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/hgHubConnect/trackHubWizard.c src/hg/hgHubConnect/trackHubWizard.c
index 9cc153d4c85..546d15e9fc0 100644
--- src/hg/hgHubConnect/trackHubWizard.c
+++ src/hg/hgHubConnect/trackHubWizard.c
@@ -1,264 +1,265 @@
 /* trackHubWizard -- a user interface for creating a track hubs configuration files */
 
 /* Copyright (C) 2019 The Regents of the University of California
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "cart.h"
 #include "cheapcgi.h"
 #include "hdb.h"
 #include "hgConfig.h"
 #include "md5.h"
 #include "trashDir.h"
 #include "hgHubConnect.h"
 #include "jsHelper.h"
 #include "web.h"
 #include "wikiLink.h"
 #include "customTrack.h"
 #include "userdata.h"
 #include "jsonWrite.h"
 #include "cartJson.h"
 #include "hubSpace.h"
 #include "hubSpaceKeys.h"
 #include "hubConnect.h"
 #include "trackHub.h"
 #include "htmshell.h"
 #include <limits.h>
 #include "errCatch.h"
 
 void removeOneFile(char *userName, char *cgiFileName, char *fullPath, char *db, char *fileType)
 /* Remove one single file for userName */
 {
 // prefixUserFile returns a canonicalized path, or NULL if the
 // canonicalized path does not begin with the hg.conf specified userDataDir
 // TODO: make the debug information from stderr go to stdout so the user
 // can know there is a mistake somewhere, and only print the debug
 // information in the event that the filename actually begins with the
 // userDataDir so we don't tell hackers what files do and do not exist
 char *fileName = prefixUserFile(userName, fullPath, NULL);
 if (fileName)
     {
     if (fileExists(fileName))
         {
         fprintf(stderr, "deleting file: '%s'\n", fileName);
         removeFileForUser(fileName, userName);
         fflush(stderr);
         }
     else
         {
         fprintf(stderr, "file '%s' does not exist\n", fileName);
         fflush(stderr);
         }
     }
 }
 
 int pathDepth(char *path)
 {
 // replace multiple occurences of '/' with just a single one to get a canonical path
 // as path///to/file and path/to/file are the same path on Linux
 char *deduped = replaceChars(path, "//", "/");
 return countChars(deduped, '/');
 }
 
 int sortByFullPathCmp(const void *va, const void *vb)
 /* Compare two fullPaths */
 {
 struct jsonElement *a = (struct jsonElement *)(*(struct slRef **)va)->val;
 struct jsonElement *b = (struct jsonElement *)(*(struct slRef **)vb)->val;
 char *aFullpath = jsonStringField(a, "fullPath");
 char *bFullpath = jsonStringField(b, "fullPath");
 int aDepth = pathDepth(aFullpath);
 int bDepth = pathDepth(bFullpath);
 // ensure subdirectories order before their parents:
 if (aDepth != bDepth)
     return bDepth - aDepth;
 // if equal depth than lexicographic sort is fine
 return strcmp(jsonStringField(a,"fullPath"), jsonStringField(b, "fullPath"));
 }
 
 void sortByFullPath(struct jsonElement *listJson)
 {
 slSort(&(listJson->val.jeList), sortByFullPathCmp);
 }
 
 void doRemoveFile(struct cartJson *cj, struct hash *paramHash)
 /* Process the request to remove a file */
 {
 char *userName = getUserName();
 if (userName)
     {
     // our array of objects, each object represents a track file
     struct jsonElement *deleteJson = hashFindVal(paramHash, "fileList");
     struct slRef *copy, *f, *fileList = deleteJson->val.jeList;
     struct jsonElement *dirListJsonEle = newJsonList(NULL);
     jsonWriteListStart(cj->jw, "deletedList");
     for (f = fileList; f != NULL; )
         {
         struct jsonElement *fileObj = (struct jsonElement *)f->val;
         char *fileName = jsonStringField(fileObj, "fileName");
         char *fileType = jsonStringField(fileObj, "fileType");
         char *db = jsonStringField(fileObj, "genome");
         char *fullPath = jsonStringField(fileObj, "fullPath");
         copy = f->next;
         if (sameString(fileType, "dir"))
             {
             f->next = NULL;
             jsonListAdd(dirListJsonEle, fileObj);
             }
         else
             {
             if (sameString(fileType, "hub.txt"))
                 {
                 // disconnect this hub from the cart if it exists
                 char *hubUrl = urlForFile(userName, fullPath);
                 char *hubId = hubNameFromUrl(hubUrl);
                 if (hubId)
                     {
                     /* remove the cart variable */
                     hubId += 4; // skip past the hub_ part
                     char buffer[1024];
                     safef(buffer, sizeof buffer, "hgHubConnect.hub.%s", hubId);
                     cartRemove(cj->cart, buffer);
                     }
                 }
             removeOneFile(userName, fileName, fullPath, db, fileType);
             // write out the fullPath so the DataTable can remove the correct row:
             jsonWriteString(cj->jw, NULL, fullPath);
             }
         f = copy;
         }
     // now attempt to delete any requested directories, but don't die if they still have contents
     sortByFullPath(dirListJsonEle);
     struct slRef *dir = NULL;
     for (dir = dirListJsonEle->val.jeList; dir != NULL; dir = dir->next)
         {
         struct jsonElement *fileObj = (struct jsonElement *)dir->val;
         char *fileName = jsonStringField(fileObj, "fileName");
         char *fileType = jsonStringField(fileObj, "fileType");
         char *db = jsonStringField(fileObj, "genome");
         char *fullPath = jsonStringField(fileObj, "fullPath");
         removeOneFile(userName, fileName, fullPath, db, fileType);
         // write out the fullPath so the DataTable can remove the correct row:
         jsonWriteString(cj->jw, NULL, fullPath);
         }
     jsonWriteListEnd(cj->jw);
     }
 }
 
 void doMoveFile(struct cartJson *cj, struct hash *paramHash)
 /* Move a file to a new hub */
 {
 }
 
 static void outUiDataForUser(struct jsonWrite *jw)
 /* List out the currently stored files for the user as well as other data
  * needed to create the hubSpace table */
 {
 char *userName = getUserName();
 jsonWriteObjectStart(jw, "userFiles");
 if (userName)
     {
     // the url for this user:
     jsonWriteString(jw, "userUrl", webDataDir(userName));
     jsonWriteListStart(jw, "fileList");
     struct hubSpace *file, *fileList = listFilesForUser(userName);
     for (file = fileList; file != NULL; file = file->next)
         {
         jsonWriteObjectStart(jw, NULL);
         jsonWriteString(jw, "fileName", file->fileName);
         jsonWriteNumber(jw, "fileSize", file->fileSize);
         jsonWriteString(jw, "fileType", file->fileType);
         jsonWriteString(jw, "parentDir", file->parentDir);
         jsonWriteString(jw, "genome", file->db);
         jsonWriteString(jw, "lastModified", file->lastModified);
         jsonWriteString(jw, "uploadTime", file->creationTime);
         jsonWriteString(jw, "fullPath", stripDataDir(file->location, userName));
         jsonWriteString(jw, "md5sum", file->md5sum);
+        jsonWriteString(jw, "hubType", file->hubType ? file->hubType : "trackHub");
         jsonWriteObjectEnd(jw);
         }
     jsonWriteListEnd(jw);
     }
 jsonWriteBoolean(jw, "isLoggedIn", getUserName() ? TRUE : FALSE);
 jsonWriteString(jw, "hubNameDefault", defaultHubNameForUser(getUserName()));
 // if the user is not logged, the 0 for the quota is ignored
 jsonWriteNumber(jw, "userQuota", getUserName() ? checkUserQuota(getUserName()) : 0);
 jsonWriteNumber(jw, "maxQuota", getUserName() ? getMaxUserQuota(getUserName()) : HUB_SPACE_DEFAULT_QUOTA);
 jsonWriteObjectEnd(jw);
 }
 
 void getHubSpaceUIState(struct cartJson *cj, struct hash *paramHash)
 /* Get all the data we need to make a users hubSpace UI table. The cartJson library
  * deals with printing the json */
 {
 outUiDataForUser(cj->jw);
 }
 
 void cjRevokeApiKey(struct cartJson *cj, struct hash *paramHash)
 /* Wrapper for cartJson to call lib function revokeApiKey, removes any api keys for the user */
 {
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     char *userName = getUserName();
     hubSpaceRevokeApiKey(userName);
     }
 errCatchEnd(errCatch);
 if (!(errCatch->gotError))
     jsonWriteString(cj->jw, "revoke", "true");
 else
     jsonWriteStringf(cj->jw, "error", "revokeApiKey() error: '%s'", errCatch->message->string);
 errCatchFree(&errCatch);
 }
 
 void cjGenerateApiKey(struct cartJson *cj, struct hash *paramHash)
 /* Wrapper for cartJson to call lib function generateApiKey, makes a random (but not crypto-secure api key for use of hubtools to upload to hubspace, or for skipping cloudflare */
 {
 struct errCatch *errCatch = errCatchNew();
 char *apiKey = NULL;
 
 if (errCatchStart(errCatch))
     {
     char *userName = getUserName();
     apiKey = hubSpaceGenerateApiKey(userName);
     }
 
 errCatchEnd(errCatch);
 if (apiKey)
     jsonWriteString(cj->jw, "apiKey", apiKey);
 else if (errCatch->gotError)
     jsonWriteStringf(cj->jw, "error", "generateApiKey() error: '%s'", errCatch->message->string);
 errCatchFree(&errCatch);
 }
 
 
 void doTrackHubWizard(char *database)
 /* Offer an upload form so users can upload all their hub files */
 {
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("lodash.3.10.0.compat.min.js", NULL);
 jsIncludeFile("cart.js", NULL);
 jsIncludeFile("autocompleteCat.js",NULL);
 webIncludeResourceFile("font-awesome.min.css");
 webIncludeResourceFile("dataTables-2.2.2.min.css");
 jsIncludeFile("dataTables-2.2.2.min.js", NULL);
 webIncludeResourceFile("dataTables.buttons-3.2.2.min.css");
 jsIncludeFile("dataTables.buttons-3.2.2.min.js", NULL);
 webIncludeResourceFile("dataTables.select-3.0.0.min.css");
 jsIncludeFile("dataTables.select-3.0.0.min.js", NULL);
 puts("<link href=\"https://releases.transloadit.com/uppy/v4.5.0/uppy.min.css\" rel=\"stylesheet\">");
 puts("<script type=\"text/javascript\" src=\"https://releases.transloadit.com/uppy/v4.5.0/uppy.min.js\"></script>");
 jsIncludeFile("hgMyData.js", NULL);
 
 // the skeleton HTML:
 webIncludeFile("inc/hgMyData.html");
 webIncludeResourceFile("hgMyData.css");
 
 jsInlineF("\nvar isLoggedIn = %s;\n", getUserName() ? "true" : "false");
 jsInlineF("\nvar cartDb=\"%s %s\";\n", trackHubSkipHubName(hGenome(database)), database);
 jsInlineF("\nvar tusdEndpoint=\"%s\";\n", cfgOptionDefault("hubSpaceTusdEndpoint", NULL));
 jsInlineF("\nvar fileListEndpoint=\"%shgHubConnect\";\n", hLoginHostCgiBinUrl());
 jsInlineF("\nvar loginHost=\"http%s://%s\";\n", loginUseHttps() ? "s" : "", wikiLinkHost());
 jsInline("$(document).ready(function() {\nhubCreate.init();\n})");
 puts("</div>");
 }