59e2bbf2d3a99e5f18436a756e1e5c8b64308e33 braney Tue Sep 8 09:21:02 2026 -0700 Copy a track collection's hub file when the program that writes it asks for a copy, instead of on every session load. cartCopyLocalHubs ran on every session load, in every CGI and in four more places in hgSession. For each customComposite-<db> cart variable it copied the collection's hub file to a fresh trash name and registered the copy in hgcentral.hubStatus to get a hub id. Nothing removed the old row. 81% of the 3.1 million rows in hubStatus on the RR are these dead registrations, and each load also took the central_hubStatus advisory lock and wrote to a MyISAM table, which serializes every concurrent load of a shared session that carries a collection. The copy itself is needed. A saved session's hub file lives under sessionDataDir and every load of that session names it, so hgCollection must not write it in place. It was just being made for every load, and almost no load is followed by an edit. hgCollection is the only program that writes one of these files, so it now asks for its own copy: main() calls cartRequestLocalHubCopy() before it opens the cart, and cartNew() makes the copy for it. That has to be a property of the program rather than of the request, and the copy has to be made at cart open, above hubConnectLoadHubs. Copying the file gives the hub a new id, the hubs are loaded during cart open, and trackList carries that id in every track name, so a copy made any later leaves printTrackDbListToHub looking for the collection under an id trackList does not have and the hub file comes out with a header and no tracks. A condition that instead tries to work out whether this particular request will write cannot be correct either: "cmd" is not in hgTracks' excludeVars, so it persists in the cart and hgCollection dispatches on the cart rather than on the CGI variable, a settings file can carry it, and a command-line run has no SCRIPT_NAME to test. Three other parts. copyLocalHubs skips a hub the cart already owns, so repeated edits reuse one file and one hub id rather than renumbering the hub on every drag; the test requires a plain file, because saveTrackFile leaves the trash name behind as a symbolic link to the durable copy and writing through that link would rewrite the saved session's own file. copyLocalHubs also screens the path with isServerUserFilePath before opening it, the way getHubName does, and selects on customComposite-<db> with the dash so that the names it acts on are the ones fileNameCartVarPrefixes screens. saveTrackFile copies when the source is a local hub outside trash that is not under this session's own directory, so loading one session and saving it under a new name gives the new session its own file instead of a reference into the first one's directory. pathIsUnderDir is no longer static in trashDir.c. All of it is behind the hg.conf gate collectionHubCopyOnWrite, default off, which reproduces the old behavior exactly. Retiring the gate is not uniform: the body of cartCopyLocalHubsOnSessionLoad is the old behavior and that function and its five callers go away with the gate, while the other three tests lose only the gate term. Measured on hgcentraltest with one binary. With the gate off, five loads of a session carrying a collection add five hubStatus rows and three later edits add none; with it on, the five loads add none and the first edit adds one. Saving a loaded session costs two rows off and one on. The resulting hub file is byte identical either way apart from the hub id, and the file the saved session names is unchanged by md5 and mtime, including after an edit made straight after a save, and including when the cart names a trash symbolic link into session storage. refs #38273 diff --git src/hg/utils/hgConfCatalog/hgConfCatalog.py src/hg/utils/hgConfCatalog/hgConfCatalog.py index b9f12b27e7f..e7e36ff3924 100755 --- src/hg/utils/hgConfCatalog/hgConfCatalog.py +++ src/hg/utils/hgConfCatalog/hgConfCatalog.py @@ -222,30 +222,44 @@ } # --------------------------------------------------------------------------- # release gates: boolean flags that exist to hold a feature back # --------------------------------------------------------------------------- # These are the reason this catalog has a sunset mode. Each was added so a # user-visible change could sit on master without shipping. Ordered by age so # the backlog is visible at a glance. RELEASE_GATES = { "what": "Boolean flags introduced to ship a feature dark during a release. " "Temporary by intent: each should be deleted once the feature it " "guards is public and mirrors have had a cycle to object.", "vars": [ + h("collectionHubCopyOnWrite", "flag", "hg/lib/cart.c", default="FALSE", + role="gate", verified=True, ticket="38273", + note="Copy a track collection's generated hub file when the program that writes " + "it (only hgCollection) asks for a copy, instead of on every session load. " + "With it off, loading any session that carries a collection copies the hub to " + "a new trash file and registers that copy in hgcentral.hubStatus, which is " + "where 81% of the RR's 3.1M hubStatus rows came from. Read in " + "cartCollectionHubCopyOnWrite() and branched on at four places in three " + "files: cart.c makes the copy when cartRequestLocalHubCopy() was called, and " + "skips a hub the cart already owns in copyLocalHubs(); " + "cartCopyLocalHubsOnSessionLoad() does nothing (that one is the old behavior, " + "and it plus its five callers in cart.c and hgSession.c go away with the " + "gate); sessionData.c's saveTrackFile splits a hub that came from another " + "session. Off during QA; flip to TRUE once released."), h("bigNet", "flag", "hg/lib/trackHub.c", default="FALSE", role="gate", verified=True, ticket="20824", note="The bigNet track type, a net of pairwise alignments in a " "bigBed, and quickLift support for it. Read once in " "trackHubBigNetEnabled(); with it off a hub that declares " "\"type bigNet\" fails to load with an unsupported-type error, " "quickLift refuses the type, and neither hubCheck nor the hubApi " "lists it among the supported types."), h("showMouseovers", "flag", "hg/hgTracks/config.c", default="FALSE", role="gate", verified=True, note="Mouseover text on track items instead of the browser's own " "title tooltips. Added v446 and still defaulting FALSE, which " "makes it the oldest gate in the tree that never shipped. Four " "call sites across config.c and imageV2.c. Either the feature " "is wanted, in which case flip it, or it is not, in which case "