From d699b8b5d1304fc6b990d9ab4541ebba88fcef5e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 25 Sep 2020 14:43:50 +0200
Subject: [PATCH] Add prescreen to the pipeline and update read_conf

* R/mix.R(read_conf): Use conf_trans function to interpret some of the
  prescreening input parameters.

* R/api.R(new_state): Update because of read_conf.

* (run_in_dir): Add call to prescreen function.
---
 R/api.R | 4 +++-
 R/mix.R | 3 +--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/api.R b/R/api.R
index 95b06ee..78d483c 100644
--- a/R/api.R
+++ b/R/api.R
@@ -15,7 +15,8 @@
 
 ##' @export
 run <- function(fn_conf) {
-    m <- new_state(fn_conf=fn_conf,
+    conf <- read_conf(fn_conf)
+    m <- new_state(conf=conf,
                    GUI=F)    
     dir.create(m$conf$project,
                showWarnings = F,
@@ -32,6 +33,7 @@ run_in_dir <- function(m) {
     m <- concurrency(m)
     m <- mk_comp_tab(m)
     m <- extr_data(m)
+    m <- prescreen(m)
     invisible(m)
     
 }
diff --git a/R/mix.R b/R/mix.R
index 15e8e1a..b6215c8 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -710,8 +710,7 @@ read_conf <- function(fn) {
         
     }
     cf$compound$lists <- fnl
-
-    cf
+    conf_trans(cf)
 }
 
 new_conf <- function() EMPTY_CONF
-- 
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