7545a188d43c6e1ea33f692b0d833ec96a7f76c5 chmalee Wed Aug 14 09:21:15 2024 -0700 refactor some methods into userdata.c for writing hub.txt files. Finish trackHubWizard.c back end for writing hub.txt and clean up the html. Start of adding a modal dialog for creating hub.txt diff --git src/hg/hgHubConnect/hooks/post-finish.c src/hg/hgHubConnect/hooks/post-finish.c index c40092e..c5e5c07 100644 --- src/hg/hgHubConnect/hooks/post-finish.c +++ src/hg/hgHubConnect/hooks/post-finish.c @@ -1,192 +1,166 @@ /* 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" 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; 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 = 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) { - 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 = NULL; - row->db = db; - row->location = location; - row->md5sum = md5HexForFile(row->location); - struct sqlConnection *conn = hConnectCentral(); - - // now write out row to hubSpace table - if (!sqlTableExistsOnMain(conn, "hubSpace")) - { - errAbort("No hubSpace MySQL table is present. Please send us an email"); - } - struct dyString *sqlUpdateStmt = dyStringNew(0); - sqlDyStringPrintf(sqlUpdateStmt, "insert into hubSpace values ('%s', '%s', %llu, " - "'%s', NULL, '%s', '', '%s', '%s', '%s')", - row->userName, row->fileName, row->fileSize, row->fileType, - row->lastModified, row->db, row->location, row->md5sum); - fprintf(stderr, "%s\n", sqlUpdateStmt->string); - fflush(stderr); - sqlUpdate(conn, sqlUpdateStmt->string); + addNewFileForUser(userName, fileName, fileSize, fileType, lastModified, NULL, db, location); } } 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(); }