aca9143822a9c12b16b33d479a5abb6495b6b4f0 braney Wed Aug 19 06:59:39 2026 -0700 lib, hgc, hgTables, hgHubConnect: share hubEncode, refs #38123 hgc.c and hgTables.c each had their own copy of hubEncode(). The two bodies were identical, so move the function to hubConnect.c next to isHubTrack() and let both CGIs call the one definition. Also use cgiEncode() rather than htmlEncode() for the db= value in the hgHubConnect assembly list. That value goes in a query string, so cgiEncode() is the right function there. Genome names are already limited to a safe character set, so this changes no output today. diff --git src/hg/inc/hubConnect.h src/hg/inc/hubConnect.h index 5b8ee7548ba..9b14a57489d 100644 --- src/hg/inc/hubConnect.h +++ src/hg/inc/hubConnect.h @@ -1,218 +1,223 @@ /* hubConnect - stuff to manage connections to track hubs. Most of this is mediated through * the hubStatus table in the hgcentral database. Here there are routines to translate between * hub symbolic names and hub URLs, to see if a hub is up or down or sideways (up but badly * formatted) etc. Note that there is no C structure corresponding to a row in the hubStatus * table by design. We just want field-by-field access to this. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HUBCONNECT_H #define HUBCONNECT_H #define hubCuratedPrefix "hub:" /* Prefix to hub path in dbDb.nibPath */ #define defaultHubPublicTableName "hubPublic" /* Name of our table with list of public hubs. read only */ #define hubPublicTableConfVariable "hub.publicTableName" /* the name of the hg.conf variable to use something other than the default */ #define defaultHubStatusTableName "hubStatus" /* Name of table that maintains status of hubs read/write. */ #define hubStatusTableConfVariable "hub.statusTableName" /* the name of the hg.conf variable to use something other than the default */ #define hgHubCheckUrl "hubCheckUrl" /* name of cgi variable containing hub name to check */ #define hgHubDataText "hubUrl" /* name of cgi variable containing new hub name */ #define hgHubGenome "genome" /* name of the cgi variable to specify a db within an assembly hub */ #define hgHubDataClearText "hubClear" /* name of cgi variable containing new hub name */ #define hubTrackPrefix "hub_" /* The names of all hub tracks begin with this. Use in cart. */ #define hgHubSearchTerms "hubSearchTerms" /* name of cart/cgi variable containing the current search terms */ #define hgHubDbFilter "hubDbFilter" /* name of cart/cgi variable containing text for filtering hubs by assembly */ #define hgHub "hgHub_" /* prefix for all control variables */ #define hgHubDo hgHub "do_" /* prefix for all commands */ #define hgHubDoClear hgHubDo "clear" #define hgHubDoRefresh hgHubDo "refresh" #define hgHubDoSearch hgHubDo "search" #define hgHubDoDeleteSearch hgHubDo "deleteSearch" #define hgHubDoFilter hgHubDo "filter" #define hgHubDoDisconnect hgHubDo "disconnect" #define hgHubDoFirstDb hgHubDo "firstDb" #define hgHubDoDecorateDb hgHubDo "decorateDb" #define hgHubDoRedirect hgHubDo "redirect" #define hgHubDoHubCheck hgHubDo "hubCheck" boolean isHubTrack(char *trackName); /* Return TRUE if it's a hub track. */ +struct trackDb; + +char *hubEncode(struct trackDb *tdb, char *text); +/* Return text escaped for HTML if it belongs to a track hub, otherwise return it unchanged. */ + struct hubConnectStatus /* Basic status in hubStatus. Note it is *not* the same as the * hubStatus table, that has a bunch of extra fields to help * keep track of whether the hub is alive. */ { struct hubConnectStatus *next; unsigned id; /* Hub ID */ char *hubUrl; /* URL to hub.ra file. */ char *shortLabel; /* shortLabel from hubStatus table. */ char *errorMessage; /* If non-empty hub has an error and this describes it. */ struct trackHub *trackHub; /* pointer to structure that describes hub */ unsigned status; /* 1 if private */ }; void hubConnectStatusFree(struct hubConnectStatus **pHub); /* Free hubConnectStatus */ void hubConnectStatusFreeList(struct hubConnectStatus **pList); /* Free a list of dynamically allocated hubConnectStatus's */ struct hubConnectStatus *hubConnectStatusForIdExt(struct sqlConnection *conn, int id, char *replaceDb, char *newDb, char *quickLiftChain); /* Given a hub ID return associated status. For quickLifted hubs, replace the db with our current db and * keep track of the quickLiftChain for updating trackDb later.*/ struct hubConnectStatus *hubConnectStatusForId( struct sqlConnection *conn, int id); /* Given a hub ID return associated status. */ struct hubConnectStatus *hubConnectStatusListFromCart(struct cart *cart, char *db); /* Return list of track hubs that are turned on by user in cart. If there are quickLifted hubs, make sure the toDb is db */ struct hubConnectStatus *hubConnectStatusListFromCartAll(struct cart *cart); /* Return list of all track hubs that are referenced by cart. */ #define hubConnectTrackHubsVarName "trackHubs" /* Name of cart variable with list of track hubs. */ #define hgHubConnectRemakeTrackHub "hgHubConnect.remakeTrackHub" /* Cart variable to indicate trackHub cart variable needs refreshing. */ #define hgHubConnectHubVarPrefix "hgHubConnect.hub." /* Prefix to temporary variable holding selected cart names. */ boolean hubConnectTableExists(); /* Return TRUE if the hubConnect table exists. */ struct slName *hubConnectHubsInCart(struct cart *cart); /* Return list of track hub ids that are turned on by user. */ int hubIdFromCartName(char *trackName); /* Given something like "hgHubConnect.hub.123" return 123 */ unsigned hubIdFromTrackName(char *trackName); /* Given something like "hub_123_myWig" return 123 */ char *hubNameFromGroupName(char *groupName); /* Given something like "hub_123_myWig" return hub_123 */ void hubConnectAddDescription(char *database, struct trackDb *tdb); /* Fetch tdb->track's html description (or nearest ancestor's non-empty description) * and store in tdb->html. */ struct trackDb *hubConnectAddHubForTrackAndFindTdb( char *database, char *trackName, struct trackDb **pTdbList, struct hash *trackHash); /* Go find hub for trackName (which will begin with hub_), and load the tracks * for it, appending to end of list and adding to trackHash. Return the * trackDb associated with trackName. */ char *hubFileVar(); /* return the name of the cart variable that holds the name of the * file in trash that has private hubs */ boolean hubWriteToFile(FILE *f, struct hubConnectStatus *el); /* write out a hubConnectStatus structure to a file */ unsigned hubFindOrAddUrlInStatusTable(struct cart *cart, char *url, char **errorMessage); /* find or add a URL to the status table */ unsigned hubResetError(char *url); /* clear the error for this url in the hubStatus table,return the id */ unsigned hubClearStatus(char *url); /* drop the information about this url from the hubStatus table,return the id */ void hubDisconnect(struct cart *cart, char *url); /* drop the information about this url from the hubStatus table, and * the cart variable the references this hub */ void hubUpdateStatus(char *errorMessage, struct hubConnectStatus *hub); /* set the error message in the hubStatus table */ boolean trackHubHasDatabase(struct trackHub *hub, char *database) ; /* Return TRUE if hub has contents for database */ struct trackDb *hubAddTracks(struct hubConnectStatus *hub, char *database, boolean *foundFirstGenome, struct hash *trackDbNameHash, struct grp **hubGroups); /* Load up stuff from data hub and append to list. The hubUrl points to * a trackDb.ra format file. Only the first example of a genome gets to * populate groups, the others get a group for the trackHub. A particular * trackDb is only read once even if referenced from more than one hub. */ char *hubConnectLoadHubs(struct cart *cart); /* load the track data hubs. Set a static global to remember them */ struct hubConnectStatus *hubConnectGetHubs(); /* return the static global to the track data hubs */ struct trackHub *hubConnectGetHub(char *hubUrl); /* Return the connected hub for hubUrl, or NULL if not found. Do not free result. */ struct trackHub *hubConnectGetHubForDb(char *db); /* Return the connected hub for db, or NULL if not found. Do not free result. */ struct trackDb *hubCollectTracks( char *database, struct grp **pGroupList); /* Generate trackDb structures for all the tracks in attached hubs. * Make grp structures for each hub. Returned group list is reversed. */ char *hubConnectSkipHubPrefix(char *trackName); /* Given something like "hub_123_myWig" return myWig. Don't free this, it's not allocated */ struct hubConnectStatus *hubFromId(unsigned hubId); /* Given a hub ID number, return corresponding trackHub structure. * ErrAbort if there's a problem. */ struct hubConnectStatus *hubFromIdNoAbort(unsigned hubId); /* Given a hub ID number, return corresponding trackHub structure. */ struct hubConnectStatus *hubConnectNewHub(); /* return the hub of the hubUrl we added (if any) */ char *hubPublicTableName(); /* Get the name of the table that lists public hubs. Don't free the result. */ char *hubNameFromUrl(char *hubUrl); /* Given the URL for a hub, return its hub_# name. */ void addPublicHubsToHubStatus(struct cart *cart, struct sqlConnection *conn, char *publicTable, char *statusTable); /* Add urls in the hubPublic table to the hubStatus table if they aren't there already */ struct hash *buildPublicLookupHash(struct sqlConnection *conn, char *publicTable, char *statusTable, struct hash **pHash); /* Return a hash linking hub URLs to struct hubEntries. Also make pHash point to a hash that just stores * the names of the public hubs (for use later when determining if hubs were added by the user) */ boolean hubConnectIsCurated(char *db); /* Look in the dbDb table to see if this hub is curated. */ boolean hubConnectGetCuratedUrl(char *db, char **hubUrl); /* Check to see if this db is a curated hub and if so return its hubUrl */ boolean hubsCanAddGroups(); /* can track hubs have their own groups? */ #endif /* HUBCONNECT_H */