748b06ac95ff2a3957be3845bd3594984e3cc3cf
chmalee
  Wed Aug 17 19:21:48 2022 -0700
Rename test cgi to official name. Always search everything, only show
categories that have matches in the result list. Add /search endpoint to
hubApi, add code to search help docs in hgSuggest but don't call it yet
in autoComplete.js. Minor fixups so search result links work correctly.

Fixing up old programs that call hgPositionsFind

diff --git src/hg/makefile src/hg/makefile
index 6a08d85..bbd83e1 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -1,307 +1,307 @@
 # Build all directories in utils
 
 kentSrc = ..
 include ${kentSrc}/inc/localEnvironment.mk
 
 BROWSER_BINS=cartReset das hgBlat makeDb/hgCgiData hgCollection hgConvert \
 	hgHubConnect hgGateway hgGene hgGenome hgIntegrator hgLogin hgPcr \
 	hgSession hgSuggest hgTables hgTracks hgTrackUi hgUserSuggestion \
 	hgc hgApi cartDump near/hgNear hgLiftOver hgLinkIn hgVai \
 	visiGene/hgVisiGene hgMenubar hgPublicSessions \
 	encode/hgEncodeDataVersions encode/hgEncodeVocab encode/hgEncodeApi \
 	phyloPng hgCustom hgPal hgFileUi hgFileSearch makeDb/hgCgiData \
 	js htdocs/style hgMirror hgBeacon hgGtexTrackSettings pyLib \
-	hgGeneGraph hgs hubApi hgPhyloPlace gar searchExample
+	hgGeneGraph hgs hubApi hgPhyloPlace gar hgSearch
 
 ifdef LOWELAB
     BROWSER_BINS += $(HOME)/lowelab/src/browser/tooltip $(HOME)/lowelab/src/browser/chooseorg
 endif
 
 BROWSER_LOADERS = makeDb/hgLoadBed makeDb/hgLoadWiggle makeDb/hgLoadMaf utils/pslToBigPsl utils/hubCheck
 
 ifneq ($(findstring $(shell hostname),hgwdev hgwbeta),)
     ENCODE_FILES = encode3/encodeDataWarehouse
 endif
 
 
 TEST_DIRS = lib cgilib autoDtd autoSql blastToPsl checkTableCoords embossToPsl \
             genePredSingleCover genePredHisto genePredToBed genePredToGtf \
 	    genePredToMafFrames gbGetEntries hgGetAnn liftAcross liftOver \
             mouseStuff mrnaToGene pslCDnaFilter pslDiff pslHisto \
             pslPartition pslSelect pslStats pslToBed spideyToPsl \
 	    sqlToXml xmlToSql utils
 
 BROKEN_TEST_DIRS = liftOver scaffoldFaToAgp
 
 BAD_DIRS = \
 	altGraph \
 	cgiExample \
 	geneOverlap \
 	hgBatch \
 	makeSeqs \
 	oneShot \
 	synMap \
 	encode \
 	wikiPlot
 
 # can not build this on Mac OSX - has functions not supported
 UNAME_S := $(shell uname -s) 
 ifeq ($(UNAME_S),Darwin)
   buildRefresh=
 else
   buildRefresh=encode3
 endif
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	autoDtd \
 	autoSql \
 	autoXml \
 	bedSort \
 	liftUp \
 	liftOver \
 	bedIntersect \
 	bedItemOverlapCount \
 	bedToGenePred \
 	blastToPsl \
 	checkCoverageGaps \
 	checkHgFindSpec \
 	checkTableCoords \
 	dbTrash \
 	encode3/validateFiles \
 	encode3/validateManifest \
 	estOrient \
 	featureBits \
 	geneBounds/clusterGenes \
 	genePredHisto \
 	genePredSingleCover \
 	genePredToBed \
 	genePredToFakePsl \
 	genePredToMafFrames \
 	getRna \
 	getRnaPred \
 	gigAssembler/checkAgpAndFa \
 	hgSpeciesRna \
 	hgsql \
 	hgsqldump \
 	maskOutFa \
 	mrnaToGene \
 	ratStuff/mafsInRegion \
 	ratStuff/mafSpeciesSubset \
 	ratStuff/mafToSnpBed \
 	pslCDnaFilter \
 	genePredCheck \
 	genePredToGtf \
 	pslCat \
 	pslCheck \
 	pslDropOverlap \
 	pslFilter \
 	pslHisto \
 	pslPairs \
 	pslPartition \
 	pslPretty \
 	pslRecalcMatch \
 	pslReps \
 	pslSelect \
 	pslSomeRecords \
 	pslSort \
 	pslSortAcc \
 	pslStats \
 	pslToBed \
 	pslToChain \
 	pslxToFa \
 	qaToQac \
 	qacAgpLift \
 	qacToQa \
 	qacToWig \
 	sqlToXml \
 	trfBig \
 	xmlCat \
 	xmlToSql
 
 # List of directories to build at UCSC
 UTIL_DIRS = \
 	affyTransciptome \
 	agpCloneCheck \
 	agpCloneList \
 	agpAllToFaFile \
 	agpMergeChromScaf \
 	agpToFa \
 	agpToGl \
 	altSplice \
 	bedOrBlocks \
 	bedSplitOnChrom \
 	borfBig \
 	ctgFaToFa \
 	ctgToChromFa \
 	embossToPsl \
 	${buildRefresh} \
 	fakeFinContigs \
 	fakeOut \
 	ffaToFa \
 	fishClones \
 	fqToQa \
 	fqToQac \
 	fragPart \
 	gbGetEntries \
 	gbOneAcc \
 	gbToFaRa \
 	geneBounds \
 	getFeatDna \
 	gpStats \
 	gpToGtf \
 	gpcrParser \
 	gsBig \
 	hgTablesTest \
 	hgChroms \
 	hgGetAnn \
 	hgKnownGeneList \
 	hgSelect \
 	hgsqladmin \
 	hgsqlimport \
         hgsqlSwapTables \
         hgsqlTableDate \
 	intronEnds \
 	lib \
 	liftAcross \
 	liftAgp \
 	liftFrags \
 	lfsOverlap \
 	makeDb \
 	mdToNcbiLift \
 	mouseStuff \
 	near/hgCeOrfToGene \
 	near/hgClusterGenes \
 	near/hgEmblProtLinks \
 	near/hgExpDistance \
 	near/hgGoAssociation \
 	near/hgKnownToSuper \
 	near/hgMapToGene \
 	near/hgMapViaSwissProt \
 	near/hgProtIdToGenePred \
 	near/hgWormLinks \
 	near/pepPredToFa \
 	near/hgNearTest \
 	near/hgNetDist \
 	near/knownToHprd \
 	nci60 \
 	orthoMap \
 	patCount \
 	perf \
 	pslCoverage \
 	pslDiff \
 	pslFilterPrimers \
 	pslGlue \
 	pslHitPercent \
 	pslIntronsOnly \
 	pslQuickFilter \
 	pslSimp \
 	pslSortAcc \
 	pslSplitOnTarget \
 	pslUnpile \
 	qa \
 	ratStuff \
 	relPairs \
 	recycleDb \
 	rnaStructure \
 	sage \
 	scanRa \
 	semiNorm \
 	sim4big \
 	snpException \
 	snp \
 	spideyToPsl \
 	splitFa \
 	splitFaIntoContigs \
 	test \
 	txCds \
 	txGene \
 	txGraph \
 	utils \
 	uniqSize \
 	updateStsInfo \
 	visiGene/knownToVisiGene
 
 APPS = $(UTIL_DIRS) $(UTILS_APPLIST)
 
 all::    cgi utils
 
 hgLib:
 	cd lib && ${MAKE}
 	cd cgilib && ${MAKE}
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
 	cd altSplice/lib && $(MAKE)
 	cd altSplice/altSplice && $(MAKE) bedToExons
 	cd mouseStuff && $(MAKE) userApps
 	cd ratStuff && $(MAKE) userApps
 
 %.userApp: hgLib
 	cd $* && echo $* && $(MAKE)
 
 utils: $(APPS:%=%.utils)
 %.utils: hgLib
 	cd $* && echo $* && $(MAKE)
 
 # Compile only, the cgi's for those builds without write access
 #	to apache cgi-bin directories  (this compiles and links executables)
 
 compile: ${BROWSER_BINS:%=%.compile} ${BROWSER_LOADERS:%=%.compile}
 %.compile: hgLib
 	cd $* && echo $* && $(MAKE) compile
 
 # Build cgi's
 #   cgi: Destination for the binaries is /usr/local/apache/cgi-bin-${USER}
 
 cgi: ${BROWSER_BINS:%=%.bins} ${BROWSER_LOADERS:%=%.cgi} ${ENCODE_FILES:%=%.cgi}
 %.bins: hgLib
 	cd $* && echo $* && $(MAKE)
 %.cgi: hgLib
 	cd $* && echo $* && $(MAKE) cgi
 
 #   alpha: Destination for the binaries is /usr/local/apache/cgi-bin/
 
 alpha:	 ${BROWSER_BINS:%=%.alpha} ${BROWSER_LOADERS:%=%.alpha} ${ENCODE_FILES:%=%.alpha}
 %.alpha: hgLib
 	cd $* && echo $* && $(MAKE) alpha
 
 #   beta: Destination for the binaries is /usr/local/apache/cgi-bin-beta/
 
 beta: ${BROWSER_BINS:%=%.beta} ${BROWSER_LOADERS:%=%.beta}
 %.beta: hgLib
 	cd $* && echo $* && $(MAKE) beta
 
 # install: Destination for the binaries is ${DESTDIR}/usr/local/apache/cgi-bin
 
 install: ${BROWSER_BINS:%=%.install} ${BROWSER_LOADERS:%=%.install}
 %.install: hgLib
 	cd $* && echo $* && $(MAKE) install
 
 clean::
 	cd lib && ${MAKE} clean
 	@for D in ${BROWSER_BINS} ${BROWSER_LOADERS}; do \
 		(cd $${D} && ${MAKE} clean;) \
 	done
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 
 clean_utils::
 	@for D in ${UTIL_DIRS}; do \
 		(cd $${D} && ${MAKE} clean;) \
 	done
 
 clean::	${TEST_DIRS:%=%.clean}
 
 %.clean:
 	cd $* && ${MAKE} clean
 
 testAll: $(APPS:%=%.testAll)
 
 %.testAll:
 	@test -s $*/tests/makefile && (echo $*; cd $* && $(MAKE) test) || true
 
 test::	${TEST_DIRS:%=%.test} testAll
 
 %.test: hgLib
 	cd $* && ${MAKE} test