From 5e3c41b058b320f5f2524d11b1f134864da30e5a Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 4 Sep 2019 16:48:13 +0200
Subject: [PATCH] C: Fixed opened DIR leak

---
 python/obitools3/commands/test.pyx |  5 +++
 src/obidmscolumn.c                 | 55 ++++++++++++++++++++++++++----
 2 files changed, 54 insertions(+), 6 deletions(-)

diff --git a/python/obitools3/commands/test.pyx b/python/obitools3/commands/test.pyx
index 80f1d2a..5bc6de7 100755
--- a/python/obitools3/commands/test.pyx
+++ b/python/obitools3/commands/test.pyx
@@ -23,6 +23,7 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
 import shutil
 import string
 import random
+#import subprocess
 
 
 VIEW_TYPES = [b"", b"NUC_SEQS_VIEW"]
@@ -516,6 +517,10 @@ def run(config):
         i+=1
         if (i%(config['test']['nbtests']/10)) == 0 :
             print("Testing......"+str(i*100/config['test']['nbtests'])+"%")
+            #lsof = subprocess.Popen("lsof | grep '/private/tmp/test_dms.obidms/'", stdin=subprocess.PIPE, shell=True )
+            #lsof.communicate( b"LSOF\n" )
+            #lsof = subprocess.Popen("lsof | wc -l", stdin=subprocess.PIPE, shell=True )
+            #lsof.communicate( b"LSOF total\n" )
  
     #print(infos)
     
diff --git a/src/obidmscolumn.c b/src/obidmscolumn.c
index 16e4f2b..6edcf21 100644
--- a/src/obidmscolumn.c
+++ b/src/obidmscolumn.c
@@ -368,11 +368,18 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
 	if (version_file_descriptor < 0)
 	{
 		if (errno == ENOENT)
+		{
+			free(version_file_name);
+			free(column_directory_name);
+			closedir(col_directory);
 			return create_version_file(column_directory);
+		}
 		else
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
 			obidebug(1, "\nError opening a version file");
+			free(column_directory_name);
+			closedir(col_directory);
 			free(version_file_name);
 			return -1;
 		}
@@ -380,7 +387,13 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
 
 	free(version_file_name);
 	free(column_directory_name);
-	closedir(col_directory);
+	if (closedir(col_directory) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening a version file");
+		close(version_file_descriptor);
+		return -1;
+	}
 
 	// Test if the version file size is ok
 	if (lseek(version_file_descriptor, 0, SEEK_END) < loc_size)
@@ -1193,7 +1206,13 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 
 	free(column_file_name);
 	free(column_directory_name);
-	closedir(col_dir);
+	if (closedir(col_dir) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError closing a column directory");
+		close(column_file_descriptor);
+		return NULL;
+	}
 
 	// Truncate the column file to the right size
 	if (ftruncate(column_file_descriptor, file_size) < 0)
@@ -1453,7 +1472,13 @@ OBIDMS_column_p obi_open_column(OBIDMS_p     dms,
 
 	free(column_file_name);
 	free(column_directory_name);
-	closedir(col_dir);
+	if (closedir(col_dir) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError closing a column directory");
+		close(column_file_descriptor);
+		return NULL;
+	}
 
 	// Allocate the memory for the column structure
 	column = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_t));
@@ -1807,7 +1832,13 @@ int obi_truncate_column(OBIDMS_column_p column)	// TODO is it necessary to unmap
 
 	free(column_file_name);
 	free(column_directory_name);
-	closedir(col_dir);
+	if (closedir(col_dir) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError closing a column directory");
+		close(column_file_descriptor);
+		return -1;
+	}
 
 	// Unmap the data before truncating the file
 	if (munmap(column->data, (column->header)->data_size) < 0)
@@ -1932,7 +1963,13 @@ int obi_enlarge_column(OBIDMS_column_p column)
 
 	free(column_file_name);
 	free(column_directory_name);
-	closedir(col_dir);
+	if (closedir(col_dir) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError closing a column directory");
+		close(column_file_descriptor);
+		return -1;
+	}
 
 	// Calculate the new file size
 	old_line_count = (column->header)->line_count;
@@ -2227,7 +2264,13 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
 
 	free(column_file_name);
 	free(column_directory_name);
-	closedir(col_dir);
+	if (closedir(col_dir) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError closing a column directory");
+		close(column_file_descriptor);
+		return NULL;
+	}
 
 	// Read the header size
 	if (read(column_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))