608044d23640516fd06338d04d98960048699b07 hiram Mon Jul 6 08:59:20 2020 -0700 adding list/schema tests and redmine25840 refs #25840 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index af35461..85cd452 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -23,31 +23,31 @@ supportedTypes: altGraphX barChart chain ctgPos expRatio \ interact netAlign peptideMapping pgSnp supportedTypes0: altGraphX barChart chain ctgPos expRatio factorSource gvf \ interact netAlign peptideMapping pgSnp errorTests: err01 err02 err03 err04 err05 err06 err07 err08 err09 err10 \ err11 err12 err13 err14 err15 err16 err17 err18 err19 err20 \ err21 err22 err23 err24 err25 err26 err27 err28 err29 err30 \ err31 err32 err33 err34 err35 err36 err37 err38 err39 err40 \ err41 err42 err43 err44 err45 err46 err47 notSupported: notSup01 notSup02 notSup03 notSup07 notSup10 -bugReports: redmine23733 redmine24089a redmine24089b redmine24666 +bugReports: redmine23733 redmine24089a redmine24089b redmine24666 redmine25840 setOutput: @if [ ! -d testOutput ]; then mkdir testOutput; fi clean:: rm -f testOutput/*.gz rmdir testOutput # exclude these lines from the JSON output for comparison with expected excludeLines = downloadTime|dataTime # testing /list/noSubCommand, /list/publicHubs and /list/ucscGenomes test0: setOutput @./jsonConsumer.pl -test0 2>&1 | sed -e 's#https://.*/list#/list#;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -1057,30 +1057,36 @@ @./jsonConsumer.pl -endpoint="/getData/sequence" -genome=hg19 -chrom=chrM -start=16560 -end=16572 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # end coordinate for get sequence past end of chromosome, asmHub genome redmine24089b: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=araTha1;chrom=chrCp;start=154470;end=154479;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=154470 -end=154479 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # full chromosome fetch from a NIB based genom redmine24666: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=ci2;chrom=scaffold_8534'\n" @./jsonConsumer.pl -endpoint="/getData/sequence" -genome=ci2 -chrom=scaffold_8534 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# full chromosome fetch from a NIB based genom +redmine25840: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?genome=hg18;track=cnpSebat2'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome="hg18" -track="cnpSebat2" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + # curl -L "https://api-test.gi.ucsc.edu/getData/sequence?genome=ci2;chrom=scaffold_8534" 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz # track types found in hg19 and hg38 trackDb 'type' column: # 4586 narrowPeak # 4472 bigWig # 3294 bed # 1745 broadPeak # 872 chain # 871 netAlign # 596 bam # 512 genePred # 438 bigBed # 368 pgSnp # 348 bedGraph # 286 wig # 106 psl