966a8c19f18ac15df06580c18bb7515c6af258fd Merge parents 8f399a0 d215717 chmalee Tue Jun 13 12:23:26 2023 -0700 Fixing merge conflict diff --cc src/hg/lib/trackHub.c index 0af7a03,d1f104d..b536e30 --- src/hg/lib/trackHub.c +++ src/hg/lib/trackHub.c @@@ -1,1419 -1,1415 +1,1421 @@@ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* trackHub - supports collections of tracks hosted on a remote site. * The basic layout of a data hub is: * hub.txt - contains information about the hub itself * genomes.txt - says which genomes are supported by hub * Contains file name of trackDb.txt for each genome * trackDb.txt - contains a stanza for each track. Stanzas * are in a subset of the usual trackDb format. * How you use the routines here most commonly is as so: * struct trackHub *hub = trackHubOpen(hubRaUrl); * struct trackHubGenome *hubGenome = trackHubFindGenome(hub, "hg19"); * struct trackDb *tdbList = trackHubTracksForGenome(hub, hubGenome); * // do something with tdbList * trackHubClose(&hub); * Note that the tdbList returned does not have the parent/subtrack pointers set. * It is just a simple list of tracks, not a tree. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "udc.h" #include "ra.h" #include "filePath.h" #include "htmlPage.h" #include "trackDb.h" #include "trackHub.h" #include "errCatch.h" #include "hgBam.h" #include "bigWig.h" #include "bigBed.h" #include "barChartUi.h" #include "hdb.h" #include "chromInfo.h" #include "grp.h" #include "twoBit.h" #include "dbDb.h" #include "net.h" #include "bbiFile.h" #include "bPlusTree.h" #include "hgFind.h" #include "hubConnect.h" #include "trix.h" #include "vcf.h" #include "vcfUi.h" #include "htmshell.h" #include "bigBedFind.h" #include "customComposite.h" #include "interactUi.h" #include "bedTabix.h" #include "hic.h" #include "hui.h" #include "chromAlias.h" +#include "asmAlias.h" #ifdef USE_HAL #include "halBlockViz.h" #endif static struct hash *hubCladeHash; // mapping of clade name to hub pointer static struct hash *hubAssemblyHash; // mapping of assembly name to genome struct static struct hash *hubAssemblyUndecoratedHash; // mapping of undecorated assembly name to genome struct static struct hash *hubOrgHash; // mapping from organism name to hub pointer static struct trackHub *globalAssemblyHubList; // list of trackHubs in the user's cart static struct hash *trackHubHash; char *trackHubRelativeUrl(char *hubUrl, char *path) /* Return full path (in URL form if it's a remote hub) given * path possibly relative to hubUrl. Do a freeMem of result * when done. */ { /* If path itself is a URL then just return a copy of it. */ if (hasProtocol(path)) return cloneString(path); /* If it's a remote hub, let html path expander handle it. */ if (hasProtocol(hubUrl)) return expandUrlOnBase(hubUrl, path); /* If we got to here hub is local, and so is path. Do standard * path parsing. */ return pathRelativeToFile(hubUrl, path); } static void badGenomeStanza(struct lineFile *lf) /* Put up semi-informative error message about a genome stanza being bad. */ { errAbort("Genome stanza should have at least two lines, one with 'genome' and one with 'trackDb'\n" "Bad stanza format ending line %d of %s", lf->lineIx, lf->fileName); } char *trackHubCladeToGenome(char *clade) /* Given a track hub clade(hub name) return the default genome. */ { if (hubCladeHash == NULL) return FALSE; struct hashEl *hel = hashLookup(hubCladeHash, clade); if (hel == NULL) return FALSE; struct trackHub *trackHub = hel->val; struct trackHubGenome *hubGenome = trackHub->genomeList; for(; hubGenome; hubGenome=hubGenome->next) if (hubGenome->twoBitPath != NULL) return hubGenome->organism ; return NULL; } struct trackHubGenome *trackHubGetGenomeUndecorated(char *database) /* Get the genome structure for an undecorated genome name. */ { if (hubAssemblyUndecoratedHash == NULL) return NULL; struct hashEl *hel = hashLookup(hubAssemblyUndecoratedHash, database); if (hel == NULL) return NULL; return (struct trackHubGenome *)hel->val; } struct trackHubGenome *trackHubGetGenome(char *database) /* get genome structure for an assembly in a trackHub */ { if (hubAssemblyHash == NULL) errAbort("requesting hub genome with no hubs loaded"); struct hashEl *hel = hashLookup(hubAssemblyHash, database); if (hel == NULL) return NULL; return (struct trackHubGenome *)hel->val; } boolean trackHubDatabase(char *database) /* Is this an assembly from an Assembly Data hub? */ { if (hubAssemblyHash == NULL) return FALSE; return trackHubGetGenome(database) != NULL; } char *trackHubDatabaseToGenome(char *db) /* get a database name that is either a genome database or a trackHub * database, return the genome assembly */ { return trackHubDatabase(db) ? trackHubAssemblyField(db, "genome") : db; } char *trackHubAssemblyField(char *database, char *field) /* Get data field from a assembly data hub. */ { struct trackHubGenome *genome = trackHubGetGenome(database); if (genome == NULL) return NULL; char *ret = hashFindVal(genome->settingsHash, field); return cloneString(ret); } static struct dbDb *makeDbDbFromAssemblyGenome(struct trackHubGenome *hubGenome) /* Make a dbdb struture from a single assembly hub database. */ { struct dbDb *db; AllocVar(db); db->genome = cloneString(hubGenome->organism); db->organism = cloneString(hubGenome->organism); db->name = cloneString(hubGenome->name); db->active = TRUE; if (hubGenome->description != NULL) db->description = cloneString(hubGenome->description); else db->description = cloneString(""); char *orderKey = hashFindVal(hubGenome->settingsHash, "orderKey"); if (orderKey != NULL) db->orderKey = sqlUnsigned(orderKey); db->defaultPos = cloneString(hubGenome->defaultPos); return db; } struct dbDb *trackHubDbDbFromAssemblyDb(char *database) /* Return a dbDb structure for just this database. */ { struct trackHubGenome *genome = trackHubGetGenome(database); if (genome == NULL) return NULL; return makeDbDbFromAssemblyGenome(genome); } struct slPair *trackHubGetCladeLabels() /* Get a list of labels describing the loaded assembly data hubs. */ { if (globalAssemblyHubList == NULL) return NULL; struct slPair *clade, *cladeList = NULL; struct trackHub *trackHub = globalAssemblyHubList; for(;trackHub; trackHub = trackHub->next) { AllocVar(clade); slAddHead(&cladeList, clade); clade->name = cloneString(trackHub->name); clade->val = cloneString(trackHub->shortLabel); } return cladeList; } struct dbDb *trackHubGetPcrServers() /* Look through attached trackHubs to see which of them have "isPcr" line in them. */ { struct dbDb *db, *dbList = NULL; if (globalAssemblyHubList != NULL) { struct trackHub *trackHub = globalAssemblyHubList; for(;trackHub; trackHub = trackHub->next) { struct trackHubGenome *hubGenome = trackHub->genomeList; for(; hubGenome; hubGenome = hubGenome->next) { if (hashFindVal(hubGenome->settingsHash,"isPcr") != NULL) { db = makeDbDbFromAssemblyGenome(hubGenome); slAddHead(&dbList, db); } } } } slReverse(&dbList); slSort(&dbList, hDbDbCmpOrderKey); return dbList; } static struct dbDb *getDbDbs(char *clade, boolean blatEnabled) /* Get a list of struct dbDbs from track hubs. Only get blat enabled ones if asked */ { struct dbDb *db, *dbList = NULL; if (globalAssemblyHubList != NULL) { struct trackHub *trackHub = globalAssemblyHubList; for(;trackHub; trackHub = trackHub->next) { if ((clade != NULL) && differentString(clade, trackHub->name)) continue; struct trackHubGenome *hubGenome = trackHub->genomeList; for(; hubGenome; hubGenome = hubGenome->next) { boolean blatCheck = !blatEnabled || ((hashFindVal(hubGenome->settingsHash,"transBlat") != NULL) || (hashFindVal(hubGenome->settingsHash,"blat") != NULL)); if ( blatCheck && (hubGenome->twoBitPath != NULL)) { db = makeDbDbFromAssemblyGenome(hubGenome); slAddHead(&dbList, db); } } } } slReverse(&dbList); slSort(&dbList, hDbDbCmpOrderKey); return dbList; } struct dbDb *trackHubGetBlatDbDbs() /* Get a list of connected track hubs that have blat servers */ { return getDbDbs(NULL, TRUE); } struct dbDb *trackHubGetDbDbs(char *clade) /* Get a list of dbDb structures for all the tracks in this clade/hub. */ { return getDbDbs(clade, FALSE); } struct slPair *trackHubDbDbToValueLabel(struct dbDb *hubDbDbList) /* Given a trackHub (list of) track hub dbDb which may be missing some info, * return an slPair of value and label suitable for making a select/menu option. */ { struct dbDb *dbDb; struct slPair *pairList = NULL; for (dbDb = hubDbDbList; dbDb != NULL; dbDb = dbDb->next) { char *db = dbDb->name; if (isEmpty(db)) db = dbDb->genome; char *label = dbDb->description; if (isEmpty(label)) label = trackHubSkipHubName(db); slAddHead(&pairList, slPairNew(db, cloneString(label))); } slReverse(&pairList); return pairList; } struct slName *trackHubAllChromNames(char *database) /* Return a list of all the chrom names in this assembly hub database. */ /* Free with slFreeList. */ { struct trackHubGenome *genome = trackHubGetGenome(database); if (genome == NULL) return NULL; struct slName *chromList = twoBitSeqNames(genome->twoBitPath); return chromList; } int trackHubChromCount(char *database) /* Return number of chromosomes in a assembly data hub. */ { struct slName *chromList = trackHubAllChromNames(database); int num = slCount(chromList); slFreeList(&chromList); return num; } char *trackHubDefaultChrom(char *database) /* Return the default chromosome for this track hub assembly. */ { struct slName *chromList = trackHubAllChromNames(database); if (chromList == NULL) return NULL; char *defaultName = cloneString( chromList->name); slFreeList(&chromList); return defaultName; } static struct twoBitFile *openTwoBit(struct trackHubGenome *genome) /* Open a twoBit file that may or may not have a bpt index. */ { if (genome->twoBitBptUrl) return twoBitOpenExternalBptIndex(genome->twoBitPath, genome->twoBitBptUrl); else return twoBitOpen(genome->twoBitPath); } struct chromInfo *trackHubMaybeChromInfo(char *database, char *chrom) /* Return a chromInfo structure for just this chrom in this database. * Return NULL if chrom doesn't exist. */ { struct trackHubGenome *genome = trackHubGetGenome(database); if (genome == NULL) return NULL; if (genome->tbf == NULL) genome->tbf = openTwoBit(genome); if (!twoBitIsSequence(genome->tbf, chrom)) return NULL; struct chromInfo *ci; AllocVar(ci); ci->chrom = cloneString(chrom); ci->fileName = genome->twoBitPath; ci->size = twoBitSeqSize(genome->tbf, chrom); return ci; } struct chromInfo *trackHubChromInfo(char *database, char *chrom) /* Return a chromInfo structure for just this chrom in this database. * errAbort if chrom doesn't exist. */ { struct chromInfo *ci = trackHubMaybeChromInfo(database, chrom); if (ci == NULL) errAbort("%s is not in %s", chrom, database); return ci; } static char *assemblyHubGenomeSetting(char *database, char *tagName) /* see if this assembly hub has specified tagName, return url if present * returns NULL when not present */ { struct trackHubGenome *genome = trackHubGetGenome(database); if (genome == NULL) return NULL; char *fileName = hashFindVal(genome->settingsHash, tagName); char *absFileName = NULL; if (fileName) absFileName = trackHubRelativeUrl((genome->trackHub)->url, fileName); if (absFileName) { hashReplace(genome->settingsHash, tagName, absFileName); fileName = absFileName; } return fileName; } char *trackHubChromSizes(char *database) /* see if this assembly hub has a chrom.sizes file, return url if present * returns NULL when not present */ { return assemblyHubGenomeSetting(database, "chromSizes"); } char *trackHubAliasBbFile(char *database) /* see if this assembly hub has an alias bigBed file, return url if present * returns NULL when not present */ { return assemblyHubGenomeSetting(database, "chromAliasBb"); } char *trackHubAliasFile(char *database) /* see if this assembly hub has an alias file, return url if present * returns NULL when not present */ { return assemblyHubGenomeSetting(database, "chromAlias"); } struct chromInfo *trackHubAllChromInfo(char *database) /* Return a chromInfo structure for all the chroms in this database. */ { struct trackHubGenome *genome = trackHubGetGenome(database); if (genome == NULL) return NULL; if (genome->tbf == NULL) genome->tbf = openTwoBit(genome); struct chromInfo *ci, *ciList = NULL; struct slName *chromList = twoBitSeqNames(genome->twoBitPath); for(; chromList; chromList = chromList->next) { AllocVar(ci); ci->chrom = cloneString(chromList->name); ci->fileName = cloneString(genome->twoBitPath); ci->size = twoBitSeqSize(genome->tbf, chromList->name); slAddHead(&ciList, ci); } slFreeList(&chromList); return ciList; } static char *getRequiredGrpSetting(struct hash *hash, char *name, struct lineFile *lf) /* Grab a group setting out of the group hash. errAbort if not found. */ { char *str; if ((str = hashFindVal(hash, name)) == NULL) errAbort("missing required setting '%s' for group on line %d in file %s\n", name, lf->lineIx, lf->fileName); return str; } static struct grp *readGroupRa(char *groupFileName) /* Read in the ra file that describes the groups in an assembly hub. */ { if (groupFileName == NULL) return NULL; struct hash *ra; struct grp *list = NULL; struct lineFile *lf = udcWrapShortLineFile(groupFileName, NULL, MAX_HUB_GROUP_FILE_SIZE); while ((ra = raNextRecord(lf)) != NULL) { struct grp *grp; AllocVar(grp); slAddHead(&list, grp); grp->name = cloneString(getRequiredGrpSetting(ra, "name", lf)); grp->label = cloneString(getRequiredGrpSetting(ra, "label", lf)); grp->priority = atof(getRequiredGrpSetting(ra, "priority", lf)); grp->defaultIsClosed = sqlUnsigned(getRequiredGrpSetting(ra,"defaultIsClosed",lf)); hashFree(&ra); } if (list) slReverse(&list); lineFileClose(&lf); return list; } struct grp *trackHubLoadGroups(char *database) /* Load the grp structures for this track hub database. */ { struct trackHubGenome *genome = trackHubGetGenome(database); if (genome == NULL) return NULL; struct grp *list = readGroupRa(genome->groups); return list; } char *trackHubGenomeNameToDb(char *genome) /* Return assembly name given a genome name if one exists, otherwise NULL. */ { struct hashEl *hel; if ((hubOrgHash != NULL) && (hel = hashLookup(hubOrgHash, genome)) != NULL) { struct trackHub *hub = hel->val; struct trackHubGenome *genomeList = hub->genomeList; for(; genomeList; genomeList=genomeList->next) if ((genomeList->organism != NULL ) && sameString(genomeList->organism, genome)) return genomeList->name; } return NULL; } char *trackHubAssemblyClade(char *genome) /* Return the clade/hub_name that contains this genome. */ { struct hashEl *hel; if ((hubOrgHash != NULL) && (hel = hashLookup(hubOrgHash, genome)) != NULL) { struct trackHub *hub = hel->val; return cloneString(hub->name); } return NULL; } static void deleteAssembly(char *name, struct trackHubGenome *genome, struct trackHub *hub) /* delete this assembly from the assembly caches */ { hashRemove(hubCladeHash, hub->name); slRemoveEl(&globalAssemblyHubList, hub); hashRemove(hubOrgHash, genome->organism); hashRemove(hubAssemblyHash, genome->name); } static void addAssembly(char *name, struct trackHubGenome *genome, struct trackHub *hub) /* Add a new assembly hub database to our global list. */ { struct hashEl *hel; if (hubCladeHash == NULL) hubCladeHash = newHash(5); if ((hel = hashLookup(hubCladeHash, hub->name)) == NULL) { hashAdd(hubCladeHash, hub->name, hub); slAddHead(&globalAssemblyHubList, hub); } if (hubOrgHash == NULL) hubOrgHash = newHash(5); if ((hel = hashLookup(hubOrgHash, genome->organism)) == NULL) { hashAdd(hubOrgHash, genome->organism, hub); } if (hubAssemblyHash == NULL) hubAssemblyHash = newHash(5); if ((hel = hashLookup(hubAssemblyHash, genome->name)) == NULL) hashAdd(hubAssemblyHash, genome->name, genome); if (hubAssemblyUndecoratedHash == NULL) hubAssemblyUndecoratedHash = newHash(5); if ((hel = hashLookup(hubAssemblyUndecoratedHash, trackHubSkipHubName(genome->name))) == NULL) hashAdd(hubAssemblyUndecoratedHash, trackHubSkipHubName(genome->name), genome); } static char *addHubName(char *base, char *hubName) { if (base == NULL) return NULL; char buffer[4096]; if (isNotEmpty(hubName)) safef(buffer, sizeof(buffer), "%s_%s", hubName, base); else safef(buffer, sizeof(buffer), "%s", base); return cloneString(buffer); } static int genomeOrderKeyCmp(const void *va, const void *vb) /* Compare to sort based on order key */ { const struct trackHubGenome *a = *((struct trackHubGenome **)va); const struct trackHubGenome *b = *((struct trackHubGenome **)vb); if (b->orderKey > a->orderKey) return -1; else if (b->orderKey < a->orderKey) return 1; else return 0; } static struct trackHubGenome *trackHubGenomeReadRa(char *url, struct trackHub *hub, char *singleFile) /* Read in a genome.ra format url and return it as a list of trackHubGenomes. * Also add it to hash, which is keyed by genome. */ { struct lineFile *lf = udcWrapShortLineFile(url, NULL, MAX_HUB_GENOME_FILE_SIZE); struct trackHubGenome *list = NULL, *el; struct hash *hash = hub->genomeHash; struct hash *ra; while ((ra = raNextRecord(lf)) != NULL) { // allow that trackDb+hub+genome is in one single file if (hashFindVal(ra, "hub")) continue; if (hashFindVal(ra, "track")) break; char *twoBitPath = hashFindVal(ra, "twoBitPath"); char *twoBitBptUrl = hashFindVal(ra, "twoBitBptUrl"); char *genome, *trackDb; if (twoBitPath != NULL) genome = addHubName(hashFindVal(ra, "genome"), hub->name); else + { genome = hashFindVal(ra, "genome"); + char *alias = asmAliasFind(genome); + if (!hDbExists(alias)) + errAbort("Error: non UCSC genome '%s' is defined without an associated twoBitPath. Please check the genomes.txt file stanzas", genome); + } + if (hasWhiteSpace(genome)) + errAbort("Bad genome name: \"%s\". Only alpha-numeric characters and \"_\" are allowed ([A-Za-z0-9_]).", genome); if (hub->defaultDb == NULL) hub->defaultDb = genome; if (genome == NULL) badGenomeStanza(lf); if (hashLookup(hash, genome) != NULL) errAbort("Duplicate genome %s in stanza ending line %d of %s", genome, lf->lineIx, lf->fileName); if (singleFile == NULL) { trackDb = hashFindVal(ra, "trackDb"); if (trackDb == NULL) badGenomeStanza(lf); } else trackDb = singleFile; AllocVar(el); el->name = cloneString(genome); el->trackDbFile = trackHubRelativeUrl(url, trackDb); el->trackHub = hub; hashAdd(hash, el->name, el); hashAdd(hash, hubConnectSkipHubPrefix(el->name), el); slAddHead(&list, el); char *orderKey = hashFindVal(ra, "orderKey"); if (orderKey != NULL) el->orderKey = sqlUnsigned(orderKey); char *groups = hashFindVal(ra, "groups"); if (twoBitPath != NULL) { el->description = hashFindVal(ra, "description"); char *organism = hashFindVal(ra, "organism"); if (organism == NULL) errAbort("must have 'organism' set in assembly hub in stanza ending line %d of %s", lf->lineIx, lf->fileName); el->organism = addHubName(organism, hub->name); hashReplace(ra, "organism", el->organism); el->defaultPos = hashFindVal(ra, "defaultPos"); if (el->defaultPos == NULL) errAbort("must have 'defaultPos' set in assembly hub in stanza ending line %d of %s", lf->lineIx, lf->fileName); el->twoBitPath = trackHubRelativeUrl(url, twoBitPath); if (twoBitBptUrl != NULL) el->twoBitBptUrl = trackHubRelativeUrl(url, twoBitBptUrl); char *htmlPath = hashFindVal(ra, "htmlPath"); if (htmlPath != NULL) hashReplace(ra, "htmlPath",trackHubRelativeUrl(url, htmlPath)); if (groups != NULL) el->groups = trackHubRelativeUrl(url, groups); addAssembly(genome, el, hub); } el->settingsHash = ra; hashAdd(ra, "hubName", hub->shortLabel); el->chromAuthority = hashFindVal(ra, "chromAuthority"); } /* Clean up and go home. */ lineFileClose(&lf); slReverse(&list); slSort(&list, genomeOrderKeyCmp); return list; } char *trackHubSetting(struct trackHub *hub, char *name) /* Return setting if it exists, otherwise NULL. */ { return hashFindVal(hub->settings, name); } char *trackHubRequiredSetting(struct trackHub *hub, char *name) /* Return named setting. Abort with error message if not found. */ { char *val = trackHubSetting(hub, name); if (val == NULL) errAbort("Missing required setting '%s' from %s", name, hub->url); return val; } static struct trackHub *grabHashedHub(char *hubName) /* see if a trackHub with this name is in the cache */ { if ( trackHubHash == NULL) trackHubHash = newHash(5); return (struct trackHub *)hashFindVal(trackHubHash, hubName); } static void cacheHub(struct trackHub *hub) { /* put this trackHub in the trackHub hash */ if ( trackHubHash == NULL) trackHubHash = newHash(5); hashAdd(trackHubHash, hub->name, hub); } void uncacheHub(struct trackHub *hub) /* take this trackHub out of the trackHub hash */ { if ( trackHubHash == NULL) return; hashMustRemove(trackHubHash, hub->name); } struct trackHub *trackHubOpen(char *url, char *hubName) /* Open up a track hub from url. Reads and parses hub.txt and the genomesFile. * The hubName is generally just the asciified ID number. */ { struct trackHub *hub = grabHashedHub(hubName); if (hub != NULL) return hub; struct lineFile *lf = udcWrapShortLineFile(url, NULL, MAX_HUB_TRACKDB_FILE_SIZE); struct hash *hubRa = raNextRecord(lf); if (hubRa == NULL) errAbort("empty %s in trackHubOpen", url); // no errAbort when more records in hub.txt file: user can stuff // trackDb into it /* Allocate hub and fill in settings field and url. */ AllocVar(hub); hub->url = cloneString(url); hub->name = cloneString(hubName); hub->settings = hubRa; /* Fill in required fields from settings. */ trackHubRequiredSetting(hub, "hub"); trackHubRequiredSetting(hub, "email"); hub->shortLabel = trackHubRequiredSetting(hub, "shortLabel"); hub->longLabel = trackHubRequiredSetting(hub, "longLabel"); boolean isOneFile = (trackHubSetting(hub, "useOneFile") != NULL); char *ourFile = NULL; if (isOneFile) { ourFile = url; char *root = strrchr(url, '/'); if (root) ourFile = root + 1; hub->genomesFile = cloneString(ourFile); } else hub->genomesFile = trackHubRequiredSetting(hub, "genomesFile"); hub->email = trackHubSetting(hub, "email"); hub->version = trackHubSetting(hub, "version"); // default to current version hub->level = trackHubSetting(hub, "level"); // "core" or "all" char *descriptionUrl = trackHubSetting(hub, "descriptionUrl"); if (descriptionUrl != NULL) hub->descriptionUrl = trackHubRelativeUrl(hub->url, descriptionUrl); lineFileClose(&lf); char *genomesUrl = trackHubRelativeUrl(hub->url, hub->genomesFile); hub->genomeHash = hashNew(8); hub->genomeList = trackHubGenomeReadRa(genomesUrl, hub, ourFile); freez(&genomesUrl); cacheHub(hub); return hub; } void trackHubClose(struct trackHub **pHub) /* Close up and free resources from hub. */ { struct trackHub *hub = *pHub; if (hub != NULL) { trackHubGenomeFreeList(hub); freeMem(hub->url); hashFree(&hub->settings); hashFree(&hub->genomeHash); uncacheHub(hub); freez(pHub); } } void trackHubGenomeFree(struct trackHubGenome **pGenome) /* Free up genome info. */ { struct trackHubGenome *genome = *pGenome; if (genome != NULL) { freeMem(genome->name); freeMem(genome->trackDbFile); freez(pGenome); } } void trackHubGenomeFreeList(struct trackHub *hub) /* Free a list of dynamically allocated trackHubGenome's */ { struct trackHubGenome *el, *next; for (el = hub->genomeList; el != NULL; el = next) { next = el->next; if (el->twoBitPath != NULL) deleteAssembly(el->name, el, hub); trackHubGenomeFree(&el); } hub->genomeList = NULL; } static char *requiredSetting(struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb, char *setting) /* Fetch setting or give an error message, a little more specific than the * error message from trackDbRequiredSetting(). */ { char *val = trackDbSetting(tdb, setting); if (val == NULL) errAbort("Missing required '%s' setting in hub %s genome %s track %s", setting, hub->url, genome->name, tdb->track); return val; } static void forbidSetting(struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb, char *setting) /* Abort if forbidden setting found. */ { if (trackDbSetting(tdb, setting)) errAbort("Forbidden setting '%s' in hub %s genome %s track %s", setting, hub->url, genome->name, tdb->track); } static void expandOneUrl(struct hash *settingsHash, char *hubUrl, char *variable) { struct hashEl *hel = hashLookup(settingsHash, variable); if (hel != NULL) { char *oldVal = hel->val; hel->val = trackHubRelativeUrl(hubUrl, oldVal); freeMem(oldVal); } } static void expandBigDataUrl(struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb) /* Expand bigDataUrls so that no longer relative to genome->trackDbFile */ { struct hashEl *hel; struct hashCookie cookie = hashFirst(tdb->settingsHash); while ((hel = hashNext(&cookie)) != NULL) { char *name = hel->name; if (trackSettingIsFile(name)) expandOneUrl(tdb->settingsHash, genome->trackDbFile, name); } } struct trackHubGenome *trackHubFindGenome(struct trackHub *hub, char *genomeName) /* Return trackHubGenome of given name associated with hub. Return NULL if no * such genome. Check genomeName without hub prefix to see if this hub * is attached to an assembly hub.*/ { struct trackHubGenome *ret = hashFindVal(hub->genomeHash, genomeName); if (ret == NULL) ret = hashFindVal(hub->genomeHash, hubConnectSkipHubPrefix(genomeName)); return ret; } static void requireBarChartBars(struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb) /* Fetch setting(s) or give an error message */ { if (!trackDbSetting(tdb, BAR_CHART_CATEGORY_URL) && !trackDbSetting(tdb, BAR_CHART_CATEGORY_LABELS)) errAbort("BarChart track '%s' is missing either %s or %s setting. Please add one of those settings to the appropriate stanza", tdb->track, BAR_CHART_CATEGORY_LABELS, BAR_CHART_CATEGORY_URL); } static void validateOneTrack( struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb) /* Validate a track's trackDb entry. */ { /* Check for existence of fields required in all tracks */ requiredSetting(hub, genome, tdb, "shortLabel"); char *shortLabel = trackDbSetting(tdb, "shortLabel"); memSwapChar(shortLabel, strlen(shortLabel), '\t', ' '); requiredSetting(hub, genome, tdb, "longLabel"); char *longLabel = trackDbSetting(tdb, "longLabel"); memSwapChar(longLabel, strlen(longLabel), '\t', ' '); /* Forbid any dangerous settings that should not be allowed */ forbidSetting(hub, genome, tdb, "idInUrlSql"); // subtracks is not NULL if a track said we were its parent if (tdb->subtracks != NULL) { boolean isSuper = FALSE; char *superTrack = trackDbSetting(tdb, "superTrack"); if ((superTrack != NULL) && startsWith("on", superTrack)) isSuper = TRUE; if (!(trackDbSetting(tdb, "compositeTrack") || trackDbSetting(tdb, "container") || isSuper)) { errAbort("Parent track %s is not compositeTrack, container, or superTrack in hub %s genome %s", tdb->track, hub->url, genome->name); } } else { /* Check type field. */ char *type = requiredSetting(hub, genome, tdb, "type"); if (! isCustomComposite(tdb)) { if (startsWithWord("mathWig", type) ) { requiredSetting(hub, genome, tdb, "mathDataUrl"); } else { /* RMH: Added bigRmsk to support RepeatMasker data in bigBed track hub format */ if (!(startsWithWord("wig", type)|| startsWithWord("bedGraph", type))) { if (!(startsWithWord("bigWig", type) || startsWithWord("bigBed", type) || #ifdef USE_HAL startsWithWord("pslSnake", type) || startsWithWord("halSnake", type) || #endif startsWithWord("vcfTabix", type) || startsWithWord("vcfPhasedTrio", type) || startsWithWord("bigPsl", type) || startsWithWord("bigMaf", type) || startsWithWord("longTabix", type) || startsWithWord("bigGenePred", type) || startsWithWord("bigNarrowPeak", type) || startsWithWord("bigChain", type) || startsWithWord("bigLolly", type) || startsWithWord("bigRmsk", type) || startsWithWord("bigBarChart", type) || startsWithWord("bigInteract", type) || startsWithWord("hic", type) || startsWithWord("bigDbSnp", type) || startsWithWord("bam", type))) { errAbort("Unsupported type '%s' in hub %s genome %s track %s", type, hub->url, genome->name, tdb->track); } requiredSetting(hub, genome, tdb, "bigDataUrl"); } } if (sameString("barChart", type) || sameString("bigBarChart", type)) requireBarChartBars(hub, genome, tdb); if (sameString("vcfPhasedTrio", type)) requiredSetting(hub, genome, tdb, VCF_PHASED_CHILD_SAMPLE_SETTING); } } } static void markContainers( struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdbList) /* Mark containers that are parents, or have them. */ { struct hash *hash = hashNew(0); struct trackDb *tdb; // add all the track names to a hash for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { if (hashLookup(hash, tdb->track)) errAbort("Track %s appears more than once in genome %s. " "Track identifiers have to be unique. Please check your track hub files, " "especially the 'track' lines. " "The most likely reason for this error is that you duplicated a " "'track' identifier. Hub URL: %s", tdb->track, genome->name, hub->url); hashAdd(hash, tdb->track, tdb); } // go through and find the container tracks for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { char *parentLine = trackDbLocalSetting(tdb, "parent"); // maybe it's a child of a supertrack? if (parentLine == NULL) { parentLine = trackDbLocalSetting(tdb, "superTrack"); if ((parentLine != NULL) && startsWith("on", parentLine)) parentLine = NULL; } if (parentLine != NULL) { char *parentName = cloneFirstWord(parentLine); struct trackDb *parent = hashFindVal(hash, parentName); if (parent == NULL) errAbort("Parent %s of track %s doesn't exist in hub %s genome %s", parentName, tdb->track, hub->url, genome->name); // mark the parent as a container parent->subtracks = tdb; // ugh...do this so requiredSetting looks at parent // in the case of views. We clear this after // validating anyway tdb->parent = parent; freeMem(parentName); } } hashFree(&hash); } static void validateTracks( struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdbList) /* Make sure a hub track list has the right settings and its parents exist. */ { // mark the containers by setting their subtracks pointer markContainers(hub, genome, tdbList); /* Loop through list checking tags */ struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { validateOneTrack(hub, genome, tdb); } errCatchEnd(errCatch); if (errCatch->gotError) { tdb->errMessage = cloneString(errCatch->message->string); } // clear these two pointers which we set in markContainers tdb->subtracks = NULL; tdb->parent = NULL; } } struct trackDb *trackHubTracksForGenome(struct trackHub *hub, struct trackHubGenome *genome, struct dyString *incFiles, boolean *foundFirstGenome) /* Get list of tracks associated with genome. Check that it only is composed of legal * types. Do a few other quick checks to catch errors early. If incFiles is not NULL, * put the list of included files in there. Only the first example of a genome * gets to populate groups, the others get a group for the trackHub. */ { struct lineFile *lf = udcWrapShortLineFile(genome->trackDbFile, NULL, MAX_HUB_TRACKDB_FILE_SIZE); struct trackDb *tdbList = trackDbFromOpenRa(lf, NULL, incFiles); lineFileClose(&lf); char *tabMetaName = hashFindVal(genome->settingsHash, "metaTab"); char *absTabName = NULL; if (tabMetaName) absTabName = trackHubRelativeUrl(hub->url, tabMetaName); char *tagStormName = hashFindVal(genome->settingsHash, "metaDb"); char *absStormName = NULL; if (tagStormName) absStormName = trackHubRelativeUrl(hub->url, tagStormName); /* Make bigDataUrls more absolute rather than relative to genome.ra dir */ struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { expandBigDataUrl(hub, genome, tdb); if (absStormName) hashReplace(tdb->settingsHash, "metaDb", absStormName); if (absTabName) hashReplace(tdb->settingsHash, "metaTab", absTabName); } validateTracks(hub, genome, tdbList); trackDbAddTableField(tdbList); if (!isEmpty(hub->name)) trackHubAddNamePrefix(hub->name, tdbList); if (genome->twoBitPath == NULL || *foundFirstGenome) trackHubAddGroupName(hub->name, tdbList); else *foundFirstGenome = TRUE; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { trackDbFieldsFromSettings(tdb); trackDbPolish(tdb); } return tdbList; } static void reprefixString(char **pString, char *prefix) /* Replace *pString with prefix + *pString, freeing * whatever was in *pString before. */ { char *oldName = *pString; *pString = catTwoStrings(prefix, oldName); freeMem(oldName); } static void addPrefixToSetting(struct hash *settings, char *key, char *prefix) /* Given a settings hash, which is string valued. Old values will be freed. */ { struct hashEl *hel = hashLookup(settings, key); if (hel != NULL) reprefixString((char **)&hel->val, prefix); } static void trackDbListAddNamePrefix(struct trackDb *tdbList, char *prefix) /* Surgically alter tdbList so that it works as if every track was * renamed so as to add a prefix to it's name. */ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { addPrefixToSetting(tdb->settingsHash, "track", prefix); addPrefixToSetting(tdb->settingsHash, "parent", prefix); reprefixString(&tdb->track, prefix); if (tdb->table != NULL) reprefixString(&tdb->table, prefix); } } void trackHubAddNamePrefix(char *hubName, struct trackDb *tdbList) /* For a hub named "hub_1" add the prefix "hub_1_" to each track and parent field. */ { char namePrefix[PATH_LEN]; safef(namePrefix, sizeof(namePrefix), "%s_", hubName); trackDbListAddNamePrefix(tdbList, namePrefix); } char *trackHubSkipHubName(char *name) /* Skip the hub_#_ prefix in a hub name. */ { if ((name == NULL) || !startsWith("hub_", name)) return name; return strchr(&name[4], '_') + 1; } void trackHubAddGroupName(char *hubName, struct trackDb *tdbList) /* Add group tag that references the hubs symbolic name. */ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { tdb->grp = cloneString(hubName); hashReplace(tdb->settingsHash, "group", tdb->grp); } } void trackHubAddOneDescription(char *trackDbFile, struct trackDb *tdb) /* Fetch tdb->track's html description and store in tdb->html. */ { /* html setting should always be set because we set it at load time */ char *htmlName = trackDbSetting(tdb, "html"); if (htmlName == NULL) return; char *simpleName = hubConnectSkipHubPrefix(htmlName); char *url = trackHubRelativeUrl(trackDbFile, simpleName); char buffer[10*1024]; char *fixedUrl = url; if (!endsWith(url, ".html")) { safef(buffer, sizeof buffer, "%s.html", url); fixedUrl = buffer; } tdb->html = udcFileReadAllIfExists(fixedUrl, NULL, 0, NULL); freez(&url); } void trackHubAddDescription(char *trackDbFile, struct trackDb *tdb) /* Fetch tdb->track's html description (or nearest ancestor's non-empty description) * and store in tdb->html. */ { trackHubAddOneDescription(trackDbFile, tdb); if (isEmpty(tdb->html)) { struct trackDb *parent; for (parent = tdb->parent; isEmpty(tdb->html) && parent != NULL; parent = parent->parent) { trackHubAddOneDescription(trackDbFile, parent); if (isNotEmpty(parent->html)) tdb->html = cloneString(parent->html); } } } void trackHubFixName(char *name) /* Change all characters other than alphanumeric, dash, and underbar * to underbar. */ { if (name == NULL) return; char *in = name; char c; for(; (c = *in) != 0; in++) { if (c == ' ') break; if (!(isalnum(c) || c == '-' || c == '_')) *in = '_'; } } static void polishOneTrack( struct trackHub *hub, struct trackDb *bt, struct hash *hash) /* Get rid of special characters in track name, squirrel away a copy * of the original name for html retrieval, make sure there aren't * two tracks with the same name. */ { char *polished = trackDbLocalSetting(bt, "polished"); if (polished != NULL) return; trackDbAddSetting(bt, "polished", "polished"); char *htmlName = trackDbSetting(bt, "html"); /* if the user didn't specify an html variable, set it to be the original * track name */ if (htmlName == NULL) trackDbAddSetting(bt, "html", bt->track); trackHubFixName(bt->track); if (hashLookup(hash, bt->track) != NULL) errAbort("more than one track called %s in hub %s\n", bt->track, hub->url); hashStore(hash, bt->track); } void trackHubPolishTrackNames(struct trackHub *hub, struct trackDb *tdbList) /* Remove all the special characters from trackHub track names. */ { struct trackDb *next, *tdb; struct hash *nameHash = hashNew(5); for (tdb = tdbList; tdb != NULL; tdb = next) { if (tdb->parent != NULL) polishOneTrack(hub, tdb->parent, nameHash); next = tdb->next; polishOneTrack(hub, tdb, nameHash); if (tdb->subtracks != NULL) { trackHubPolishTrackNames(hub, tdb->subtracks); } } } void trackHubFindPos(struct cart *cart, char *db, char *term, struct hgPositions *hgp, boolean measureTiming) /* Look for term in track hubs. Update hgp if found */ { findBigBedPosInTdbList(cart, db, hubCollectTracks(db, NULL), term, hgp, NULL, measureTiming); } static void parseBlatPcrParams(char *database, char *type, char *setting, char **pHost, char **pPort, char **pGenomeDataDir) /* parser parameters for either blat or pcr */ { char *conf = trimSpaces(cloneString(setting)); int numWords = chopByWhite(conf, NULL, 5); if ((numWords < 2) || (numWords > 4)) errAbort("invalid configuration for hub %s server, expect 2 or 4 arguments: %s", type, setting); char *words[4]; chopByWhite(conf, words, numWords); *pHost = words[0]; *pPort = words[1]; if (numWords > 2) { if (!sameString(words[2], "dynamic")) errAbort("invalid configuration for hub %s server, third argument should be 'dynamic' or omitted, got: %s", type, words[2]); *pGenomeDataDir = words[3]; } else *pGenomeDataDir = NULL; } boolean trackHubGetPcrParams(char *database, char **pHost, char **pPort, char **pGenomeDataDir) /* Get the isPcr params from a trackHub genome. */ { char *type = "isPcr"; char *setting = trackHubAssemblyField(database, type); parseBlatPcrParams(database, type, setting, pHost, pPort, pGenomeDataDir); return TRUE; } boolean trackHubGetBlatParams(char *database, boolean isTrans, char **pHost, char **pPort, char **pGenomeDataDir) { char *type = isTrans ? "transBlat" : "blat"; char *setting = trackHubAssemblyField(database, type); if (setting == NULL) return FALSE; parseBlatPcrParams(database, type, setting, pHost, pPort, pGenomeDataDir); return TRUE; } void hubCheckBigDataUrl(struct trackHub *hub, struct trackHubGenome *genome, struct trackDb *tdb) /* Check remote file exists and is of correct type. Wrap this in error catcher */ { char *relativeUrl = trackDbSetting(tdb, "bigDataUrl"); if (relativeUrl != NULL) { char *type = trackDbRequiredSetting(tdb, "type"); char *bigDataUrl = trackHubRelativeUrl(genome->trackDbFile, relativeUrl); char *bigDataIndex = NULL; char *relIdxUrl = trackDbSetting(tdb, "bigDataIndex"); if (relIdxUrl != NULL) bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl); verbose(2, "checking %s.%s type %s at %s\n", genome->name, tdb->track, type, bigDataUrl); if (startsWithWord("bigWig", type)) { /* Just open and close to verify file exists and is correct type. */ struct bbiFile *bbi = bigWigFileOpen(bigDataUrl); bbiFileClose(&bbi); } /* RMH: Added support for bigRmsk track hub data type */ else if (startsWithWord("bigNarrowPeak", type) || startsWithWord("bigBed", type) || startsWithWord("bigGenePred", type) || startsWithWord("bigPsl", type)|| startsWithWord("bigChain", type)|| startsWithWord("bigMaf", type) || startsWithWord("bigBarChart", type) || startsWithWord("bigInteract", type) || startsWithWord("bigLolly", type) || startsWithWord("bigRmsk",type)) { /* Just open and close to verify file exists and is correct type. */ struct bbiFile *bbi = bigBedFileOpen(bigDataUrl); char *typeString = cloneString(type); nextWord(&typeString); if (startsWithWord("bigBed", type) && (typeString != NULL)) { unsigned numFields = sqlUnsigned(nextWord(&typeString)); if (numFields > bbi->fieldCount) errAbort("fewer fields in bigBed (%d) than in type statement (%d) for track %s with bigDataUrl %s", bbi->fieldCount, numFields, trackHubSkipHubName(tdb->track), bigDataUrl); } bbiFileClose(&bbi); } else if (startsWithWord("vcfTabix", type) || startsWithWord("vcfPhasedTrio", type)) { /* Just open and close to verify file exists and is correct type. */ struct vcfFile *vcf = vcfTabixFileAndIndexMayOpen(bigDataUrl, bigDataIndex, NULL, 0, 0, 1, 1); if (vcf == NULL) // Warnings already indicated whether the tabix file is missing etc. errAbort("Couldn't open %s and/or its tabix index (.tbi) file. " "See http://genome.ucsc.edu/goldenPath/help/vcf.html", bigDataUrl); vcfFileFree(&vcf); } else if (startsWithWord("bam", type)) { bamFileAndIndexMustExist(bigDataUrl, bigDataIndex); } else if (startsWithWord("longTabix", type)) { struct bedTabixFile *btf = bedTabixFileMayOpen(bigDataUrl, NULL, 0, 0); if (btf == NULL) errAbort("Couldn't open %s and/or its tabix index (.tbi) file.", bigDataUrl); bedTabixFileClose(&btf); } #ifdef USE_HAL else if (startsWithWord("halSnake", type)) { char *errString; int handle = halOpenLOD(bigDataUrl, &errString); if (handle < 0) errAbort("HAL open error: %s", errString); if (halClose(handle, &errString) < 0) errAbort("HAL close error: %s", errString); } #endif else if (startsWithWord("hic", type)) { struct hicMeta *header; char *errString = hicLoadHeader(bigDataUrl, &header, genome->name); if (errString != NULL) errAbort("hic file error: %s", errString); } else errAbort("unrecognized type %s in genome %s track %s", type, genome->name, tdb->track); freez(&bigDataUrl); } }