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/inc/trashDir.h src/hg/inc/trashDir.h index c752ac3e694..172a3f65c53 100644 --- src/hg/inc/trashDir.h +++ src/hg/inc/trashDir.h @@ -1,56 +1,61 @@ /* trashDir.c - temporary file creation and directory creation in /trash */ /* Copyright (C) 2010 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef TRASHDIR_H #define TRASHDIR_H #include "portable.h" void trashDirFile(struct tempName *tn, char *dirName, char *base, char *suffix); /* obtain a trash file name trash/dirName/base*.suffix */ void trashDirDateFile(struct tempName *tn, char *dirName, char *base, char *suffix); /* obtain a trash file name trash/dirName.dayOfYear/base*.suffix */ boolean trashDirReusableFile(struct tempName *tn, char *dirName, char *base, char *suffix); /* obtain a resusable trash file name as trash/dirName/base.suffix * returns TRUE if already exists. */ void copyFileToTrash(char **pFileName, char *dirName, char *base, char *suffix); /* If *pFileName is not NULL and exists, then create a new file in the * given dirName of trash/ with the given base and suffix, copy *pFileName's * contents to it, and set *pFileName to the new filename. */ +boolean pathIsUnderDir(char *dir, char *path); +/* Return TRUE if path names something underneath dir. A '/' is required at the directory + * boundary, so a sibling directory whose name merely starts the same way (trashBackup next + * to trash) does not match. ".." below the boundary is refused. */ + boolean isTrashPath(char *path); /* Return TRUE if path names a file inside the trash directory. */ boolean isTrashOrSessionDataPath(char *path); /* Return TRUE if path is under the trash directory, or under one of the durable session-data * directories that trash files are moved to when a session is saved. This is the allow-list * isValidBigDataUrl() uses for a bigDataUrl that names a local file. */ boolean isServerUserFilePath(char *path); /* Return TRUE if path is under one of the directories where the server keeps files it made * for a user: the trash directory, the session-data directories, or a per-feature data * directory such as myVariantsDataDir. * * Use this on any file name that comes back out of the cart before opening, reading, writing * or deleting it. Cart values are not ours: they arrive from CGI parameters, from an uploaded * or fetched hgSession file, and from another user's shared session. Note that a trash file * may itself be a symbolic link pointing at session storage, so a realpath() check is not * usable here -- sessionDataSaveTrashFile() creates exactly those links on purpose. */ boolean isRemoteUrl(char *path); /* Return TRUE if path is a URL fetched over the network rather than a file name. */ boolean isServerUserFileOrUrl(char *path); /* Return TRUE if path is either a remote URL or a file the server made for a user. * * Use this instead of isServerUserFilePath() on the cart variables that legitimately hold * either one, such as multiRegionsBedUrl and the hgSession load-from-URL name. Both are read * by code that decides between the two by looking for a protocol and falls through to opening * a local file, so a value with no protocol has to be one of ours. */ #endif /* TRASHDIR_H */