404d5bb6d8c0418d5f06535ef470e36c35d2a237
chmalee
  Thu Apr 16 15:57:56 2026 -0700
Add assembly hub support to hubSpace.

Users can upload a .2bit to create an assembly hub, optionally alongside
their own *.hub.txt (prefix names like araTha1.hub.txt are recognized)
and sibling track files. Uploads run in parallel; hub.txt mutations are
serialized per-hub via flock so arrival order does not matter.

- hubSpace table gains a hubType column ('trackHub' or 'assemblyHub');
ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an
upgraded hub.
- writeHubText can now emit an assembly stanza derived from the 2bit;
upgradeHubTxtForAssembly promotes an existing plain hub.txt in place
when a 2bit arrives after tracks.
- pre-finish decides synthesize vs upgrade vs leave-alone from server
state (existing rows, hub.txt on disk) plus a single client flag
(batchHasHubTxt); client-supplied hubType is no longer trusted.
- Client UI adds 2bit as a file type, locks the genome field when the
hub is authoritative (drilled-in or batch hub.txt), defaults new
uploads to an existing assembly hub at top level, and routes
hgTracks URLs through 'genome=' vs 'db=' by hubType.
- Fix pre-existing nested-path bug in hubPathFromParentDir
(*firstSlash = 0).

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

diff --git src/hg/inc/userdata.h src/hg/inc/userdata.h
index 31ef0d8834b..36f5124ebb2 100644
--- src/hg/inc/userdata.h
+++ src/hg/inc/userdata.h
@@ -1,103 +1,130 @@
 /* userdata.c - code for managing data stored on a per user basis */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #ifndef USERDATA_H
 #define USERDATA_H
 
 #include "hubSpace.h"
 
 struct userFiles
 {
 char *userName;
 struct fileInfo *fileList; // list of files for this user
 };
 
 struct userHubs
 {
 struct userHubs *next;
 char *hubName; // name of this hub
 char *genome; // only one genome allowed per hub for now
 char *userName; // for convenience
 time_t lastModified; // actually last access time but this works
 struct userFiles *fileList; // list of files (tracks) in the hub
 };
 
 char *getUserName();
 /* Query the right system for the users name */
 
 char *emailForUserName(char *userName);
 /* Fetch the email for this user from gbMembers hgcentral table */
 
 // the various quota helper variables:
 #define HUB_SPACE_DEFAULT_QUOTA_BYTES 10000000000
 #define HUB_SPACE_DEFAULT_QUOTA HUB_SPACE_DEFAULT_QUOTA_BYTES 
 // for defining the quota in hg.conf
 #define HUB_SPACE_CONF_QUOTA_VAR "hubspace.quota"
 
 char *webDataDir(char *userName);
 /* Return a web accesible path to the userDataDir, this is different from the full path tusd uses */
 
 char *urlForFile(char *userName, char *filePath);
 /* Return a web accessible URL to filePath */
 
 char *getEncodedUserNamePath(char *userName);
 /* Compute the path for just the userName part of the users upload */
 
 char *getDataDir(char *userName);
 /* Return the full path to the user specific data directory, can be configured via hg.conf
  * on hgwdev, this is /data/apache/userdata/userStore/hash/userName/
  * on the RR, this is /userdata/userStore/hash/userName/ */
 
 char *stripDataDir(char *fname, char *userName);
 /* Strips the getDataDir(userName) off of fname */
 
 char *swapDataDir(char *userName, char *in);
 /* Try replacing the current dataDir with what is defined in hg.conf:tusdMountPoint as
  * the data server may be somewhere else and mounted over NFS. In this case, when
  * tusd saves files, it is writing it's local tusdDataDir value into the hgcentral
  * file location. When the CGI running somewhere else needs to verify file existence,
  * the tusdDataDir won't exist on the CGI filesystem, but will instead be mounted as some
  * different path.  In this case, replace tusdDataDir with tusdMountPoint */
 
 char *prefixUserFile(char *userName, char *fname, char *parentDir);
 /* Allocate a new string that contains the full per-user path to fname. return NULL if
  * we cannot construct a full path because of a realpath(3) failure.
  * parentDir is optional and will go in between the per-user dir and the fname */
 
 char *hubNameFromPath(char *path);
 /* Return the last directory component of path. Assume that a '.' char in the last component
  * means that component is a filename and go back further */
 
-char *writeHubText(char *path, char *userName, char *db);
-/* Create a hub.txt file, optionally creating the directory holding it. For convenience, return
- * the file name of the created hub, which can be freed. */
+char *writeHubText(char *path, char *userName, char *db, char *twoBitFileName);
+/* Create a hub.txt file, optionally creating the directory holding it.
+ * If twoBitFileName is non-NULL, write an assembly hub stanza referencing it
+ * (with stub organism / scientificName / description / defaultPos derived from
+ * the 2bit). For convenience, return the file name of the created hub, which
+ * can be freed. */
 
 void createNewTempHubForUpload(char *requestId, struct hubSpace *rowForFile, char *userDataDir, char *parentDir);
 /* Creates a hub.txt for this upload, and updates the hubSpace table for the
  * hub.txt and any parentDirs we need to create. */
 
+boolean userHasOwnNamedHubTxtInDir(char *userName, char *parentDir);
+/* Return TRUE if user uploaded a *.hub.txt NOT literally named 'hub.txt' in parentDir.
+ * Used to decide whether the backend can modify hub.txt (synthesize / append / upgrade)
+ * or should leave it alone because the user has their own authoritative config. */
+
+char *existingHubTypeForDir(char *userName, char *hubName);
+/* Return the hubType of this user's hub dir row, or NULL if no such row exists. */
+
+void upgradeExistingHubToAssembly(struct hubSpace *rowForFile, char *userDataDir, char *encodedParentDir);
+/* Race-proofing: when a 2bit arrives into a hub that already has a synthesized
+ * hub.txt, upgrade that hub.txt to include the assembly stanza and mark every
+ * hubSpace row for this hub as hubType='assemblyHub'. No-op unless rowForFile
+ * is a 2bit, or the synthesized hub.txt does not exist. */
+
+boolean literalHubTxtExistsOnDisk(char *parentDir, char *userDataDir);
+/* Return TRUE if path/hub.txt exists as a real file in this user's parentDir. */
+
+int lockHubDir(char *hubDir);
+/* Acquire an exclusive flock on hubDir/.hub.lock; returns a file descriptor.
+ * Hold while mutating hub.txt to serialize parallel pre-finish processes. */
+
+void unlockHubDir(int fd);
+/* Release an exclusive hub lock acquired by lockHubDir. */
+
 void addHubSpaceRowForFile(struct hubSpace *row);
 /* We created a file for a user, now add an entry to the hubSpace table for it */
 
-void makeParentDirRows(char *userName, time_t lastModified, char *db, char *parentDirStr, char *userDataDir);
+void makeParentDirRows(char *userName, time_t lastModified, char *db, char *parentDirStr, char *userDataDir, char *hubType);
 /* For each '/' separated component of parentDirStr, create a row in hubSpace. Return the
  * final subdirectory component of parentDirStr */
 
 void removeFileForUser(char *fname, char *userName);
 /* Remove a file for this user if it exists */
 
 struct hubSpace *listFilesForUser(char *userName);
 /* Return the files the user has uploaded */
 
 char *defaultHubNameForUser(char *userName);
 /* Return a name to use as a default for a hub, starts with myFirstHub, then myFirstHub2, ... */
 
 long long getMaxUserQuota(char *userName);
 /* Return how much space is allocated for this user or the default */
 
 long long checkUserQuota(char *userName);
 /* Return the amount of space a user is currently using */
 
 #endif /* USERDATA_H */