2f0d3fa3d2bcbf3e23e834ca68565c470f73939d
chmalee
  Mon Oct 21 12:32:08 2024 -0700
Back end for auto-generating a hub with every user upload done

diff --git src/hg/hgHubConnect/hooks/post-finish.c src/hg/hgHubConnect/hooks/post-finish.c
index a70a16d..1335cd5 100644
--- src/hg/hgHubConnect/hooks/post-finish.c
+++ src/hg/hgHubConnect/hooks/post-finish.c
@@ -1,167 +1,186 @@
 /* post-finish  - tus daemon post-finish hook program. Reads
  * a JSON encoded request to finsh an upload from a tus
  * client and moves a downloaded file to a specific user
  * directory. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "wikiLink.h"
 #include "customTrack.h"
 #include "userdata.h"
 #include "jsonQuery.h"
 #include "jsHelper.h"
 #include "errCatch.h"
 #include "obscure.h"
 #include "hooklib.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hubSpace.h"
 #include "md5.h"
 #include "cheapcgi.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "post-finish - tus daemon post-finish hook program\n"
   "usage:\n"
   "   post-finish < input\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 int postFinish()
 /* post-finish hook for tus daemon. Read JSON encoded hook request from
  * stdin and write a JSON encoded hook to stdout. Writing to stderr
  * will be redirected to the tusd log and not seen by the user, so for
  * errors that the user needs to see, they need to be in the JSON response */
 {
 // TODO: create response object and do all error catching through that
 char *reqId = getenv("TUS_ID");
 // always return an exit status to the daemon and print to stdout, as
 // stdout gets sent by the daemon back to the client
 int exitStatus = 0;
 struct jsonElement *response = makeDefaultResponse();
 if (!(reqId))
     {
     rejectUpload(response, "not a TUS request");
     exitStatus = 1;
     }
 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;
 
         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
             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);
                 // 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))
                     {
                     errAbort("file '%s' exists already, not overwriting", newFile);
                     }
                 else
                     {
                     // set our mysql table location:
                     location = 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);
                     // the files definitely should not be executable!
                     chmod(newFile, 0666);
                     mustRemove(tusFile);
                     mustRemove(tusInfo);
                     }
                 }
             }
 
         // 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)
             {
-            addNewFileForUser(userName, fileName, fileSize, fileType, lastModified, NULL, db, location);
+            // create a hub for this upload, which can be edited later
+            char *hubName = createNewTempHubForUpload(reqId, userName, db, fileName, fileType);
+            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);
+            hubSpaceFree(&row);
+            fprintf(stderr, "added hubSpace row for file '%s'\n", fileName);
+            fflush(stderr);
             }
         }
     if (errCatch->gotError)
         {
         rejectUpload(response, errCatch->message->string);
         exitStatus = 1;
         }
     errCatchEnd(errCatch);
     }
 // always print a response no matter what
 jsonPrintToFile(response, NULL, stdout, 0);
 return exitStatus;
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 1)
     usage();
 return postFinish();
 }