6bbfd4220159b66826230dfaf577a67c4a2d7236 hiram Mon Mar 1 10:52:48 2021 -0800 add full table psl test and bring tests up to date no redmine diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 85cd452..784ebb2 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1,28 +1,28 @@ test:: all all:: test0 listFunctions getFunctions listSchema getSequence wigData \ supportedTypes errorTests notSupported bugReports listFunctions: list01 list02 list03 list04 list05 list06 list07 list08 list09 \ list10 list11 list12 list13 list14 list15 list16 list17 list18 getFunctions: test8 test9 test10 test11 test12 test13 test14 \ test15 test16 test19 test21 test26 test27 test28 \ test29 test39 test40 test41 test42 test43 test44 test45 test46 test47 \ - test48 test49 test50 test51 test52 test53 test54 test55 test56 + test48 test49 test50 test51 test52 test53 test54 test55 test56 test57 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 \ schema08 schema09 schema10 schema11 schema12 getSequence: getSeq01 getSeq02 getSeq03 getSeq04 getSeq05 wigData: wig01 wig02 wig03 wig04 wig05 wig06 wig07 wig08 wig09 wig10 \ wig11 wig12 wig13 wig14 wig15 wig16 wig17 wig18 wig19 wig20 \ wig21 wig22 wig23 wig24 supportedTypes: altGraphX barChart chain ctgPos expRatio \ interact netAlign peptideMapping pgSnp supportedTypes0: altGraphX barChart chain ctgPos expRatio factorSource gvf \ interact netAlign peptideMapping pgSnp @@ -352,30 +352,38 @@ @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from clonePos track with chrom specified test55: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr22'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays -chrom=chr22 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # get data from clonePos track with chrom and start,end specified test56: setOutput @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=clonePos;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5;chrom=chr21;start=20000000;end=30000000'\n" @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=clonePos -maxItemsOutput=5 -jsonOutputArrays -chrom=chr21 -start=20000000 -end=30000000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?genome=ce11;track=mrna;maxItemsOutput=5 + +# PSL track, no chrom specified, exercise column name tName instead of chrom +test57: setOutput + @printf "### $@ ### 'https://api-test.gi.soe.ucsc.edu/getData/track?track=mrna;genome=ce11;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=mrna -maxItemsOutput=5 -jsonOutputArrays | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + ############################################################################### # /getData/sequence testing ############################################################################### # testing /getData/sequence? hubUrl genome=hg19&chrom=chrCp&start=4321&end=5647 getSeq01: setOutput @printf "### $@ " @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="araTha1" -chrom="chrCp" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence? hubUrl Bejerano genome=hg19&chrom=chrM&start=4321&end=5647 getSeq02: setOutput @printf "### $@ " @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -chrom="chrM" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -1035,50 +1043,50 @@ @./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="hapmapLdPhCeu" -chrom="chr1" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # 34 bam - not supported</li> # 2 bigBarChart - not supported</li> # 3 bigInteract - not supported</li> # 18 bigMaf - not supported</li> # 152 composite container - not supported</li> # 93 composite view - not supported</li> # 37 halSnake - not supported</li> # 31 superTrack child - not supported</li> # 5 vcfTabix - not supported</li> redmine23733: setOutput - @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=knownGene;genome=hg38;chrom=chr1;end=48000;start=47000'\n" - @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg38 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | tail -5 | gzip -c > testOutput/$@.gz + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=knownGene;genome=hg19;chrom=chr1;end=48000;start=47000'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=knownGene -chrom=chr1 -start=47000 -end=48000 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | sort | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # end coordinate for get sequence past end of chromosome, database genome redmine24089a: setOutput @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/sequence?genome=hg19;chrom=chrM;start=16560;end=16572'\n" @./jsonConsumer.pl -endpoint="/getData/sequence" -genome=hg19 -chrom=chrM -start=16560 -end=16572 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${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/$@.gz + @./jsonConsumer.pl -endpoint="/getData/sequence" -genome=ci2 -chrom=scaffold_8534 2>&1 | sed -e 's/, /,\n/g;' | egrep -v "${excludeLines}" | grep -v "^#" | 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