544b4db19ee0f7f92c9d338d6900c34a53d9f032
chmalee
  Wed Jun 11 15:45:15 2025 -0700
Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook

diff --git src/hg/hgHubConnect/hooks/pre-finish.c src/hg/hgHubConnect/hooks/pre-finish.c
index 850b1a06147..e135c7ab9f5 100644
--- src/hg/hgHubConnect/hooks/pre-finish.c
+++ src/hg/hgHubConnect/hooks/pre-finish.c
@@ -54,31 +54,30 @@
     exitStatus = 1;
     }
 else
     {
     char *tusFile = NULL, *tusInfo = NULL;
     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 *dataDir = NULL, *userDataDir = NULL;
         char *fileName = NULL;
         long long fileSize = 0;
         char *fileType = NULL;
         char *db = NULL;
-        char *location = NULL;
         char *reqLm = NULL;
         time_t lastModified = 0;
         boolean isHubToolsUpload = FALSE;
         char *parentDir = NULL, *encodedParentDir = NULL;
 
         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);
             }
@@ -88,114 +87,89 @@
             {
             // maybe an apiKey was provided, use that instead to look up the userName
             char *apiKey = jsonQueryString(req, "", "Event.Upload.MetaData.apiKey", NULL);
             userName = userNameForApiKey(apiKey);
             if (!userName)
                 errAbort("You are not logged in. Please navigate to My Data -> My Sessions and log in or create an account.");
             }
         fprintf(stderr, "userName='%s'\n'", userName);
         // 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
-        char *hubtoolsStr = jsonQueryString(req, "", "Event.Upload.MetaData.hubtools", NULL);
-        if (hubtoolsStr)
-            isHubToolsUpload = sameString(hubtoolsStr, "TRUE") || sameString(hubtoolsStr, "true");
         parentDir = jsonQueryString(req, "", "Event.Upload.MetaData.parentDir", NULL);
         fprintf(stderr, "parentDir = '%s'\n", parentDir);
         fflush(stderr);
         // strip out plain leading '.' and '/' components
         // middle '.' components are dealt with later
         if (startsWith("./", parentDir) || startsWith("/", parentDir))
             parentDir = skipBeyondDelimit(parentDir, '/');
         fprintf(stderr, "parentDir = '%s'\n", parentDir);
         fflush(stderr);
         tusFile = jsonQueryString(req, "", "Event.Upload.Storage.Path", NULL);
+        tusInfo = jsonQueryString(req, "", "Event.Upload.Storage.InfoPath", NULL);
         if (fileName == NULL)
             {
             errAbort("No Event.Upload.fileName setting");
             }
         else if (tusFile == NULL)
             {
             errAbort("No Event.Path setting");
             }
         else
             {
-            tusInfo = catTwoStrings(tusFile, ".info");
             userDataDir = dataDir = getDataDir(userName);
-            struct dyString *newFile = dyStringNew(0);
             // if parentDir provided we are throwing the files in there
             if (parentDir)
                 {
                 encodedParentDir = encodePath(parentDir);
                 if (!endsWith(encodedParentDir, "/"))
                     encodedParentDir = catTwoStrings(encodedParentDir, "/");
                 dataDir = catTwoStrings(dataDir, encodedParentDir);
                 }
-            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
-            // hubtools uploads always overwrite because we assume those users
-            // know what they are doing
-            if (fileExists(dyStringContents(newFile)) && !isHubToolsUpload)
-                {
-                errAbort("file '%s' exists already, not overwriting", dyStringContents(newFile));
-                }
-            else
-                {
-                // set our mysql table location:
-                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, dyStringContents(newFile));
-                // the files definitely should not be executable!
-                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
             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->db = db;
-            row->location = location;
+            row->location = tusFile;
             row->md5sum = md5HexForFile(row->location);
             row->parentDir = encodedParentDir ? encodedParentDir : "";
             if (!isHubToolsUpload && !(sameString(fileType, "hub.txt")))
                 {
                 createNewTempHubForUpload(reqId, row, userDataDir, encodedParentDir);
                 fprintf(stderr, "added hub.txt and hubSpace row for hub for file: '%s'\n", fileName);
                 fflush(stderr);
                 }
             // first make the parentDir rows
             makeParentDirRows(row->userName, sqlDateToUnixTime(row->lastModified), row->db, row->parentDir, userDataDir);
             row->parentDir = hubNameFromPath(encodedParentDir);
             addHubSpaceRowForFile(row);
             fprintf(stderr, "added hubSpace row for file '%s'\n", fileName);
             fflush(stderr);
             }