Vdb 4796

build/env.cmake

@@ -709,19 +709,21 @@ int main(int argc, char *argv[]) {
 endif()
 
 if( NOT SINGLE_CONFIG )
-    set( COMMON_LINK_LIBRARIES kapp tk-version )
+#    set( COMMON_LINK_LIBRARIES kapp tk-version )
+    set( COMMON_LINK_LIBRARIES tk-version )
     set( COMMON_LIBS_READ  $<$<CONFIG:Debug>:${NCBI_VDB_LIBDIR_DEBUG}>$<$<CONFIG:Release>:${NCBI_VDB_LIBDIR_RELEASE}>/${LIBPFX}ncbi-vdb.${STLX} ${MBEDTLS_LIBS} )
     set( COMMON_LIBS_WRITE $<$<CONFIG:Debug>:${NCBI_VDB_LIBDIR_DEBUG}>$<$<CONFIG:Release>:${NCBI_VDB_LIBDIR_RELEASE}>/${LIBPFX}ncbi-wvdb.${STLX} ${MBEDTLS_LIBS} )
 else()
     # single-config generators need full path to ncbi-vdb libraries in order to handle the dependency correctly
-    set( COMMON_LINK_LIBRARIES ${NCBI_VDB_LIBDIR}/libkapp.${STLX} tk-version )
+#    set( COMMON_LINK_LIBRARIES ${NCBI_VDB_LIBDIR}/libkapp.${STLX} tk-version )
+    set( COMMON_LINK_LIBRARIES tk-version )
     set( COMMON_LIBS_READ   ${NCBI_VDB_LIBDIR}/libncbi-vdb.${STLX} pthread dl m ${MBEDTLS_LIBS} )
     set( COMMON_LIBS_WRITE  ${NCBI_VDB_LIBDIR}/libncbi-wvdb.${STLX} pthread dl m ${MBEDTLS_LIBS} )
 endif()
 
 if( WIN32 )
     add_compile_definitions( UNICODE _UNICODE )
-    set( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /ENTRY:wmainCRTStartup" )
+   set( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /ENTRY:wmainCRTStartup" )
     set( CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>" )
     set( COMMON_LINK_LIBRARIES  ${COMMON_LINK_LIBRARIES} Ws2_32 Crypt32 ${MBEDTLS_LIBS} )
 endif()

test/external/driver-tool/CMakeLists.txt

@@ -39,7 +39,7 @@ AddExecutableTest( Test_Drivertool_JsonParsing "test-json-parse.cpp" "" "${SOURC
 AddExecutableTest( Test_Drivertool_SDLResponse "test-sdl-response.cpp" "" "${SOURCEDIR}" )
 AddExecutableTest( Test_Drivertool_Accession "test-accession.cpp" "" "${SOURCEDIR}" )
 AddExecutableTest( Test_Drivertool_UUID "test-uuid.cpp" "" "${SOURCEDIR}" )
-AddExecutableTest( Test_Drivertool_RunSource "test-run-source.cpp;${SOURCEDIR}/run-source.cpp;${SOURCEDIR}/command-line.cpp;${SOURCEDIR}/SDL-response.cpp;${SOURCEDIR}/${FILE_PATH_CPP};${SOURCEDIR}/json-parse.cpp;${SOURCEDIR}/build-version.cpp;${SOURCEDIR}/tool-args.cpp;" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "${SOURCEDIR}")
+AddExecutableTest( Test_Drivertool_RunSource "test-run-source.cpp;${SOURCEDIR}/run-source.cpp;${SOURCEDIR}/command-line.cpp;${SOURCEDIR}/SDL-response.cpp;${SOURCEDIR}/${FILE_PATH_CPP};${SOURCEDIR}/json-parse.cpp;${SOURCEDIR}/build-version.cpp;${SOURCEDIR}/tool-args.cpp;" "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "${SOURCEDIR}")
 AddExecutableTest( Test_Drivertool_ToolArgs "test-tool-args.cpp;${SOURCEDIR}/tool-args.cpp;${SOURCEDIR}/command-line.cpp;${SOURCEDIR}/build-version.cpp;${SOURCEDIR}/${FILE_PATH_CPP}" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "${SOURCEDIR}")
 
 if ( CMAKE_BUILD_TYPE STREQUAL "Debug" )

test/external/ngs-pileup/CMakeLists.txt

@@ -24,6 +24,7 @@
 
 include_directories( ${CMAKE_SOURCE_DIR} )
 set( NGS_PILEUP_LIBS
+    kapp
     ncbi-ngs-c++
     ngs-c++
     ngs

test/external/ngs-pileup/test-ngs-pileup.cpp

@@ -153,15 +153,6 @@ ver_t CC KAppVersion ( void )
 {
     return 0x1000000;
 }
-rc_t CC UsageSummary (const char * progname)
-{
-    return 0;
-}
-
-rc_t CC Usage ( const Args * args )
-{
-    return 0;
-}
 
 const char UsageDefaultName[] = "test-ngs-pileup";
 

test/external/ngs/testy-the-bear/CMakeLists.txt

@@ -24,7 +24,7 @@
 
 if( NOT WIN32 )
     GenerateExecutableWithDefs( testy-the-bear "testy-the-bear" "__mod__=\"test/ngs/testy-the-bear\""
-                                "" "${COMMON_LINK_LIBRARIES};ncbi-ngs-c++;ncbi-ngs" )
+                                "" "kapp;${COMMON_LINK_LIBRARIES};ncbi-ngs-c++;ncbi-ngs" )
     add_compile_definitions( __mod__="test/ngs/testy-the-bear" )
     add_test( NAME SlowTest_testy-the-bear
         COMMAND runtestcase.sh "${TESTBINDIR}/testy-the-bear" "1" "0"

test/external/prefetch/CMakeLists.txt

@@ -33,7 +33,7 @@ add_compile_definitions( __mod__="test/external/prefetch" )
 if ( NOT WIN32 )
 	ToolsRequired(prefetch srapath)
 
-	GenerateExecutableWithDefs( test-quality "test-quality" "" "" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+	GenerateExecutableWithDefs( test-quality "test-quality" "" "" "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
 
 	add_test( NAME Test_Prefetch_In_PATH
 		COMMAND

test/external/sra-info/CMakeLists.txt

@@ -27,7 +27,7 @@ add_compile_definitions( __mod__="test/external/sra-info" )
 # unit tests
 
 AddExecutableTest( Test_SraInfo_Unit "test-sra-info"
-                                "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}"
+                                "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}"
                                 "${PROJECT_SOURCE_DIR}/tools/external/sra-info" )
 
 ToolsRequired(sra-info)

test/external/sra-info/test-sra-info.cpp

@@ -563,23 +563,8 @@ FIXTURE_TEST_CASE(Contents_SRA, SraInfoFixture)
 extern "C"
 {
 
-ver_t CC KAppVersion ( void )
-{
-    return 0x1000000;
-}
-
 const char UsageDefaultName[] = "test-sra-info";
 
-rc_t CC UsageSummary (const char * progname)
-{
-    return KOutMsg ( "Usage:\n" "\t%s [options] -o path\n\n", progname );
-}
-
-rc_t CC Usage( const Args* args )
-{
-    return 0;
-}
-
 rc_t CC KMain ( int argc, char *argv [] )
 {
     KConfigDisableUserSettings();

test/external/sra-stat/CMakeLists.txt

@@ -28,7 +28,7 @@ if ( NOT WIN32 )
     ToolsRequired(sra-stat)
 
 	#add_executable( testAssemblyStatistics testAssemblyStatistics )
-	GenerateExecutableWithDefs( testAssemblyStatistics "testAssemblyStatistics" "" "" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+	GenerateExecutableWithDefs( testAssemblyStatistics "testAssemblyStatistics" "" "" "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
 	#target_link_libraries( testAssemblyStatistics ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} )
 
 	add_test( NAME Test_Sra_stat_dflt

test/external/sra-stat/testAssemblyStatistics.cpp

@@ -145,7 +145,6 @@ TEST_CASE ( test7 ) {
 }
 
 extern "C" {
-    ver_t CC KAppVersion ( void ) { return 0; }
     rc_t CC KMain ( int argc, char * argv [] ) {
         return TestAssemblyStatistics ( argc, argv );
     }

test/external/vdb-config/CMakeLists.txt

@@ -26,7 +26,7 @@ add_compile_definitions( __mod__="test/external/vdb-config" )
 
 if ( NOT WIN32 )
 
-	GenerateExecutableWithDefs( test-vdb-config-model "test-vdb-config-model" "" "" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+	GenerateExecutableWithDefs( test-vdb-config-model "test-vdb-config-model" "" "" "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
 
 	add_test( NAME Test_VDB_Config_model
 		COMMAND model.sh ${TESTBINDIR}/test-vdb-config-model

test/external/vdb-config/test-vdb-config-model.cpp

@@ -183,20 +183,6 @@ extern "C"
 #include <kapp/args.h>
 #include <kfg/config.h>
 
-ver_t CC KAppVersion ( void )
-{
-    return 0x1000000;
-}
-rc_t CC UsageSummary (const char * progname)
-{
-    return 0;
-}
-
-rc_t CC Usage ( const Args * args )
-{
-    return 0;
-}
-
 const char UsageDefaultName[] = "wb-test-fastq";
 
 rc_t CC KMain ( int argc, char *argv [] )

test/external/vdb-dump/CMakeLists.txt

@@ -39,13 +39,13 @@ set(TOOL_HOME ${CMAKE_SOURCE_DIR}/tools/external/vdb-dump)
 file ( MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/db )
 AddExecutableTest( Test_Vdb_dump_view-spec
     "test-view-spec;${TOOL_HOME}/vdb-dump-view-spec.c;${TOOL_HOME}/vdb-dump-helper.c;${TOOL_HOME}/vdb-dump-context.c;${TOOL_HOME}/vdb-dump-coldefs.c;${TOOL_HOME}/vdb-dump-str.c"
-    "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE}"
+    "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE}"
     "${CMAKE_SOURCE_DIR}/tools/external/vdb-dump" )
 
 if ( NOT WIN32 )
 
 	add_executable( vdb-dump-makedb makedb )
-	target_link_libraries( vdb-dump-makedb ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_WRITE} )
+	target_link_libraries( vdb-dump-makedb kapp ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_WRITE} )
 	add_dependencies(vdb-dump-makedb vdb-dump)
 	if( TARGET vdb-dump-asan )
 		add_dependencies(vdb-dump-makedb vdb-dump-asan)
@@ -81,7 +81,7 @@ if ( NOT WIN32 )
     # run this test after Test_Vdb_dump to make sure the test database has been created
     AddExecutableTest( Test_Vdb_dump_view-alias
         "test-view-alias"
-        "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}"
+        "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}"
         "${CMAKE_SOURCE_DIR}/tools/external/vdb-dump"
     )
 

test/external/vdb-dump/makedb.cpp

@@ -288,20 +288,6 @@ extern "C"
 #include <kapp/args.h>
 #include <kfg/config.h>
 
-ver_t CC KAppVersion ( void )
-{
-    return 0x1000000;
-}
-rc_t CC UsageSummary (const char * progname)
-{
-    return 0;
-}
-
-rc_t CC Usage ( const Args * args )
-{
-    return 0;
-}
-
 const char UsageDefaultName[] = "makedb";
 
 rc_t CC KMain ( int argc, char *argv [] )

test/external/vdb-dump/test-view-alias.cpp

@@ -79,20 +79,6 @@ extern "C"
 #include <kfg/config.h>
 #include <klib/debug.h>
 
-ver_t CC KAppVersion ( void )
-{
-    return 0x1000000;
-}
-rc_t CC UsageSummary (const char * progname)
-{
-    return 0;
-}
-
-rc_t CC Usage ( const Args * args )
-{
-    return 0;
-}
-
 const char UsageDefaultName[] = "test-view-alias";
 
 rc_t CC KMain ( int argc, char *argv [] )

test/external/vdb-dump/test-view-spec.cpp

@@ -383,20 +383,6 @@ extern "C"
 #include <kapp/args.h>
 #include <kfg/config.h>
 
-ver_t CC KAppVersion ( void )
-{
-    return 0x1000000;
-}
-rc_t CC UsageSummary (const char * progname)
-{
-    return 0;
-}
-
-rc_t CC Usage ( const Args * args )
-{
-    return 0;
-}
-
 const char UsageDefaultName[] = "test-view-spec";
 
 rc_t CC KMain ( int argc, char *argv [] )

test/external/vdb-validate/CMakeLists.txt

@@ -30,7 +30,7 @@ if( NOT DEFINED VDB_SRCDIR )
 endif()
 
 AddExecutableTest( Test_VdbValidate_Unit "test-vdb-validate"
-                                "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}"
+                                "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}"
                                 "${PROJECT_SOURCE_DIR}/tools/external/vdb-validate" )
 
 

test/external/vdb-validate/test-vdb-validate.cpp

@@ -83,25 +83,17 @@ TEST_CASE(is_sorted_unsorted)
 extern "C"
 {
 
-ver_t CC KAppVersion ( void )
-{
-    return 0x1000000;
-}
-
 const char UsageDefaultName[] = "test-sra-info";
 
 rc_t CC UsageSummary (const char * progname)
 {
     return KOutMsg ( "Usage:\n" "\t%s [options] -o path\n\n", progname );
 }
 
-rc_t CC Usage( const Args* args )
-{
-    return 0;
-}
-
 rc_t CC KMain ( int argc, char *argv [] )
 {
+    SetUsageSummary( UsageSummary );
+
     KConfigDisableUserSettings();
 
     rc_t rc=VdbValidateTestSuite(argc, argv);

test/internal/align/CMakeLists.txt

@@ -26,10 +26,10 @@ add_compile_definitions( __mod__="test/internal/align" )
 
 if( NOT WIN32 )
   if ( NOT CMAKE_SYSTEM_NAME STREQUAL "FreeBSD" ) # Test_Align_samextract hangs on FreeBSD
-    AddExecutableTest( Test_Align_samextract "test-samextract" "sam-extract;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "" )
+    AddExecutableTest( Test_Align_samextract "test-samextract" "sam-extract;kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "" )
   endif()
 endif()
 
 include_directories( ${VDB_INTERFACES_DIR}/ext/ ) # zlib.h
 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};${COMMON_LIBS_READ}" "" )
+AddExecutableTest( SlowTest_Align_estimator "pileup_estimator" "kapp;ncbi-ngs-c++;ngs-c++;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "" )

test/internal/copycat/CMakeLists.txt

@@ -36,7 +36,7 @@ if ( NOT HAVE_MAGIC STREQUAL "HAVE_MAGIC-NOTFOUND" )
                 ${SRC_DIR}/kff/fileformat.c
                 ${SRC_DIR}/kff/ffmagic.c
         )
-        AddExecutableTest( Test_KFF "kfftest.cpp;${KFF_SRC}" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ};magic" "${SRC_DIR}" )
+        AddExecutableTest( Test_KFF "kfftest.cpp;${KFF_SRC}" "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ};magic" "${SRC_DIR}" )
 
         add_test( NAME Test_Copycat_Help
             COMMAND sh -c "ls ${DIRTOTEST}/copycat>/dev/null 2>&1 && ${DIRTOTEST}/copycat -h || echo no copycat"

test/loaders/fastq-loader/CMakeLists.txt

@@ -36,12 +36,12 @@ if( NOT WIN32 )
     endmacro()
 
     if( NOT "bsd" STREQUAL ${OS} )
-        LatfExeTest( SlowTest_FastqLoader_id2name     "test-id2name.cpp"          "fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+        LatfExeTest( SlowTest_FastqLoader_id2name     "test-id2name.cpp"          "kapp;fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
     endif()
-    LatfExeTest( Test_FastqLoader_WbFastq_dflt    "wb-test-fastq.cpp"         "fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
-    LatfExeTest( Test_FastqLoader_WbFastqParse    "wb-test-fastq-parse.cpp"   "fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+    LatfExeTest( Test_FastqLoader_WbFastq_dflt    "wb-test-fastq.cpp"         "kapp;fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+    LatfExeTest( Test_FastqLoader_WbFastqParse    "wb-test-fastq-parse.cpp"   "kapp;fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
 
-    LatfExeTest( Test_FastqLoader_WbFastqLoader   "test-fastq-loader.cpp"     "fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE}" )
+    LatfExeTest( Test_FastqLoader_WbFastqLoader   "test-fastq-loader.cpp"     "kapp;fastqloader;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE}" )
     set_tests_properties( Test_FastqLoader_WbFastqLoader
         PROPERTIES ENVIRONMENT "NCBI_SETTINGS=/;VDB_CONFIG=${CMAKE_CURRENT_SOURCE_DIR}"
     )

test/loaders/loader/CMakeLists.txt

@@ -30,6 +30,6 @@ else()
     set( ADDITIONAL_LIBS "" )
 endif()
 
-AddExecutableTest( Test_KAPP_qfile  "qfiletest"             "loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ};" "" )
-AddExecutableTest( Test_LOADERFILE  "test-loaderfile.cpp"   "loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "" )
-AddExecutableTest( Test_LOADER      "loadertest"            "loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE};${ADDITIONAL_LIBS}" "" )
+AddExecutableTest( Test_KAPP_qfile  "qfiletest"             "kapp;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ};" "" )
+AddExecutableTest( Test_LOADERFILE  "test-loaderfile.cpp"   "kapp;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" "" )
+AddExecutableTest( Test_LOADER      "loadertest"            "kapp;loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE};${ADDITIONAL_LIBS}" "" )

test/search/CMakeLists.txt

@@ -24,4 +24,4 @@
 
 add_compile_definitions( __mod__="test/search" )
 
-AddExecutableTest( Test_SEARCH_agrep "test-agrep;agrep-main;search-vdb" "${COMMON_LINK_LIBRARIES};ncbi-vdb;ksrch" "" )
+AddExecutableTest( Test_SEARCH_agrep "test-agrep;agrep-main;search-vdb" "kapp;${COMMON_LINK_LIBRARIES};ncbi-vdb;ksrch" "" )

tools/external/align-info/CMakeLists.txt

@@ -26,5 +26,5 @@ set( SRC
     align-info
 )
 
-GenerateExecutableWithDefs( align-info "${SRC}" "__mod__=\"tools/align-info\"" "" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+GenerateExecutableWithDefs( align-info "${SRC}" "__mod__=\"tools/align-info\"" "" "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
 MakeLinksExe( align-info false )

tools/external/align-info/align-info.c

@@ -114,6 +114,8 @@ rc_t CC UsageSummary (const char * progname) {
 
 static const char* param_usage[] = { "Path to the database", NULL };
 
+const char UsageDefaultName[] = "align-info";
+
 rc_t CC Usage(const Args* args) {
     rc_t rc = 0 ;
 
@@ -149,8 +151,6 @@ rc_t CC Usage(const Args* args) {
     return rc;
 }
 
-const char UsageDefaultName[] = "align-info";
-
 static rc_t bam_header(const VDatabase* db) {
     rc_t rc = 0;
     const char path[] = "BAM_HEADER";
@@ -481,6 +481,9 @@ rc_t CC KMain(int argc, char* argv[]) {
     Params prm;
     memset(&prm, 0, sizeof prm);
 
+    SetUsage( Usage );
+    SetUsageSummary( UsageSummary );
+
     do {
         uint32_t pcount = 0;
 

tools/external/cache-mgr/CMakeLists.txt

@@ -23,5 +23,5 @@
 # ===========================================================================
 
 # External
-GenerateExecutableWithDefs( cache-mgr "cache-mgr" "__mod__=\"tools/cache-mgr\"" "" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
+GenerateExecutableWithDefs( cache-mgr "cache-mgr" "__mod__=\"tools/cache-mgr\"" "" "kapp;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}" )
 MakeLinksExe( cache-mgr false )