2ba572dc8bbe18b3398dcf17205dafdd52ab396a braney Sat May 24 10:01:21 2014 -0700 updates to hgHubConnect to interface to make it less confusing. Nowconnection and disconnection put you on the gateway page. diff --git src/hg/inc/trackHub.h src/hg/inc/trackHub.h index 60d7121..1fa4ae3 100644 --- src/hg/inc/trackHub.h +++ src/hg/inc/trackHub.h @@ -1,170 +1,170 @@ /* trackHub - supports collections of tracks hosted on a remote site. * The basic layout of a data hub is: * hub.ra - contains information about the hub itself * genomes.ra - says which genomes are supported by hub * Contains file name of trackDb.ra for each genome * trackDb.ra - 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. */ #ifndef TRACKHUB_H #define TRACKHUB_H struct trackHub /* A track hub. */ { struct trackHub *next; char *url; /* URL of hub.ra file. */ struct trackHubGenome *genomeList; /* List of associated genomes. */ struct hash *genomeHash; /* Hash of genomeList keyed by genome name. */ struct hash *settings; /* Settings from hub.ra file. */ /* Required settings picked out for convenience. All allocated in settings hash */ char *shortLabel; /* Hub short label. Not allocated here. */ char *longLabel; /* Hub long label. Not allocated here. */ char *genomesFile; /* URL to genome.ra file. Not allocated here. */ char *name; /* Symbolic name of hub in cart, etc. From trackHubOpen hubName parameter. */ char *descriptionUrl; /* URL to description file */ }; struct trackHubGenome /* A genome serviced within a track hub. */ { struct trackHubGenome *next; char *name; /* Something like hg18 or mm9, a UCSC assembly database name. */ char *trackDbFile; /* The base trackDb.ra file. */ struct hash *settingsHash; /* Settings from hub.ra file. */ char *twoBitPath; /* URL to twoBit. If not null, this is an assmebly hub*/ struct twoBitFile *tbf; /* open handle to two bit file */ char *groups; /* URL to group.txt file */ char *defaultPos; /* default position */ char *organism; /* organism name, like Human */ char *description; /* description, also called freeze name */ struct trackHub *trackHub; /* associated track hub */ }; void trackHubClose(struct trackHub **pHub); /* Close up and free resources from hub. */ struct trackHub *trackHubOpen(char *url, char *hubName); /* Open up a track hub from url. Reads and parses hub.ra and the genomesFile. * The hubName is generally just the asciified ID number. */ struct trackHubGenome *trackHubFindGenome(struct trackHub *hub, char *genomeName); /* Return trackHubGenome of given name associated with hub. Return NULL if no * such genome. */ struct trackDb *trackHubTracksForGenome(struct trackHub *hub, struct trackHubGenome *genome); /* 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. */ void trackHubAddNamePrefix(char *hubName, struct trackDb *tdbList); /* For a hub named "xyz" add the prefix "hub_xyz_" to each track and parent field. * This is useful to the genome browser which directly puts tracks into it's * user settings name space.... */ void trackHubAddGroupName(char *hubName, struct trackDb *tdbList); /* Add group tag that references the hubs symbolic name. */ char *trackHubSetting(struct trackHub *hub, char *name); /* Return setting if it exists, otherwise NULL. */ char *trackHubRequiredSetting(struct trackHub *hub, char *name); /* Return named setting. Abort with error message if not found. */ 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. */ void trackHubGenomeFree(struct trackHubGenome **pGenome); /* Free up genome info. */ -void trackHubGenomeFreeList(struct trackHubGenome **pList); +void trackHubGenomeFreeList(struct trackHub *hub); /* Free a list of dynamically allocated trackHubGenome's. */ int trackHubCheck(char *hubUrl, struct dyString *errors, boolean checkTracks, FILE *searchFp); /* trackHubCheck - Check a track data hub for integrity. Put errors in dyString. * if checkTracks is TRUE, individual tracks are checked * if searchFp is non-null, then put search terms in there * return 0 if hub has no errors, 1 otherwise */ void trackHubPolishTrackNames(struct trackHub *hub, struct trackDb *tdbList); /* Remove all the special characters from trackHub track names. */ char *trackHubCladeToGenome(char *clade); /* Given a track hub clade(hub name) return the default genome. */ boolean trackHubDatabase(char *database); /* Is this an assembly from an Assembly Data hub? */ char *trackHubDefaultChrom(char *database); /* Return the default chromosome for this track hub assembly. */ char *trackHubAssemblyField(char *database, char *field); /* Get data field from a assembly data hub. */ int trackHubChromCount(char *database); /* Return number of chromosomes in a assembly data hub. */ struct slName *trackHubAllChromNames(char *database); /* Return a list of all the chrom names in this assembly hub database. */ struct chromInfo *trackHubAllChromInfo(char *database); /* Return a chromInfo structure for all the chroms in this database. */ 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 chromInfo *trackHubChromInfo(char *database, char *chrom); /* Return a chromInfo structure for just this chrom in this database. * errAbort if chrom doesn't exist. */ char *trackHubGenomeNameToDb(char *genome); /* Return assembly name given a genome name if one exists, otherwise NULL. */ struct dbDb *trackHubGetDbDbs(char *clade); /* Get a list of dbDb structures for all the tracks in this clade/hub. */ struct slPair *trackHubGetCladeLabels(); /* Get a list of labels describing the loaded assembly data hubs. */ char *trackHubAssemblyClade(char *genome); /* Return the clade/hub_name that contains this genome. */ void trackHubFixName(char *name); /* Change all characters other than alphanumeric, dash, and underbar * to underbar. */ struct grp *trackHubLoadGroups(char *database); /* Load the grp structures for this track hub database. */ char *trackHubSkipHubName(char *name); /* Skip the hub_#_ prefix in a hub name. */ struct dbDb *trackHubDbDbFromAssemblyDb(char *database); /* Return a dbDb structure for just this database. */ struct hgPositions; void trackHubFindPos(char *db, char *term, struct hgPositions *hgp); /* Look for term in track hubs. Update hgp if found */ 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. */ #endif /* TRACKHUB_H */