[med-svn] [Git][med-team/simka][master] Patch to display originating error for easier diagnostic.
Shayan Doust
gitlab at salsa.debian.org
Fri Sep 13 21:59:53 BST 2019
Shayan Doust pushed to branch master at Debian Med / simka
Commits:
1a14c59a by Shayan Doust at 2019-09-13T07:30:28Z
Patch to display originating error for easier diagnostic.
- - - - -
3 changed files:
- + debian/patches/detailed_errors.patch
- debian/patches/fix_test_path.patch
- debian/patches/series
Changes:
=====================================
debian/patches/detailed_errors.patch
=====================================
@@ -0,0 +1,119 @@
+Description: display more information in caught errors
+ The errors are unmarked and understanding the originating source file is not easy, so append the file names and other diagnostic information before the error messages. Do not apply this patch when uploading.
+Author: Shayan Doust <hello at shayandoust.me>
+Last-Update: 2019-09-13
+---
+
+Index: simka/src/core/main.cpp
+===================================================================
+--- simka.orig/src/core/main.cpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/core/main.cpp 2019-09-13 08:27:17.187648345 +0100
+@@ -33,7 +33,7 @@
+ }
+ catch (Exception& e)
+ {
+- std::cout << "EXCEPTION: " << e.getMessage() << std::endl;
++ std::cout << "[main.cpp] EXCEPTION: " << e.getMessage() << std::endl;
+ return EXIT_FAILURE;
+ }
+
+Index: simka/src/core/SimkaAlgorithm.cpp
+===================================================================
+--- simka.orig/src/core/SimkaAlgorithm.cpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/core/SimkaAlgorithm.cpp 2019-09-13 08:27:17.187648345 +0100
+@@ -162,7 +162,7 @@
+ layoutInputFilename();
+ }
+ catch (Exception& e){
+- cout << "Syntax error in input file" << endl;
++ cout << "[SimkaAlgorithm.cpp] Syntax error in input file" << endl;
+ return false;
+ }
+
+@@ -363,7 +363,7 @@
+ LOCAL(bank);
+ }
+ catch (Exception& e){
+- cerr << "ERROR: Can't open dataset: " << _bankNames[i] << endl;
++ cerr << "[SimkaAlgorithm.cpp] ERROR: Can't open dataset: " << _bankNames[i] << endl;
+ return false;
+ }
+
+Index: simka/src/core/SimkaCommons.hpp
+===================================================================
+--- simka.orig/src/core/SimkaCommons.hpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/core/SimkaCommons.hpp 2019-09-13 08:27:17.187648345 +0100
+@@ -129,7 +129,7 @@
+ nbDatasets += 1;
+ }
+ catch (Exception& e){
+- cerr << "ERROR: Can't open dataset: " << bankId << endl;
++ cerr << "[SimkaCommons.hpp] ERROR: Can't open dataset: " << bankId << endl;
+ error = true;
+ }
+
+Index: simka/src/SimkaCount.cpp
+===================================================================
+--- simka.orig/src/SimkaCount.cpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/SimkaCount.cpp 2019-09-13 08:27:17.187648345 +0100
+@@ -385,7 +385,7 @@
+ }
+ catch (Exception& e)
+ {
+- std::cout << "EXCEPTION: " << e.getMessage() << std::endl;
++ std::cout << "[SimkaCount.cpp] EXCEPTION: " << e.getMessage() << std::endl;
+ return EXIT_FAILURE;
+ }
+ }
+Index: simka/src/SimkaMerge.cpp
+===================================================================
+--- simka.orig/src/SimkaMerge.cpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/SimkaMerge.cpp 2019-09-13 08:27:17.187648345 +0100
+@@ -1585,7 +1585,7 @@
+ }
+ catch (Exception& e)
+ {
+- std::cout << "EXCEPTION: " << e.getMessage() << std::endl;
++ std::cout << "[SimkaMerge.cpp] EXCEPTION: " << e.getMessage() << std::endl;
+ return EXIT_FAILURE;
+ }
+ }
+Index: simka/src/SimkaPotara.hpp
+===================================================================
+--- simka.orig/src/SimkaPotara.hpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/SimkaPotara.hpp 2019-09-13 08:27:17.187648345 +0100
+@@ -572,7 +572,7 @@
+ }
+ catch (Exception& e)
+ {
+- cout << "\tcan't open config, computing it again" << endl;
++ cout << "\t[SimkaPotara.hpp] can't open config, computing it again" << endl;
+ System::file().remove(filename);
+ createConfig();
+ return;
+Index: simka/src/simkaMin/SimkaMin.cpp
+===================================================================
+--- simka.orig/src/simkaMin/SimkaMin.cpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/simkaMin/SimkaMin.cpp 2019-09-13 08:27:17.187648345 +0100
+@@ -114,7 +114,7 @@
+ }
+ catch (Exception& e)
+ {
+- std::cout << "EXCEPTION: " << e.getMessage() << std::endl;
++ std::cout << "[SimkaMin.cpp] EXCEPTION: " << e.getMessage() << std::endl;
+ return EXIT_FAILURE;
+ }
+
+Index: simka/src/SimkaPotara.cpp
+===================================================================
+--- simka.orig/src/SimkaPotara.cpp 2019-09-13 08:27:17.191648329 +0100
++++ simka/src/SimkaPotara.cpp 2019-09-13 08:27:17.187648345 +0100
+@@ -155,7 +155,7 @@
+ }
+ catch (Exception& e)
+ {
+- std::cout << "EXCEPTION: " << e.getMessage() << std::endl;
++ std::cout << "[SimkaPotara.cpp] EXCEPTION: " << e.getMessage() << std::endl;
+ return EXIT_FAILURE;
+ }
+
=====================================
debian/patches/fix_test_path.patch
=====================================
@@ -5,8 +5,8 @@ Last-Update: 2019-09-13
Index: simka/tests/simkaMin/test_simkaMin.py
===================================================================
---- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 07:39:12.023233040 +0100
-+++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 07:39:12.019233056 +0100
+--- simka.orig/tests/simkaMin/test_simkaMin.py 2019-09-13 08:06:40.164613706 +0100
++++ simka/tests/simkaMin/test_simkaMin.py 2019-09-13 08:06:40.160613722 +0100
@@ -48,7 +48,7 @@
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
@@ -74,8 +74,8 @@ Index: simka/tests/simkaMin/test_simkaMin.py
if ret != 0: exit(1)
Index: simka/tests/simple_test.py
===================================================================
---- simka.orig/tests/simple_test.py 2019-09-13 07:39:12.023233040 +0100
-+++ simka/tests/simple_test.py 2019-09-13 07:40:08.951004314 +0100
+--- simka.orig/tests/simple_test.py 2019-09-13 08:06:40.164613706 +0100
++++ simka/tests/simple_test.py 2019-09-13 08:06:40.160613722 +0100
@@ -91,7 +91,7 @@
#test k=31 t=0
clear()
@@ -126,8 +126,8 @@ Index: simka/tests/simple_test.py
Index: simka/example/simple_test.sh
===================================================================
---- simka.orig/example/simple_test.sh 2019-09-13 07:39:12.023233040 +0100
-+++ simka/example/simple_test.sh 2019-09-13 07:39:12.019233056 +0100
+--- simka.orig/example/simple_test.sh 2019-09-13 08:06:40.164613706 +0100
++++ simka/example/simple_test.sh 2019-09-13 08:07:06.216509113 +0100
@@ -3,19 +3,19 @@
# look for simka binary. In devel mode, it's in ../build/bin directory.
@@ -156,7 +156,7 @@ Index: simka/example/simple_test.sh
+bindir="/usr/bin"
# run simka
-command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"
-+command="$bindir/simka -in simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"
++command="simka -in simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"
#printf "$command\n\n"
# DO NOT add lines between '$command' exec and 'var...' !
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+detailed_errors.patch
fix_test_path.patch
2to3.patch
use_debian_packaged_libraries.patch
View it on GitLab: https://salsa.debian.org/med-team/simka/commit/1a14c59a82bea04af0e3ca35202362988a3fa5bd
--
View it on GitLab: https://salsa.debian.org/med-team/simka/commit/1a14c59a82bea04af0e3ca35202362988a3fa5bd
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