02af9dedd3443875fc2b3eee09c48a5e6f85b1c3
chmalee
  Wed Nov 6 15:27:22 2024 -0800
Start of work on optional subdir and hubName metadata for hubtools uploads

diff --git src/hg/hgHubConnect/hooks/post-finish.c src/hg/hgHubConnect/hooks/post-finish.c
index 1335cd5..9988612 100644
--- src/hg/hgHubConnect/hooks/post-finish.c
+++ src/hg/hgHubConnect/hooks/post-finish.c
@@ -54,108 +54,118 @@
     }
 else
     {
     struct errCatch *errCatch = errCatchNew(0);
     if (errCatchStart(errCatch))
         {
         // the variables for the row entry for this file, some can be NULL
         char *userName = NULL;
         char *fileName = NULL;
         long long fileSize = 0;
         char *fileType = NULL;
         char *db = NULL;
         char *location = NULL;
         char *reqLm = NULL;
         time_t lastModified = 0;
+        char *subdir = NULL; // special optional argument from hubtools commands
+        char *reqHubName = NULL; // special optional argument from hubtools commands
 
         struct lineFile *lf = lineFileStdin(FALSE);
         char *request = lineFileReadAll(lf);
         struct jsonElement *req = jsonParse(request);
         fprintf(stderr, "Hook request:\n");
         jsonPrintToFile(req, NULL, stderr, 0);
         char *reqCookie= jsonQueryString(req, "", "Event.HTTPRequest.Header.Cookie[0]", NULL);
         if (reqCookie)
             {
             setenv("HTTP_COOKIE", reqCookie, 0);
             }
         fprintf(stderr, "reqCookie='%s'\n", reqCookie);
         userName = (loginSystemEnabled() || wikiLinkEnabled()) ? wikiLinkUserName() : NULL;
         fprintf(stderr, "userName='%s'\n'", userName);
         if (!userName)
             {
             errAbort("not logged in");
             }
         else
             {
             // NOTE: All Upload.MetaData values are strings
             fileName = cgiEncodeFull(jsonQueryString(req, "", "Event.Upload.MetaData.fileName", NULL));
             fileSize = jsonQueryInt(req, "",  "Event.Upload.Size", 0, NULL);
             fileType = jsonQueryString(req, "", "Event.Upload.MetaData.fileType", NULL);
             db = jsonQueryString(req, "", "Event.Upload.MetaData.genome", NULL);
             reqLm = jsonQueryString(req, "", "Event.Upload.MetaData.lastModified", NULL);
             lastModified = sqlLongLong(reqLm) / 1000; // yes Javascript dates are in millis
+            subdir = jsonQueryString(req, "", "Event.Upload.MetaData.subdir", NULL);
+            reqHubName = jsonQueryString(req, "", "Event.Upload.MetaData.hubName", NULL);
             char *tusFile = jsonQueryString(req, "", "Event.Upload.Storage.Path", NULL);
             if (fileName == NULL)
                 {
                 errAbort("No Event.Upload.fileName setting");
                 }
             else if (tusFile == NULL)
                 {
                 errAbort("No Event.Path setting");
                 }
             else
                 {
                 char *tusInfo = catTwoStrings(tusFile, ".info");
                 char *dataDir = getDataDir(userName);
-                char *newFile = catTwoStrings(dataDir, fileName);
-                fprintf(stderr, "moving %s to %s\n", tusFile, newFile);
+                struct dyString *newFile = dyStringNew(0);
+                // if subdir provided we are throwing the files in there
+                if (subdir)
+                    dataDir = catTwoStrings(dataDir, subdir);
+                dyStringPrintf(newFile, "%s%s", dataDir, fileName);
+
+                fprintf(stderr, "moving %s to %s\n", tusFile, dyStringContents(newFile));
                 // TODO: check if file exists or not and let user choose to overwrite
                 // and re-call this hook, for now just exit if the file exists
-                if (fileExists(newFile))
+                if (fileExists(dyStringContents(newFile)))
                     {
-                    errAbort("file '%s' exists already, not overwriting", newFile);
+                    errAbort("file '%s' exists already, not overwriting", dyStringContents(newFile));
                     }
                 else
                     {
                     // set our mysql table location:
-                    location = newFile;
+                    location = dyStringContents(newFile);
                     // the directory may not exist yet
                     int oldUmask = 00;
                     if (!isDirectory(dataDir))
                         {
                         fprintf(stderr, "making directory '%s'\n", dataDir);
                         // the directory needs to be 777, so ignore umask for now
                         oldUmask = umask(0);
                         makeDirsOnPath(dataDir);
                         // restore umask
                         umask(oldUmask);
                         }
-                    copyFile(tusFile, newFile);
+                    copyFile(tusFile, dyStringContents(newFile));
                     // the files definitely should not be executable!
-                    chmod(newFile, 0666);
+                    chmod(dyStringContents(newFile), 0666);
                     mustRemove(tusFile);
                     mustRemove(tusInfo);
+                    dyStringCannibalize(&newFile);
                     }
                 }
             }
 
         // we've passed all the checks so we can write a new or updated row
         // to the mysql table and return to the client that we were successful
         if (exitStatus == 0)
             {
             // create a hub for this upload, which can be edited later
-            char *hubName = createNewTempHubForUpload(reqId, userName, db, fileName, fileType);
+            char *hubName = createNewTempHubForUpload(reqId, userName, db, fileName, fileType, reqHubName);
             fprintf(stderr, "added hub.txt and hubSpace row for hub for file: '%s'\n", fileName);
             fflush(stderr);
             struct hubSpace *row = NULL;
             AllocVar(row);
             row->userName = userName;
             row->fileName = fileName;
             row->fileSize = fileSize;
             row->fileType = fileType;
             row->creationTime = NULL; // automatically handled by mysql
             row->lastModified = sqlUnixTimeToDate(&lastModified, TRUE);
             row->hubNameList = hubName;
             row->db = db;
             row->location = location;
             row->md5sum = md5HexForFile(row->location);
             addHubSpaceRowForFile(row);