e8405f0a3004ccb304cd7b061b9b94d63d29197f markd Sat Apr 19 19:12:00 2025 -0700 Exit non-zero if an error occurs creating the bigBed. Enhance test to check exit code for error cases #35551 diff --git src/utils/bedToBigBed/tests/makefile src/utils/bedToBigBed/tests/makefile index 50e1729a3a1..d4167478edf 100644 --- src/utils/bedToBigBed/tests/makefile +++ src/utils/bedToBigBed/tests/makefile @@ -1,63 +1,68 @@ kentSrc = ../../.. A = bedToBigBed include ../../../inc/common.mk test: testOddSorted testRgb testMultiInsAtEnd itemsRgb tabSep testBadChrom1 testBbSize1 testBbSize2 testDevStdin testStdin testCompress testNotSorted +# use ! cmd 2> output/$@.err || (${shouldHaveFailed}) +shouldHaveFailed = echo "Error: command should have failed" >&2 && false + +fakeGenomeTwoBit = output/fakeGenome.2bit + testBadChrom1: outputDir - -${BINDIR}/${A} input/colored.genbank.bed input/human.chrom.sizes.txt output/noFile.chromAlias.bb -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/testBadChrom1.err + ! ${BINDIR}/${A} input/colored.genbank.bed input/human.chrom.sizes.txt output/noFile.chromAlias.bb -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/testBadChrom1.err || (${shouldHaveFailed}) diff expected/testBadChrom1.err output/testBadChrom1.err output/human.chromAlias.bb: outputDir ${BINDIR}/${A} input/human.chromAlias.bed input/human.chrom.sizes.txt output/human.chromAlias.bb -tab -type=bed3+4 -as=input/chromAliasIndex.as -extraIndex=genbank,ensembl,ncbi,ucsc testBbSize1: outputDir output/human.chromAlias.bb ${BINDIR}/${A} input/colored.genbank.bed output/human.chromAlias.bb output/colored.genbank.bb -sizesIsChromAliasBb -tab -type=bed12+13 -as=input/bigGenePred.as bigBedToBed output/colored.genbank.bb output/colored.genbank.bed diff input/colored.genbank.bed output/colored.genbank.bed testBbSize2: outputDir output/human.chromAlias.bb - -${BINDIR}/${A} input/mixed.bed output/human.chromAlias.bb output/noFile.chromAlias.bb -sizesIsChromAliasBb -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/mixed.err + ! ${BINDIR}/${A} input/mixed.bed output/human.chromAlias.bb output/noFile.chromAlias.bb -sizesIsChromAliasBb -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/mixed.err || (${shouldHaveFailed}) diff expected/mixed.err output/mixed.err testRgb: outputDir ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as input/itemRgb.bed input/chrom.sizes output/itemRgb.bb 2> /dev/null bigBedToBed output/itemRgb.bb output/test_itemRgb.bed diff input/itemRgb.bed output/test_itemRgb.bed testCompress: outputDir ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as input/itemRgb.bed.gz input/chrom.sizes output/itemRgbGz.bb 2> /dev/null bigBedToBed output/itemRgbGz.bb output/test_itemRgbGz.bed diff input/itemRgb.bed output/test_itemRgbGz.bed testOddSorted: outputDir - -${BINDIR}/${A} -extraIndex=name -type=bed12+16 -tab -as=../../..//hg/lib/gencodeBGP.as input/oddSorted.bed input/hg38.chrom.sizes output/oddSorted.bb + ${BINDIR}/${A} -extraIndex=name -type=bed12+16 -tab -as=../../..//hg/lib/gencodeBGP.as input/oddSorted.bed input/hg38.chrom.sizes output/oddSorted.bb bigBedToBed output/oddSorted.bb output/oddSorted.bed LC_ALL=C sort -k1,1 -k2,2n input/oddSorted.bed > output/oddSorted.check.bed diff output/oddSorted.check.bed output/oddSorted.bed cut -f 4 input/oddSorted.bed > output/oddSorted.names bigBedNamedItems output/oddSorted.bb output/oddSorted.names -nameFile stdout | LC_ALL=C sort -k1,1 -k2,2n > output/searchNames.bed diff output/oddSorted.bed output/searchNames.bed testSortNotSorted: outputDir - -${BINDIR}/${A} -tab -type=bed9+3 -sort input/notSorted.bed input/notSorted.chrom.sizes output/notSorted.bb + ${BINDIR}/${A} -tab -type=bed9+3 -sort input/notSorted.bed input/notSorted.chrom.sizes output/notSorted.bb bigBedToBed output/notSorted.bb output/notSorted.bed diff expected/notSorted.bed output/notSorted.bed testNotSorted: outputDir - -${BINDIR}/${A} -type=bed12 input/notSorted.bed input/notSorted.chrom.sizes /dev/null 2> output/notSorted.err || true + ! ${BINDIR}/${A} -type=bed12 input/notSorted.bed input/notSorted.chrom.sizes /dev/null 2> output/notSorted.err || (${shouldHaveFailed}) diff expected/notSorted.err output/notSorted.err testMultiInsAtEnd: outputDir ${BINDIR}/${A} input/multiInsAtEnd.bed input/chrom.sizes output/multiInsAtEnd.bb 2> /dev/null bigBedToBed output/multiInsAtEnd.bb output/test_multiInsAtEnd.bed diff -w input/multiInsAtEnd.bed output/test_multiInsAtEnd.bed itemsRgb: outputDir ${BINDIR}/${A} input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed diff input/reservedBed12.bed output/test_reservedBed12.bed ${BINDIR}/${A} -type=bed12 input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed diff input/reservedBed12.bed output/test_reservedBed12.bed ${BINDIR}/${A} -type=bed9+ -as=input/reservedBed12.as input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null @@ -73,29 +78,34 @@ bigBedToBed output/itemRgbBed12.bb output/test_itemRgbBed12.bed diff input/itemRgbBed12.bed output/test_itemRgbBed12.bed ${BINDIR}/${A} -type=bed12 -as=input/reservedBed12.as input/itemRgbBed12.bed input/chrom.sizes output/itemRgbBed12.bb 2> /dev/null bigBedToBed output/itemRgbBed12.bb output/test_itemRgbBed12.bed diff input/itemRgbBed12.bed output/test_itemRgbBed12.bed ${BINDIR}/${A} -type=bed12 -as=input/itemRgbBed12.as input/itemRgbBed12.bed input/chrom.sizes output/itemRgbBed12.bb 2> /dev/null bigBedToBed output/itemRgbBed12.bb output/test_itemRgbBed12.bed diff input/itemRgbBed12.bed output/test_itemRgbBed12.bed tabSep: outputDir ${BINDIR}/${A} -tab -type=bed4 -as=input/tabSep.as input/tabSep.bed input/chrom.sizes output/tabSep.bb 2> /dev/null bigBedToBed output/tabSep.bb output/test_tabSep.bed diff input/tabSep.bed output/test_tabSep.bed testDevStdin: outputDir - -cat input/itemRgb.bed | ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as /dev/stdin input/chrom.sizes output/$@.bb 2> output/$@.err + cat input/itemRgb.bed | (! ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as /dev/stdin input/chrom.sizes output/$@.bb 2> output/$@.err) || (${shouldHaveFailed}) diff expected/$@.err output/$@.err testStdin: outputDir - -cat input/itemRgb.bed | ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as stdin input/chrom.sizes output/$@.bb 2> output/$@.err + cat input/itemRgb.bed | (! ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as stdin input/chrom.sizes output/$@.bb 2> output/$@.err) || (${shouldHaveFailed}) diff expected/$@.err output/$@.err +test2bitMissingSeq: outputDir ${fakeGenomeTwoBit} + ! ${BINDIR}/${A} -tab -type=bed4 -as=input/tabSep.as -sizesIs2Bit input/tabSep.bed ${fakeGenomeTwoBit} output/tabSep.bb 2> output/$@.err || (${shouldHaveFailed}) + diff expected/$@.err output/$@.err +${fakeGenomeTwoBit}: outputDir input/fakeGenome.fa + faToTwoBit input/fakeGenome.fa $@ clean:: @rm -rf output outputDir: @${MKDIR} -p output