[med-svn] [Git][med-team/sra-sdk][master] label_online_tests.patch: 55 additional tests need network access.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Fri Apr 12 22:16:35 BST 2024
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
0de80a43 by Aaron M. Ucko at 2024-04-12T17:15:22-04:00
label_online_tests.patch: 55 additional tests need network access.
- - - - -
2 changed files:
- debian/changelog
- debian/patches/label_online_tests.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -11,17 +11,18 @@ 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/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.
+ - Label 55 additional tests as needing network access.
* 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 21:27:35 -0400
+ -- Aaron M. Ucko <ucko at debian.org> Fri, 12 Apr 2024 17:15:20 -0400
sra-sdk (3.0.3+dfsg-6) unstable; urgency=high
=====================================
debian/patches/label_online_tests.patch
=====================================
@@ -1,9 +1,7 @@
Author: Aaron M. Ucko
-Last-Update: 2023-01-15 20:56:15
+Last-Update: 2024-04-12 17:15;20
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 )
@@ -15,8 +13,6 @@ Index: b/ngs/ngs-sdk/examples/CMakeLists.txt
)
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 )
@@ -28,8 +24,6 @@ Index: b/ngs/ngs-java/examples/CMakeLists.txt
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 )
@@ -40,8 +34,6 @@ Index: b/ngs/ngs-python/examples/CMakeLists.txt
)
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()
@@ -49,8 +41,6 @@ Index: b/test/internal/align/CMakeLists.txt
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 )
@@ -61,8 +51,6 @@ Index: b/test/loaders/kar/CMakeLists.txt
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 )
@@ -73,8 +61,6 @@ Index: b/test/external/kdbmeta/CMakeLists.txt
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 )
@@ -84,8 +70,6 @@ Index: b/test/external/ngs/ngs-java/CMakeLists.txt
+ 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
@@ -170,8 +154,6 @@ Index: b/test/external/ngs-pileup/CMakeLists.txt
-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 )
@@ -182,8 +164,6 @@ Index: b/test/external/ngs/ngs-python/CMakeLists.txt
)
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 )
@@ -231,8 +211,6 @@ Index: b/test/external/prefetch/CMakeLists.txt
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 )
@@ -243,8 +221,6 @@ Index: b/test/external/srapath/CMakeLists.txt
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
@@ -65,4 +65,8 @@ if( NOT WIN32 )
@@ -256,18 +232,22 @@ Index: b/test/internal/vdb-diff/CMakeLists.txt
+ Test_VDB_Diff_Check_success Test_VDB_Diff_Check_failure
+ PROPERTIES LABELS "online")
endif()
-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 )
+@@ -58,6 +58,7 @@ if ( NOT WIN32 )
+ bash -c "./vdb_dump.sh ${TESTBINDIR}/vdb-dump-makedb ${DIRTOTEST} vdb-dump"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ )
++ set_tests_properties(Test_Vdb_dump PROPERTIES LABELS "online")
+
+ if( RUN_SANITIZER_TESTS )
+ add_test( NAME Test_Vdb_dump_asan
+@@ -81,4 +82,5 @@ if ( NOT WIN32 )
"${CMAKE_SOURCE_DIR}/tools/external/vdb-dump"
)
-+ set_tests_properties(Test_Vdb_dump PROPERTIES LABELS "online")
++ set_tests_properties(Test_Vdb_dump_view-alias 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
@@ -363,8 +343,6 @@ Index: b/libs/ngs-vdb/test/CMakeLists.txt
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 )
@@ -375,8 +353,6 @@ Index: b/test/external/ngs/testy-the-bear/CMakeLists.txt
+ 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
@@ -390,3 +366,297 @@ Index: b/tools/external/sra-search/test/CMakeLists.txt
# command line tests
if ( NOT WIN32)
+@@ -105,40 +106,70 @@ if ( NOT WIN32)
+ # single run
+ add_test ( NAME SlowTest_SraSearch-3.0-single-run-default WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.0-single-run-default --args "AGCTAGCTAGCT -T 1 SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.0-single-run-default
++ PROPERTIES LABELS online )
+ add_test ( NAME SraSearch-3.05-single-run-default-WGS WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.05-single-run-default-WGS --sort --args "AGCTAGCTA ALAI01" )
++ set_tests_properties( SlowTest_SraSearch-3.05-single-run-default-WGS
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.1-single-run-fgrep-standard WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.1-single-run-fgrep-standard --args "AGCTAGCTAGCT -T 1 -a FgrepStandard SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.1-single-run-fgrep-standard
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.2-single-run-fgrep-boyer-moore WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.2-single-run-fgrep-boyer-moore --args "AGCTAGCTAGCT -T 1 --algorithm FgrepBoyerMoore SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.2-single-run-fgrep-boyer-moore
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.3-single-run-fgrep-aho WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.3-single-run-fgrep-aho --args "AGCTAGCTAGCT -T 1 --algorithm FgrepAho SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.3-single-run-fgrep-aho
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.4-single-run-agrep-dp WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.4-single-run-agrep-dp --args "AGCTAGCTAGCT -T 1 --algorithm AgrepDP SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.4-single-run-agrep-dp
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.5-single-run-agrep-wumanber WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.5-single-run-agrep-wumanber --args "AGCTAGCTAGCT -T 1 --algorithm AgrepWuManber SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.5-single-run-agrep-wumanber
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.6-single-run-agrep-myers WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.6-single-run-agrep-myers --args "AGCTAGCTAGCT -T 1 --algorithm AgrepMyers SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.6-single-run-agrep-myers
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.7-single-run-agrep-myers-unltd WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.7-single-run-agrep-myers-unltd --args "AGCTAGCTAGCT -T 1 --algorithm AgrepMyersUnltd SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.7-single-run-agrep-myers-unltd
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.8-single-run-nucstrstr WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.8-single-run-nucstrstr --args "AGCTAGCTAGCT -T 1 --algorithm NucStrstr SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.8-single-run-nucstrstr
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-3.9-single-run-smith-waterman WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.9-single-run-smith-waterman --args "AGCTAGCTAGCT -T 1 --algorithm SmithWaterman -m 4 SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-3.9-single-run-smith-waterman
++ PROPERTIES LABELS online )
+
+ # single run, fasta format
+ add_test ( NAME SraSearch-3.10-single-run-fasta WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.10-single-run-fasta --args "AGCTAGCTA ALAI01 --fasta --max 2" )
++ set_tests_properties( SraSearch-3.10-single-run-fasta
++ PROPERTIES LABELS online )
+ add_test ( NAME SraSearch-3.11-single-run-fasta-custom-line-size WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 3.11-single-run-fasta-custom-line-size --args "AGCTAGCTA ALAI01 --fasta 80 --max 2" )
++ set_tests_properties( SraSearch-3.11-single-run-fasta-custom-line-size
++ PROPERTIES LABELS online )
+
+ # multiple runs, single threaded
+ add_test ( NAME SraSearch-4.0-multiple-runs WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 4.0-multiple-runs --args "TACTGGGCGTAAAGCGTGCGCAGGCGGT -T 1 --algorithm NucStrstr SRR600096 SRR600097" )
++ set_tests_properties( SraSearch-4.0-multiple-runs
++ PROPERTIES LABELS online )
+
+ # query expressions
+ add_test ( NAME SlowTest_SraSearch-5.0-run-nucstrstr-with-expression WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 5.0-run-nucstrstr-with-expression --sort --args "AAAAAAACCCCCCCAAAAAAACCCCCCC\\|\\|AGCTAGCTAGCT -T 1 --algorithm NucStrstr --expression SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-5.0-run-nucstrstr-with-expression
++ PROPERTIES LABELS online )
+
+ # query expressions, bad arguments
+ add_test ( NAME SraSearch-5.1-run-not-nucstrstr-with-expression WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+@@ -160,16 +191,26 @@ if ( NOT WIN32)
+ # imperfect match
+ add_test ( NAME SlowTest_SraSearch-6.4-imperfect-match-agrep-dp WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 6.4-imperfect-match-agrep-dp --args "AGCTAGCTAGCT -T 1 --score 90 --algorithm AgrepDP SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-6.4-imperfect-match-agrep-dp
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-6.5-imperfect-match-agrep-wumanber WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 6.5-imperfect-match-agrep-wumanber --args "AGCTAGCTAGCT -T 1 --score 90 --algorithm AgrepWuManber SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-6.5-imperfect-match-agrep-wumanber
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-6.6-imperfect-match-agrep-myers WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 6.6-imperfect-match-agrep-myers --args "AGCTAGCTAGCT -T 1 --score 90 --algorithm AgrepMyers SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-6.6-imperfect-match-agrep-myers
++ PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearch-6.7-imperfect-match-agrep-myers-unltd WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 6.7-imperfect-match-agrep-myers-unltd --args "AGCTAGCTAGCT -T 1 --score 90 --algorithm AgrepMyersUnltd SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-6.7-imperfect-match-agrep-myers-unltd
++ PROPERTIES LABELS online )
+ add_test ( NAME SraSearch-6.8-imperfect-match-nucstrstr WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 6.8-imperfect-match-nucstrstr --args "AGCTAGCTAGCT --score 90 --algorithm NucStrstr SRR000001" --rc 3 )
+ add_test ( NAME SlowTest_SraSearch-6.9-imperfect-match-smith-waterman WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 6.9-imperfect-match-smith-waterman --args "AGCTAGCTAGCT -T 1 --score 90 --algorithm SmithWaterman -m 100 SRR000001" )
++ set_tests_properties( SlowTest_SraSearch-6.9-imperfect-match-smith-waterman
++ PROPERTIES LABELS online )
+
+ # multi-threading, bad arguments
+ add_test ( NAME SraSearch-7.0.1-threads-no-arg WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+@@ -180,15 +221,23 @@ if ( NOT WIN32)
+ # multiple runs, thread per accession
+ add_test ( NAME SlowTest_SraSearch-7.1-threads-unsorted WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 7.1-threads-unsorted --sort --args "ACGTAGGGTCC --threadperacc --threads 4 SRR600094 SRR600095 SRR600096 SRR600099" )
++ set_tests_properties( SlowTest_SraSearch-7.1-threads-unsorted
++ PROPERTIES LABELS online )
+ # single run, thread per blob
+ add_test ( NAME SlowTest_SraSearch-7.2-threads-single WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 7.2-threads-single --sort --args "ACGTAGGGTCC --threads 2 SRR600094" )
++ set_tests_properties( SlowTest_SraSearch-7.2-threads-single
++ PROPERTIES LABELS online )
+ # multiple runs, thread per blob
+ add_test ( NAME SlowTest_SraSearch-7.3-threads-multiple WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 7.3-threads-multiple --sort --args "ACGTAGGGTCC --threads 2 SRR600094 SRR600095 SRR600096 SRR600099" )
++ set_tests_properties( SlowTest_SraSearch-7.3-threads-multiple
++ PROPERTIES LABELS online )
+ # sorting the output
+ add_test ( NAME SlowTest_SraSearch-7.4-threads-sort WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 7.4-threads-sort --args "ACGTAGGGTCC --threads 4 SRR600096 SRR600095 --sort" )
++ set_tests_properties( SlowTest_SraSearch-7.4-threads-sort
++ PROPERTIES LABELS online )
+
+ # nothing found
+ add_test ( NAME SlowTest_SraSearch-8.0-nothing-found WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+@@ -197,14 +246,20 @@ if ( NOT WIN32)
+ # reference mode
+ add_test ( NAME SlowTest_SraSearch-9.0-reference WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 9.0-reference --sort --args "ACGTAGGGTCC SRR600094 --reference -T 6" )
++ set_tests_properties( SlowTest_SraSearch-9.0-reference
++ PROPERTIES LABELS online )
+
+ # reference mode, multiple references, one accession
+ add_test ( NAME SlowTest_SraSearch-9.1-reference-multiple-refs WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 9.1-reference --sort --args "ACGTAGGGTCC SRR600094 --reference NC_000007.13,doesnotexist,NC_000001.10 -T 6" )
++ set_tests_properties( SlowTest_SraSearch-9.1-reference-multiple-refs
++ PROPERTIES LABELS online )
+
+ # reference mode, multiple references, accessions
+ add_test ( NAME SlowTest_SraSearch-9.2-reference-multiple-refs-multiple-runs WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 9.2-reference --sort --args "ACGTAGGGTCC SRR600095 SRR600094 --reference NC_000007.13,NC_000001.10 -T 6" )
++ set_tests_properties( SlowTest_SraSearch-9.2-reference-multiple-refs-multiple-runs
++ PROPERTIES LABELS online )
+
+ # reference mode, expressions not allowed
+ add_test ( NAME SraSearch-9.3-reference-expression WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+@@ -213,5 +268,7 @@ if ( NOT WIN32)
+ # unaligned reads only
+ add_test ( NAME SlowTest_SraSearch-10.0-unaligned WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
+ ${SRA_SEARCH} 10.0-unaligned --args "AGCTAGCTAGCT SRR600099 --unaligned" )
++ set_tests_properties( SlowTest_SraSearch-10.0-unaligned
++ PROPERTIES LABELS online )
+
+ endif ()
+--- a/test/external/sra-info/CMakeLists.txt
++++ b/test/external/sra-info/CMakeLists.txt
+@@ -29,6 +29,7 @@ add_compile_definitions( __mod__="test/e
+ AddExecutableTest( Test_SraInfo_Unit "test-sra-info"
+ "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ}"
+ "${PROJECT_SOURCE_DIR}/tools/external/sra-info" )
++set_tests_properties( Test_SraInfo_Unit PROPERTIES LABELS "online" )
+
+ ToolsRequired(sra-info)
+
+@@ -70,6 +71,13 @@ AddQueryTest( Test_Sra_Info_Platform_CSR
+ AddQueryTest( Test_Sra_Info_Platform_WGS 1.2 "-P AAAAAA01" )
+ AddQueryTest( Test_Sra_Info_Platform_Multiple 2.0 "-P ./input/MultiPlatform_Long.sra" )
+ AddQueryTest( Test_Sra_Info_Platform_Reference 3.0 "-P NC_000001.11" )
++set_tests_properties( Test_Sra_Info_Platform_Table PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_Platform_CSRA PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_Platform_WGS PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_Platform_Multiple
++ PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_Platform_Reference
++ PROPERTIES LABELS "online" )
+
+ # formatting
+ AddQueryTest( Test_Sra_Info_Platform_Format_CSV 4.1 "-P ./input/MultiPlatform.sra -f csv" )
+@@ -80,10 +88,13 @@ AddQueryTest( Test_Sra_Info_Platform_For
+ # is-aligned
+ AddQueryTest( Test_Sra_Info_IsAligned_No 5.1 "-A SRR000123" )
+ AddQueryTest( Test_Sra_Info_IsAligned_Yes 5.2 "--is-aligned ERR334733" )
++set_tests_properties( Test_Sra_Info_IsAligned_Yes PROPERTIES LABELS "online" )
+
+ # quality
+ AddQueryTest( Test_Sra_Info_Quality_Physical 6.1 "--quality ./input/MultiPlatform.sra" )
+ AddQueryTest( Test_Sra_Info_Quality_Physical_Refseq 6.2 "-Q NC_000001.10" )
++set_tests_properties( Test_Sra_Info_Quality_Physical_Refseq
++ PROPERTIES LABELS "online" )
+
+ # spot layout
+ AddQueryTest( Test_Sra_Info_SpotLayout_Default 7.1 "--spot-layout SRR000123" )
+@@ -91,22 +102,43 @@ AddQueryTest( Test_Sra_Info_SpotLayout_J
+ AddQueryTest( Test_Sra_Info_SpotLayout_CSV 7.3 "--spot-layout -f csv SRR000123" )
+ AddQueryTest( Test_Sra_Info_SpotLayout_Tab 7.4 "--spot-layout -f tab SRR000123" )
+ AddQueryTest( Test_Sra_Info_SpotLayout_XML 7.5 "--spot-layout -f xml SRR000123" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Default
++ PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Json
++ PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_SpotLayout_CSV PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Tab PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_SpotLayout_XML PROPERTIES LABELS "online" )
+
+ # PACBIO, uses the CONSENSUS table
+ AddQueryTest( Test_Sra_Info_SpotLayout_Pacbio_Consensus 7.6.1 "--spot-layout DRR032985 --limit 100" )
+ # PACBIO, uses the SEQUENCE table
+ AddQueryTest( Test_Sra_Info_SpotLayout_Pacbio_Sequence 7.6.2 "--spot-layout DRR032985 --limit 100 --sequence" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Pacbio_Consensus
++ PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Pacbio_Sequence
++ PROPERTIES LABELS "online" )
+
+ # TODO: find a smaller CG run
+ AddQueryTest( SlowTest_Sra_Info_SpotLayout_CG 7.7 "--spot-layout SRR546160 --limit 100" )
++set_tests_properties( SlowTest_Sra_Info_SpotLayout_CG
++ PROPERTIES LABELS "online" )
+
+ # spot layout, detail level
+ AddQueryTest( Test_Sra_Info_SpotLayout_Detail_Short 7.8.1 "--spot-layout SRR000123 --detail 0" )
+ AddQueryTest( Test_Sra_Info_SpotLayout_Detail_Abbreviated 7.8.2 "--spot-layout SRR000123 --detail 1" )
+ AddQueryTest( Test_Sra_Info_SpotLayout_Detail_Full 7.8.3 "--spot-layout SRR000123 --detail 2" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Detail_Short
++ PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Detail_Abbreviated
++ PROPERTIES LABELS "online" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Detail_Full
++ PROPERTIES LABELS "online" )
+
+ # spot layout, first N rows only
+ AddQueryTest( Test_Sra_Info_SpotLayout_Rows 7.9 "--spot-layout SRR000123 --rows 5" )
++set_tests_properties( Test_Sra_Info_SpotLayout_Rows
++ PROPERTIES LABELS "online" )
+
+ # # multiple queries
+ # add_test( NAME Test_Sra_Info_MultipleQueries_8.0
+--- a/test/external/sra-pileup/CMakeLists.txt
++++ b/test/external/sra-pileup/CMakeLists.txt
+@@ -42,4 +42,5 @@ if ( NOT WIN32 AND Python3_EXECUTABLE )
+ bash -c "./runtests-slow.sh ${DIRTOTEST} ${Python3_EXECUTABLE}"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ )
++ set_tests_properties( SlowTest_SraPileup PROPERTIES LABELS online )
+ endif()
+--- a/test/external/sra-stat/CMakeLists.txt
++++ b/test/external/sra-stat/CMakeLists.txt
+@@ -34,6 +34,7 @@ if ( NOT WIN32 )
+ add_test( NAME Test_Sra_stat_dflt
+ COMMAND test-sra-stat.sh ${DIRTOTEST} sra-stat
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties( Test_Sra_stat_dflt PROPERTIES LABELS online )
+ if( RUN_SANITIZER_TESTS )
+ add_test( NAME Test_Sra_stat-asan
+ COMMAND test-sra-stat.sh ${DIRTOTEST} sra-stat-asan
+@@ -64,6 +65,7 @@ if ( NOT WIN32 )
+ add_test( NAME SlowTest_Sra_stat
+ COMMAND test-sra-stat-slow.sh ${DIRTOTEST} sra-stat
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties( SlowTest_Sra_stat PROPERTIES LABELS online )
+ if( RUN_SANITIZER_TESTS )
+ add_test( NAME SlowTest_Sra_stat-asan
+ COMMAND test-sra-stat-slow.sh ${DIRTOTEST} sra-stat-asan
+--- a/test/external/vdb-validate/CMakeLists.txt
++++ b/test/external/vdb-validate/CMakeLists.txt
+@@ -36,10 +36,12 @@ if ( NOT WIN32 )
+ add_test( NAME Test_Vdb_validate
+ COMMAND vdb_validate.sh "${DIRTOTEST}" vdb-validate
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Vdb_validate PROPERTIES LABELS "online")
+
+ add_test( NAME Test_Vdb_validate_redact
+ COMMAND bash -c "./vdb_validate_redact.sh '${DIRTOTEST}' '${VDB_LIBDIR}' '${VDB_INCDIR}'"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Vdb_validate_redact PROPERTIES LABELS "online")
+
+ if( RUN_SANITIZER_TESTS )
+ add_test( NAME Test_Vdb_validate-asan
+--- a/test/internal/vdb-copy/CMakeLists.txt
++++ b/test/internal/vdb-copy/CMakeLists.txt
+@@ -45,6 +45,8 @@ if( Python3_EXECUTABLE )
+ COMMAND bash -c "./copy_and_compare.sh ${DIRTOTEST} SRR000123"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
+
++ set_tests_properties( Test_VDB_Copy_On_Short_Accession
++ PROPERTIES LABELS online )
+ add_test( NAME Test_VDB_Copy_Should_Fail_On_Invalid_Accession
+ COMMAND bash -c "./return_code_on_error.sh ${DIRTOTEST}"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
+@@ -53,6 +55,8 @@ if( Python3_EXECUTABLE )
+ COMMAND bash -c "./test-redaction.sh '${DIRTOTEST}' '${VDB_LIBDIR}' '${VDB_INCDIR}'"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ )
++ set_tests_properties( Test_VDB_Copy_Redaction
++ PROPERTIES LABELS online )
+ endif()
+
+ else()
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/0de80a43ef22f01493fad333e5457db19c47be36
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/0de80a43ef22f01493fad333e5457db19c47be36
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