From 73cd1f02f33b36e762786421f44c1b700f7464d8 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 21 Nov 2024 15:04:29 +0100
Subject: [PATCH 01/21] wip: new auth method + prepopulation of upload

---
 components/app/R/server.R                 |   7 ++
 components/board.upload/R/upload_server.R |  23 ++++-
 components/board.upload/R/upload_utils.R  |  19 ++++
 components/modules/AuthenticationModule.R | 106 ++++++++++++++++++++++
 4 files changed, 154 insertions(+), 1 deletion(-)

diff --git a/components/app/R/server.R b/components/app/R/server.R
index 568c08d06..c05be43ca 100644
--- a/components/app/R/server.R
+++ b/components/app/R/server.R
@@ -117,6 +117,13 @@ app_server <- function(input, output, session) {
       allow_new_users = opt$ALLOW_NEW_USERS,
       redirect_login = TRUE
     )
+  } else if (authentication == "email-encrypted") {
+    auth <- EmailEncryptedAuthenticationModule(
+      id = "auth",
+      show_modal = TRUE,
+      # TODO add argument for location of crypto key (probably on ETC)
+      domain = opt$DOMAIN
+    )
   } else if (authentication == "shinyproxy") {
     username <- Sys.getenv("SHINYPROXY_USERNAME")
     auth <- NoAuthenticationModule(
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 878d0bbcb..92310214b 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -945,7 +945,7 @@ UploadBoard <- function(id,
         wizardR::reset("upload_wizard")
 
         # skip upload trigger at first startup
-        if (new_upload() == 0) {
+        if (new_upload() == 1) {
           return(NULL)
         }
 
@@ -976,6 +976,27 @@ UploadBoard <- function(id,
               ## compute_info(list( "name" = pgx$name,"description" = pgx$description))
               compute_settings$name <- pgx$name
               compute_settings$description <- pgx$description
+            } else if (opt$AUTHENTICATION == "email-encrypted") { # Only data preloading on email-encrypted authentication
+              query_files <- check_query_files()
+              # TODO unencrypt links!!! to do inside check_query_files
+              if (!is.null(query_files$counts)) {
+                file <- read_query_files(query_files$counts)
+                df <- playbase::read_counts(file)
+                uploaded$counts.csv <- df
+                ## if counts file contains annotation
+                af <- playbase::read_annot(file)
+                uploaded$annot.csv <- af
+              }
+              if (!is.null(query_files$samples)) {
+                file <- read_query_files(query_files$samples)
+                df <- playbase::read_samples(file)
+                uploaded$samples.csv <- df
+              }
+              if (!is.null(query_files$contrasts)) {
+                file <- read_query_files(query_files$contrasts)
+                df <- playbase::read_contrasts(file)
+                uploaded$contrasts.csv <- df
+              }
             }
           } else {
             shinyalert::shinyalert(
diff --git a/components/board.upload/R/upload_utils.R b/components/board.upload/R/upload_utils.R
index 9b968a73a..10d022d73 100644
--- a/components/board.upload/R/upload_utils.R
+++ b/components/board.upload/R/upload_utils.R
@@ -308,3 +308,22 @@ write_check_output <- function(
     write(unlist(lines), file.path(raw_dir, "CHECKS_OUTPUT"), append = TRUE)
   }
 }
+
+# Check if there are counts/samples file links on the query parameters
+check_query_files <- function() {
+  counts <- shiny::getQueryString()$counts
+  samples <- shiny::getQueryString()$samples
+  contrasts <- shiny::getQueryString()$contrasts
+  return(list(
+    counts = counts,
+    samples = samples,
+    contrasts = contrasts
+  ))
+}
+
+# Read query files
+read_query_files <- function(url) {
+  destination <- tempfile(fileext = ".csv")
+  download.file(url, destination)
+  return(destination)
+}
diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index b49015c3c..5320ed1c7 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1227,6 +1227,112 @@ LoginCodeAuthenticationModule <- function(id,
 }
 
 
+EmailEncryptedAuthenticationModule <- function(
+  id = "auth",
+  show_modal = TRUE,
+  # TODO add argument for location of crypto key (probably on ETC)
+  domain = opt$DOMAIN) {
+  shiny::moduleServer(id, function(input, output, session) {
+    message("[AuthenticationModule] >>>> using EmailEncrypted authentication <<<<")
+    ns <- session$ns
+
+    # TODO add key and uncomment this code
+    # encryption_key <- readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+    # if (!file.exists(crypto_key)) {
+    #   ## we continue but email is not working
+    #   warning("[EmailHeaderAuthenticationModule] ERROR : missing crypto_key file!!!")
+    # }
+
+    USER <- shiny::reactiveValues(
+      method = "email-encrypted",
+      logged = FALSE,
+      username = NA,
+      email = NA,
+      level = "",
+      limit = "",
+      options = opt, ## global
+      user_dir = PGX.DIR ## global
+    )
+
+    if (show_modal) {
+      m <- splashLoginModal(
+        ns = ns,
+        with.username = FALSE,
+        with.email = FALSE,
+        with.password = FALSE,
+        title = "Sign in",
+        subtitle = "Ready to explore your data?",
+        button.text = "Sure I am!"
+      )
+      shiny::showModal(m)
+    }
+
+    resetUSER <- function() {
+      dbg("[EmailEncryptedAuthenticationModule] resetUSER called")
+      USER$logged <- FALSE
+      USER$username <- NA
+      USER$email <- NA
+      USER$password <- NA
+      USER$level <- ""
+      USER$limit <- ""
+
+      PLOT_DOWNLOAD_LOGGER <<- reactiveValues(log = list(), str = "")
+    }
+
+    output$showLogin <- shiny::renderUI({
+      resetUSER()
+    })
+
+    output$login_warning <- shiny::renderText("")
+
+    ## --------------------------------------
+    ## Step 1: Get email query field
+    ## --------------------------------------
+
+    query_email <- shiny::reactive({
+      # aqui fer que pilli el header enlloc del query string
+      query_email <- shiny::getQueryString()$email
+      query_email
+    })
+
+    ## --------------------------------------
+    ## Step 2: Decrypt email query field
+    ## --------------------------------------
+
+    # TODO decrypt email
+
+    ## --------------------------------------
+    ## Step 3: Login user
+    ## --------------------------------------
+    # TODO place decrypted email instead of query_email
+    shiny::observeEvent(input$login_submit_btn, {
+      if (is.null(query_email())) {
+        dbg("[EmailEncryptedAuthenticationModule] invalid email")
+        output$login_warning <- shiny::renderText("invalid email hash")
+        # TODO show some error on the UI
+      } else {
+        USER$email <- query_email()
+        USER$username <- query_email()
+        USER$logged <- TRUE
+        # TODO Use some sort of user_database to see if email allowed??
+        # TODO check domain (?)
+        USER$user_dir <- file.path(PGX.DIR, USER$email)
+        create_user_dir_if_needed(USER$user_dir, PGX.DIR)
+        if (!opt$ENABLE_USERDIR) {
+          USER$user_dir <- file.path(PGX.DIR)
+        }
+        dbg("[EmailEncryptedAuthenticationModule] using user OPTIONS")
+        USER$options <- read_user_options(USER$user_dir)
+        session$sendCustomMessage("set-user", list(user = USER$email))
+      }
+    })
+
+    ## export as 'public' functions
+    USER$resetUSER <- resetUSER
+
+    return(USER)
+  })
+}
 ## ================================================================================
 ## ================================= END OF FILE ==================================
 ## ================================================================================

From 7f0dbf63f3a2c05efc6ea3a442dee04de994a8a5 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 21 Nov 2024 15:29:46 +0100
Subject: [PATCH 02/21] wip: decrypt email

---
 components/board.upload/R/upload_utils.R  |  7 +++++++
 components/modules/AuthenticationModule.R | 16 +++++++++-------
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/components/board.upload/R/upload_utils.R b/components/board.upload/R/upload_utils.R
index 10d022d73..a140d1d52 100644
--- a/components/board.upload/R/upload_utils.R
+++ b/components/board.upload/R/upload_utils.R
@@ -327,3 +327,10 @@ read_query_files <- function(url) {
   download.file(url, destination)
   return(destination)
 }
+
+# Decrypt email
+decrypt_email <- function(query_email, encryption_key) {
+  ciphertext <- base64enc::base64decode(query_email)
+  email <- rawToChar(sodium::data_decrypt(ciphertext, encryption_key))
+  return(email)
+}
diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index 5320ed1c7..4250c14f3 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1237,11 +1237,12 @@ EmailEncryptedAuthenticationModule <- function(
     ns <- session$ns
 
     # TODO add key and uncomment this code
-    # encryption_key <- readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
-    # if (!file.exists(crypto_key)) {
-    #   ## we continue but email is not working
-    #   warning("[EmailHeaderAuthenticationModule] ERROR : missing crypto_key file!!!")
-    # }
+    encryption_key <- readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+    if (!file.exists(encryption_key)) {
+      ## we continue without decryption, just to test, unsafe
+      warning("[EmailEncryptedAuthenticationModule] ERROR : missing encryption_key file!!!")
+      encryption_key <- NULL
+    }
 
     USER <- shiny::reactiveValues(
       method = "email-encrypted",
@@ -1290,7 +1291,6 @@ EmailEncryptedAuthenticationModule <- function(
     ## --------------------------------------
 
     query_email <- shiny::reactive({
-      # aqui fer que pilli el header enlloc del query string
       query_email <- shiny::getQueryString()$email
       query_email
     })
@@ -1299,7 +1299,9 @@ EmailEncryptedAuthenticationModule <- function(
     ## Step 2: Decrypt email query field
     ## --------------------------------------
 
-    # TODO decrypt email
+    if (!is.null(encryption_key)) {
+      query_email <- decrypt_mail(query_email, encryption_key)
+    }
 
     ## --------------------------------------
     ## Step 3: Login user

From 0003ae9f16c4fbf1a8c1918403bfe16101608ed2 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 21 Nov 2024 15:36:17 +0100
Subject: [PATCH 03/21] wip: decrypt url

---
 components/board.upload/R/upload_server.R | 13 +++++++++----
 components/board.upload/R/upload_utils.R  | 13 ++++++++-----
 components/modules/AuthenticationModule.R |  2 +-
 3 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 92310214b..7efd3cb0e 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -978,9 +978,14 @@ UploadBoard <- function(id,
               compute_settings$description <- pgx$description
             } else if (opt$AUTHENTICATION == "email-encrypted") { # Only data preloading on email-encrypted authentication
               query_files <- check_query_files()
-              # TODO unencrypt links!!! to do inside check_query_files
+              # Get encryption key
+              encryption_key <- readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+              if (!file.exists(encryption_key)) {
+                encryption_key <- NULL
+              }
+              # Populate upload data with available
               if (!is.null(query_files$counts)) {
-                file <- read_query_files(query_files$counts)
+                file <- read_query_files(query_files$counts, encryption_key)
                 df <- playbase::read_counts(file)
                 uploaded$counts.csv <- df
                 ## if counts file contains annotation
@@ -988,12 +993,12 @@ UploadBoard <- function(id,
                 uploaded$annot.csv <- af
               }
               if (!is.null(query_files$samples)) {
-                file <- read_query_files(query_files$samples)
+                file <- read_query_files(query_files$samples, encryption_key)
                 df <- playbase::read_samples(file)
                 uploaded$samples.csv <- df
               }
               if (!is.null(query_files$contrasts)) {
-                file <- read_query_files(query_files$contrasts)
+                file <- read_query_files(query_files$contrasts, encryption_key)
                 df <- playbase::read_contrasts(file)
                 uploaded$contrasts.csv <- df
               }
diff --git a/components/board.upload/R/upload_utils.R b/components/board.upload/R/upload_utils.R
index a140d1d52..3b70983ea 100644
--- a/components/board.upload/R/upload_utils.R
+++ b/components/board.upload/R/upload_utils.R
@@ -322,15 +322,18 @@ check_query_files <- function() {
 }
 
 # Read query files
-read_query_files <- function(url) {
+read_query_files <- function(url, encryption_key = NULL) {
+  if (!is.null(encryption_key)) {
+    url <- decrypt_util(url, encryption_key)
+  }
   destination <- tempfile(fileext = ".csv")
   download.file(url, destination)
   return(destination)
 }
 
 # Decrypt email
-decrypt_email <- function(query_email, encryption_key) {
-  ciphertext <- base64enc::base64decode(query_email)
-  email <- rawToChar(sodium::data_decrypt(ciphertext, encryption_key))
-  return(email)
+decrypt_util <- function(query, encryption_key) {
+  ciphertext <- base64enc::base64decode(query)
+  decrypted_query <- rawToChar(sodium::data_decrypt(ciphertext, encryption_key))
+  return(decrypted_query)
 }
diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index 4250c14f3..1fd108f0b 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1236,7 +1236,7 @@ EmailEncryptedAuthenticationModule <- function(
     message("[AuthenticationModule] >>>> using EmailEncrypted authentication <<<<")
     ns <- session$ns
 
-    # TODO add key and uncomment this code
+    # Get encryption key
     encryption_key <- readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
     if (!file.exists(encryption_key)) {
       ## we continue without decryption, just to test, unsafe

From d579b6b6af23d581eab99f73f355f7c6dd323f55 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 21 Nov 2024 16:15:19 +0100
Subject: [PATCH 04/21] wip: re-order stuff

---
 components/modules/AuthenticationModule.R | 30 +++++++++++------------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index 1fd108f0b..90f453bf7 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1237,11 +1237,12 @@ EmailEncryptedAuthenticationModule <- function(
     ns <- session$ns
 
     # Get encryption key
-    encryption_key <- readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
-    if (!file.exists(encryption_key)) {
+    encryption_key <- tryCatch({
+      readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+    }, error = function(w){NULL})
+    if (is.null(encryption_key)) {
       ## we continue without decryption, just to test, unsafe
       warning("[EmailEncryptedAuthenticationModule] ERROR : missing encryption_key file!!!")
-      encryption_key <- NULL
     }
 
     USER <- shiny::reactiveValues(
@@ -1296,25 +1297,22 @@ EmailEncryptedAuthenticationModule <- function(
     })
 
     ## --------------------------------------
-    ## Step 2: Decrypt email query field
+    ## Step 2: Decrypt and Login user
     ## --------------------------------------
-
-    if (!is.null(encryption_key)) {
-      query_email <- decrypt_mail(query_email, encryption_key)
-    }
-
-    ## --------------------------------------
-    ## Step 3: Login user
-    ## --------------------------------------
-    # TODO place decrypted email instead of query_email
     shiny::observeEvent(input$login_submit_btn, {
       if (is.null(query_email())) {
-        dbg("[EmailEncryptedAuthenticationModule] invalid email")
+        dbg("[EmailEncryptedAuthenticationModule] invalid email hash")
         output$login_warning <- shiny::renderText("invalid email hash")
         # TODO show some error on the UI
       } else {
-        USER$email <- query_email()
-        USER$username <- query_email()
+        # Decrypt
+        if (!is.null(encryption_key)) {
+          query_email <- decrypt_util(query_email(), encryption_key)
+        } else {
+          query_email <- query_email()
+        }
+        USER$email <- query_email
+        USER$username <- query_email
         USER$logged <- TRUE
         # TODO Use some sort of user_database to see if email allowed??
         # TODO check domain (?)

From 8536905198147de2f4213828b7c5f634da5482b9 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 21 Nov 2024 16:17:06 +0100
Subject: [PATCH 05/21] add some info

---
 components/board.upload/R/upload_utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/board.upload/R/upload_utils.R b/components/board.upload/R/upload_utils.R
index 3b70983ea..b89495d17 100644
--- a/components/board.upload/R/upload_utils.R
+++ b/components/board.upload/R/upload_utils.R
@@ -331,7 +331,7 @@ read_query_files <- function(url, encryption_key = NULL) {
   return(destination)
 }
 
-# Decrypt email
+# Decrypt utility, used in email-encrypted authentication + population of data upload (only on that auth)
 decrypt_util <- function(query, encryption_key) {
   ciphertext <- base64enc::base64decode(query)
   decrypted_query <- rawToChar(sodium::data_decrypt(ciphertext, encryption_key))

From bc640e9298c1b8ad2368d830422429397f4f9e33 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Fri, 13 Dec 2024 11:44:50 +0100
Subject: [PATCH 06/21] feat: startup modal as an OPTION

---
 components/app/R/global.R | 1 +
 components/app/R/server.R | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/components/app/R/global.R b/components/app/R/global.R
index d0f8af61b..d74e55c64 100644
--- a/components/app/R/global.R
+++ b/components/app/R/global.R
@@ -169,6 +169,7 @@ opt.default <- list(
   ENABLE_HEARTBEAT = TRUE,
   ENABLE_INACTIVITY = TRUE,
   ENABLE_ANNOT = FALSE,
+  ENABLE_STARTUP_MODAL = TRUE,
   MAX_DATASETS = 25,
   MAX_SAMPLES = 1000,
   MAX_COMPARISONS = 20,
diff --git a/components/app/R/server.R b/components/app/R/server.R
index c05be43ca..a066f68eb 100644
--- a/components/app/R/server.R
+++ b/components/app/R/server.R
@@ -1221,7 +1221,7 @@ app_server <- function(input, output, session) {
   ## Startup Message
   dbg("[MAIN] showing startup modal")
   observeEvent(auth$logged, {
-    if (auth$logged) {
+    if (auth$logged && opt$ENABLE_STARTUP_MODAL) {
       shinyjs::delay(500, {
         ## read startup messages
         msg <- readLines(file.path(ETC, "MESSAGES"))

From 2661e7ec4136cced3fe4263838ba38a85c6d00ee Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Fri, 13 Dec 2024 11:45:17 +0100
Subject: [PATCH 07/21] feat: redirect to upload/data

---
 components/modules/AuthenticationModule.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index 90f453bf7..ad8f721e4 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1324,6 +1324,14 @@ EmailEncryptedAuthenticationModule <- function(
         dbg("[EmailEncryptedAuthenticationModule] using user OPTIONS")
         USER$options <- read_user_options(USER$user_dir)
         session$sendCustomMessage("set-user", list(user = USER$email))
+        # If data is sent, trigger upload, if not, go to datasets
+        query_files <- check_query_files() |> unlist()
+        if (!is.null(query_files)) {
+          bigdash.selectTab(session, "upload-tab")
+          shinyjs::runjs("$('#upload-start_upload').click();")
+        } else {
+          bigdash.selectTab(session, "load-tab")
+        }
       }
     })
 

From 13775777b4e4ea65cf16a45f930c43f4b78598e9 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Fri, 13 Dec 2024 14:31:10 +0100
Subject: [PATCH 08/21] feat: datatype and organism on url

---
 components/board.upload/R/upload_server.R | 28 +++++++++++++++++++----
 components/board.upload/R/upload_utils.R  |  7 +++++-
 2 files changed, 30 insertions(+), 5 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 7efd3cb0e..468c0def0 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -684,11 +684,31 @@ UploadBoard <- function(id,
     # change upload_datatype to selected_datatype
     observeEvent(input$selected_datatype, {
       upload_datatype(input$selected_datatype)
+      query_files <- check_query_files()
+      if (!is.null(query_files$datatype)) {
+        # Get encryption key
+        encryption_key <- NULL# readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+        # if (!file.exists(encryption_key)) {
+        #   encryption_key <- NULL
+        # }
+        datatype <- decrypt_util(query_files$datatype, encryption_key)
+        upload_datatype(datatype)
+      }
     })
 
     # change upload_organism to selected_organism
     observeEvent(input$selected_organism, {
       upload_organism(input$selected_organism)
+      query_files <- check_query_files()
+      if (!is.null(query_files$organism)) {
+        # Get encryption key
+        encryption_key <- NULL# readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+        # if (!file.exists(encryption_key)) {
+        #   encryption_key <- NULL
+        # }
+        organism <- decrypt_util(query_files$organism, encryption_key)
+        upload_organism(organism)
+      }
     })
 
     observeEvent(input$start_upload, {
@@ -979,10 +999,10 @@ UploadBoard <- function(id,
             } else if (opt$AUTHENTICATION == "email-encrypted") { # Only data preloading on email-encrypted authentication
               query_files <- check_query_files()
               # Get encryption key
-              encryption_key <- readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
-              if (!file.exists(encryption_key)) {
-                encryption_key <- NULL
-              }
+              encryption_key <- NULL# readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+              # if (!file.exists(encryption_key)) {
+              #   encryption_key <- NULL
+              # }
               # Populate upload data with available
               if (!is.null(query_files$counts)) {
                 file <- read_query_files(query_files$counts, encryption_key)
diff --git a/components/board.upload/R/upload_utils.R b/components/board.upload/R/upload_utils.R
index b89495d17..6cef01859 100644
--- a/components/board.upload/R/upload_utils.R
+++ b/components/board.upload/R/upload_utils.R
@@ -314,10 +314,14 @@ check_query_files <- function() {
   counts <- shiny::getQueryString()$counts
   samples <- shiny::getQueryString()$samples
   contrasts <- shiny::getQueryString()$contrasts
+  datatype <- shiny::getQueryString()$datatype
+  organism <- shiny::getQueryString()$organism
   return(list(
     counts = counts,
     samples = samples,
-    contrasts = contrasts
+    contrasts = contrasts,
+    datatype = datatype,
+    organism = organism
   ))
 }
 
@@ -333,6 +337,7 @@ read_query_files <- function(url, encryption_key = NULL) {
 
 # Decrypt utility, used in email-encrypted authentication + population of data upload (only on that auth)
 decrypt_util <- function(query, encryption_key) {
+  if (is.null(encryption_key)) return(query)
   ciphertext <- base64enc::base64decode(query)
   decrypted_query <- rawToChar(sodium::data_decrypt(ciphertext, encryption_key))
   return(decrypted_query)

From 9528b5fac20dacc5e51073d1799935b5f69a24ea Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Tue, 17 Dec 2024 15:50:09 +0100
Subject: [PATCH 09/21] second dictionary for integration

---
 components/app/R/global.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/components/app/R/global.R b/components/app/R/global.R
index d74e55c64..0b568586d 100644
--- a/components/app/R/global.R
+++ b/components/app/R/global.R
@@ -170,6 +170,7 @@ opt.default <- list(
   ENABLE_INACTIVITY = TRUE,
   ENABLE_ANNOT = FALSE,
   ENABLE_STARTUP_MODAL = TRUE,
+  INTEGRATION_TRANSLATION = FALSE,
   MAX_DATASETS = 25,
   MAX_SAMPLES = 1000,
   MAX_COMPARISONS = 20,
@@ -277,3 +278,10 @@ library(shiny.i18n)
 DICTIONARY <- file.path(FILES, "translation.json")
 i18n <- shiny.i18n::Translator$new(translation_json_path = DICTIONARY)
 i18n$set_translation_language("RNA-seq")
+
+## Init integration translator
+if (opt$INTEGRATION_TRANSLATION) {
+  DICTIONARY2 <- file.path(FILES, "translation_integration.json")
+  i18n_int <- shiny.i18n::Translator$new(translation_json_path = DICTIONARY2)
+  i18n_int$set_translation_language("integration")
+}

From 045a7aaf19434d83361b38bc0221dd458651465e Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Tue, 17 Dec 2024 15:50:15 +0100
Subject: [PATCH 10/21] add tspan to steps

---
 components/board.upload/R/upload_server.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 468c0def0..148b92286 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -522,7 +522,7 @@ UploadBoard <- function(id,
       )
 
       samples_ui <- wizardR::wizard_step(
-        step_title = "Step 2: Upload samples",
+        step_title = tspan("Step 2: Upload samples", js = FALSE),
         step_id = "step_samples",
         server = TRUE,
         upload_table_preview_samples_ui(
@@ -531,7 +531,7 @@ UploadBoard <- function(id,
       )
 
       contrasts_ui <- wizardR::wizard_step(
-        step_title = "Step 3: Create comparisons",
+        step_title = tspan("Step 3: Create comparisons", js = FALSE),
         step_id = "step_comparisons",
         server = TRUE,
         upload_table_preview_contrasts_ui(
@@ -540,7 +540,7 @@ UploadBoard <- function(id,
       )
 
       normalization_panel <- wizardR::wizard_step(
-        step_title = "Step 4: QC/BC",
+        step_title = tspan("Step 4: QC/BC", js = FALSE),
         step_id = "step_qc",
         server = TRUE,
         upload_module_normalization_ui(ns("checkqc"))

From f0b8fb00c708d84cd23bd919a66599561ba9ecd7 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Tue, 17 Dec 2024 15:50:52 +0100
Subject: [PATCH 11/21] new translation on tspan

just available when integration_translation is true
---
 components/ui/ui-utils.R | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/components/ui/ui-utils.R b/components/ui/ui-utils.R
index 790b2e678..22456e70e 100644
--- a/components/ui/ui-utils.R
+++ b/components/ui/ui-utils.R
@@ -457,7 +457,7 @@ tspan <- function(text, js = TRUE) {
   if (nchar(text) == 0) {
     return("")
   }
-  if (!grepl("gene|counts|transcriptomics|rna-seq|logcpm",
+  if (!grepl("gene|counts|transcriptomics|rna-seq|logcpm|step",
     text,
     ignore.case = TRUE
   )) {
@@ -481,6 +481,18 @@ tspan <- function(text, js = TRUE) {
     text <- paste0("<span>", text, "</span>")
     text <- shiny::HTML(text)
   }
+
+  # Integration translator (does not accept JS TRUE)
+  if (opt$INTEGRATION_TRANSLATION) {
+    keys <- c(
+      "Step"
+    )
+    i18n.tr <- function(key) as.character(i18n_int$get_translations()[key, "integration"])
+    for (k in keys) {
+      tt <- i18n.tr(k)
+      if (grepl(k, text)) text <- gsub(k, tt, text, ignore.case = FALSE)
+    }
+  }
   text
 }
 

From d9aeb99de301db02e069cd778d2e5b1d923a1bfb Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Mon, 23 Dec 2024 11:56:50 +0100
Subject: [PATCH 12/21] feat: skip modal and log in user

---
 components/app/R/server.R                 | 1 +
 components/modules/AuthenticationModule.R | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/components/app/R/server.R b/components/app/R/server.R
index a066f68eb..4ef741c3b 100644
--- a/components/app/R/server.R
+++ b/components/app/R/server.R
@@ -121,6 +121,7 @@ app_server <- function(input, output, session) {
     auth <- EmailEncryptedAuthenticationModule(
       id = "auth",
       show_modal = TRUE,
+      skip_modal = TRUE,
       # TODO add argument for location of crypto key (probably on ETC)
       domain = opt$DOMAIN
     )
diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index ad8f721e4..45756c7b5 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1267,6 +1267,9 @@ EmailEncryptedAuthenticationModule <- function(
         button.text = "Sure I am!"
       )
       shiny::showModal(m)
+      if (skip_modal) {
+        shinyjs::runjs("$('#auth-login_submit_btn').click();")
+      }
     }
 
     resetUSER <- function() {

From d7fe73b0ed4c8dbfd87e6bcc2aa98c0e5f81517a Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Mon, 23 Dec 2024 12:43:09 +0100
Subject: [PATCH 13/21] fix: correct translation

---
 components/board.upload/R/upload_server.R |  4 ++--
 components/ui/ui-utils.R                  |  2 +-
 lib/translation_integration.json          | 13 +++++++++++++
 3 files changed, 16 insertions(+), 3 deletions(-)
 create mode 100644 lib/translation_integration.json

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 148b92286..8a333a0ae 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -531,7 +531,7 @@ UploadBoard <- function(id,
       )
 
       contrasts_ui <- wizardR::wizard_step(
-        step_title = tspan("Step 3: Create comparisons", js = FALSE),
+        step_title = "Step 3: Create comparisons",
         step_id = "step_comparisons",
         server = TRUE,
         upload_table_preview_contrasts_ui(
@@ -540,7 +540,7 @@ UploadBoard <- function(id,
       )
 
       normalization_panel <- wizardR::wizard_step(
-        step_title = tspan("Step 4: QC/BC", js = FALSE),
+        step_title = "Step 4: QC/BC",
         step_id = "step_qc",
         server = TRUE,
         upload_module_normalization_ui(ns("checkqc"))
diff --git a/components/ui/ui-utils.R b/components/ui/ui-utils.R
index 22456e70e..c88c06b9e 100644
--- a/components/ui/ui-utils.R
+++ b/components/ui/ui-utils.R
@@ -485,7 +485,7 @@ tspan <- function(text, js = TRUE) {
   # Integration translator (does not accept JS TRUE)
   if (opt$INTEGRATION_TRANSLATION) {
     keys <- c(
-      "Step"
+      "Upload"
     )
     i18n.tr <- function(key) as.character(i18n_int$get_translations()[key, "integration"])
     for (k in keys) {
diff --git a/lib/translation_integration.json b/lib/translation_integration.json
new file mode 100644
index 000000000..2c1bb6532
--- /dev/null
+++ b/lib/translation_integration.json
@@ -0,0 +1,13 @@
+{
+    "cultural_date_format": "%d-%m-%Y",
+    "languages": [
+        "default",
+        "integration"
+    ],
+    "translation": [
+        {
+            "default": "Upload",
+            "integration": "Review"
+        }
+    ]
+}

From d3bf5b4d793bc88353a4944fb1779e6bba53afe1 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 9 Jan 2025 12:19:57 +0100
Subject: [PATCH 14/21] fix: add missing argument `skip_modal`

---
 components/modules/AuthenticationModule.R | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index 45756c7b5..cd98922f0 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1228,18 +1228,24 @@ LoginCodeAuthenticationModule <- function(id,
 
 
 EmailEncryptedAuthenticationModule <- function(
-  id = "auth",
-  show_modal = TRUE,
-  # TODO add argument for location of crypto key (probably on ETC)
-  domain = opt$DOMAIN) {
+    id = "auth",
+    show_modal = TRUE,
+    skip_modal = FALSE,
+    # TODO add argument for location of crypto key (probably on ETC)
+    domain = opt$DOMAIN) {
   shiny::moduleServer(id, function(input, output, session) {
     message("[AuthenticationModule] >>>> using EmailEncrypted authentication <<<<")
     ns <- session$ns
 
     # Get encryption key
-    encryption_key <- tryCatch({
-      readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
-    }, error = function(w){NULL})
+    encryption_key <- tryCatch(
+      {
+        readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+      },
+      error = function(w) {
+        NULL
+      }
+    )
     if (is.null(encryption_key)) {
       ## we continue without decryption, just to test, unsafe
       warning("[EmailEncryptedAuthenticationModule] ERROR : missing encryption_key file!!!")

From 92bc19b7e6eb7077d3448870ebdb0132d0ab23b0 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Mon, 13 Jan 2025 17:51:00 +0100
Subject: [PATCH 15/21] feat: decryption

---
 components/board.upload/R/upload_server.R     |  60 +++++++-
 components/board.upload/R/upload_utils.R      |  15 +-
 components/modules/AuthenticationModule.R     |  74 +++++----
 .../modules/AuthenticationModule_functions.R  | 143 +++++++++++-------
 4 files changed, 190 insertions(+), 102 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 8a333a0ae..80f6649ca 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -687,7 +687,15 @@ UploadBoard <- function(id,
       query_files <- check_query_files()
       if (!is.null(query_files$datatype)) {
         # Get encryption key
-        encryption_key <- NULL# readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+        encryption_key <- tryCatch(
+          {
+            readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+          },
+          error = function(w) {
+            warning("[UploadServer] ERROR: missing encryption_key file!!!")
+            NULL
+          }
+        )
         # if (!file.exists(encryption_key)) {
         #   encryption_key <- NULL
         # }
@@ -702,7 +710,15 @@ UploadBoard <- function(id,
       query_files <- check_query_files()
       if (!is.null(query_files$organism)) {
         # Get encryption key
-        encryption_key <- NULL# readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+        encryption_key <- tryCatch(
+          {
+            readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+          },
+          error = function(w) {
+            warning("[UploadServer] ERROR: missing encryption_key file!!!")
+            NULL
+          }
+        )
         # if (!file.exists(encryption_key)) {
         #   encryption_key <- NULL
         # }
@@ -999,13 +1015,29 @@ UploadBoard <- function(id,
             } else if (opt$AUTHENTICATION == "email-encrypted") { # Only data preloading on email-encrypted authentication
               query_files <- check_query_files()
               # Get encryption key
-              encryption_key <- NULL# readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+              encryption_key <- tryCatch(
+                {
+                  readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
+                },
+                error = function(w) {
+                  warning("[UploadServer] ERROR: missing encryption_key file!!!")
+                  NULL
+                }
+              )
               # if (!file.exists(encryption_key)) {
               #   encryption_key <- NULL
               # }
               # Populate upload data with available
               if (!is.null(query_files$counts)) {
-                file <- read_query_files(query_files$counts, encryption_key)
+                # Decrypt the URL if encryption key is available
+                counts_url <- if (!is.null(encryption_key)) {
+                  decrypt_util(query_files$counts, encryption_key)
+                } else {
+                  warning("[UploadServer] No encryption key available, using raw URL")
+                  query_files$counts
+                }
+
+                file <- read_query_files(counts_url)
                 df <- playbase::read_counts(file)
                 uploaded$counts.csv <- df
                 ## if counts file contains annotation
@@ -1013,12 +1045,28 @@ UploadBoard <- function(id,
                 uploaded$annot.csv <- af
               }
               if (!is.null(query_files$samples)) {
-                file <- read_query_files(query_files$samples, encryption_key)
+                # Decrypt the URL if encryption key is available  
+                samples_url <- if (!is.null(encryption_key)) {
+                  decrypt_util(query_files$samples, encryption_key)
+                } else {
+                  warning("[UploadServer] No encryption key available, using raw URL")
+                  query_files$samples
+                }
+
+                file <- read_query_files(samples_url)
                 df <- playbase::read_samples(file)
                 uploaded$samples.csv <- df
               }
               if (!is.null(query_files$contrasts)) {
-                file <- read_query_files(query_files$contrasts, encryption_key)
+                # Decrypt the URL if encryption key is available
+                contrasts_url <- if (!is.null(encryption_key)) {
+                  decrypt_util(query_files$contrasts, encryption_key)
+                } else {
+                  warning("[UploadServer] No encryption key available, using raw URL")
+                  query_files$contrasts
+                }
+
+                file <- read_query_files(contrasts_url)
                 df <- playbase::read_contrasts(file)
                 uploaded$contrasts.csv <- df
               }
diff --git a/components/board.upload/R/upload_utils.R b/components/board.upload/R/upload_utils.R
index 6cef01859..f01356a32 100644
--- a/components/board.upload/R/upload_utils.R
+++ b/components/board.upload/R/upload_utils.R
@@ -326,19 +326,8 @@ check_query_files <- function() {
 }
 
 # Read query files
-read_query_files <- function(url, encryption_key = NULL) {
-  if (!is.null(encryption_key)) {
-    url <- decrypt_util(url, encryption_key)
-  }
+read_query_files <- function(url) {
   destination <- tempfile(fileext = ".csv")
   download.file(url, destination)
   return(destination)
-}
-
-# Decrypt utility, used in email-encrypted authentication + population of data upload (only on that auth)
-decrypt_util <- function(query, encryption_key) {
-  if (is.null(encryption_key)) return(query)
-  ciphertext <- base64enc::base64decode(query)
-  decrypted_query <- rawToChar(sodium::data_decrypt(ciphertext, encryption_key))
-  return(decrypted_query)
-}
+}
\ No newline at end of file
diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index cd98922f0..63a91997c 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1226,12 +1226,14 @@ LoginCodeAuthenticationModule <- function(id,
   })
 }
 
+## ================================================================================
+## Utility functions for authentication
+## ================================================================================
 
 EmailEncryptedAuthenticationModule <- function(
     id = "auth",
     show_modal = TRUE,
     skip_modal = FALSE,
-    # TODO add argument for location of crypto key (probably on ETC)
     domain = opt$DOMAIN) {
   shiny::moduleServer(id, function(input, output, session) {
     message("[AuthenticationModule] >>>> using EmailEncrypted authentication <<<<")
@@ -1312,35 +1314,49 @@ EmailEncryptedAuthenticationModule <- function(
       if (is.null(query_email())) {
         dbg("[EmailEncryptedAuthenticationModule] invalid email hash")
         output$login_warning <- shiny::renderText("invalid email hash")
-        # TODO show some error on the UI
+        return(NULL)
+      }
+
+      # Decrypt email if encryption key is available
+      decrypted_email <- if (!is.null(encryption_key)) {
+        decrypt_util(query_email(), encryption_key)
       } else {
-        # Decrypt
-        if (!is.null(encryption_key)) {
-          query_email <- decrypt_util(query_email(), encryption_key)
-        } else {
-          query_email <- query_email()
-        }
-        USER$email <- query_email
-        USER$username <- query_email
-        USER$logged <- TRUE
-        # TODO Use some sort of user_database to see if email allowed??
-        # TODO check domain (?)
-        USER$user_dir <- file.path(PGX.DIR, USER$email)
-        create_user_dir_if_needed(USER$user_dir, PGX.DIR)
-        if (!opt$ENABLE_USERDIR) {
-          USER$user_dir <- file.path(PGX.DIR)
-        }
-        dbg("[EmailEncryptedAuthenticationModule] using user OPTIONS")
-        USER$options <- read_user_options(USER$user_dir)
-        session$sendCustomMessage("set-user", list(user = USER$email))
-        # If data is sent, trigger upload, if not, go to datasets
-        query_files <- check_query_files() |> unlist()
-        if (!is.null(query_files)) {
-          bigdash.selectTab(session, "upload-tab")
-          shinyjs::runjs("$('#upload-start_upload').click();")
-        } else {
-          bigdash.selectTab(session, "load-tab")
-        }
+        warning("[EmailEncryptedAuthenticationModule] No encryption key available, using raw email")
+        query_email()
+      }
+
+      # Validate decrypted email
+      if (is.null(decrypted_email)) {
+        dbg("[EmailEncryptedAuthenticationModule] failed to decrypt email")
+        output$login_warning <- shiny::renderText("invalid email format")
+        return(NULL)
+      }
+
+      USER$email <- decrypted_email
+      USER$username <- decrypted_email
+      USER$logged <- TRUE
+
+      # TODO Use some sort of user_database to see if email allowed??
+      # TODO check domain (?)
+
+      # Set up user directory
+      USER$user_dir <- file.path(PGX.DIR, USER$email)
+      create_user_dir_if_needed(USER$user_dir, PGX.DIR)
+      if (!opt$ENABLE_USERDIR) {
+        USER$user_dir <- file.path(PGX.DIR)
+      }
+
+      dbg("[EmailEncryptedAuthenticationModule] using user OPTIONS")
+      USER$options <- read_user_options(USER$user_dir)
+      session$sendCustomMessage("set-user", list(user = USER$email))
+
+      # Handle query files and navigation
+      query_files <- check_query_files() |> unlist()
+      if (!is.null(query_files)) {
+        bigdash.selectTab(session, "upload-tab")
+        shinyjs::runjs("$('#upload-start_upload').click();")
+      } else {
+        bigdash.selectTab(session, "load-tab")
       }
     })
 
diff --git a/components/modules/AuthenticationModule_functions.R b/components/modules/AuthenticationModule_functions.R
index be54cc9c4..9d0ec4bc8 100644
--- a/components/modules/AuthenticationModule_functions.R
+++ b/components/modules/AuthenticationModule_functions.R
@@ -18,7 +18,7 @@ check_user_options_db <- function(email, user_database = NULL) {
   if (is.null(user_database)) {
     return(FALSE)
   }
-  connection <- connect_db(user_database)
+  connection <- DBI::dbConnect(RSQLite::SQLite(), dbname = user_database)
   user_opt <- query_by_email(email, connection)
   if (is.null(user_opt)) {
     return(FALSE) # user NOT in db
@@ -47,16 +47,14 @@ read_user_options <- function(user_dir) {
       new_opt[[opt_name]] <- user_opt[[opt_name]]
     }
   }
-  # add user dir to opt file (IK: this is not an option!)
-  ##  new_opt$user_dir <- user_dir
   new_opt
 }
 
 read_user_options_db <- function(email, user_database = NULL) {
-  connection <- connect_db(user_database)
+  connection <- DBI::dbConnect(RSQLite::SQLite(), dbname = user_database)
   user_opt <- query_by_email(email, connection)
   new_opt <- opt ## opt from global
-  disconnect_db(connection)
+  DBI::dbDisconnect(connection)
   if (!is.null(user_opt)) {
     ## restrict user options only to these options.
     ALLOWED_USER_OPTS <- c(
@@ -93,71 +91,71 @@ upgrade.dialog <- function(ns, current.plan) {
   if (current.plan == "starter") btn_starter <- "Current Plan"
   if (current.plan == "premium") btn_premium <- "Current Plan"
 
-  modalDialog(
-    title = h3("Find the right OmicsPlayground plan for you"),
+  shiny::modalDialog(
+    title = shiny::h3("Find the right OmicsPlayground plan for you"),
     size = "m",
-    div(
+    shiny::div(
       class = "row",
       style = "padding-left:4rem;padding-right:4rem;text-align:center;",
-      div(
+      shiny::div(
         class = "col-md-4",
         style = "background:#F2FAFF;",
-        HTML("<h4><b>Basic</b></h4>"),
-        p("Try for free"),
-        h3("Free!"),
-        tags$ul(
+        shiny::HTML("<h4><b>Basic</b></h4>"),
+        shiny::p("Try for free"),
+        shiny::h3("Free!"),
+        shiny::tags$ul(
           class = "list-unstyled",
-          tags$li("Host up to 3 datasets"),
-          tags$li("45 minutes time limit"),
-          tags$li("Up to 25 samples / dataset"),
-          tags$li("Up to 5 comparisons")
+          shiny::tags$li("Host up to 3 datasets"),
+          shiny::tags$li("45 minutes time limit"),
+          shiny::tags$li("Up to 25 samples / dataset"),
+          shiny::tags$li("Up to 5 comparisons")
         ),
         shiny::actionButton(ns("get_basic"), btn_basic),
-        br()
+        shiny::br()
       ),
-      div(
+      shiny::div(
         class = "col-md-4",
         style = "background:#E8F8FF;",
-        h4(HTML("<b>Starter</b>")),
-        p("Great to start"),
-        h3("Soon!"),
-        tags$ul(
+        shiny::h4(shiny::HTML("<b>Starter</b>")),
+        shiny::p("Great to start"),
+        shiny::h3("Soon!"),
+        shiny::tags$ul(
           class = "list-unstyled",
-          tags$li("Host up to 10 datasets"),
-          tags$li("3 hours time limit"),
-          tags$li("Up to 100 samples / dataset"),
-          tags$li("Up to 10 comparisons")
+          shiny::tags$li("Host up to 10 datasets"),
+          shiny::tags$li("3 hours time limit"),
+          shiny::tags$li("Up to 100 samples / dataset"),
+          shiny::tags$li("Up to 10 comparisons")
         ),
         shiny::actionButton(ns("get_starter"), btn_starter),
-        br()
+        shiny::br()
       ),
-      div(
+      shiny::div(
         class = "col-md-4",
         style = "background:#E2F4FF;",
-        HTML("<h4><b>Premium</b></h4>"),
-        p("For power users or small groups"),
-        h3("Soon!"),
-        tags$ul(
+        shiny::HTML("<h4><b>Premium</b></h4>"),
+        shiny::p("For power users or small groups"),
+        shiny::h3("Soon!"),
+        shiny::tags$ul(
           class = "list-unstyled",
-          tags$li("Host up to 100 datasets"),
-          tags$li("8 hours time limit"),
-          tags$li("Up to 2000 samples / dataset"),
-          tags$li("Up to 100 comparisons")
+          shiny::tags$li("Host up to 100 datasets"),
+          shiny::tags$li("8 hours time limit"),
+          shiny::tags$li("Up to 2000 samples / dataset"),
+          shiny::tags$li("Up to 100 comparisons")
         ),
         shiny::actionButton(ns("get_premium"), btn_premium),
-        br()
+        shiny::br()
       )
     ), ## content div
-    div(
+    shiny::div(
       style = "margin-top:3rem;text-align:center;",
-      HTML("Looking for OmicsPlayground for <b>Enterprise</b>? <a href='mailto:info@bigomics.com'>Contact sales for info and pricing</a>.")
+      shiny::HTML("Looking for OmicsPlayground for <b>Enterprise</b>? <a href='mailto:info@bigomics.com'>Contact sales for info and pricing</a>.")
     ),
-    footer = tagList(
-      fillRow(
+    footer = shiny::tagList(
+      shiny::fillRow(
         flex = c(NA, 0.03, NA, 1, NA, NA),
-        tags$label(
+        shiny::tags$label(
           class = "radio-inline",
-          tags$input(
+          shiny::tags$input(
             id = "yearlyCheck",
             type = "radio",
             name = "yearly",
@@ -166,10 +164,10 @@ upgrade.dialog <- function(ns, current.plan) {
           ),
           "Billed yearly"
         ),
-        br(),
-        tags$label(
+        shiny::br(),
+        shiny::tags$label(
           class = "radio-inline",
-          tags$input(
+          shiny::tags$input(
             id = "monthlyCheck",
             type = "radio",
             name = "monthly",
@@ -177,9 +175,9 @@ upgrade.dialog <- function(ns, current.plan) {
           ),
           "Billed monthly"
         ),
-        br(),
+        shiny::br(),
         shiny::actionButton(ns("manage"), "Manage Subscription"),
-        modalButton("Dismiss")
+        shiny::modalButton("Dismiss")
       )
     )
   ) ## modalDialog
@@ -227,7 +225,7 @@ checkAuthorizedUser <- function(email, credentials_file = NULL) {
   if (!file.exists(credentials_file)) {
     return(TRUE)
   }
-  CREDENTIALS <- read.csv(credentials_file, colClasses = "character")
+  CREDENTIALS <- utils::read.csv(credentials_file, colClasses = "character")
   valid_user <- tolower(email) %in% tolower(CREDENTIALS$email)
   if (!valid_user) {
     return(FALSE)
@@ -245,15 +243,13 @@ checkExpiredUser <- function(email, user_database) {
   if (!file.exists(user_database)) {
     return(TRUE)
   }
-  connection <- connect_db(user_database)
-  # connection <- DBI::dbConnect(RSQLite::SQLite(), dbname = user_database)
+  connection <- DBI::dbConnect(RSQLite::SQLite(), dbname = user_database)
   query_result <- DBI::dbGetQuery(connection, paste0("
     SELECT expiry
     FROM users
     WHERE email = '", email, "'
   "))
-  # DBI::dbDisconnect(connection)
-  disconnect_db(connection)
+  DBI::dbDisconnect(connection)
   if (nrow(query_result) == 0) {
     return(TRUE)
   } else {
@@ -332,6 +328,45 @@ chueckHubspotData <- function(user_email) {
   }
 }
 
+## -----------------------------------------------------------------
+## Encryption/Decryption functions
+## -----------------------------------------------------------------
+
+#' Decrypt text using AES-256-CBC
+#' @param encrypted_text The encrypted text to decrypt
+#' @param key The encryption key as a string
+#' @return The decrypted text
+decrypt_util <- function(encrypted_text, key) {
+  if (is.null(encrypted_text) || is.null(key)) return(NULL)
+
+  # Convert key to raw bytes
+  key_raw <- charToRaw(key)
+
+  # URL decode the encrypted text
+  encrypted_text <- utils::URLdecode(encrypted_text)
+
+  # Split the IV and encrypted data
+  parts <- strsplit(encrypted_text, ":")[[1]]
+  if (length(parts) != 2) return(NULL)
+
+  # Decode base64 components
+  iv <- openssl::base64_decode(parts[1])
+  encrypted_data <- openssl::base64_decode(parts[2])
+
+  # Decrypt using AES-256-CBC
+  tryCatch({
+    decrypted <- openssl::aes_cbc_decrypt(
+      encrypted_data,
+      key = key_raw,
+      iv = iv
+    )
+    rawToChar(decrypted)
+  }, error = function(e) {
+    warning("[decrypt_util] Decryption failed: ", e$message)
+    NULL
+  })
+}
+
 ## ================================================================================
 ## ================================= END OF FILE ==================================
 ## ================================================================================

From dc870369387f9bc1c7f1b18992ffed0ba245f631 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 15 Jan 2025 09:45:48 +0100
Subject: [PATCH 16/21] feat: datatype and organism not encrypted

---
 components/board.upload/R/upload_server.R | 30 ++---------------------
 1 file changed, 2 insertions(+), 28 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 80f6649ca..98a2dc431 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -686,20 +686,7 @@ UploadBoard <- function(id,
       upload_datatype(input$selected_datatype)
       query_files <- check_query_files()
       if (!is.null(query_files$datatype)) {
-        # Get encryption key
-        encryption_key <- tryCatch(
-          {
-            readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
-          },
-          error = function(w) {
-            warning("[UploadServer] ERROR: missing encryption_key file!!!")
-            NULL
-          }
-        )
-        # if (!file.exists(encryption_key)) {
-        #   encryption_key <- NULL
-        # }
-        datatype <- decrypt_util(query_files$datatype, encryption_key)
+        datatype <- query_files$datatype
         upload_datatype(datatype)
       }
     })
@@ -709,20 +696,7 @@ UploadBoard <- function(id,
       upload_organism(input$selected_organism)
       query_files <- check_query_files()
       if (!is.null(query_files$organism)) {
-        # Get encryption key
-        encryption_key <- tryCatch(
-          {
-            readLines(file.path(OPG, "etc/keys/encryption.txt"))[1]
-          },
-          error = function(w) {
-            warning("[UploadServer] ERROR: missing encryption_key file!!!")
-            NULL
-          }
-        )
-        # if (!file.exists(encryption_key)) {
-        #   encryption_key <- NULL
-        # }
-        organism <- decrypt_util(query_files$organism, encryption_key)
+        organism <- query_files$organism
         upload_organism(organism)
       }
     })

From 3a1ab6d2551739ab4b46f5fa4b3dcbe1a294531a Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Tue, 21 Jan 2025 14:01:33 +0100
Subject: [PATCH 17/21] feat: remove trailin 8 characters from email decryption

---
 components/modules/AuthenticationModule.R           |  2 +-
 components/modules/AuthenticationModule_functions.R | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/components/modules/AuthenticationModule.R b/components/modules/AuthenticationModule.R
index 63a91997c..a26505024 100644
--- a/components/modules/AuthenticationModule.R
+++ b/components/modules/AuthenticationModule.R
@@ -1319,7 +1319,7 @@ EmailEncryptedAuthenticationModule <- function(
 
       # Decrypt email if encryption key is available
       decrypted_email <- if (!is.null(encryption_key)) {
-        decrypt_util(query_email(), encryption_key)
+        decrypt_util(query_email(), encryption_key, remove_suffix = TRUE)
       } else {
         warning("[EmailEncryptedAuthenticationModule] No encryption key available, using raw email")
         query_email()
diff --git a/components/modules/AuthenticationModule_functions.R b/components/modules/AuthenticationModule_functions.R
index 9d0ec4bc8..3877f0ca6 100644
--- a/components/modules/AuthenticationModule_functions.R
+++ b/components/modules/AuthenticationModule_functions.R
@@ -336,7 +336,7 @@ chueckHubspotData <- function(user_email) {
 #' @param encrypted_text The encrypted text to decrypt
 #' @param key The encryption key as a string
 #' @return The decrypted text
-decrypt_util <- function(encrypted_text, key) {
+decrypt_util <- function(encrypted_text, key, remove_suffix = FALSE) {
   if (is.null(encrypted_text) || is.null(key)) return(NULL)
 
   # Convert key to raw bytes
@@ -360,7 +360,13 @@ decrypt_util <- function(encrypted_text, key) {
       key = key_raw,
       iv = iv
     )
-    rawToChar(decrypted)
+    decrypted_text <- rawToChar(decrypted)
+
+    if (remove_suffix) {
+      decrypted_text <- substr(decrypted_text, 1, nchar(decrypted_text) - 8)
+    }
+ 
+    decrypted_text
   }, error = function(e) {
     warning("[decrypt_util] Decryption failed: ", e$message)
     NULL

From 05d0086240810226912fa65a75fb2f69ea0a7f48 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Tue, 21 Jan 2025 14:15:38 +0100
Subject: [PATCH 18/21] feat: blacklist email suffix

---
 components/modules/AuthenticationModule_functions.R | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/components/modules/AuthenticationModule_functions.R b/components/modules/AuthenticationModule_functions.R
index 3877f0ca6..a2bebdc96 100644
--- a/components/modules/AuthenticationModule_functions.R
+++ b/components/modules/AuthenticationModule_functions.R
@@ -363,9 +363,20 @@ decrypt_util <- function(encrypted_text, key, remove_suffix = FALSE) {
     decrypted_text <- rawToChar(decrypted)
 
     if (remove_suffix) {
+      BLACKLIST_FILE <- file.path(ETC, "blacklisted_suffixes.txt")
+      suffix <- substr(decrypted_text, nchar(decrypted_text) - 7, nchar(decrypted_text))
+      if (!file.exists(BLACKLIST_FILE)) {
+        dir.create(dirname(BLACKLIST_FILE), recursive = TRUE, showWarnings = FALSE)
+        file.create(BLACKLIST_FILE)
+      }
+      if (system(paste("grep -q", shQuote(suffix), shQuote(BLACKLIST_FILE)), 
+                 ignore.stdout = TRUE, ignore.stderr = TRUE) == 0) {
+        warning("[decrypt_util] Blacklisted suffix detected")
+        return(NULL)
+      }
       decrypted_text <- substr(decrypted_text, 1, nchar(decrypted_text) - 8)
+      write(suffix, file = BLACKLIST_FILE, append = TRUE)
     }
- 
     decrypted_text
   }, error = function(e) {
     warning("[decrypt_util] Decryption failed: ", e$message)

From c6ecb3d93888e2ee72b6ae464cf98acc82eecea3 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Tue, 21 Jan 2025 17:33:11 +0100
Subject: [PATCH 19/21] feat: do not populate on second upload

---
 components/board.upload/R/upload_server.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 98a2dc431..db419163a 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -685,7 +685,7 @@ UploadBoard <- function(id,
     observeEvent(input$selected_datatype, {
       upload_datatype(input$selected_datatype)
       query_files <- check_query_files()
-      if (!is.null(query_files$datatype)) {
+      if (!is.null(query_files$datatype) && new_upload() == 2) {
         datatype <- query_files$datatype
         upload_datatype(datatype)
       }
@@ -695,7 +695,7 @@ UploadBoard <- function(id,
     observeEvent(input$selected_organism, {
       upload_organism(input$selected_organism)
       query_files <- check_query_files()
-      if (!is.null(query_files$organism)) {
+      if (!is.null(query_files$organism) && new_upload() == 2) {
         organism <- query_files$organism
         upload_organism(organism)
       }
@@ -1002,7 +1002,7 @@ UploadBoard <- function(id,
               #   encryption_key <- NULL
               # }
               # Populate upload data with available
-              if (!is.null(query_files$counts)) {
+              if (!is.null(query_files$counts) && new_upload() == 2) {
                 # Decrypt the URL if encryption key is available
                 counts_url <- if (!is.null(encryption_key)) {
                   decrypt_util(query_files$counts, encryption_key)
@@ -1018,8 +1018,8 @@ UploadBoard <- function(id,
                 af <- playbase::read_annot(file)
                 uploaded$annot.csv <- af
               }
-              if (!is.null(query_files$samples)) {
-                # Decrypt the URL if encryption key is available  
+              if (!is.null(query_files$samples) && new_upload() == 2) {
+                # Decrypt the URL if encryption key is available
                 samples_url <- if (!is.null(encryption_key)) {
                   decrypt_util(query_files$samples, encryption_key)
                 } else {
@@ -1031,7 +1031,7 @@ UploadBoard <- function(id,
                 df <- playbase::read_samples(file)
                 uploaded$samples.csv <- df
               }
-              if (!is.null(query_files$contrasts)) {
+              if (!is.null(query_files$contrasts) && new_upload() == 2) {
                 # Decrypt the URL if encryption key is available
                 contrasts_url <- if (!is.null(encryption_key)) {
                   decrypt_util(query_files$contrasts, encryption_key)

From b4371496d9197f00d68999e70f7b5a601b275265 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 22 Jan 2025 10:01:05 +0100
Subject: [PATCH 20/21] wip

---
 components/board.upload/R/upload_server.R | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index db419163a..067dea5c9 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -1003,7 +1003,6 @@ UploadBoard <- function(id,
               # }
               # Populate upload data with available
               if (!is.null(query_files$counts) && new_upload() == 2) {
-                # Decrypt the URL if encryption key is available
                 counts_url <- if (!is.null(encryption_key)) {
                   decrypt_util(query_files$counts, encryption_key)
                 } else {
@@ -1011,12 +1010,21 @@ UploadBoard <- function(id,
                   query_files$counts
                 }
 
-                file <- read_query_files(counts_url)
-                df <- playbase::read_counts(file)
-                uploaded$counts.csv <- df
-                ## if counts file contains annotation
-                af <- playbase::read_annot(file)
-                uploaded$annot.csv <- af
+                future_promise({
+                  file <- read_query_files(counts_url)
+                  df <- playbase::read_counts(file)
+                  af <- playbase::read_annot(file)
+                  list(counts = df, annot = af)
+                }) %...>% 
+                (function(result) {
+                  message("[UploadServer] Future completed successfully")
+                  uploaded$counts.csv <- result$counts
+                  uploaded$annot.csv <- result$annot
+                }) %...!% 
+                (function(error) {
+                  message("[UploadServer] Future failed with error: ", error$message)
+                  warning("[UploadServer] Error processing counts file: ", error)
+                })
               }
               if (!is.null(query_files$samples) && new_upload() == 2) {
                 # Decrypt the URL if encryption key is available

From 2bf5d142b958426acba67aab157504ae87d036e3 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 22 Jan 2025 11:00:31 +0100
Subject: [PATCH 21/21] feat: async+loader while data is not there

---
 .../R/upload_module_preview_counts.R             | 16 ++++++++++++++++
 components/board.upload/R/upload_server.R        |  3 +++
 2 files changed, 19 insertions(+)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 4ff9b8384..d976cd787 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -128,6 +128,22 @@ upload_table_preview_counts_server <- function(
             action_buttons
           )
         },
+        if (is.matrix(uploaded$counts.csv) && nrow(uploaded$counts.csv) == 1 && ncol(uploaded$counts.csv) == 1) {
+          bslib::layout_columns(
+            col_widths = 12,
+            div(
+              style = "display: flex; justify-content: center; align-items: center; position: absolute; top: 21px; left: 21px; right: 21px; bottom: 21px; z-index: 9999; background: white;",
+              shiny::tags$div(
+                style = "width: 100%; display: flex; justify-content: center; align-items: center;",
+                shiny::tags$div(
+                  class = "spinner-border text-primary", 
+                  style = "width: 5rem; height: 5rem;",
+                  shiny::tags$span(class = "visually-hidden", "Loading...")
+                )
+              )
+            )
+          )
+        },
         if (!is.null(uploaded$counts.csv)) {
           bslib::layout_columns(
             col_widths = 12,
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 067dea5c9..a2cfacc55 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -1010,6 +1010,9 @@ UploadBoard <- function(id,
                   query_files$counts
                 }
 
+                # Set initial loading state
+                uploaded$counts.csv <- matrix(data = 1, nrow = 1, ncol = 1)
+                
                 future_promise({
                   file <- read_query_files(counts_url)
                   df <- playbase::read_counts(file)