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/lib/hubSpace.c src/hg/lib/hubSpace.c
index 35e8fd4d2b3..c91b1157740 100644
--- src/hg/lib/hubSpace.c
+++ src/hg/lib/hubSpace.c
@@ -1,312 +1,328 @@
 /* hubSpace.c was originally generated by the autoSql program, which also
  * generated hubSpace.h and hubSpace.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "hubSpace.h"
 
-char *hubSpaceCommaSepFieldNames = "userName,fileName,fileSize,fileType,creationTime,lastModified,db,location,md5sum,parentDir";
+char *hubSpaceCommaSepFieldNames = "userName,fileName,fileSize,fileType,creationTime,lastModified,db,location,md5sum,parentDir,hubType";
 
 void hubSpaceStaticLoad(char **row, struct hubSpace *ret)
 /* Load a row from hubSpace table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->userName = row[0];
 ret->fileName = row[1];
 ret->fileSize = sqlLongLong(row[2]);
 ret->fileType = row[3];
 ret->creationTime = row[4];
 ret->lastModified = row[5];
 ret->db = row[6];
 ret->location = row[7];
 ret->md5sum = row[8];
 ret->parentDir = row[9];
+ret->hubType = row[10];
 }
 
 struct hubSpace *hubSpaceLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all hubSpace from table that satisfy the query given.
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something =
  * anotherTable.something'.
  * Dispose of this with hubSpaceFreeList(). */
 {
 struct hubSpace *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = hubSpaceLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void hubSpaceSaveToDb(struct sqlConnection *conn, struct hubSpace *el, char *tableName, int updateSize)
 /* Save hubSpace as a row to the table specified by tableName.
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. This function automatically escapes quoted strings for mysql.
  * Uses ON DUPLICATE KEY UPDATE to handle file overwrites. */
 {
 struct dyString *update = dyStringNew(updateSize);
-sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%lld,'%s',NULL,'%s','%s','%s','%s','%s') "
+char *hubType = el->hubType ? el->hubType : "trackHub";
+// Exclude hubType from the UPDATE clause so a re-upload does not revert a
+// row's hubType back to trackHub after the hub was promoted to assemblyHub
+// (e.g. by a 2bit arriving later). The initial INSERT value stands.
+sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%lld,'%s',NULL,'%s','%s','%s','%s','%s','%s') "
 	"ON DUPLICATE KEY UPDATE fileSize=%lld, lastModified='%s', md5sum='%s', location='%s', db='%s'",
-	tableName, el->userName, el->fileName, el->fileSize, el->fileType, el->lastModified, el->db, el->location, el->md5sum, el->parentDir,
+	tableName, el->userName, el->fileName, el->fileSize, el->fileType, el->lastModified, el->db, el->location, el->md5sum, el->parentDir, hubType,
 	el->fileSize, el->lastModified, el->md5sum, el->location, el->db);
-fprintf(stderr, "hubSpace row insert:\n\n%s\n\n", update->string);
-fflush(stderr);
 sqlUpdate(conn, update->string);
 dyStringFree(&update);
-fprintf(stderr, "hubSpace update successful\n");
-fflush(stderr);
 }
 
 struct hubSpace *hubSpaceLoad(char **row)
 /* Load a hubSpace from row fetched with select * from hubSpace
  * from database.  Dispose of this with hubSpaceFree(). */
 {
 struct hubSpace *ret;
 
 AllocVar(ret);
 ret->userName = cloneString(row[0]);
 ret->fileName = cloneString(row[1]);
 ret->fileSize = sqlLongLong(row[2]);
 ret->fileType = cloneString(row[3]);
 ret->creationTime = cloneString(row[4]);
 ret->lastModified = cloneString(row[5]);
 ret->db = cloneString(row[6]);
 ret->location = cloneString(row[7]);
 ret->md5sum = cloneString(row[8]);
 ret->parentDir = cloneString(row[9]);
+ret->hubType = cloneString(row[10]);
 return ret;
 }
 
 struct hubSpace *hubSpaceLoadAll(char *fileName)
 /* Load all hubSpace from a whitespace-separated file.
  * Dispose of this with hubSpaceFreeList(). */
 {
 struct hubSpace *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
+char *row[11];
 
 while (lineFileRow(lf, row))
     {
     el = hubSpaceLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubSpace *hubSpaceLoadAllByChar(char *fileName, char chopper)
 /* Load all hubSpace from a chopper separated file.
  * Dispose of this with hubSpaceFreeList(). */
 {
 struct hubSpace *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
+char *row[11];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hubSpaceLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubSpace *hubSpaceCommaIn(char **pS, struct hubSpace *ret)
 /* Create a hubSpace out of a comma separated string.
  * This will fill in ret if non-null, otherwise will
  * return a new hubSpace */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->userName = sqlStringComma(&s);
 ret->fileName = sqlStringComma(&s);
 ret->fileSize = sqlLongLongComma(&s);
 ret->fileType = sqlStringComma(&s);
 ret->creationTime = sqlStringComma(&s);
 ret->lastModified = sqlStringComma(&s);
 ret->db = sqlStringComma(&s);
 ret->location = sqlStringComma(&s);
 ret->md5sum = sqlStringComma(&s);
 ret->parentDir = sqlStringComma(&s);
+ret->hubType = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void hubSpaceFree(struct hubSpace **pEl)
 /* Free a single dynamically allocated hubSpace such as created
  * with hubSpaceLoad(). */
 {
 struct hubSpace *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->userName);
 freeMem(el->fileName);
 freeMem(el->fileType);
 freeMem(el->creationTime);
 freeMem(el->lastModified);
 freeMem(el->db);
 freeMem(el->location);
 freeMem(el->md5sum);
 freeMem(el->parentDir);
+freeMem(el->hubType);
 freez(pEl);
 }
 
 void hubSpaceFreeList(struct hubSpace **pList)
 /* Free a list of dynamically allocated hubSpace's */
 {
 struct hubSpace *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hubSpaceFree(&el);
     }
 *pList = NULL;
 }
 
 void hubSpaceOutput(struct hubSpace *el, FILE *f, char sep, char lastSep)
 /* Print out hubSpace.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->userName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fileName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%lld", el->fileSize);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fileType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->creationTime);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->lastModified);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->db);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->location);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->md5sum);
 if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->parentDir);
 if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->hubType ? el->hubType : "trackHub");
+if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void hubSpaceJsonOutput(struct hubSpace *el, FILE *f)
 /* Print out hubSpace in JSON format. */
 {
 fputc('{',f);
 fputc('"',f);
 fprintf(f,"userName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->userName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"fileName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->fileName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"fileSize");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%lld", el->fileSize);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"fileType");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->fileType);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"creationTime");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->creationTime);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"lastModified");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->lastModified);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"db");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->db);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"location");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->location);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"md5sum");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->md5sum);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"hubNameList");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->parentDir);
 fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"hubType");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+fprintf(f, "%s", el->hubType ? el->hubType : "trackHub");
+fputc('"',f);
 fputc('}',f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */