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Fixed bug where column directories weren't closed correctly, leading to

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too many file descriptors open, and added error checking when closing
file descriptors
This commit is contained in:
Celine Mercier
2016-09-15 12:18:40 +02:00
parent a240ec0169
commit 986f90c59e
1 changed files with 55 additions and 19 deletions
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70
src/obidmscolumn.c
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@ -317,7 +317,12 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
return -1;
}
close(version_file_descriptor);
if (close(version_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a version file");
return -1;
}
return new_version_number;
}
@ -403,7 +408,12 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
return -1;
}
close(version_file_descriptor);
if (close(version_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a version file");
return -1;
}
return version_number;
}
@ -480,7 +490,12 @@ obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_dire
return -1;
}
close(version_file_descriptor);
if (close(version_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a version file");
return -1;
}
return latest_version_number;
}
@ -794,7 +809,12 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
// Fill the data with NA values
obi_ini_to_NA_values(new_column, 0, nb_lines);
close(column_file_descriptor);
if (close(column_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a column file");
return NULL;
}
// Add in the list of opened columns
obi_dms_list_column(dms, new_column);
@ -940,7 +960,12 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
}
}
close(column_file_descriptor);
if (close(column_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a column file");
return NULL;
}
// Add in the list of opened columns
obi_dms_list_column(dms, column);
@ -999,10 +1024,11 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError creating the new column when cloning a column");
// The new file is deleted
const char* column_file_name = build_column_file_name(column_name, version_number);
if (remove(column_file_name) < 0)
obidebug(1, "\nError deleting a bad cloned file");
// The new file is deleted TODO check if it exists before
//const char* column_file_name = build_column_file_name(column_name, version_number);
//if (remove(column_file_name) < 0)
// obidebug(1, "\nError deleting a bad cloned file");
return NULL;
}
(new_column->header)->cloned_from = (column_to_clone->header)->version;
@ -1036,7 +1062,6 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
int obi_close_column(OBIDMS_column_p column)
{
bool close_dir;
int ret_val = 0;
// Truncate the column to the number of lines used if it's not read-only
@ -1051,9 +1076,6 @@ int obi_close_column(OBIDMS_column_p column)
if (obi_dms_unlist_column(column->dms, column) < 0)
ret_val = -1;
// Close column directory if it was the last column opened from that directory
close_dir = obi_dms_is_column_name_in_list(column->dms, (column->header)->name);
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
if (obi_close_indexer(column->indexer) < 0)
@ -1076,7 +1098,6 @@ int obi_close_column(OBIDMS_column_p column)
}
// Close column directory
if (close_dir)
if (obi_close_column_directory(column->column_directory) < 0)
ret_val = -1;
@ -1164,7 +1185,12 @@ int obi_truncate_column(OBIDMS_column_p column) // TODO is it necessary to unmap
(column->header)->line_count = new_line_count;
(column->header)->data_size = data_size;
close(column_file_descriptor);
if (close(column_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a column file");
return -1;
}
return 0;
}
@ -1264,7 +1290,12 @@ int obi_enlarge_column(OBIDMS_column_p column)
// Initialize new data lines to NA
obi_ini_to_NA_values(column, old_line_count, new_line_count - old_line_count);
close(column_file_descriptor);
if (close(column_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a column file");
return -1;
}
return 0;
}
@ -1407,7 +1438,12 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
return NULL;
}
close(column_file_descriptor);
if (close(column_file_descriptor) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError closing a column file");
return NULL;
}
return header;
}