From bd14ea7aee583d7262f514a3debb9961e8f1d79f Mon Sep 17 00:00:00 2001
From: Chai Bandlamudi <bandlamc@mskcc.org>
Date: Mon, 9 Mar 2020 06:30:11 -0400
Subject: [PATCH] removing jsonvalidate for now because installing it on the
 servers will be a nightmare

---
 DESCRIPTION                      |  3 +--
 NAMESPACE                        |  2 +-
 R/generate_genomic_annotations.R | 11 +++++++++++
 inst/application/server.R        | 24 +++++++++++++-----------
 4 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d215831..87de6a2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,8 +29,7 @@ Imports:
     doParallel,
     parallel,
     configr,
-    R.utils,
-    jsonvalidate
+    R.utils
 License: GNU Affero General Public License v3.0
 Encoding: UTF-8
 LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
index ca23823..7025531 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -40,4 +40,4 @@ import(doParallel)
 import(parallel)
 import(configr)
 import(R.utils)
-import(jsonvalidate)
\ No newline at end of file
+#import(jsonvalidate)
\ No newline at end of file
diff --git a/R/generate_genomic_annotations.R b/R/generate_genomic_annotations.R
index 72097c5..e188889 100755
--- a/R/generate_genomic_annotations.R
+++ b/R/generate_genomic_annotations.R
@@ -18,6 +18,17 @@ generate_genomic_annotations = function(sample_id, sample_path, config_file, reg
   if (!file.exists(config_file)) {
     stop("invalid config file provided to generate_genomic_annotations")
   }
+
+  ### NOTE: Removing json validation because installing 'jsonvalidate' on juno is a nightmare. 
+  ### Need to figure out an alternative or somehow install it.  
+  # json_validation_status = jsonvalidate::json_validate(values$config_file, 
+  #                                                      system.file("data/config_schema.json", package="facetsPreview"), 
+  #                                                      verbose=T)
+  # if (!json_validation_status) {
+  #   print(json_validation_status)
+  #   stop('Error parsing config file')
+  # }
+  
   config = configr::read.config(config_file)
   source(config$facets_qc_script)
   library(facetsSuite, lib.loc = config$facets_suite_lib)
diff --git a/inst/application/server.R b/inst/application/server.R
index 3d6e076..80703d6 100755
--- a/inst/application/server.R
+++ b/inst/application/server.R
@@ -28,17 +28,19 @@ function(input, output, session) {
       return(NULL)
     }
 
-    json_validation_status = jsonvalidate::json_validate(values$config_file, 
-                                                         system.file("data/config_schema.json", package="facetsPreview"), 
-                                                         verbose=T)
-    if (!json_validation_status) {
-      showModal(modalDialog( title = "config file parsing error",  
-                             'likely missing or incorrectly set parameters in config file. check console for error information',
-                             easyClose = TRUE))
-      print(json_validation_status)
-      stop('Error parsing config file')
-      stopApp(1)
-    }
+    ### NOTE: Removing json validation because installing 'jsonvalidate' on juno is a nightmare. 
+    ### Need to figure out an alternative or somehow install it.
+    # json_validation_status = jsonvalidate::json_validate(values$config_file, 
+    #                                                      system.file("data/config_schema.json", package="facetsPreview"), 
+    #                                                      verbose=T)
+    # if (!json_validation_status) {
+    #   showModal(modalDialog( title = "config file parsing error",  
+    #                          'likely missing or incorrectly set parameters in config file. check console for error information',
+    #                          easyClose = TRUE))
+    #   print(json_validation_status)
+    #   stop('Error parsing config file')
+    #   stopApp(1)
+    # }
     
     values$config = configr::read.config(values$config_file)