From f147715a1fc95b5b636c0e8efd5bcb1d52d114d6 Mon Sep 17 00:00:00 2001
From: pontus_pih <pontus_pih>
Date: Wed, 14 May 2008 17:09:02 +0000
Subject: [PATCH] removed "remove_temp_files" option and documented "clean" a
 bit

---
 lib/common_options.pm      | 17 ++++-------------
 lib/tool/bootstrap_subs.pm |  1 -
 lib/tool/cdd_subs.pm       |  2 --
 lib/tool/llp_subs.pm       |  3 ---
 lib/tool/modelfit_subs.pm  |  3 +--
 5 files changed, 5 insertions(+), 21 deletions(-)

diff --git a/lib/common_options.pm b/lib/common_options.pm
index 286594d..733c357 100644
--- a/lib/common_options.pm
+++ b/lib/common_options.pm
@@ -534,22 +534,13 @@ EOF
     five units above than the lowest ofv value among all models.  
 EOF
 
-    $help_hash{-remove_temp_files} = <<'EOF';
-    <p class="style2">-remove_temp_files</p>
-
-    If the <span class="style2">-remove_temp_files</span> option is set to 1, execute will remove
-    the 'FCON', 'FDATA', 'FREPORT', 'FSUBS', 'FSUBS.f', 'LINK.LNK',
-    'FSTREAM', 'PRDERR' and 'nonmem' files from the 'NM_runX'
-    directory. The default value is 0.
-EOF
-
     $help_hash{-clean} = <<'EOF';
     <p class="style2">-clean</p>
 
-    If the <span class="style2">-clean</span>
-    option is set to 1, execute will remove the entire 'NM_runX'
-    directory after the NONMEM run is finished. The default value of
-    <span class="style2">-clean </span>is 0.
+    The <span class="style2">-clean</span> clean option can take four different values:
+    0 - means that nothing is removed, 1 - NONMEM intermediate files and binary is removed (this is the default), 
+    2 - model and output files generated by PsN restarts are removed, 3 - the wholde NM_run directory is removed 
+    and if it is not an "execute" command, all modelfit_dir's will be removed.
 EOF
 
     $help_hash{-missing_data_token} = <<'EOF';
diff --git a/lib/tool/bootstrap_subs.pm b/lib/tool/bootstrap_subs.pm
index c7b22ec..737bc14 100644
--- a/lib/tool/bootstrap_subs.pm
+++ b/lib/tool/bootstrap_subs.pm
@@ -607,7 +607,6 @@ start general_setup
 # 		retries		 => $self -> {'retries'},
 # 		tweak_inits	 => $self -> {'tweak_inits'},
 # 		handle_maxevals	 => $self -> {'handle_maxevals'},
-# 		remove_temp_files	 => $self -> {'remove_temp_files'},
 # 		_raw_results_callback => $self ->
 # 		_modelfit_raw_results_callback( model_number => $model_number ),
 # 		threads		      => $subm_threads,
diff --git a/lib/tool/cdd_subs.pm b/lib/tool/cdd_subs.pm
index 8c39bc0..91b0f36 100644
--- a/lib/tool/cdd_subs.pm
+++ b/lib/tool/cdd_subs.pm
@@ -412,7 +412,6 @@ start general_setup
 # 	      compress       => $self -> {'compress'},
 # 	      threads        => $subm_threads,
 # 	      retries        => $self -> {'retries'},
-# 	      remove_temp_files  => $self -> {'remove_temp_files'},
 # 	      base_directory => $self -> {'directory'},
 # 	      directory      => $self -> {'directory'}.'/orig_modelfit_dir'.$model_number,
 # 	      parent_threads => $own_threads );
@@ -822,7 +821,6 @@ start general_setup
 # 		compress       => $self -> {'compress'},
 #		threads        => $subm_threads,
 # 		retries        => $self -> {'retries'},
-# 		remove_temp_files  => $self -> {'remove_temp_files'},
 # 		base_directory => $self -> {'directory'},
 #  		directory      => $self -> {'directory'}.'/'.$subdir.'_dir'.$model_number,
 # 		_raw_results_callback => $self ->
diff --git a/lib/tool/llp_subs.pm b/lib/tool/llp_subs.pm
index f1a9f10..81bff08 100644
--- a/lib/tool/llp_subs.pm
+++ b/lib/tool/llp_subs.pm
@@ -186,7 +186,6 @@ start modelfit_setup
 # 	      compress              => $self -> {'compress'},
 # 	      threads               => $mfit_threads,
 # 	      retries               => $self -> {'retries'},
-# 	      remove_temp_files         => $self -> {'remove_temp_files'},
 # 	      base_directory        => $self -> {'directory'},
 # 	      directory             => $self -> {'directory'}.'/orig_modelfit_dir'.$model_number.'/',
 # 	      parent_tool_id        => $self -> {'tool_id'},
@@ -285,7 +284,6 @@ start modelfit_setup
 # 		compress       => $self -> {'compress'},
 # 		threads        => $mfit_threads,
 # 		retries        => $self -> {'retries'},
-# 		remove_temp_files  => $self -> {'remove_temp_files'},
 # 		base_directory => $self -> {'directory'},
 #  		directory      => $self -> {'directory'}.'/modelfit_dir'.$model_number.'/',
 # 		subtools       => [],
@@ -758,7 +756,6 @@ start modelfit_analyze
 # 			compress	   =>  $self -> {'compress'},
 # 			threads		   =>  $self -> {'threads'},
 # 			retries		   =>  $self -> {'retries'},
-# 			remove_temp_files	   =>  $self -> {'remove_temp_files'},
 # 			base_directory	   =>  $self -> {'directory'},
 # 			directory	   =>  $self -> {'directory'}.'/llp_dir'.$model_number.'/',
 # 			logfile		   => [$self -> {'logfile'}[$model_number-1]],
diff --git a/lib/tool/modelfit_subs.pm b/lib/tool/modelfit_subs.pm
index 160c4ad..ca142ee 100644
--- a/lib/tool/modelfit_subs.pm
+++ b/lib/tool/modelfit_subs.pm
@@ -779,7 +779,7 @@ start copy_model_and_input
 	my $msfi_names = $candidate_model -> msfi_names;
 	my $msfi_in;
 
-	print "msfos: ". Dumper $msfo_names, $msfi_names;
+	print "Model already has msfi: ". Dumper $msfi_names . "and msfo: " . Dumper $msfo_names;
 
 	if( defined $msfo_names ){
 	  $msfi_in = $msfo_names -> [0][0];
@@ -1603,7 +1603,6 @@ end ud_retrieve
 start sge_submit
 {
   my $fsubs = join( ',' , @{$model -> subroutine_files} );
-
   if( system( 'qsub -cwd -b y ' . 
 	      ($self -> {'sge_resource'} ? '-l '.$self -> {'sge_resource'}.' ' : ' ') .
 	      ($self -> {'sge_queue'} ? '-q '.$self -> {'sge_queue'}.' ' : ' ') .
-- 
2.11.4.GIT