afd7d0d912aa376f0f214448f3e83d5967f35d50 hiram Mon Jun 17 12:55:03 2024 -0700 allow list functions to work on a genark genome without hubUrl specified no redmine diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index e06893c..1be34f5 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -21,31 +21,32 @@ hgwdev:: SERVERNAME="https://api-test.gi.ucsc.edu" make test alpha:: SERVERNAME="https://genome-test.gi.ucsc.edu" make test beta:: SERVERNAME="https://apibeta.soe.ucsc.edu" make test all:: test0 listFunctions getFunctions listSchema getSequence wigData \ search supportedTypes errorTests notSupported bugReports listFunctions: list01 list02 list03 list04 list05 list06 list07 list08 list09 \ list10 list11 list12 list13 list14 list15 list16 list17 list18 list19 \ - list20 list21 list22 list23 list24 list25 list26 + list20 list21 list22 list23 list24 list25 list26 list27 list28 list29 \ + list30 list31 list32 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 test57 \ multiTrack01 multiTrack02 multiTrack03 findGenome: findGenome01 listSchema: schema01 schema02 schema03 schema04 schema05 schema06 schema07 \ schema08 schema09 schema10 schema11 schema12 getSequence: getSeq01 getSeq02 getSeq03 getSeq04 getSeq05 getSeq06 getSeq07 wigData: wig01 wig02 wig03 wig04 wig05 wig06 wig07 wig08 wig09 wig10 \ @@ -253,30 +254,60 @@ @ curl -L "${SERVERNAME}/list/files?genome=ce2;maxItemsOutput=5;format=text" 2> /dev/null | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/genarkGenomes list26: setOutput @printf "### $@ '${SERVERNAME}/list/genarkGenomes?maxItemsOutput=5'\n" @./jsonConsumer.pl -maxItemsOutput=5 -serverName="${SERVERNAME}" -endpoint="/list/genarkGenomes" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/genarkGenomes verify existence of genome GCA_000002765.3 list27: setOutput @printf "### $@ '${SERVERNAME}/list/genarkGenomes?genome=GCA_000002765.3;maxItemsOutput=5'\n" @./jsonConsumer.pl -genome=GCA_000002765.3 -maxItemsOutput=5 -serverName="${SERVERNAME}" -endpoint="/list/genarkGenomes" 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#; s#/hubs/.*/hub#/hubs/hub#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz +# testing /list/tracks?genome=GCA_021951015.1 without hubUrl +list28: setOutput + @printf "### $@ '${SERVERNAME}/list/tracks?genome=GCA_021951015.1'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="GCA_021951015.1" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /list/tracks?genome=GCA_021951015.1 with hubUrl +list29: setOutput + @printf "### $@ '${SERVERNAME}/list/tracks?genome=GCA_021951015.1;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/tracks" -genome="GCA_021951015.1" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /list/chromosomes?genome=GCA_021951015.1 without hubUrl +list30: setOutput + @printf "### $@ '${SERVERNAME}/list/chromosomes?genome=GCA_021951015.1'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="GCA_021951015.1" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /list/chromosomes?genome=GCA_021951015.1 with hubUrl +list31: setOutput + @printf "### $@ '${SERVERNAME}/list/chromosomes?genome=GCA_021951015.1;hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/chromosomes" -genome="GCA_021951015.1" -hubUrl="https://hgdownload.soe.ucsc.edu/hubs/GCA/021/951/015/GCA_021951015.1/hub.txt" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# testing /list/schema?genome=GCA_021951015.1;track=cpgIslandExt without hubUrl +list32: setOutput + @printf "### $@ '${SERVERNAME}/list/schema?genome=GCA_021951015.1;track=cpgIslandExt'\n" + @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/list/schema" -genome="GCA_021951015.1" -track="cpgIslandExt" 2>&1 | egrep -v "${excludeLines}" | egrep -v "dateTime" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + ########################## getData functions ############################# # testing /getData/track?genome=ce11&track=gold test8: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce11" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrM test9: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrM" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce11&track=gold&chrom=chrI&start=1&end=1024 test10: setOutput @./jsonConsumer.pl -serverName="${SERVERNAME}" -endpoint="/getData/track" -genome="ce11" -track="gold" -chrom="chrI" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz