541933ca6a407a10621c3110fb0873529d78e11e chmalee Wed Feb 26 12:42:38 2025 -0800 Don't error out if trying to do a hubspace re-upload of a file if the upload is coming from hubtools. Assume hubtools users want to overwrite existing files, ref Max email diff --git src/hg/hgHubConnect/hooks/pre-finish.c src/hg/hgHubConnect/hooks/pre-finish.c index 29c15dc897c..d70c4612af2 100644 --- src/hg/hgHubConnect/hooks/pre-finish.c +++ src/hg/hgHubConnect/hooks/pre-finish.c @@ -1,219 +1,221 @@ /* pre-finish - tus daemon pre-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 "hubSpaceKeys.h" #include "md5.h" #include "cheapcgi.h" void usage() /* Explain usage and exit. */ { errAbort( "pre-finish - tus daemon pre-finish hook program\n" "usage:\n" " pre-finish < input\n" ); } /* Command line validation table. */ static struct optionSpec options[] = { {NULL, 0}, }; int preFinish() /* pre-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 *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); } fprintf(stderr, "reqCookie='%s'\n", reqCookie); userName = getUserName(); if (!userName) { // 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); 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"); 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 - if (fileExists(dyStringContents(newFile))) + // 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->md5sum = md5HexForFile(row->location); row->parentDir = encodedParentDir ? encodedParentDir : ""; if (!isHubToolsUpload) { 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); } } 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 preFinish(); }