571aecdf42c832e61ee921e977589ca386467d13
max
  Fri Sep 4 12:24:17 2026 -0700
hubCheck: report a bigDataUrl that cannot be opened instead of dropping the track, refs #38260

hubCheckGenome() called trackDbPolishAfterLinkup(), whose pruneEmpties() step hands
each track to addTrackIfDataAccessible(), which frees any track whose data cannot be
reached. That is right for the browser, which should degrade gracefully rather than
draw a broken track, and wrong for hubCheck, whose main job is to say that the file
is unreachable. The track was gone before the file check ran, so hubCheck printed
nothing and exited 0:

cd hubCheck/tests/input
sed 's|test6field.bb|noSuchFile.bb|' fieldCountMismatch.txt > tmp.txt
hubCheck tmp.txt      # only the descriptionUrl warning, missing file not mentioned

Split the non-pruning part of trackDbPolishAfterLinkup() into
trackDbPolishAfterLinkupKeepAll() and call that from hubCheck. Every other caller
still goes through trackDbPolishAfterLinkup() and still prunes, so browser behaviour
is unchanged.

Added a tests/ case whose bigDataUrl does not exist. Before this change it produced
no output and exit 0; now it reports "Couldn't open input/relPath/data/noSuchFile.bb".

Of the existing tests, only badType changes, and it gains a real error that the prune
had been hiding: 'unrecognized type "wig" for track "invalidType"'. badType was
already failing before this commit and still is, for an unrelated reason: seven tests
carry expected output with per-track "missing description page" warnings that no
longer appear, because those hubs point at remote URLs that no longer resolve and
hubCheckTrack aborts at the file check before reaching the description check. That is
stale test data, not addressed here.

diff --git src/hg/utils/hubCheck/hubCheck.c src/hg/utils/hubCheck/hubCheck.c
index 2ec999e3bd1..2729c1e6df1 100644
--- src/hg/utils/hubCheck/hubCheck.c
+++ src/hg/utils/hubCheck/hubCheck.c
@@ -1237,31 +1237,34 @@
         // groups and htmlPath are optional settings, again only warn if they are malformed
         char *groupsFile = genome->groups;
         if (groupsFile != NULL && !extFileExists(groupsFile))
             warn("warning: '%s' groups file does not exist or is not accessible: '%s'", genome->name, groupsFile);
 
         char *htmlPath = hashFindVal(genome->settingsHash, "htmlPath");
         if (htmlPath == NULL)
             warn("warning: missing htmlPath setting for assembly hub '%s'", genome->name);
         else if (!extFileExists(htmlPath))
             warn("warning: '%s' htmlPath file does not exist or is not accessible: '%s'", genome->name, htmlPath);
 
         }
     boolean foundFirstGenome = FALSE;
     tdbList = trackHubTracksForGenome(hub, genome, NULL, &foundFirstGenome);
     tdbList = trackDbLinkUpGenerations(tdbList);
-    tdbList = trackDbPolishAfterLinkup(tdbList, genome->name);
+    /* Deliberately not trackDbPolishAfterLinkup(): its prune step silently drops any
+     * track whose data file cannot be opened, which is the single most important thing
+     * for hubCheck to complain about. */
+    tdbList = trackDbPolishAfterLinkupKeepAll(tdbList);
     checkTrackNamesForDots(tdbList);
     trackHubPolishTrackNames(hub, tdbList);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError || errCatch->gotWarning)
     {
     openedGenome = TRUE;
     genomeErr(errors, errCatch->message->string, hub, genome, options->htmlOut);
     if (errCatch->gotError || !options->allowWarnings)
         genomeErrorCount += 1;
     }
 errCatchFree(&errCatch);
 
 verbose(2, "%d tracks in %s\n", slCount(tdbList), genome->name);
 struct trackDb *tdb;