL, exclude_schemas=NULL) {
+write_dca_template_config <- function(data_model, file, include_schemas = NULL, exclude_schemas = NULL) {
   df <- create_dca_template_config(data_model, include_schemas, exclude_schemas)
   jsonlite::write_json(df, file, pretty = TRUE, auto_unbox = TRUE)
 }

From 18db322be9cf7e8f1ab0f207cacc0c18e6244990 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Fri, 10 Nov 2023 10:19:18 -0800
Subject: [PATCH 30/41] Update info panel for json config

---
 server.R | 54 ++++++++++++++++++++----------------------------------
 1 file changed, 20 insertions(+), 34 deletions(-)

diff --git a/server.R b/server.R
index d594bb74..1be601b8 100644
--- a/server.R
+++ b/server.R
@@ -34,12 +34,6 @@ shinyServer(function(input, output, session) {
   
   ######## session global variables ########
   # read config in
-  if (grepl("dev", dcc_config_file)) {
-    def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev-old/demo/dca-template-config.json")
-  } else if (grepl("staging", dcc_config_file)) {
-    def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/staging/demo/dca-template-config.json")
-  } else def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/dca-template-config.json")
-  
   config <- reactiveVal()
   config_schema <- reactiveVal()
   
@@ -57,6 +51,8 @@ shinyServer(function(input, output, session) {
   validation_res <- reactiveVal()
   manifest_id <- reactiveVal()
   
+  primary_col <- reactiveVal()
+  
   data_list <- list(
     projects = reactiveVal(NA), folders = reactiveVal(NULL),
     template = reactiveVal(NULL),
@@ -188,7 +184,7 @@ shinyServer(function(input, output, session) {
     tags$head(tags$style(css()))
     })
     
-    primary_col <- reactive(col2rgba(dcc_config_react()$dca$primary_col, 255*0.9))
+    primary_col(col2rgba(dcc_config_react()$dca$primary_col, 255*0.9))
     css <- reactive({
     # Don't change theme for default projects
     sass(input = list(primary_col=dcc_config_react()$dca$primary_col,
@@ -242,28 +238,7 @@ shinyServer(function(input, output, session) {
     }
     # Use the template dropdown config file from the appropriate branch of
     # data_curator_config
-    conf_file <- reactiveVal(template_config_files[input$dropdown_asset_view])
-    if (!file.exists(conf_file())){
-      if (grepl("dev", dcc_config_file)) {
-        conf_file(
-          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev-old",
-                    conf_file()
-          )
-        )
-      } else if (grepl("staging", dcc_config_file)) {
-        conf_file(
-          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/staging",
-                    conf_file()
-          )
-        )
-      } else {
-        conf_file(
-          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main",
-                    conf_file()
-          )
-        )
-      }
-    }
+    conf_file <- reactiveVal(file.path(config_dir, template_config_files[input$dropdown_asset_view]))
     config_df <- jsonlite::fromJSON(conf_file())
     
     conf_template <- setNames(config_df[[1]]$schema_name, config_df[[1]]$display_name)
@@ -335,13 +310,24 @@ shinyServer(function(input, output, session) {
   })
   
   observeEvent(input$info_box, {
-    
+    has_dcc <- ifelse(is.na(dcc_config_react()$dcc$dcc_help_link) |
+                      dcc_config_react()$dcc$dcc_help_link == "" |
+                      is.null(dcc_config_react()$dcc$dcc_help_link),
+                      FALSE, TRUE)
+    has_portal <- ifelse(is.na(dcc_config_react()$dcc$portal_help_link) |
+                        dcc_config_react()$dcc$portal_help_link == "" |
+                        is.null(dcc_config_react()$dcc$portal_help_link),
+                      FALSE, TRUE)
+    has_dm <- ifelse(is.na(dcc_config_react()$dcc$data_model_info) |
+                           dcc_config_react()$dcc$data_model_info == "" |
+                           is.null(dcc_config_react()$dcc$data_model_info),
+                         FALSE, TRUE)
     nx_report_info(
-      title = sprintf("DCA for %s", dcc_config_react()$project_name),
+      title = sprintf("DCA for %s", dcc_config_react()$dcc$project_name),
       tags$ul(
-        if (!is.na(dcc_config_react()$dca_help_link)) tags$li(tags$a(href = dcc_config_react()$dca_help_link, "DCA Help Docs", target = "_blank")),
-        if (!is.na(dcc_config_react()$portal_help_link)) tags$li(tags$a(href = dcc_config_react()$portal_help_link, "Portal Help Docs", target = "_blank")),
-        if (!is.na(dcc_config_react()$data_model_info)) tags$li(tags$a(href = dcc_config_react()$data_model_info, "Data Model Info", target = "_blank")),
+        if (has_dcc) tags$li(tags$a(href = dcc_config_react()$dcc$dcc_help_link, "DCA Help Docs", target = "_blank")),
+        if (has_portal) tags$li(tags$a(href = dcc_config_react()$dcc$portal_help_link, "Portal Help Docs", target = "_blank")),
+        if (has_dm) tags$li(tags$a(href = dcc_config_react()$dcc$data_model_info, "Data Model Info", target = "_blank")),
         tags$li(tags$a(href = paste0("https://www.synapse.org/#!Synapse:", selected$master_asset_view()), paste("Asset View:", selected$master_asset_view()), target = "_blank")),
         tags$li("DCA version: ", dca_version),
         tags$li("Schematic version: ", schematic_version),

From 2cd381a618e79e8ac155dc97d2bcced0de020f5b Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 15 Nov 2023 08:47:15 -0800
Subject: [PATCH 31/41] WIP: add project_scope to validation endpoint

---
 R/schematic_rest_api.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/schematic_rest_api.R b/R/schematic_rest_api.R
index b2e39e0e..31d032e2 100644
--- a/R/schematic_rest_api.R
+++ b/R/schematic_rest_api.R
@@ -115,12 +115,13 @@ manifest_populate <- function(url="http://localhost:3001/v1/manifest/populate",
 #' @export
 manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
                               schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #nolint
-                              data_type, file_name, restrict_rules=FALSE) {
+                              data_type, file_name, restrict_rules=FALSE, project_scope = NULL) {
   req <- httr::POST(url,
                      query=list(
                        schema_url=schema_url,
                        data_type=data_type,
-                       restrict_rules=restrict_rules),
+                       restrict_rules=restrict_rules,
+                       project_scope = project_scope),
                     body=list(file_name=httr::upload_file(file_name))
   )
   

From a9f25f0622d75a077236213dd745bc0245097cf5 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 15 Nov 2023 08:49:04 -0800
Subject: [PATCH 32/41] WIP: add asset view as project scope to validation
 endpoint

---
 server.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/server.R b/server.R
index a6a22874..7a60e62d 100644
--- a/server.R
+++ b/server.R
@@ -727,7 +727,8 @@ shinyServer(function(input, output, session) {
     .infile_data <- inFile$data()
     .dd_template <- input$dropdown_template
     .restrict_rules <- dcc_config_react()$validate_restrict_rules
-    
+    .project_scope <- selected$master_asset_view()    
+
     promises::future_promise({
       annotation_status <- switch(dca_schematic_api,
         reticulate = manifest_validate_py(
@@ -740,7 +741,8 @@ shinyServer(function(input, output, session) {
         schema_url=.data_model,
         data_type=.schema,
         file_name=.datapath,
-        restrict_rules = .restrict_rules),
+        restrict_rules = .restrict_rules,
+        project_scope = .project_scope),
       {
         Sys.sleep(0)
         list(list(

From 38ed6dd56fb38428481a24246d04b6cbbfa3ee51 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 16 Nov 2023 16:12:46 -0800
Subject: [PATCH 33/41] remove config dir from urls in config files

---
 server.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/server.R b/server.R
index 1be601b8..66918c8b 100644
--- a/server.R
+++ b/server.R
@@ -198,7 +198,7 @@ shinyServer(function(input, output, session) {
       color = primary_col())
     
     logo_img <- ifelse(!is.na(dcc_config_react()$dcc$logo_location),
-        file.path(config_dir, dcc_config_react()$dcc$logo_location),
+        dcc_config_react()$dcc$logo_location,
       "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/Logo_Sage_Logomark.png")
     
     logo_link <- ifelse(!is.na(dcc_config_react()$dcc$logo_link),
@@ -238,7 +238,7 @@ shinyServer(function(input, output, session) {
     }
     # Use the template dropdown config file from the appropriate branch of
     # data_curator_config
-    conf_file <- reactiveVal(file.path(config_dir, template_config_files[input$dropdown_asset_view]))
+    conf_file <- reactiveVal(template_config_files[input$dropdown_asset_view])
     config_df <- jsonlite::fromJSON(conf_file())
     
     conf_template <- setNames(config_df[[1]]$schema_name, config_df[[1]]$display_name)
@@ -323,7 +323,7 @@ shinyServer(function(input, output, session) {
                            is.null(dcc_config_react()$dcc$data_model_info),
                          FALSE, TRUE)
     nx_report_info(
-      title = sprintf("DCA for %s", dcc_config_react()$dcc$project_name),
+      title = sprintf("DCA for %s", dcc_config_react()$dcc$name),
       tags$ul(
         if (has_dcc) tags$li(tags$a(href = dcc_config_react()$dcc$dcc_help_link, "DCA Help Docs", target = "_blank")),
         if (has_portal) tags$li(tags$a(href = dcc_config_react()$dcc$portal_help_link, "Portal Help Docs", target = "_blank")),
@@ -599,7 +599,7 @@ shinyServer(function(input, output, session) {
     .schema_url <- data_model()
     .asset_view <- selected$master_asset_view()
     .template <- paste(
-      dcc_config_react()$dcc$project_name,
+      dcc_config_react()$dcc$name,
       "-",
       input$dropdown_template
     )

From aef9d0b686de011d2cc3164b7a11a397dfc39f44 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 28 Nov 2023 15:55:56 -0800
Subject: [PATCH 34/41] WIP: add ability to pass multiple project_scope to
 manifest_validate

---
 R/schematic_rest_api.R | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/R/schematic_rest_api.R b/R/schematic_rest_api.R
index c691b822..794c1afa 100644
--- a/R/schematic_rest_api.R
+++ b/R/schematic_rest_api.R
@@ -115,13 +115,36 @@ manifest_populate <- function(url="http://localhost:3001/v1/manifest/populate",
 #' @export
 manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
                               schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #nolint
-                              data_type, file_name, restrict_rules=FALSE, project_scope = NULL) {
+                              data_type, file_name, restrict_rules=FALSE, project_scope = NULL,
+                              access_token, asset_view = NULL) {
+  
+  flattenbody <- function(x) {
+    # A form/query can only have one value per name, so take
+    # any values that contain vectors length >1 and
+    # split them up
+    # list(x=1:2, y="a") becomes list(x=1, x=2, y="a")
+    if (all(lengths(x)<=1)) return(x);
+    do.call("c", mapply(function(name, val) {
+      if (length(val)==1 || any(c("form_file", "form_data") %in% class(val))) {
+        x <- list(val)
+        names(x) <- name
+        x
+      } else {
+        x <- as.list(val)
+        names(x) <- rep(name, length(val))
+        x
+      }
+    }, names(x), x, USE.NAMES = FALSE, SIMPLIFY = FALSE))
+  }
+  
   req <- httr::POST(url,
-                     query=list(
+                    httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
+                     query=flattenbody(list(
                        schema_url=schema_url,
                        data_type=data_type,
                        restrict_rules=restrict_rules,
-                       project_scope = project_scope),
+                       project_scope = project_scope,
+                       asset_view = asset_view)),
                     body=list(file_name=httr::upload_file(file_name))
   )
   

From e9a4aece5db6c83c08504057645003fba6096731 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 28 Nov 2023 15:56:10 -0800
Subject: [PATCH 35/41] Add asset view to manifest_validate

---
 server.R | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/server.R b/server.R
index 644affc1..8e202fb7 100644
--- a/server.R
+++ b/server.R
@@ -723,9 +723,11 @@ shinyServer(function(input, output, session) {
     .data_model <- data_model()
     .infile_data <- inFile$data()
     .dd_template <- input$dropdown_template
-    .restrict_rules <- dcc_config_react()$validate_restrict_rules
-    .project_scope <- selected$master_asset_view()    
-
+    .restrict_rules <- dcc_config_react()$schematic$model_validate$restrict_rules
+    .project_scope <- data_list$projects()
+    .access_token <- access_token
+    .asset_view <- selected$master_asset_view()
+browser()
     promises::future_promise({
       annotation_status <- switch(dca_schematic_api,
         reticulate = manifest_validate_py(
@@ -739,7 +741,9 @@ shinyServer(function(input, output, session) {
         data_type=.schema,
         file_name=.datapath,
         restrict_rules = .restrict_rules,
-        project_scope = .project_scope),
+        project_scope = .project_scope,
+        access_token = .access_token,
+        asset_view <- .asset_view),
       {
         Sys.sleep(0)
         list(list(

From 99854d044d6fc7a5318ed0b8871f7910bba0d871 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 5 Dec 2023 11:17:20 -0800
Subject: [PATCH 36/41] Remove node uninstall/install from Dockerfile.

---
 Dockerfile | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 98204915..65dfda63 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,10 +13,6 @@ RUN apt-get install -y libxml2 libglpk-dev libicu-dev libicu70 curl
 COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
 RUN chmod 777 /etc/shiny-server/shiny-server.conf
 
-# Update node. https://github.com/nodesource/distributions
-RUN apt-get remove nodejs
-RUN curl -fsSL https://deb.nodesource.com/setup_16.x | sudo -E bash - && apt-get install -y nodejs
-
 USER shiny
 
 WORKDIR /srv/shiny-server/app

From 4f0e69b7e742ac3d588cbb2d090c8cd044c44f2d Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 28 Nov 2023 15:56:10 -0800
Subject: [PATCH 37/41] remove browser statement

---
 server.R | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/server.R b/server.R
index 644affc1..c08c288f 100644
--- a/server.R
+++ b/server.R
@@ -723,8 +723,10 @@ shinyServer(function(input, output, session) {
     .data_model <- data_model()
     .infile_data <- inFile$data()
     .dd_template <- input$dropdown_template
-    .restrict_rules <- dcc_config_react()$validate_restrict_rules
-    .project_scope <- selected$master_asset_view()    
+    .restrict_rules <- dcc_config_react()$schematic$model_validate$restrict_rules
+    .project_scope <- data_list$projects()
+    .access_token <- access_token
+    .asset_view <- selected$master_asset_view()
 
     promises::future_promise({
       annotation_status <- switch(dca_schematic_api,
@@ -739,7 +741,9 @@ shinyServer(function(input, output, session) {
         data_type=.schema,
         file_name=.datapath,
         restrict_rules = .restrict_rules,
-        project_scope = .project_scope),
+        project_scope = .project_scope,
+        access_token = .access_token,
+        asset_view <- .asset_view),
       {
         Sys.sleep(0)
         list(list(

From 1c8626189ce764b9f62c1d22f96f50e2ca1ef38c Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 14 Dec 2023 14:50:47 -0800
Subject: [PATCH 38/41] fix argument assignment operator in manifest_validation
 function call

---
 server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server.R b/server.R
index c08c288f..41d51847 100644
--- a/server.R
+++ b/server.R
@@ -743,7 +743,7 @@ shinyServer(function(input, output, session) {
         restrict_rules = .restrict_rules,
         project_scope = .project_scope,
         access_token = .access_token,
-        asset_view <- .asset_view),
+        asset_view = .asset_view),
       {
         Sys.sleep(0)
         list(list(

From 7042e23ac9c01cce46c5ade84737e2a862cea409 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 14 Dec 2023 15:46:09 -0800
Subject: [PATCH 39/41] WIP: check the template config for project scope. If no
 project scope, set project_scope and asset_view to NULL in manifest_validate
 to avoid cross-manifest validation

---
 server.R | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/server.R b/server.R
index 41d51847..954189ea 100644
--- a/server.R
+++ b/server.R
@@ -64,7 +64,8 @@ shinyServer(function(input, output, session) {
     project = reactiveVal(NULL), folder = reactiveVal(""),
     schema = reactiveVal(NULL), schema_type = reactiveVal(NULL),
     master_asset_view = reactiveVal(NULL),
-    master_asset_view_label = reactiveVal(NULL)
+    master_asset_view_label = reactiveVal(NULL),
+    project_scope = reactiveVal(NULL)
   )
   
   isUpdateFolder <- reactiveVal(FALSE)
@@ -540,6 +541,14 @@ shinyServer(function(input, output, session) {
     selected$schema(data_list$template()[input$dropdown_template])
     schema_type <- config_schema()[[1]]$type[which(config_schema()[[1]]$display_name == input$dropdown_template)]
     selected$schema_type(schema_type)
+    
+    # set project scope for each template for cross-manifest validation.
+    # If project_scope is missing from dca_template_config.json then
+    # this value will be NULL and cross-manifest validation won't happen.
+    # validation will occur.
+    project_scope <- config_schema()[[1]]$project_scope[which(config_schema()[[1]]$display_name == input$dropdown_template)]
+    selected$project_scope(project_scope)
+    
     # clean all tags related with selected template
     sapply(clean_tags, FUN = hide)
   }, ignoreInit = TRUE)
@@ -724,9 +733,12 @@ shinyServer(function(input, output, session) {
     .infile_data <- inFile$data()
     .dd_template <- input$dropdown_template
     .restrict_rules <- dcc_config_react()$schematic$model_validate$restrict_rules
-    .project_scope <- data_list$projects()
+    .project_scope <- selected$project_scope()
     .access_token <- access_token
-    .asset_view <- selected$master_asset_view()
+    # asset view must be NULL to avoid cross-manifest validation.
+    # doing this in a verbose way to avoid warning with ifelse
+    .asset_view <- NULL
+    if (!is.null(.project_scope)) .asset_view <- selected$master_asset_view()
 
     promises::future_promise({
       annotation_status <- switch(dca_schematic_api,
@@ -754,7 +766,7 @@ shinyServer(function(input, output, session) {
         ))
       }
       )
-      
+
       # validation messages
       validationResult(annotation_status, .dd_template, .infile_data)
     

From c397b7a722b302376634996db1a4e8766002a59b Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 2 Jan 2024 08:55:15 -0800
Subject: [PATCH 40/41] Remove two obsolete  statements.

---
 server.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/server.R b/server.R
index 954189ea..8e3ce26d 100644
--- a/server.R
+++ b/server.R
@@ -635,7 +635,6 @@ shinyServer(function(input, output, session) {
         ),
         {
           message("Downloading offline manifest")
-          Sys.sleep(0)
           tibble(a="b", c="d")
         }
       )
@@ -757,7 +756,6 @@ shinyServer(function(input, output, session) {
         access_token = .access_token,
         asset_view = .asset_view),
       {
-        Sys.sleep(0)
         list(list(
         "errors" = list(
         Row = NA, Column = NA, Value = NA,

From c28db5ade71145420970aa9c09abe07b10f3f5a0 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 2 Jan 2024 13:50:38 -0800
Subject: [PATCH 41/41] Read the project scope into a vector from the template
 config file.

---
 server.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/server.R b/server.R
index 8e3ce26d..21177f24 100644
--- a/server.R
+++ b/server.R
@@ -546,9 +546,9 @@ shinyServer(function(input, output, session) {
     # If project_scope is missing from dca_template_config.json then
     # this value will be NULL and cross-manifest validation won't happen.
     # validation will occur.
-    project_scope <- config_schema()[[1]]$project_scope[which(config_schema()[[1]]$display_name == input$dropdown_template)]
+    project_scope <- config_schema()[[1]]$project_scope[[which(config_schema()[[1]]$display_name == input$dropdown_template)]]
     selected$project_scope(project_scope)
-    
+
     # clean all tags related with selected template
     sapply(clean_tags, FUN = hide)
   }, ignoreInit = TRUE)