3ada7f009d11ce5c390942bc207b40ec538c5279 kate Sun May 17 23:42:43 2015 -0700 Add checkSettings option to hubCheck instead of having setting check be default. This is to maintain current behavior for initial release. Also hide version options for now (they are in additional -help). refs #10015 diff --git src/hg/inc/trackHub.h src/hg/inc/trackHub.h index 646d324..a0ec3bb 100644 --- src/hg/inc/trackHub.h +++ src/hg/inc/trackHub.h @@ -1,216 +1,217 @@ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ /* 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 #include "dystring.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 *defaultDb; /* the default database */ char *name; /* Symbolic name of hub in cart, etc. From trackHubOpen hubName parameter. */ char *descriptionUrl; /* URL to description file */ char *email; /* email address of contact person */ char *version; /* version compliance of hub ("V1.0", etc.) */ char *level; /* support level of hub ("core", "full") */ }; 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 */ unsigned orderKey; /* the orderKey for changing the order from the order in the file */ }; struct trackHubCheckOptions /* How to check track hub */ { + boolean checkFiles; /* check remote files exist and are correct type */ + boolean checkSettings; /* check trackDb settings to spec */ char *version; /* hub spec version to check */ boolean strict; /* check hub is valid to 'core' level for version */ - boolean checkFiles; /* check remote files exist and are correct type */ char *extraFile; /* name of extra file/url with additional settings to accept */ /* intermediate data */ struct hash *settings; /* supported settings for this version */ struct hash *extra; /* additional trackDb settings to accept */ struct slName *suggest; /* list of supported settings for suggesting */ }; struct trackHubSetting /* Setting name and support level, from trackDbHub.html (the spec) */ { struct trackHubSetting *next; char *name; /* setting name */ char *level; /* support level (core, full, new, deprecated) */ }; struct trackHubSetting *trackHubSettingsForVersion(char *version); /* Return list of settings with support level */ char *trackHubVersionDefault(); /* Return current hub version */ 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 trackHub *hub); /* Free a list of dynamically allocated trackHubGenome's. */ int trackHubCheck(char *hubUrl, struct trackHubCheckOptions *options, struct dyString *errors); /* 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. */ struct trackHubGenome *trackHubGetGenome(char *database); /* get genome structure for an assembly in a trackHub */ boolean trackHubGetBlatParams(char *database, boolean isTrans, char **pHost, char **pPort); /* get "blat" and "transBlat" entries (if any) for an assembly hub */ struct dbDb *trackHubGetBlatDbDbs(); /* Get a list of connected track hubs that have blat servers */ #endif /* TRACKHUB_H */