Update KVFinder-web to v1.1.1 (#46)

* Update KVFinder-web to v1.1.1 (#45) * Update CITATION.cff * Update CITATION.cff * Change background color to LNBio colorscheme, add LNBio/CNPEM logo to footer, conditionalPanel for Run Cavity Analysis tab * Update layout of jumbotron in main page * Remove emojis from jumbotron title * Update layout of choose_input card in main page * Update laytout of choose_run_mode card in main page * Separate functions into individual files * Separate functions into individual files * conditionalPanel for Submit, Check Results and View buttons in Run Cavity Analysis tab and conditionalPanel for Get Results and View buttons in Retrieve Results page * Fix typos and code formatting * Update Get latest results color in card * Update Tutorial tab and remove debug prints * Add partial solution to Get Results bugs and remove debug prints * Fix bugs in tab 2 (Get latest results) - hide job status and ngl viewer, and show error for empty job ID and alphanumeric job ID * var_status was not defined when receiving a http error code, now it is set to error * Update layout and information in Help tab - missing TOML results file description * Update tutorial layout * Update Help tab layout and add description of TOML-formatted results file * Update DESCRIPTION * Remove .Rproj from repository * Update layout of about tab * Fix typo * Update app_server.R * Update README.md * Update app_ui.R
LBC-LNBio · Oct 10, 2023 · 08b4e53 · 08b4e53
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diff --git a/.gitignore b/.gitignore
@@ -20,6 +20,7 @@
 
 # RStudio files
 .Rproj.user/
+.Rproj
 
 # produced vignettes
 vignettes/*.html

diff --git a/README.md b/README.md
@@ -35,13 +35,33 @@ To run locally the KVFinder-web portal in Linux distributions, it is necessary t
 sudo apt install docker-compose
 ```
 
-After the docker-compose installation and clone of this repository. First, you have to build our KVFinder-web interface:
+Before using the KVFinder-web portal, you need to configure the URL address for the KVFinder-web service. Open the [app_server.R](kvfinder-web-portal/R/app_server.R#L14-L24) file and define the URL address:
+
+If KVFinder-web service is running on your local machine, use the first configuration:
+
+```r
+url_address <- "http://localhost:8081/"
+```
+
+If KVFinder-web service is on a different containers in the same network, replace <ip> in the second configuration with the actual IP address of that machine.
+
+```r
+url_address <- "http://<ip>:8081/"
+```
+
+If KVFinder-web service and portal are in the same container, use the third configuration (http://kv-server:8081/).
+
+```r
+url_address <- "http://kv-server:8081/"
+```
+
+Afterwards, you have to build our KVFinder-web portal:
 
 ```bash
 docker build -t kvfinder-web-portal .
 ```
 
-To start KVFinder-web interface:
+To start KVFinder-web portal:
 
 ```bash
 docker run -p 3838:3838 kvfinder-web-portal

diff --git a/kvfinder-web-portal/DESCRIPTION b/kvfinder-web-portal/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: KVFinderWebPortal
 Title: KVFinder-web portal
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: 
     c(
         person(
@@ -12,7 +12,7 @@ Authors@R:
         person(
             given = "João",
             family = "Guerra",
-            role = c("ctb"),
+            role = c("aut", "cre"),
         ),
         person(
             given = "José",

diff --git a/kvfinder-web-portal/KVserver.Rproj b/kvfinder-web-portal/KVserver.Rproj
diff --git a/kvfinder-web-portal/R/app_config.R b/kvfinder-web-portal/R/app_config.R
@@ -21,6 +21,8 @@ app_sys <- function(...) {
 #' @param use_parent Logical, scan the parent directory for config file.
 #'
 #' @noRd
+#' 
+
 get_golem_config <- function(value,
                              config = Sys.getenv(
                                "GOLEM_CONFIG_ACTIVE",

diff --git a/kvfinder-web-portal/R/app_server.R b/kvfinder-web-portal/R/app_server.R
@@ -2,22 +2,25 @@
 #'
 #' @param input,output,session Internal parameters for {shiny}.
 #'     DO NOT REMOVE.
+#'
 #' @import shiny
 #' @import shinyjs
 #' @import ggplot2
 #'
-#'
 #' @noRd
 #'
 
 app_server <- function(input, output, session) {
-  # url address to connection. This is used in submition and check results functions.
+  # URL address for KVFinder-web service
+  # Use this if KVFinder-web service is on the same machine
   url_address <- "http://localhost:8081/"
 
   # KVFinder-web portal outside KVFinder-web service container
+  # Uncomment and replace <ip> with the actual IP address if service is on a different container
   # url_address <- "http://<ip>:8081/"
 
   # KVFinder-web portal inside the same container of KVFinder-web service
+  # Uncomment and use this if service and portal are in the same container
   # url_address <- "http://kv-server:8081/"
 
   #-----------------------------------------------
@@ -75,11 +78,9 @@ app_server <- function(input, output, session) {
       # title = tags$a('Structure preview', style = "text-align: right;" ),
       # NGLVieweROutput("structure_prev", width = "100%", height = "75vh"),
       if (!is.null(input$input_pdb)) {
-        # print(get_nonstand_check)
         renderNGLVieweR({
           # get input protein PDB with output cavities
           pdb <- input$input_pdb$datapath
-          print(paste("/", as.numeric(input$model_number), sep = ""))
           # create initial scene
           NGLVieweR(pdb) %>%
             # start protein with visible cartoon representation
@@ -104,7 +105,6 @@ app_server <- function(input, output, session) {
   #-----------------------------------------------------
   # Fetch PDB section
   observeEvent(input$send_pdb_id, {
-    print(input$pdb_id)
     # save number of clicks in load button
     pdb_name_click_load <<- input$pdb_id
     # check if the PDB code is valid by using get_nonstand
@@ -114,20 +114,17 @@ app_server <- function(input, output, session) {
     if (length(which(is.na(get_nonstand_check))) != 0) {
       shinyWidgets::sendSweetAlert(session = session, title = "Oops!", text = "Please insert a valid PDB ID.", type = "error")
     } else {
-      print("PDB ID ok")
       process_fetch(input = input, output = output)
     }
     # run process_fetch of mod_server_fetch module to create boxes and buttons of run mode
     # process_fetch(input = input, output = output)
   })
 
   observeEvent(input$show_preview_fetch, {
-    print(pdb_name_click_load)
     showModal(modalDialog(
       # title = tags$a('Structure preview', style = "text-align: right;" ),
       # NGLVieweROutput("structure_prev", width = "100%", height = "75vh"),
       if (pdb_name_click_load != "init") {
-        print(get_nonstand_check)
         renderNGLVieweR({
           # get input protein PDB with output cavities
           pdb <- input$pdb_id
@@ -291,7 +288,6 @@ app_server <- function(input, output, session) {
     observe({
       result_pdb <<- check_results(input = input, output = output, run_id = current_run_id, is_pg2 = FALSE, url_address = url_address, session = session)
       if (length(result_pdb) == 1) { # if results_pdb corresponds to output status and not kvfinder results
-        print(result_pdb)
         if (result_pdb %in% c("queued", "running")) {
           invalidateLater(5000) # means 5 seconds
         }
@@ -317,10 +313,47 @@ app_server <- function(input, output, session) {
 
   # Check results in the secondary page ("get latest results" page)
   observeEvent(input$check_loc_pg2, {
-    result_pdb <<- check_results(input = input, output = output, run_id = trimws(input$insert_ID), is_pg2 = TRUE, url_address = url_address, session = session)
-    # When check results button in page 2 is clicked, the structure visualization and all buttons related to NGL viewer will be hidden
-    # to allow an update if the check button is used multiple times
-    output[["structure_pg2"]] <- renderNGLVieweR({})
+
+    # When Get results button in tab 2 is clicked, the job information and the results table will be hidden
+    # Hide elements
+    hideElement(
+      id = "output_status_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "download_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "download2_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "download_results_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "download_results2_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "results_table_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "table_out_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "view_output_pg2",
+      time = 0
+    )
+    hideElement(
+      id = "view_str_pg2",
+      time = 0
+    )
+
+    # When View button in tab 2 is clicked, the structure visualization and all buttons related to NGL viewer will be hidden
     hideElement(
       id = "structure_pg2",
       time = 0
@@ -389,6 +422,70 @@ app_server <- function(input, output, session) {
       id = "scale_plot",
       time = 0
     )
+
+    # Remove whitespaces from input$insert_ID
+    id <- trimws(input$insert_ID)
+
+    # Check if run_id is empty or an alphanumeric string
+    if ((nchar(id) == 0) || (is.na(as.numeric(id)))) {
+      shinyWidgets::sendSweetAlert(
+        session = session,
+        title = "Oops!",
+        text = "An error occurred when retrieving your job! \ 
+        Please insert a valid Job ID!",
+        type = "error"
+      )
+
+      return(NULL)
+    }
+
+    # Check results of a Job ID
+    result_pdb <<- check_results(input = input, output = output, run_id = id, is_pg2 = TRUE, url_address = url_address, session = session)
+
+    # Sucessfully got results, so show elements
+    showElement(
+      id = "output_status_pg2",
+      time = 0
+    )
+    if ("result_toml" %in% names(result_pdb)) {
+
+      showElement(
+        id = "download_pg2",
+        time = 0
+      )
+      showElement(
+        id = "download2_pg2",
+        time = 0
+      )
+      showElement(
+        id = "download_results_pg2",
+        time = 0
+      )
+      showElement(
+        id = "download_results2_pg2",
+        time = 0
+      )
+      showElement(
+        id = "results_table_pg2",
+        time = 0
+      )
+      showElement(
+        id = "table_out_pg2",
+        time = 0
+      )
+      showElement(
+        id = "view_output_pg2",
+        time = 0
+      )
+      showElement(
+        id = "view_str_pg2",
+        time = 0
+      )
+    }
+
+    # Show NGL viewer and buttons
+    output[["structure_pg2"]] <- renderNGLVieweR({})
+
   })
   #----------------------------------------------------
 
@@ -508,7 +605,6 @@ app_server <- function(input, output, session) {
       current_rep_cav <- input$input_cavity_rep
       # fed the protein list of representations
       cav_rep_list <<- c(cav_rep_list, current_rep_cav)
-      print(cav_rep_list)
       # Create the work scene
       create_work_scene(input = input, output = output, protein_rep_list = protein_rep_list, protein_col_list = protein_col_list, protein_col_scheme_list = protein_col_scheme_list, result_pdb_list = result_pdb, is_pg2 = FALSE, scheme_color_list = scheme_color_list, prot_or_cav = "cav", cav_rep_list = cav_rep_list)
       # clean protein color selector
@@ -567,7 +663,7 @@ app_server <- function(input, output, session) {
       updateCheckboxInput(session, "input_cavity_hyd", value = FALSE)
     }
 
-    color_cavity_deepth(input = input, output = output, is_pg2 = FALSE, cav_rep_list = cav_rep_list, result_pdb_list = result_pdb)
+    color_cavity_depth(input = input, output = output, is_pg2 = FALSE, cav_rep_list = cav_rep_list, result_pdb_list = result_pdb)
 
     output$scale_plot_deep <- renderPlot(
       {
@@ -609,7 +705,6 @@ app_server <- function(input, output, session) {
 
   # Click view in the secondary page to initialize the result visualization with the NGL engine
   observeEvent(input$view_str_pg2, {
-    print(protein_rep_list)
     protein_rep_list <<- c() # always initialize an empty list of protein representations when clicking on view button
     cav_rep_list <<- c()
     cav_rep_list <<- c(cav_rep_list, 'point') # add initial rep for the cavities to avoid NULL when running a second job
@@ -719,12 +814,10 @@ app_server <- function(input, output, session) {
   # Create a work scene every time users click on cavity representation selector and change biomolecular structure representation
   observeEvent(input$input_cavity_rep_pg2,
     {
-      print("Inside cav rep pg2")
       # save the current representation
       current_rep_cav <- input$input_cavity_rep_pg2
       # fed the protein list of representations
       cav_rep_list <<- c(cav_rep_list, current_rep_cav)
-      # print(cav_rep_list)
       # Create the work scene
       create_work_scene(input = input, output = output, protein_rep_list = protein_rep_list, protein_col_list = protein_col_list, protein_col_scheme_list = protein_col_scheme_list, result_pdb_list = result_pdb, is_pg2 = TRUE, scheme_color_list = scheme_color_list, prot_or_cav = "cav", cav_rep_list = cav_rep_list)
       # clean protein color selector
@@ -778,7 +871,7 @@ app_server <- function(input, output, session) {
       updateCheckboxInput(session, "input_cavity_hyd_pg2", value = FALSE)
     }
 
-    color_cavity_deepth(input = input, output = output, is_pg2 = TRUE, cav_rep_list = cav_rep_list, result_pdb_list = result_pdb)
+    color_cavity_depth(input = input, output = output, is_pg2 = TRUE, cav_rep_list = cav_rep_list, result_pdb_list = result_pdb)
 
     output$scale_plot_deep_pg2 <- renderPlot(
       {