[med-svn] [Git][med-team/sra-sdk][master] label_online_tests.patch: Fix test/internal/vdb-diff/CMakeLists.txt.

Aaron M. Ucko (@ucko) gitlab at salsa.debian.org
Fri Apr 12 02:29:06 BST 2024 


Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk


Commits:
a8886776 by Aaron M. Ucko at 2024-04-11T21:27:37-04:00
label_online_tests.patch: Fix test/internal/vdb-diff/CMakeLists.txt.

Its set_tests_properties call accidentally wound up ahead of the
corresponding add_test calls.

- - - - -


2 changed files:

- debian/changelog
- debian/patches/label_online_tests.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -11,13 +11,17 @@ sra-sdk (3.0.9+dfsg-1) UNRELEASED; urgency=medium
     - Drop explicit B-D on python3-distutils, currently redundant with
       dh-python (which depends on it via python3-setuptools) and found
       unnecessary regardless in Ubuntu.  (Closes: #1065961.)
+  * debian/patches/label_online_tests.patch: Correctly place
+    test/internal/vdb-diff/CMakeLists.txt's change; its
+    set_tests_properties call accidentally wound up ahead of the
+    corresponding add_test calls.
   * debian/salsa-ci.yml: Try to ensure availability of experimental VDB,
     both by setting RELEASE to experimental and by reinstating aptly, now
     using job 5576517.
   * debian/sra-toolkit.links: Drop; its only entry has dangled since
     vdb-get retired (in upstream version 3.0.1).  (Closes: #1040391.)
 
- -- Aaron M. Ucko <ucko at debian.org>  Thu, 11 Apr 2024 20:42:53 -0400
+ -- Aaron M. Ucko <ucko at debian.org>  Thu, 11 Apr 2024 21:27:35 -0400
 
 sra-sdk (3.0.3+dfsg-6) unstable; urgency=high
 


=====================================
debian/patches/label_online_tests.patch
=====================================
@@ -2,6 +2,8 @@ Author: Aaron M. Ucko
 Last-Update: 2023-01-15 20:56:15
 Description: Label tests "online" to have an easy option to run/ignore them properly
 
+Index: b/ngs/ngs-sdk/examples/CMakeLists.txt
+===================================================================
 --- a/ngs/ngs-sdk/examples/CMakeLists.txt
 +++ b/ngs/ngs-sdk/examples/CMakeLists.txt
 @@ -52,7 +52,7 @@ if ( NOT TOOLS_ONLY )
@@ -13,6 +15,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
          )
      endif()
  
+Index: b/ngs/ngs-java/examples/CMakeLists.txt
+===================================================================
 --- a/ngs/ngs-java/examples/CMakeLists.txt
 +++ b/ngs/ngs-java/examples/CMakeLists.txt
 @@ -56,6 +56,8 @@ if ( Java_FOUND )
@@ -24,6 +28,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
              endmacro()
  
              RunAndDiff( FragTest "ERR225922 10000 2" )
+Index: b/ngs/ngs-python/examples/CMakeLists.txt
+===================================================================
 --- a/ngs/ngs-python/examples/CMakeLists.txt
 +++ b/ngs/ngs-python/examples/CMakeLists.txt
 @@ -44,6 +44,7 @@ if( Python3_EXECUTABLE )
@@ -34,6 +40,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
                      )
              endmacro()
  
+Index: b/test/internal/align/CMakeLists.txt
+===================================================================
 --- a/test/internal/align/CMakeLists.txt
 +++ b/test/internal/align/CMakeLists.txt
 @@ -31,3 +31,4 @@ endif()
@@ -41,6 +49,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
  include_directories( ${CMAKE_SOURCE_DIR} ${CMAKE_SOURCE_DIR}/../ncbi-vdb/interfaces/ext/ )
  AddExecutableTest( SlowTest_Align_estimator "pileup_estimator" "ncbi-ngs-c++;ngs-c++;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "" )
 +set_tests_properties(SlowTest_Align_estimator PROPERTIES LABELS "online")
+Index: b/test/loaders/kar/CMakeLists.txt
+===================================================================
 --- a/test/loaders/kar/CMakeLists.txt
 +++ b/test/loaders/kar/CMakeLists.txt
 @@ -30,6 +30,7 @@ if ( NOT WIN32 )
@@ -51,6 +61,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
  
      if( RUN_SANITIZER_TESTS )
          add_test( NAME Test_Kar-asan
+Index: b/test/external/kdbmeta/CMakeLists.txt
+===================================================================
 --- a/test/external/kdbmeta/CMakeLists.txt
 +++ b/test/external/kdbmeta/CMakeLists.txt
 @@ -28,6 +28,7 @@ if ( NOT WIN32 )
@@ -61,6 +73,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
  
      if( RUN_SANITIZER_TESTS )
          add_test( NAME Test_Kdbmeta-asan
+Index: b/test/external/ngs/ngs-java/CMakeLists.txt
+===================================================================
 --- a/test/external/ngs/ngs-java/CMakeLists.txt
 +++ b/test/external/ngs/ngs-java/CMakeLists.txt
 @@ -81,5 +81,6 @@ if ( Java_FOUND )
@@ -70,6 +84,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
 +    set_tests_properties(SlowTest_NgsJava_CSRA1 PROPERTIES LABELS "online")
  
  endif()
+Index: b/test/external/ngs-pileup/CMakeLists.txt
+===================================================================
 --- a/test/external/ngs-pileup/CMakeLists.txt
 +++ b/test/external/ngs-pileup/CMakeLists.txt
 @@ -31,6 +31,7 @@ set( NGS_PILEUP_LIBS
@@ -154,6 +170,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
 -endif()
 \ No newline at end of file
 +endif()
+Index: b/test/external/ngs/ngs-python/CMakeLists.txt
+===================================================================
 --- a/test/external/ngs/ngs-python/CMakeLists.txt
 +++ b/test/external/ngs/ngs-python/CMakeLists.txt
 @@ -33,6 +33,7 @@ if( Python3_EXECUTABLE )
@@ -164,6 +182,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
          )
      elseif( WIN32 )
          add_test( NAME SlowTest_NgsPython
+Index: b/test/external/prefetch/CMakeLists.txt
+===================================================================
 --- a/test/external/prefetch/CMakeLists.txt
 +++ b/test/external/prefetch/CMakeLists.txt
 @@ -38,6 +38,8 @@ if ( NOT WIN32 )
@@ -211,6 +231,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
  	if( RUN_SANITIZER_TESTS )
  		add_test( NAME SlowTest_Prefetch_vdbcache-asan
  			COMMAND perl vdbcache.pl ${BINDIR} prefetch-asan
+Index: b/test/external/srapath/CMakeLists.txt
+===================================================================
 --- a/test/external/srapath/CMakeLists.txt
 +++ b/test/external/srapath/CMakeLists.txt
 @@ -42,6 +42,7 @@ if ( NOT WIN32 )
@@ -221,10 +243,12 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
      if( RUN_SANITIZER_TESTS )
          add_test( NAME Test_Srapath-asan
              COMMAND
+Index: b/test/internal/vdb-diff/CMakeLists.txt
+===================================================================
 --- a/test/internal/vdb-diff/CMakeLists.txt
 +++ b/test/internal/vdb-diff/CMakeLists.txt
-@@ -38,6 +38,10 @@ if( Python3_EXECUTABLE )
- 			COMMAND ${Python3_EXECUTABLE} ${CMAKE_SOURCE_DIR}/build/check-exit-code.py ${DIRTOTEST}/vdb-diff-tsan${EXE}
+@@ -65,4 +65,8 @@ if( NOT WIN32 )
+ 			COMMAND test_failure.sh "${DIRTOTEST}" ${ACCESSION} vdb-diff-tsan
  			WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
  	endif()
 +
@@ -232,8 +256,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
 +            Test_VDB_Diff_Check_success Test_VDB_Diff_Check_failure
 +            PROPERTIES LABELS "online")
  endif()
- 
- if( NOT WIN32 )
+Index: b/test/external/vdb-dump/CMakeLists.txt
+===================================================================
 --- a/test/external/vdb-dump/CMakeLists.txt
 +++ b/test/external/vdb-dump/CMakeLists.txt
 @@ -81,4 +81,5 @@ if ( NOT WIN32 )
@@ -242,6 +266,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
  
 +    set_tests_properties(Test_Vdb_dump PROPERTIES LABELS "online")
  endif()
+Index: b/libs/ngs-vdb/test/CMakeLists.txt
+===================================================================
 --- a/libs/ngs-vdb/test/CMakeLists.txt
 +++ b/libs/ngs-vdb/test/CMakeLists.txt
 @@ -70,32 +70,39 @@ add_test ( NAME Test_Ngs COMMAND test-ng
@@ -337,6 +363,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
  add_test ( NAME SlowTest_NgsVdbWhiteBox COMMAND test-ngs-vdb )
 +set_tests_properties( SlowTest_NgsVdbWhiteBox PROPERTIES LABELS online )
  
+Index: b/test/external/ngs/testy-the-bear/CMakeLists.txt
+===================================================================
 --- a/test/external/ngs/testy-the-bear/CMakeLists.txt
 +++ b/test/external/ngs/testy-the-bear/CMakeLists.txt
 @@ -30,6 +30,6 @@ if( NOT WIN32 )
@@ -347,6 +375,8 @@ Description: Label tests "online" to have an easy option to run/ignore them prop
 +        PROPERTIES ENVIRONMENT "NCBI_VDB_QUALITY=R" LABELS online
      )
  endif()
+Index: b/tools/external/sra-search/test/CMakeLists.txt
+===================================================================
 --- a/tools/external/sra-search/test/CMakeLists.txt
 +++ b/tools/external/sra-search/test/CMakeLists.txt
 @@ -73,8 +73,9 @@ add_executable ( test-searchblock



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/a88867765412f9ab198f6704a43e9a7e9b62b8f4

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/a88867765412f9ab198f6704a43e9a7e9b62b8f4
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