fix: typo in default_golem_opts path

CNAG-Biomedical-Informatics · Mar 26, 2024 · 9d7f39c · 9d7f39c
1 parent b67accd
commit 9d7f39c
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Showing 5 changed files with 25 additions and 23 deletions.
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -2,8 +2,8 @@ version: '3.3'
 services:
   shiny:
     container_name: pheno-ranker-shiny
-    # image: phenorankerui:${DOCKER_IMG_TAG}
-    image: phenorankerui:latest
+    image: phenorankerui:${DOCKER_IMG_TAG}
+    # image: phenorankerui:latest
     # image: leistivo/pheno-ranker-ui:${DOCKER_IMG_TAG}
     # build:
     #   context: phenoRankeR/deploy

diff --git a/phenoRankeR/R/mod_patient_mode.R b/phenoRankeR/R/mod_patient_mode.R
@@ -694,7 +694,6 @@ mod_patient_mode_server <- function(
 
       simDataPath <- paste0(
         get_golem_options("simulationOutputFolder"),
-        # "./data/output/simulatedData/",
         rv_sim$simulationId,
         ".",
         rv$inputFormat,
@@ -703,15 +702,13 @@ mod_patient_mode_server <- function(
 
       convDataPath <- paste0(
         get_golem_options("conversionOutputFolder"),
-        # "./data/output/convertedData/",
         paste0(rv_conversion$id,"/"),
         rv_conversion$id,
         ".json"
       )
 
       upload_dir <- paste0(
         get_golem_options("rankInputFolder"),
-        # "./data/uploads/rankInput/",
         mode,
         "/"
       )
@@ -827,13 +824,9 @@ mod_patient_mode_server <- function(
 
       output$phenoBlastRunId <- renderText(runId)
 
-      # cfg <- fromJSON(readLines("config/cfg.json"))
       outDir <- paste0(
-        # dirname(getwd()),
         paste0(
           get_golem_options("patientModeOutputFolder"),
-          # cfg$patientModeOutputFolder,
-          # "/data/output/rankedPatients/",
           timestamp,
           "/"
         )
@@ -848,8 +841,6 @@ mod_patient_mode_server <- function(
         rv_patient$mappingDf,
         file = paste0(
           get_golem_options("patientModeOutputFolder"),
-          # cfg$patientModeOutputFolder,
-          # "./data/output/rankedPatients/",
           rv_patient$runId,
           "/",
           rv_patient$runId,
@@ -858,12 +849,6 @@ mod_patient_mode_server <- function(
         row.names = FALSE
       )
 
-      # TODO
-      # add a reactive value depending if the weights
-      # are used or not
-
-      # it should be set to NULL if the weights editor is empty
-      # or if every yaml value is set to 1
       weights_file_path <- NULL
       if (input$yamlEditor_weights != "") {
         fn <- paste0(
@@ -872,7 +857,6 @@ mod_patient_mode_server <- function(
         )
         weights_file_path <- file.path(
           get_golem_options("weightsUploadFolder"),
-          # "./data/uploads/weights",
           fn
         )
 
@@ -884,15 +868,18 @@ mod_patient_mode_server <- function(
 
       extra_config_file_path <- NULL
       if (input$yamlEditor_config != "") {
+
         extra_config_file_path <- file.path(
           get_golem_options("extraConfigsUploadFolder"),
-          # "./data/uploads/config",
           paste0(timestamp,"_config.yaml")
         )
 
+        print("extra_config_file_path")
+        print(extra_config_file_path)
+
         print("input$yamlEditor_config")
         print(input$yamlEditor_config)
-
+        
         writeLines(
           input$yamlEditor_config,
           extra_config_file_path
@@ -991,8 +978,6 @@ mod_patient_mode_server <- function(
         )
       }
 
-      # cfg <- fromJSON(readLines("config/cfg.json"))
-      # phenoRankBin <- cfg$PHENO_RANK_BIN 
       phenoRankBin <- get_golem_options("PHENO_RANK_BIN") 
 
       cmd <- paste0(

diff --git a/phenoRankeR/deploy/cfg_bk.json b/phenoRankeR/deploy/cfg_bk.json
@@ -0,0 +1,17 @@
+{
+  "simulationOutputFolder": "/app/data/output/simulatedData/",
+  "ontologyUploadFolder": "/app/data/uploads/ontologies/",
+  "runWithDocker": "True",
+  "LD_LIB_PATH":"/usr/local/lib/perl5/5.36.1/x86_64-linux-gnu/CORE",
+  "PHENO_SIM_BIN": "/opt/pheno-ranker/sim/create_random_bff_pxf.pl",
+  "PHENO_RANK_BIN": "/opt/pheno-ranker/pheno-ranker",
+  "ODBCSYSINI": "/app/config/odbc",
+  "dbSettings": {
+    "driver": "PostgreSQL",
+    "server": "pheno-ranker-db",
+    "port": 5432,
+    "database": "shiny",
+    "user": "shiny",
+    "password": "shiny"
+  }
+}
diff --git a/phenoRankeR/deploy/phenoRankeR_0.0.0.9011.tar.gz b/phenoRankeR/deploy/phenoRankeR_0.0.0.9011.tar.gz
diff --git a/phenoRankeR/deploy/run_phenoRankeR.R b/phenoRankeR/deploy/run_phenoRankeR.R
@@ -30,7 +30,7 @@ default_golem_opts <- list(
   cohortRankInputFolder="/app/data/uploads/rankInput/cohortMode/cohorts",
 
   weightsUploadFolder="/app/data/uploads/weights",
-  extraConfigsUploadFolder="app/data/uploads/config",
+  extraConfigsUploadFolder="/app/data/uploads/config",
   ontologyUploadFolder="/app/data/uploads/ontologies/",
 
   simulationOutputFolder="/app/data/output/simulatedData/",