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Added signal catching and handling in C and Cython

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This commit is contained in:
Celine Mercier
2019-09-21 16:47:22 +02:00
parent 06f9d6da60
commit ec0737a600
23 changed files with 178 additions and 25 deletions
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3
src/CMakeLists.txt
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@ -14,7 +14,8 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR})
file(GLOB_RECURSE CSRC "*.c")
add_library(cobitools3 SHARED obierrno.c
add_library(cobitools3 SHARED obisig.c
obierrno.c
obidms_taxonomy.c
obiblob_indexer.c
obi_lcs.c

9
src/build_reference_db.c
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@ -24,6 +24,7 @@
#include "obidms.h"
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include "obitypes.h"
#include "obiview.h"
#include "obi_lcs.h"
@ -171,6 +172,8 @@ int build_reference_db(const char* dms_name,
char threshold_str[5];
char* new_comments;
signal(SIGINT, sig_handler);
// Discuss keeping the matrix view or not
matrix_view_name = calloc((strlen(o_view_name)+strlen("_matrix")+1), sizeof(char));
if (matrix_view_name == NULL)
@ -321,6 +324,9 @@ int build_reference_db(const char* dms_name,
// For each pair
for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++)
{
if (! keep_running)
return -1;
// Read all taxids associated with the first sequence and compute their LCA
// Read line index
idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
@ -440,6 +446,9 @@ int build_reference_db(const char* dms_name,
// Going through matrix once, filling refs arrays on the go for efficiency
for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++)
{
if (! keep_running)
return -1;
// Read ref line indexes
idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
idx2 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx2_column, i, 0);

8
src/obi_clean.c
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@ -24,6 +24,7 @@
#include "obidms.h"
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include "obitypes.h"
#include "obiview.h"
#include "sse_banded_LCS_alignment.h"
@ -202,6 +203,8 @@ int obi_clean(const char* dms_name,
int max_threads = 1;
signal(SIGINT, sig_handler);
#ifdef _OPENMP
max_threads = omp_get_max_threads();
if ((thread_count == -1) || (thread_count > max_threads))
@ -408,7 +411,7 @@ int obi_clean(const char* dms_name,
#pragma omp parallel default(none) \
shared(thread_count, seq_count, blob_array, complete_sample_count_array, alignment_result_array, \
stop, blob1, i, obi_errno, stderr, max_ratio, iseq_column, i_view, \
stop, blob1, i, obi_errno, keep_running, stderr, max_ratio, iseq_column, i_view, \
similarity_mode, reference, normalize, threshold, ktable, status_column, o_view, sample_count)
{
index_t j;
@ -430,6 +433,9 @@ int obi_clean(const char* dms_name,
#pragma omp for schedule(dynamic, sample_count/thread_count + (sample_count % thread_count != 0)) // Avoid 0 which blocks the program
for (sample=0; sample < sample_count; sample++)
{
if (! keep_running)
stop = true;
sample_count_array = complete_sample_count_array+(sample*seq_count);
// Get count for this sample

6
src/obi_ecopcr.c
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@ -25,6 +25,7 @@
#include "obiview.h"
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include "obitypes.h"
#include "obiview.h"
@ -718,6 +719,8 @@ int obi_ecopcr(const char* i_dms_name,
int32_t erri;
int32_t errj;
signal(SIGINT, sig_handler);
if (circular)
{
circular = strlen(primer1);
@ -999,6 +1002,9 @@ int obi_ecopcr(const char* i_dms_name,
fprintf(stderr,"\rDone : %f %% ", p);
}
if (! keep_running)
return -1;
checkedSequence++;
// Get the taxid

6
src/obi_ecotag.c
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@ -25,6 +25,7 @@
#include "obidms.h"
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include "obitypes.h"
#include "obiview.h"
#include "obidmscolumn.h"
@ -273,6 +274,8 @@ int obi_ecotag(const char* dms_name,
buffer_size = 1024;
best_match_ids_buffer_size = 1024;
signal(SIGINT, sig_handler);
// Open main DMS containing the query sequences and where the output will be written
dms = obi_open_dms(dms_name, false);
if (dms == NULL)
@ -471,6 +474,9 @@ int obi_ecotag(const char* dms_name,
for (j=0; j < ref_count; j++)
{
if (! keep_running)
return -1;
// Get reference sequence and its index
ref_seq_idx = obi_get_index_with_elt_idx_and_col_p_in_view(ref_view, ref_seq_column, j, 0);
blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(ref_view, ref_seq_column, j, 0);

11
src/obi_lcs.c
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@ -21,6 +21,7 @@
#include "obi_lcs.h"
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include "obitypes.h"
#include "obiview.h"
#include "sse_banded_LCS_alignment.h"
@ -428,6 +429,8 @@ int obi_lcs_align_one_column(const char* dms_name,
OBIDMS_column_p ali_length_column = NULL;
OBIDMS_column_p score_column = NULL;
signal(SIGINT, sig_handler);
k = 0;
// Open DMS
@ -574,6 +577,9 @@ int obi_lcs_align_one_column(const char* dms_name,
if (i%100 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) seq_count)*100);
if (! keep_running)
return -1;
// Get first id idx
id1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, id_column, i, 0); // TODO Could there be multiple IDs per line?
// Get first sequence and its index
@ -725,6 +731,8 @@ int obi_lcs_align_two_columns(const char* dms_name,
OBIDMS_column_p ali_length_column = NULL;
OBIDMS_column_p score_column = NULL;
signal(SIGINT, sig_handler);
k = 0;
// Open DMS
@ -979,6 +987,9 @@ int obi_lcs_align_two_columns(const char* dms_name,
for (j=0; j < seq2_count; j++)
{
if (! keep_running)
return -1;
// Get second sequence and its index
seq2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx);
blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx);

12
src/obidms.c
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@ -32,6 +32,7 @@
#include "utils.h"
#include "obilittlebigman.h"
#include "libjson/json_utils.h"
#include "obisig.h"
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
@ -1627,6 +1628,8 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
OBIDMS_column_header_p header = NULL;
OBIDMS_column_header_p header_2 = NULL;
signal(SIGINT, sig_handler);
dms_1 = obi_open_dms(dms_path_1, false);
if (dms_1 == NULL)
{
@ -1676,6 +1679,9 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
// Import each column and update with the new version number
for (i=0; i < (view_1->infos->column_count); i++)
{
if (! keep_running)
return -1;
new_version = obi_import_column(dms_path_1, dms_path_2, ((((view_1->infos)->column_references)[i]).column_refs).column_name, ((((view_1->infos)->column_references)[i]).column_refs).version);
if (new_version == -1)
{
@ -1708,6 +1714,9 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
// Go through columns again to update associated columns
for (i=0; i < (view_1->infos->column_count); i++)
{
if (! keep_running)
return -1;
header = obi_column_get_header_from_name(dms_1, ((((view_1->infos)->column_references)[i]).column_refs).column_name, ((((view_1->infos)->column_references)[i]).column_refs).version);
if (header == NULL)
{
@ -1747,6 +1756,9 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
}
}
if (! keep_running)
return -1;
// Close the views
if (obi_save_and_close_view(view_1) < 0)
{

3
src/obierrno.h
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@ -136,6 +136,9 @@ extern int obi_errno;
*/
#define OBIDMS_WORKING (38) /** OBIDMS is tagged as being currently used by a process.
*/
#define OBI_SIGNAL_CAUGHT (39) /** Caught an interrupting signal.
*/
/**@}*/
#endif /* OBIERRNO_H_ */

31
src/obisig.c Executable file
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@ -0,0 +1,31 @@
/****************************************************************************
* Functions for signal catching and handling *
****************************************************************************/
/**
* @file obisig.c
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date September 2019
* @brief Functions for signal catching and handling.
*/
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include <stdbool.h>
#include <signal.h>
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
bool volatile keep_running = true;
void sig_handler(int signum)
{
obi_set_errno(OBI_SIGNAL_CAUGHT);
obidebug(1, "\nCaught signal: %s\n", strsignal(signum));
keep_running = false;
}

32
src/obisig.h Executable file
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@ -0,0 +1,32 @@
/****************************************************************************
* Header file for obisig *
****************************************************************************/
/**
* @file obisig.h
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date September 2019
* @brief Header file for signal catching and handling.
*/
#ifndef OBISIG_H_
#define OBISIG_H_
#include <stdint.h>
#include <signal.h>
#include <stdbool.h>
/**
* @brief Signal handling.
*
* @since September 2019
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*
*/
bool volatile keep_running;
void sig_handler(int signum);
#endif /* OBISIG_H_ */