i think the current working version

BrentLab · Apr 23, 2024 · c322eaa · c322eaa
1 parent 9ff8207
commit c322eaa
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Showing 8 changed files with 138 additions and 100 deletions.
diff --git a/R/data.R b/R/data.R
@@ -1,7 +1,7 @@
 #' Base url of the database API
 #'
 #' @export
-base_url <- "http://ec2-13-59-35-163.us-east-2.compute.amazonaws.com"
+base_url <- "http://ec2-3-143-144-93.us-east-2.compute.amazonaws.com"
 
 #' Rank Response Plot Example
 #'

diff --git a/R/qcTableModule.R b/R/qcTableModule.R
@@ -74,84 +74,112 @@ qcTableServer <- function(id, tf_id, token) {
       }
     }
 
+    # instantiate reactives
+    rv <- shiny::reactiveValues(data = NULL, trigger=FALSE)
+    tf_manual_review_changes <- reactiveValues(data = NULL)
+
     proxy <- DT::dataTableProxy("tf_manual_review_table")
 
     # Initialize the reactiveValues object with your data frame
-    rv <- shiny::reactiveValues(data = labretriever::retrieve(
-      labretriever::create_url("qcreview",
-        base_url = yeastCCDBShiny::base_url
-      ),
-      token(),
-      filter_list = list(tf_id = tf_id())
-    ) %>%
-      dplyr::arrange(experiment_id))
-
-    tf_manual_review_changes = reactiveValues(data = NULL)
-
-    output$tf_manual_review_table <- DT::renderDataTable({
-      DT::datatable(
-        rv$data,
-        editable = TRUE,
-        selection = "single",
-        options = list(
-          scrollX = TRUE,
-          width = "100%"
+    shiny::observe({
+      shiny::req(token(), tf_id())
+      qc_df <- labretriever::retrieve(
+        labretriever::create_url("qcreview",
+          base_url = yeastCCDBShiny::base_url
+        ),
+        token(),
+        filter_list = list(tf_id = tf_id())
+      ) %>%
+        dplyr::arrange(experiment_id)
+      rv$data <- qc_df
+
+      output$tf_manual_review_table <- DT::renderDataTable({
+        DT::datatable(
+          rv$data,
+          editable = TRUE,
+          selection = "single",
+          options = list(
+            scrollX = TRUE,
+            width = "100%"
+          )
         )
-      )
-    }) # Set server to FALSE to make proxy work
+      }) # Set server to FALSE to make proxy work
+    })
 
     observeEvent(input$update_button,
-       {
-         shiny::req(tf_id())
-         # Check if there are any changes
-         if (length(tf_manual_review_changes$data) > 0) {
-           # Process the changes and send updates to the database
-           tryCatch({
-             # Iterate through the changes and send updates for each changed field
-             for (change in tf_manual_review_changes$data) {
-               labretriever::send(
-                 df = change,
-                 url = labretriever::create_url(
-                   "qcreview",
-                   base_url = yeastCCDBShiny::base_url
-                 ),
-                 token = token(),
-                 update = TRUE
-               )
-             }
-             # Update the showButtons reactive value
-             shiny::updateCheckboxInput(session, "showButtons", value = FALSE)
-           }, error = function(err) {
-             # If an error occurs, show a modal with the error message
-             showModal(modalDialog(
-               title = "Error",
-               paste0(
-                 "An error occurred while updating the data: ",
-                 err$message, "\n\n",
-                 "ALL CHANGES CLEARED"
-               ),
-               easyClose = TRUE
-             ))
-           }, finally = {
-             # retrieve the updated data and update the reactive
-             updated_data <- labretriever::retrieve(
-               labretriever::create_url("qcreview",
-                                        base_url = yeastCCDBShiny::base_url
-               ),
-               token(),
-               filter_list = list(tf_id = tf_id())
-             )
-             # update the review reactive
-             rv$data <- updated_data
-
-             # Clear the changes list
-             tf_manual_review_changes$data <- list()
-           })
-         }
-       },
-       ignoreInit = TRUE
+      {
+        shiny::req(tf_id())
+        # Check if there are any changes
+        if (length(tf_manual_review_changes$data) > 0) {
+          # Process the changes and send updates to the database
+          tryCatch({
+            # Iterate through the changes and send updates for each changed field
+            for (change in tf_manual_review_changes$data) {
+              res = labretriever::send(
+                df = change,
+                url = labretriever::create_url(
+                  "qcreview",
+                  base_url = yeastCCDBShiny::base_url
+                ),
+                token = token(),
+                update = TRUE
+              )
+            }
+            # Update the showButtons reactive value
+            shiny::updateCheckboxInput(session, "showButtons", value = FALSE)
+          }, error = function(err) {
+            # If an error occurs, show a modal with the error message
+            showModal(modalDialog(
+              title = "Error",
+              paste0(
+                "An error occurred while updating the data: ",
+                err$message, "\n\n",
+                "ALL CHANGES CLEARED"
+              ),
+              easyClose = TRUE
+            ))
+          }, finally = {
+            # retrieve the updated data and update the reactive
+            updated_data <- labretriever::retrieve(
+              labretriever::create_url("qcreview",
+                base_url = yeastCCDBShiny::base_url
+              ),
+              token(),
+              filter_list = list(tf_id = tf_id())
+            )
+            # update the review reactive
+            rv$data <- updated_data
+
+            # Clear the changes list
+            tf_manual_review_changes$data <- list()
+          })
+        }
+      },
+      ignoreInit = TRUE
     )
 
+    shiny::observeEvent(input$cancel_update_button, {
+      # Update the showButtons reactive value
+      shiny::updateCheckboxInput(session, "showButtons", value = FALSE)
+      # Clear the changes list
+      tf_manual_review_changes$data <- list()
+      rv$trigger <- !rv$trigger
+    }, ignoreInit = TRUE)
+
+    shiny::observeEvent(rv$trigger, {
+      output$tf_manual_review_table <- DT::renderDataTable({
+        DT::datatable(
+          rv$data,
+          editable = TRUE,
+          selection = "single",
+          options = list(
+            scrollX = TRUE,
+            width = "100%"
+          )
+        )
+      }) # Set server to FALSE to make proxy work
+    })
+
     shiny::observeEvent(input$tf_manual_review_table_cell_edit, {
       # Code to handle the table cell edit event
       # Update the showButtons reactive value

diff --git a/R/rankResponsePlotModule.R b/R/rankResponsePlotModule.R
@@ -116,6 +116,9 @@ rankResponsePlotServer <- function(id,
     rr_df <- reactiveVal(NULL)
 
     shiny::observeEvent(tf_id(), {
+
+      shiny::req(tf_id())
+
       if (test) {
         if (tf_gene() == "HAP5") {
           rr_df(yeastCCDBShiny::hap5_rr_data)
@@ -135,6 +138,7 @@ rankResponsePlotServer <- function(id,
 
     shiny::observeEvent(hops_source(),
       {
+        shiny::req(tf_id())
         if (test) {
           if (tf_gene() == "HAP5") {
             rr_df(yeastCCDBShiny::hap5_rr_data)
@@ -156,6 +160,7 @@ rankResponsePlotServer <- function(id,
 
     shiny::observeEvent(background_source(),
       {
+        shiny::req(tf_id())
         if (test) {
           if (tf_gene() == "HAP5") {
             rr_df(yeastCCDBShiny::hap5_rr_data)
@@ -177,6 +182,7 @@ rankResponsePlotServer <- function(id,
 
     shiny::observeEvent(promoter_source(),
       {
+        shiny::req(tf_id())
         if (test) {
           if (tf_gene() == "HAP5") {
             rr_df(yeastCCDBShiny::hap5_rr_data)
@@ -201,7 +207,8 @@ rankResponsePlotServer <- function(id,
         rr_df(),
         tf_gene(),
         normalize_selector(),
-        bin_size()
+        bin_size(),
+        confidence_intervals()
       )
       flog.info(paste0('names of gen_plot_data_out: ',
                        paste(names(gen_plot_data_out), collapse = '", "')))
@@ -254,7 +261,8 @@ rankResponsePlotServer <- function(id,
           rr_df(),
           tf_gene(),
           normalize_selector(),
-          bin_size()
+          bin_size(),
+          confidence_intervals()
         )
         rr_plots$kemmeren_tfko <- gen_plot_data_out$plt$kemmeren_tfko
         rr_plots$mcisaac_zev <- gen_plot_data_out$plt$mcisaac_zev

diff --git a/R/rank_response_utils.R b/R/rank_response_utils.R
@@ -300,8 +300,7 @@ stable_rank_response <- function(df,
     dplyr::mutate(
       test_result = list(binom.test(n_successes,
         rank,
-        p = random,
-        alternative = "greater"
+        p = random
       )),
       response_ratio = test_result$estimate,
       p_value = test_result$p.value,

diff --git a/R/retrieve_rank_response_data.R b/R/retrieve_rank_response_data.R
@@ -163,6 +163,8 @@ retrieve_rank_response_data <- function(tf_gene,
                                         background_source,
                                         promoter_source,
                                         token) {
+
+  rank_response_df = NA
   N_STEPS <- 5
   result <- shiny::withProgress(
     message = "Fetching data...",

diff --git a/R/tfSelectorModule.R b/R/tfSelectorModule.R
@@ -116,6 +116,9 @@ tfSelectorServer <- function(id,
 
     # retrieve list of active TFs
     shiny::observe({
+
+      shiny::req(token())
+
       tf_list_df <- labretriever::retrieve(
         labretriever::create_url("cctf_tf_list",
           base_url = yeastCCDBShiny::base_url

diff --git a/data/rank_response_df.rda b/data/rank_response_df.rda
diff --git a/inst/app/server.R b/inst/app/server.R
@@ -46,33 +46,31 @@ server <- function(input, output, session) {
     )
   })
 
-  shiny::observeEvent(rank_threshold(), {
-    goServer('go_module', rank_response_df, rank_threshold)
-  }, ignoreNULL = TRUE)
-
-  shiny::observeEvent(selected_tf_tracker(),
+  shiny::observeEvent(rank_threshold(),
     {
-      rankResponsePlotServer(
-        "rr_plot",
-        shiny::reactive(selected_tf$tf_id),
-        shiny::reactive(selected_tf$tf_gene),
-        rank_response_df,
-        selected_row,
-        hops_source,
-        background_source,
-        promoter_source,
-        bin_size,
-        normalize_selector,
-        confidence_intervals,
-        token
-      )
-      qcTableServer(
-        "qc_table",
-        shiny::reactive(selected_tf$tf_id),
-        token
-      )
+      goServer("go_module", rank_response_df, rank_threshold)
     },
-    ignoreInit = TRUE,
     ignoreNULL = TRUE
   )
+
+  rankResponsePlotServer(
+    "rr_plot",
+    shiny::reactive(selected_tf$tf_id),
+    shiny::reactive(selected_tf$tf_gene),
+    rank_response_df,
+    selected_row,
+    hops_source,
+    background_source,
+    promoter_source,
+    bin_size,
+    normalize_selector,
+    confidence_intervals,
+    token
+  )
+
+  qcTableServer(
+    "qc_table",
+    shiny::reactive(selected_tf$tf_id),
+    token
+  )
 }