9358ec5d40af122594470fa05e1adc23e33f2cba
braney
  Mon Nov 14 14:17:26 2011 -0800
add an option to hubCheck to not check all the tracks, just check the trackDb.  Useful in crawling the hubs to pull the trackDb's into the udc cache where they can be parsed.  #5088
diff --git src/hg/inc/trackHub.h src/hg/inc/trackHub.h
index c06e7e8..2e70c22 100644
--- src/hg/inc/trackHub.h
+++ src/hg/inc/trackHub.h
@@ -1,93 +1,94 @@
 /* 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. */
     };
 
 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. */
     };
 
 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);
 /* Free a list of dynamically allocated trackHubGenome's */
 
-int trackHubCheck(char *hubUrl, struct dyString *errors);
+int trackHubCheck(char *hubUrl, struct dyString *errors, boolean checkTracks);
 /* trackHubCheck - Check a track data hub for integrity. Put errors in dyString.
+ *      if checkTracks is TRUE, individual tracks are checked
  *      return 0 if hub has no errors, 1 otherwise */
 
 
 #endif /* TRACKHUB_H */