Andreas Tille pushed to branch master at Debian Med / sra-sdk
Commits:
2ee65f2b by Andreas Tille at 2024-12-12T14:32:58+01:00
Fix regression I injected into patch
- - - - -
1 changed file:
- debian/patches/label_online_tests.patch
Changes:
=====================================
debian/patches/label_online_tests.patch
=====================================
@@ -437,16 +437,7 @@ 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
-@@ -147,6 +178,8 @@ if ( NOT WIN32)
- # imperfect match, bad arguments
- add_test ( NAME SraSearch-6.0.1-imperfect-match-no-arg
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
- ${SRA_SEARCH} 6.0.1-imperfect-match-no-arg
--args "AGCTAGCTAGCT SRR000001 -S" --rc 3 )
-+ set_tests_properties( SlowTest_SraSearch-6.0.1-imperfect-match-agrep-dp
-+ PROPERTIES LABELS online )
- add_test ( NAME SraSearch-6.0.2-imperfect-match-bad-arg
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
- ${SRA_SEARCH} 6.0.2-imperfect-match-bad-arg
--args "AGCTAGCTAGCT SRR000001 -S qq" --rc 3 )
- add_test ( NAME SraSearch-6.0.3-imperfect-match-default
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND bash runtestcase.sh
-@@ -160,16 +193,26 @@ if ( NOT WIN32)
+@@ -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 bash runtestcase.sh
${SRA_SEARCH} 6.4-imperfect-match-agrep-dp
--args "AGCTAGCTAGCT -T 1 --score 90 --algorithm AgrepDP
SRR000001" )
@@ -473,7 +464,7 @@ 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 +223,21 @@ if ( NOT WIN32)
+@@ -180,15 +221,21 @@ 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" )
@@ -495,7 +486,7 @@ 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 +246,8 @@ if ( NOT WIN32)
+@@ -197,6 +244,8 @@ 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" )
@@ -504,7 +495,7 @@ 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 +256,8 @@ if ( NOT WIN32)
+@@ -205,6 +254,8 @@ 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" )
@@ -513,7 +504,7 @@ 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 +266,7 @@ if ( NOT WIN32)
+@@ -213,5 +264,7 @@ 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" )
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/2ee65f2baefa3097e895c1c6cd81396ba66d97c5
--
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/2ee65f2baefa3097e895c1c6cd81396ba66d97c5
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