Andreas Tille pushed to branch master at Debian Med / sra-sdk
Commits:
a109c9a5 by Andreas Tille at 2024-12-13T11:16:13+01:00
Do not try to set properties of removed tests
- - - - -
17f6c98a by Andreas Tille at 2024-12-13T11:16:48+01:00
Force finding RE2
- - - - -
2 changed files:
- debian/patches/label_online_tests.patch
- debian/patches/use_debian_packaged_re2.patch
Changes:
=====================================
debian/patches/label_online_tests.patch
=====================================
@@ -192,25 +192,6 @@ Description: Label tests "online" to have an easy option
to run/ignore them prop
if( RUN_SANITIZER_TESTS )
add_test( NAME SlowTest_Prefetch_dflt-asan
COMMAND
-@@ -86,6 +91,9 @@ if ( NOT WIN32 )
- add_test( NAME Test_Prefetch_outs
- COMMAND perl test-prefetch-outs.pl ${DIRTOTEST} prefetch 0 #
1234
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
-+ # Trivially succeeds in the absence of Aspera ascp, but any
-+ # meaningful testing would require online resources regardless.
-+ set_tests_properties(SlowTest_Prefetch_1GB PROPERTIES LABELS "online")
- if( RUN_SANITIZER_TESTS )
- add_test( NAME Test_Prefetch_outs-asan
- COMMAND perl test-prefetch-outs.pl ${DIRTOTEST} prefetch-asan
-@@ -98,6 +106,8 @@ if ( NOT WIN32 )
- add_test( NAME SlowTest_Prefetch_1GB
- COMMAND perl ncbi1GB.pl ${DIRTOTEST} prefetch # 23
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
-+ set_tests_properties(SlowTest_Prefetch_vdbcache PROPERTIES
-+ LABELS "online")
- if( RUN_SANITIZER_TESTS )
- add_test( NAME SlowTest_Prefetch_1GB-asan
- COMMAND perl ncbi1GB.pl ${BINDIR} prefetch-asan
--- a/test/external/srapath/CMakeLists.txt
+++ b/test/external/srapath/CMakeLists.txt
@@ -42,6 +42,7 @@ if ( NOT WIN32 )
@@ -437,7 +418,7 @@ Description: Label tests "online" to have an easy option to
run/ignore them prop
# query expressions, bad arguments
add_test ( NAME SraSearch-5.1-run-not-nucstrstr-with-expression
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
-@@ -160,16 +191,26 @@ if ( NOT WIN32)
+@@ -160,16 +193,26 @@ if ( NOT WIN32)
# imperfect match
add_test ( NAME SlowTest_SraSearch-6.4-imperfect-match-agrep-dp
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
${SRA_SEARCH} 6.4-imperfect-match-agrep-dp
--args "AGCTAGCTAGCT -T 1 --score 90 --algorithm AgrepDP
SRR000001" )
@@ -464,7 +445,7 @@ Description: Label tests "online" to have an easy option to
run/ignore them prop
# multi-threading, bad arguments
add_test ( NAME SraSearch-7.0.1-threads-no-arg WORKING_DIRECTORY
${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
-@@ -180,15 +221,21 @@ if ( NOT WIN32)
+@@ -180,15 +223,21 @@ if ( NOT WIN32)
# multiple runs, thread per accession
add_test ( NAME SlowTest_SraSearch-7.1-threads-unsorted
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
${SRA_SEARCH} 7.1-threads-unsorted --sort
--args "ACGTAGGGTCC --threadperacc --threads 4 SRR600094 SRR600095 SRR600096
SRR600099" )
@@ -486,7 +467,7 @@ Description: Label tests "online" to have an easy option to
run/ignore them prop
# nothing found
add_test ( NAME SlowTest_SraSearch-8.0-nothing-found WORKING_DIRECTORY
${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
-@@ -197,6 +244,8 @@ if ( NOT WIN32)
+@@ -197,6 +246,8 @@ if ( NOT WIN32)
# reference mode
add_test ( NAME SlowTest_SraSearch-9.0-reference WORKING_DIRECTORY
${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
${SRA_SEARCH} 9.0-reference --sort --args
"ACGTAGGGTCC SRR600094 --reference -T 6" )
@@ -495,7 +476,7 @@ Description: Label tests "online" to have an easy option to
run/ignore them prop
# reference mode, multiple references, one accession
add_test ( NAME SlowTest_SraSearch-9.1-reference-multiple-refs
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
-@@ -205,6 +254,8 @@ if ( NOT WIN32)
+@@ -205,6 +256,8 @@ if ( NOT WIN32)
# reference mode, multiple references, accessions
add_test ( NAME
SlowTest_SraSearch-9.2-reference-multiple-refs-multiple-runs WORKING_DIRECTORY
${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
${SRA_SEARCH} 9.2-reference --sort --args
"ACGTAGGGTCC SRR600095 SRR600094 --reference NC_000007.13,NC_000001.10 -T 6" )
@@ -504,7 +485,7 @@ Description: Label tests "online" to have an easy option to
run/ignore them prop
# reference mode, expressions not allowed
add_test ( NAME SraSearch-9.3-reference-expression WORKING_DIRECTORY
${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
-@@ -213,5 +264,7 @@ if ( NOT WIN32)
+@@ -213,5 +266,7 @@ if ( NOT WIN32)
# unaligned reads only
add_test ( NAME SlowTest_SraSearch-10.0-unaligned WORKING_DIRECTORY
${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
${SRA_SEARCH} 10.0-unaligned --args
"AGCTAGCTAGCT SRR600099 --unaligned" )
=====================================
debian/patches/use_debian_packaged_re2.patch
=====================================
@@ -5,7 +5,27 @@ Description: use Debian packaged re2
--- a/tools/loaders/sharq/CMakeLists.txt
+++ b/tools/loaders/sharq/CMakeLists.txt
-@@ -89,28 +89,29 @@ set(LOCAL_LIBDIR ${LOCAL_BUILD_DIR}/lib)
+@@ -48,17 +48,8 @@ find_package(ZLIB)
+ find_package(BZip2)
+ find_package (Threads)
+
+-# check whether RE2 is accessible
+-set(RE2_URL https://github.com/google/re2)
+-execute_process(COMMAND curl -Is ${RE2_URL}
+- COMMAND head -n 1
+- COMMAND grep -q 200
+- RESULTS_VARIABLE RE2_RC)
+-if ("${RE2_RC}" EQUAL 0)
+- set( RE2_FOUND TRUE CACHE INTERNAL "" )
+-else()
+- set( RE2_FOUND FALSE CACHE INTERNAL "" )
+-endif()
++# Debian ensures RE2 via Build-Depends
++set( RE2_FOUND TRUE CACHE INTERNAL "" )
+ message(RE2_FOUND = ${RE2_FOUND} )
+ # RE2_FOUND will be used by sharQ tests
+
+@@ -89,28 +80,29 @@ set(LOCAL_LIBDIR ${LOCAL_BUILD_DIR}/lib)
set(RE2_TAG 2021-09-01)
#set(RE2_TAG 2023-03-01)
@@ -57,7 +77,7 @@ Description: use Debian packaged re2
#file(COPY ${CMAKE_SOURCE_DIR}/tools/sharq/sharq.py DESTINATION ${BINDIR})
-@@ -122,7 +123,7 @@ add_custom_target(
+@@ -122,7 +114,7 @@ add_custom_target(
${BINDIR}/sharq.py)
add_executable(sharq fastq_parse.cpp)
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/compare/2ee65f2baefa3097e895c1c6cd81396ba66d97c5...17f6c98a0e0231f23c32df5441a44de790503707
--
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/compare/2ee65f2baefa3097e895c1c6cd81396ba66d97c5...17f6c98a0e0231f23c32df5441a44de790503707
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