d121edc0bd2809f1d6de6185a497e6a288958479
braney
  Tue May 12 09:18:29 2026 -0700
hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535

In hgConvert / trackHubBuild:
- Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination.
- Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file.

New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive).

hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings).

hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group.

hubConnect cart handling fixes shaken out by the above:
- hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL.
- hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/inc/quickLift.h src/hg/inc/quickLift.h
index 3968cc1fb30..4c992fa3081 100644
--- src/hg/inc/quickLift.h
+++ src/hg/inc/quickLift.h
@@ -1,93 +1,97 @@
 /* quickLift genome annotations on the fly between assemblies using chain files */
 
 /* Copyright (C) 2023 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef QUICKLIFT_H      
 #define QUICKLIFT_H      
 
 #define quickLiftCartName     "hubQuickLift"
 
 #define quickLiftChainTableConfVariable      "quickLiftChainName"
 #define defaultQuickLiftChainTableName       "quickLiftChain"
 
 struct quickLiftRegions
 // store highlight information
 {
 struct quickLiftRegions *next;
 unsigned type;
 char *chrom;
 long chromStart;
 long chromEnd;
 char *bases;
 unsigned baseCount;
 char *oChrom;
 long oChromStart;
 long oChromEnd;
 char *otherBases;
 unsigned otherBaseCount;
 char * id;
 };
 
 #define QUICKTYPE_INSERT     0
 #define QUICKTYPE_DEL      1
 #define QUICKTYPE_DOUBLE     2
 #define QUICKTYPE_MISMATCH     3
 
 extern char *quickTypeStrings[];
 
 typedef struct slList *(*ItemLoader2)(char **row, int numFields);
 /* Load a bed file from an SQL query result. */
 
 struct bigBedInterval *quickLiftGetIntervals(char *instaPortFile, struct bbiFile *bbi,   char *chrom, int start, int end, struct hash **pChainHash);
 /* Return intervals from "other" species that will map to the current window.
  * These intervals are NOT YET MAPPED to the current assembly.
  */
 
 struct bed *quickLiftIntervalsToBed(struct bbiFile *bbi, struct hash *chainHash, struct bigBedInterval *bb);
 /* Using chains stored in chainHash, port a bigBedInterval from another assembly to a bed
  * on the reference.
  */
 
 struct slList *quickLiftSql(struct sqlConnection *conn, char *quickLiftFile, char *table, char *chromName, int winStart, int winEnd,  char *query, char *extraWhere, ItemLoader2 loader, int numFields, struct hash *chainHash);
 /* Load a list of items (usually beds) from another database in a region that corresponds to chromName:winStart-winEnd in the reference database.
  * Fill a hash with the chains that were used to map the desired range.  These chains will be used to map the query side items back to the reference. */
 
 unsigned quickLiftGetChainId(struct cart *, char *fromDb, char *toDb);
 /* Return the id from the quickLiftChain table for given assemblies. */
 
 char *quickLiftGetChainPath(struct cart *, char *fromDb, char *toDb);
 /* Return the path from the quickLiftChain table for given assemblies. */
 
 struct bed *quickLiftBeds(struct bed *bedList, struct hash *chainHash, boolean blocked);
 // Map a list of bedd in query coordinates to our current reference
 
 boolean quickLiftEnabled(struct cart *cart);
 /* Return TRUE if feature is available */
 
 struct quickLiftRegions *quickLiftGetRegions(char *ourDb, char *liftDb, char *quickLiftFile, char *chrom, int seqStart, int seqEnd);
 /* Figure out the highlight regions and cache them. */
 
 char *quickLiftChainTable();
 /* Return the name of the quickLiftChain table. */
 
 void quickLiftResolveTable(struct trackDb *tdb, char *trackTable, char **retTable, char **retLiftDb);
 /* Resolve the table name and liftDb for a quickLift track.  For custom tracks,
  * sets *retLiftDb to CUSTOM_TRASH and *retTable to the dbTableName setting;
  * otherwise sets *retTable to trackTable. Caller should have already set
  * *retLiftDb to trackDbSetting(tdb, "quickLiftDb"). */
 
 struct bed *quickLiftSqlLoadBeds(struct trackDb *tdb, char *trackTable, char *liftDb,
     char *chrom, int start, int end, char *extraWhere,
     ItemLoader2 loader, int numFields, boolean blocked);
 /* Load items from another assembly via quickLift SQL, map them back to the reference,
  * and return the lifted beds.  Handles custom track table resolution internally.
  * Caller provides liftDb from trackDbSetting(tdb, "quickLiftDb"). */
 
 boolean quickLiftLiftPos(char *sourceDb, char *destDb,
     char *chrom, int start, int end,
     char **retChrom, int *retStart, int *retEnd);
 /* Map a position from source (sourceDb) coords to destination (destDb) coords
  * using the liftOver chain for sourceDb -> destDb.  Used to remap hgFind
  * results from quickLifted bigBed tracks back to the destination assembly. */
+
+boolean quickLiftHubRemoveTrack(struct cart *cart, char *sourceDb, char *trackName);
+/* Remove a track stanza from the quickLift hub file for sourceDb.  Returns
+ * TRUE if a stanza matching trackName was found and removed. */
 #endif