c3788110e8d865774fff8197cf5b47350472ba64 chmalee Tue Aug 4 11:26:55 2026 -0700 Fix hubSpace hook error handling and nested hub path handling, refs #37964 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/hgHubConnect/hooks/hooklib.c src/hg/hgHubConnect/hooks/hooklib.c index 6c4caf6cb62..23d5bc3bcc7 100644 --- src/hg/hgHubConnect/hooks/hooklib.c +++ src/hg/hgHubConnect/hooks/hooklib.c @@ -1,203 +1,203 @@ /* hooklib.c - functions common to all the different tusd hooks */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #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 "cheapcgi.h" #include "hooklib.h" char *prettyFileSize(long size) /* Return a string representing the size of a file */ { char buf[32]; sprintWithGreekByte(buf, sizeof(buf), size); return cloneString(buf); } char *encodePath(char *path) /* Return a string where each individual component of a '/' separated * string has been cgiEncoded, but not the '/' chars themselves */ { int maxSeps = 256; char *pathArr[maxSeps]; // errAbort if more than maxSeps subdirs char *copy = cloneString(path); int numChops = chopString(copy, "/", pathArr, maxSeps); if (numChops >= maxSeps) errAbort("Too many subdirectories. Fix filesystem layout of upload and try again"); struct dyString *ret = dyStringNew(0); int i = 0; for (; i < numChops; i++) { // we can ignore .. and . in paths, it is an error if hubtools is creating these names // don't errAbort right now because hubtools does send things like 'hubName/.' // as a parentDir, but that should be fixed soon if (sameString(pathArr[i], ".") || sameString(pathArr[i], "..")) { continue; } dyStringPrintf(ret, "%s/", cgiEncodeFull(pathArr[i])); } return dyStringCannibalize(&ret); } char *normalizeParentDir(char *parentDir) /* Return parentDir with any surrounding whitespace trimmed off, or NULL if it was NULL. * The pre-create and pre-finish hooks each build paths from this metadata value * independently, so they have to normalize it identically or they end up disagreeing * about which directory the upload belongs in */ { if (parentDir == NULL) return NULL; return trimSpaces(cloneString(parentDir)); } boolean isValidParentDir(char *parentDir) /* Return TRUE if every '/' separated component of parentDir holds only alphanumeric, - * period or underscore characters. NULL or empty means the top level of the user's - * directory, which is allowed. Mirrors the same named check in hgMyData.js, which the - * browser does first, but hubtools and any other tus client come straight here */ + * period or underscore characters. NULL or empty is invalid, every upload belongs to + * a hub. Mirrors the same named check in hgMyData.js, which the browser does first, + * but hubtools and any other tus client come straight here */ { if (isEmpty(parentDir)) - return TRUE; + return FALSE; if (startsWith("/", parentDir) || endsWith(parentDir, "/")) return FALSE; int maxSeps = 256; char *pathArr[maxSeps]; char *copy = cloneString(parentDir); int numChops = chopString(copy, "/", pathArr, maxSeps); int i = 0; for (; i < numChops; i++) { char *component = pathArr[i]; if (isEmpty(component) || sameString(component, ".") || sameString(component, "..")) return FALSE; char *c = component; for (; *c != '\0'; c++) { if (!isalnum((unsigned char)*c) && *c != '.' && *c != '_') return FALSE; } } return TRUE; } char *setUploadPath(char *userName, char *fileName, char *parentDir, boolean forceOverwrite) /* return the path, relative to hg.conf tusdDataDir, where we will store this upload * ensures all subdirectories on the final path will exist, and then returns * userPrefix/userName/parentDir/fileName * NOTE: This must be a relative path or tusd will complain */ { char *dataDir = getDataDir(userName); struct dyString *fullFilePath = dyStringNew(0); struct dyString *retPath = dyStringNew(0); // if parentDir provided we are throwing the files in there. Stays empty when there // is no parentDir so the path we return below is still correct char *encodedParentDir = ""; if (parentDir) { encodedParentDir = encodePath(parentDir); if (!endsWith(encodedParentDir, "/")) encodedParentDir = catTwoStrings(encodedParentDir, "/"); dataDir = catTwoStrings(dataDir, encodedParentDir); } dyStringPrintf(fullFilePath, "%s%s", dataDir, fileName); fprintf(stderr, "DEBUG: setUploadPath of '%s' to '%s'\n", fileName, dyStringContents(fullFilePath)); // 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(fullFilePath)) && !forceOverwrite) { errAbort("file '%s' exists already, not overwriting", dyStringContents(fullFilePath)); } else { // since we are returning a ChangeFileInfo response in pre-create, tusd will write // the uploaded file into the users directory for us, ensure the subdirs exist int oldUmask = 00; if (!isDirectory(dataDir)) { fprintf(stderr, "making directory '%s'\n", dataDir); // the directory needs to be 777 for apache, ignore umask for now oldUmask = umask(0); makeDirsOnPath(dataDir); // restore umask umask(oldUmask); } // now we can construct the path relative to tusd uploadDir. This must use the // same encoded parentDir as the dataDir we just made above: if it doesn't, tusd // creates the unencoded directory itself when it writes the file, leaving two // directories for one hub and the file in the one we never made dyStringPrintf(retPath, "%s/%s%s", getEncodedUserNamePath(userName), encodedParentDir, fileName); return dyStringCannibalize(&retPath); } // on error return NULL return NULL; } void fillOutHttpResponseError(struct jsonElement *response) { fprintf(stderr, "http response error!\n"); } void fillOutHttpResponseSuccess(struct jsonElement *response) { fprintf(stderr, "http response success!\n"); // DEBUG: comment out after a few releases jsonPrintToFile(response, NULL, stderr, 0); } struct jsonElement *makeDefaultResponse() /* Create the default response json with some fields pre-filled */ { struct hash *defHash = hashNew(0); struct jsonElement *response = newJsonObject(defHash); // only the HTTP Response object is important to have by default, the other // fields will be created as needed struct jsonElement *httpResponse = newJsonObject(hashNew(0)); jsonObjectAdd(httpResponse, HTTP_STATUS, newJsonNumber(200)); // default to a successful response jsonObjectAdd(httpResponse, HTTP_BODY, newJsonString("")); struct jsonElement *header = newJsonObject(hashNew(0)); jsonObjectAdd(header, HTTP_CONTENT_TYPE, newJsonString(HTTP_CONTENT_TYPE_STR)); jsonObjectAdd(httpResponse, HTTP_HEADER, header); jsonObjectAdd(response, HTTP_NAME, httpResponse); return response; } void rejectUpload(struct jsonElement *response, char *msg, ...) /* Set the keys for stopping an upload */ { // first set the necessary keys to reject the request jsonObjectAdd(response, REJECT_SETTING, newJsonBoolean(TRUE)); jsonObjectAdd(response, STOP_SETTING, newJsonBoolean(TRUE)); // now format the message va_list args; va_start(args, msg); struct dyString *ds = dyStringNew(0); dyStringVaPrintf(ds, msg, args); va_end(args); // find the HTTPResponse object and fill it out with msg: struct jsonElement *httpResponse = jsonFindNamedField(response, "", HTTP_NAME); jsonObjectAdd(httpResponse, HTTP_STATUS, newJsonNumber(500)); jsonObjectAdd(httpResponse, HTTP_BODY, newJsonString(dyStringCannibalize(&ds))); } boolean isFileTypeRecognized(char *fileName) /* Return true if this file one of our recognized types */ { return TRUE; }