Commit 1a14c59a authored by Shayan Doust's avatar Shayan Doust
Browse files

Patch to display originating error for easier diagnostic.

parent 2375e4a1

debian/patches/detailed_errors.patch

0 → 100644
+119 −0
Original line number Diff line number Diff line 
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@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

+7 −7
Original line number Diff line number Diff line
@@ -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 −0
Original line number Diff line number Diff line 
detailed_errors.patch

fix_test_path.patch

2to3.patch

use_debian_packaged_libraries.patch