From 9a20abd69b466ce22246c67d69859a9d067edcfa Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Fri, 1 Jul 2022 12:40:54 +0200
Subject: [PATCH] Temporarily remove DisGeNET integration

Supplying the custom background results in internal server errors on the
DisGeNET backend. We don't want to present results without a proper
background set.
---
 DESCRIPTION |  1 -
 R/server.R  | 43 -------------------------------------------
 R/ui.R      |  7 -------
 3 files changed, 51 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 72f3a1f..8eaf5f5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -19,7 +19,6 @@ RoxygenNote: 7.2.0
 Imports:
     bslib,
     data.table,
-    disgenet2r,
     DT,
     geposan,
     glue,
diff --git a/R/server.R b/R/server.R
index 2b37685..30e9578 100644
--- a/R/server.R
+++ b/R/server.R
@@ -267,48 +267,5 @@ server <- function(options) {
         digits = 1
       )
     })
-
-    output$disgenet <- DT::renderDT({
-      withProgress(
-        message = "Querying DisGeNET",
-        value = 0.0,
-        { # nolint
-          setProgress(0.2)
-
-          all_gene_names <- unique(results()[name != "", name])
-          filtered_gene_names <- unique(results_filtered()[name != "", name])
-
-          diseases <- suppressMessages(
-            disgenet2r::disease_enrichment(
-              all_gene_names,
-              custom_universe = list(filtered_gene_names)
-            )
-          )
-
-          data <- data.table(diseases@qresult)
-
-          data <- data[, .(Description, Ratio, BgRatio, pvalue)]
-          setorder(data, pvalue)
-
-          dt <- DT::datatable(
-            data,
-            rownames = FALSE,
-            colnames = c(
-              "Disease",
-              "Query ratio",
-              "Total ratio",
-              "p-value"
-            ),
-            options = list(
-              pageLength = 25
-            )
-          )
-
-          dt <- DT::formatRound(dt, "pvalue", digits = 4)
-
-          dt
-        }
-      )
-    })
   }
 }
diff --git a/R/ui.R b/R/ui.R
index becbe67..0a35a0c 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -101,13 +101,6 @@ ui <- function(options) {
                   style = "margin-top: 16px",
                   DT::DTOutput("gost_details")
                 )
-              ),
-              tabPanel(
-                title = "DisGeNET",
-                div(
-                  style = "margin-top: 16px",
-                  DT::DTOutput("disgenet")
-                )
               )
             )
           )