6d5eab1bc6022f0ed9c79637a98016d8e91d1516 angie Thu Jun 27 10:33:42 2019 -0700 Instead of adding special cases for CGIs that are surprised by empty cart vars for lost trash files, just leave the lost trash file paths in place because the CGIs already know how to deal with those. refs #22440 diff --git src/hg/hgSession/sessionData.c src/hg/hgSession/sessionData.c index 41cc38c..b14caaa 100644 --- src/hg/hgSession/sessionData.c +++ src/hg/hgSession/sessionData.c @@ -1,505 +1,505 @@ /* sessionData -- if hg.conf defines sessionDataDir & sessionDataDbPrefix, scan cart for trash filesb * and customTrash tables; move them to a safe location and update paths in cart, files, tables. */ /* Copyright (C) 2019 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "cart.h" #include "cheapcgi.h" #include "customComposite.h" #include "customTrack.h" #include "hdb.h" #include "hgConfig.h" #include "md5.h" #include "trashDir.h" INLINE boolean isTrashPath(char *path) /* Return TRUE if path starts with trashDir. */ { return startsWith(trashDir(), path); } static char *sessionDataPathFromTrash(char *trashPath, char *sessionDir) /* Make a new path from a trash path -- replace "../trash" with safe location. */ { if (!isTrashPath(trashPath)) errAbort("sessionDataPathFromTrash: input is non-trash path '%s'", trashPath); return replaceChars(trashPath, trashDir(), sessionDir); } static char *maybeReadlink(char *path) /* If path is a symbolic link, then alloc & return the link target, otherwise NULL. */ { char *linkTarget = NULL; struct stat stat; if (lstat(path, &stat) != 0) // expired file return NULL; if (S_ISLNK(stat.st_mode)) { linkTarget = needMem(stat.st_size + 1); int len = readlink(path, linkTarget, stat.st_size); if (len < 0) errnoAbort("maybeReadlink: lstat says '%s' is symbolic link but readlink failed", path); else if (len != stat.st_size) errAbort("maybeReadLink: st_size is %d but readlink read %d bytes", (int)stat.st_size, len); // readlink doesn't null-terminate linkTarget[len] = '\0'; } return linkTarget; } static void makeDirsForFile(char *path) /* If path has directories before filename, create them if they don't already exist. */ { if (path && strchr(path, '/')) { char pathCopy[strlen(path)+1]; safecpy(pathCopy, sizeof(pathCopy), path); char *p = strrchr(pathCopy, '/'); *p = '\0'; makeDirsOnPath(pathCopy); } } static void moveAndLink(char *oldPath, char *newPath) /* Make a hard link from newPath to oldPath; unlink oldPath; symlink oldPath to newPath. */ { if (link(oldPath, newPath) != 0) errnoAbort("moveAndLink: link(oldPath='%s', newPath='%s') failed", oldPath, newPath); if (unlink(oldPath) != 0) errnoAbort("moveAndLink: unlink(oldPath='%s') failed", oldPath); if (symlink(newPath, oldPath) != 0) errnoAbort("moveAndLink: symlink(newPath='%s', oldPath='%s') failed", newPath, oldPath); } static char *saveTrashFile(char *trashPath, char *sessionDir) /* If trashPath exists and is not already a soft-link to sessionDir, alloc and return a new path in * sessionDir; move trashPath to new path and soft-link from trashPath to new path. * If trashPath is already a soft-link, return the path that it links to. * Return NULL if trashPath does not exist (can happen with expired custom track files). */ { char *newPath = NULL; if (fileExists(trashPath)) { char *existingLink = maybeReadlink(trashPath); if (existingLink) { // It may be a multi-directory-level relative symlink created by the trashCleaner scripts if (existingLink[0] != '/') { char trashPathDir[PATH_LEN]; splitPath(trashPath, trashPathDir, NULL, NULL); char fullLinkPath[strlen(trashPathDir) + strlen(existingLink) + 1]; safef(fullLinkPath, sizeof fullLinkPath, "%s%s", trashPathDir, existingLink); newPath = realpath(fullLinkPath, NULL); } else newPath = existingLink; } else { newPath = sessionDataPathFromTrash(trashPath, sessionDir); if (fileExists(newPath)) errAbort("saveTrashFile: new path '%s' already exists", newPath); makeDirsForFile(newPath); moveAndLink(trashPath, newPath); } } return newPath; } static char *nextTrashPath(char *string, char *trashDirPrefix) /* Alloc & return the next file path in string that starts with "../trash/", or NULL. */ { char *trashPath = NULL; if (isNotEmpty(string)) { char *pathStart = stringIn(trashDirPrefix, string); if (pathStart) { char *end = pathStart + strlen(trashDirPrefix); // Assume our trash paths don't contain spaces, quotes, '+' or '&', and will be followed by // a space, quote, '+', '&', or end of string. while (*end && !isspace(*end) && *end != '\'' && *end != '"' && *end != '+' && *end != '&') end++; trashPath = cloneStringZ(pathStart, (end - pathStart)); } } return trashPath; } struct stealthFile /* Info for detecting stealth files, i.e. files not explicitly named in the cart or track lines, * but whose names are just a suffix added to a trash file that is explicitly named. */ { char *contains; // Trash path contains this string char *ending; // Trash path ends with this char *suffix; // Stealth file is trash path plus this suffix }; static struct stealthFile stealthFiles[] = { { "custRgn", ".bed", ".sha1" }, { "hggUp", ".cgb", ".cgm" }, }; static void saveStealthFile(char *trashPath, char *sessionDir) /* Some trash files have shadow files -- similarly named, but not in any cart var. */ { int i; for (i = 0; i < ArraySize(stealthFiles); i++) { struct stealthFile *sf = &stealthFiles[i]; if (endsWith(trashPath, sf->ending) && stringIn(sf->contains, trashPath)) { char stealthPath[strlen(trashPath) + strlen(sf->suffix) + 1]; safef(stealthPath, sizeof stealthPath, "%s%s", trashPath, sf->suffix); saveTrashFile(stealthPath, sessionDir); break; } } } static void saveTrashPaths(char **retString, char *sessionDir, boolean urlEncoded) /* If sessionDir is provided, then for each instance of "../trash" in *retString, move * the trash file into an analogous location in sessionDir and replace the path in retString. * If urlEncoded, look for encoded "..%2ftrash" and replace with encoded new path. */ { if (retString && sessionDir) { char *trashDirPrefix = urlEncoded ? cgiEncode(trashDir()) : trashDir(); char *encTrashPath; while ((encTrashPath = nextTrashPath(*retString, trashDirPrefix)) != NULL) { int encLen = strlen(encTrashPath); char trashPath[encLen+1]; if (urlEncoded) cgiDecode(encTrashPath, trashPath, encLen); else safecpy(trashPath, sizeof(trashPath), encTrashPath); char *newPath = saveTrashFile(trashPath, sessionDir); if (newPath) { saveStealthFile(trashPath, sessionDir); char *encNewPath = urlEncoded ? cgiEncode(newPath) : newPath; char *newString = replaceChars(*retString, encTrashPath, encNewPath); freez(retString); *retString = newString; if (urlEncoded) freeMem(encNewPath); } else { // No new path -- trash file doesn't exist. Remove from retString to avoid inf loop. char *newString = replaceChars(*retString, encTrashPath, ""); freez(retString); *retString = newString; } freeMem(encTrashPath); freeMem(newPath); } if (urlEncoded) freeMem(trashDirPrefix); } } static char *sessionDataDbTableName(char *tableName, char *sessionDataDbPrefix, char *dbSuffix) /* Alloc and return a new table name that includes a db derived from sessionDataDbPrefix. */ { struct dyString *dy = dyStringCreate("%s%s.%s", sessionDataDbPrefix, dbSuffix, tableName); return dyStringCannibalize(&dy); } static char *findTableInSessionDataDbs(struct sqlConnection *conn, char *sessionDataDbPrefix, char *tableName) /* Given a tableName (no db. prefix), if it exists in any of the sessionDataPrefix* dbs * then return the full db.tableName, otherwise NULL. */ { int day; for (day = 1; day <= 31; day++) { char dbDotTable[strlen(sessionDataDbPrefix) + 3 + strlen(tableName) + 1]; safef(dbDotTable, sizeof dbDotTable, "%s%02d.%s", sessionDataDbPrefix, day, tableName); if (sqlTableExists(conn, dbDotTable)) return cloneString(dbDotTable); } return NULL; } static char *saveTrashTable(char *tableName, char *sessionDataDbPrefix, char *dbSuffix) /* Move trash tableName out of customTrash to a sessionDataDbPrefix database, unless that * has been done already. If table does not exist in either customTrash or customData*, * then return NULL; otherwise return the new database.table name. */ { char *newDbTableName = sessionDataDbTableName(tableName, sessionDataDbPrefix, dbSuffix); struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); if (! sqlTableExists(conn, newDbTableName)) { if (! sqlTableExists(conn, tableName)) { // It's possible that this table was already saved and moved out of customTrash as part // of some other saved session. We don't have a way of leaving a symlink in customTrash. newDbTableName = findTableInSessionDataDbs(conn, sessionDataDbPrefix, tableName); } else { struct dyString *dy = sqlDyStringCreate("rename table %s to %s", tableName, newDbTableName); sqlUpdate(conn, dy->string); dyStringFree(&dy); } } else if (sqlTableExists(conn, tableName)) errAbort("saveTrashTable: both %s and %s exist", tableName, newDbTableName); hFreeConn(&conn); return newDbTableName; } static void replaceColumnValue(struct sqlConnection *conn, char *tableName, char *columnName, char *newVal) /* Replace all tableName.columnName values with newVal. */ { struct dyString *dy = sqlDyStringCreate("update %s set %s = '%s'", tableName, columnName, newVal); sqlUpdate(conn, dy->string); dyStringFree(&dy); } static char *fileColumnNames[] = { "file", // wiggle tables "extFile", // maf tables "fileName", // vcf tables }; static void updateSessionDataTablePaths(char *tableName, char *sessionDir) /* If table contains a trash path and sessionDir is given, then replace * the old trash path in the table with the new sessionDir location. * NOTE: this supports only wiggle, maf and vcf customTrash tables, and relies * on the assumption that each customTrash table refers to only one trash path in all rows. */ { if (sessionDir) { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); int ix; for (ix = 0; ix < ArraySize(fileColumnNames); ix++) { char *columnName = fileColumnNames[ix]; if (sqlFieldIndex(conn, tableName, columnName) >= 0) { struct dyString *dy = sqlDyStringCreate("select %s from %s limit 1", columnName, tableName); char *trashPath = sqlQuickString(conn, dy->string); // For some reason, customTrash tables' filename paths can begin with "./../trash" char *actualTrashPath = trashPath; if (startsWith("./", trashPath) && isTrashPath(trashPath+2)) actualTrashPath = trashPath+2; if (isTrashPath(actualTrashPath)) { char *newPath = saveTrashFile(actualTrashPath, sessionDir); if (newPath) replaceColumnValue(conn, tableName, columnName, newPath); freeMem(newPath); } dyStringFree(&dy); freeMem(trashPath); break; } } hFreeConn(&conn); } } static void saveDbTableName(char **retString, char *sessionDataDbPrefix, char *dbSuffix, char *sessionDir) /* If sessionDataDbPrefix is given then scan for dbTableName setting; if found, move table and * update retString with new location. Also, if table contains a trash path and sessionDir * is given, then replace the old trash path in the table with the new sessionDir location. */ { char *prefix = "dbTableName"; if (sessionDataDbPrefix) { int prefixLen = strlen(prefix); char *setting = stringIn(prefix, *retString); if (setting && (setting[prefixLen] == '=' || setting[prefixLen] == ' ')) { char *start = setting + prefixLen + 1; char quote = *start; if (quote == '\'' || quote == '"') start++; else quote = '\0'; char *end = start; while (*end && ((quote && *end != quote) || (!quote && !isspace(*end)))) end++; if (stringIn(prefix, end)) errAbort("saveDbTableName: encountered two instances of '%s', expected 0 or 1", prefix); char *tableName = cloneStringZ(start, (end - start)); if (!startsWith(sessionDataDbPrefix, tableName)) { char *newDbTableName = saveTrashTable(tableName, sessionDataDbPrefix, dbSuffix); if (newDbTableName) { updateSessionDataTablePaths(newDbTableName, sessionDir); char *newString = replaceChars(*retString, tableName, newDbTableName); freez(retString); *retString = newString; freeMem(newDbTableName); } } freeMem(tableName); } } } static char *newCtTrashFile() /* Alloc and return the name of a new trash file to hold custom track metadata. */ { struct tempName tn; trashDirFile(&tn, "ct", CT_PREFIX, ".ctfile"); return cloneString(tn.forCgi); } static char *saveTrackFile(struct cart *cart, char *varName, char *oldFile, char *sessionDataDbPrefix, char *dbSuffix, char *sessionDir) /* oldFile contains custom track lines or track collection hub trackDb; scan for trashDir paths * and/or customTrash tables and move files and tables to safe locations per sessionDataDbPrefix and * sessionDir. If oldFile does not exist or has already been saved, return NULL. */ { char *newFile = NULL; if (fileExists(oldFile)) { if (isTrashPath(oldFile)) { struct lineFile *lf = lineFileOpen(oldFile, TRUE); if (isNotEmpty(sessionDir)) newFile = sessionDataPathFromTrash(oldFile, sessionDir); else newFile = newCtTrashFile(); if (fileExists(newFile)) errAbort("saveTrackFile: new file '%s' already exists", newFile); makeDirsForFile(newFile); FILE *newF = mustOpen(newFile, "w"); char *line; while (lineFileNext(lf, &line, NULL)) { char *s = skipLeadingSpaces(line); if (*s != '\0' && *s != '#') { char *trackLine = cloneString(line); saveTrashPaths(&trackLine, sessionDir, FALSE); saveDbTableName(&trackLine, sessionDataDbPrefix, dbSuffix, sessionDir); fprintf(newF, "%s\n", trackLine); freeMem(trackLine); } else fprintf(newF, "%s\n", line); } carefulClose(&newF); fprintf(stderr, "Wrote new file %s\n", newFile); if (isNotEmpty(sessionDir)) { if (unlink(oldFile) != 0) errnoAbort("saveTrackFile: unlink(oldFile='%s') failed", oldFile); if (symlink(newFile, oldFile) != 0) errnoAbort("saveTrackFile: symlink(newFile='%s', oldFile='%s') failed", newFile, oldFile); fprintf(stderr, "symlinked %s to %s\n", oldFile, newFile); } cartSetString(cart, varName, newFile); } } else cartRemove(cart, varName); return newFile; } char *sessionDirFromNames(char *sessionDataDir, char *encUserName, char *encSessionName) /* Alloc and return session data directory: * sessionDataDir/2ByteHashOfEncUserName/encUserName/8ByteHashOfEncSessionName * 2ByteHashOfEncUserName spreads userName values across up to 256 subdirectories because * we have ~15000 distinct namedSessionDb.userName values in 2019. * 8ByteHashOfEncSessionName because session names can be very long. */ { char *dir = NULL; if (isNotEmpty(sessionDataDir)) { if (sessionDataDir[0] != '/') errAbort("config setting sessionDataDir must be an absolute path (starting with '/')"); char *userHash = md5HexForString(encUserName); userHash[2] = '\0'; char *sessionHash = md5HexForString(encSessionName); sessionHash[8] = '\0'; struct dyString *dy = dyStringCreate("%s/%s/%s/%s", sessionDataDir, userHash, encUserName, sessionHash); dir = dyStringCannibalize(&dy); freeMem(sessionHash); } return dir; } INLINE boolean cartVarIsCustomComposite(char *cartVar) /* Return TRUE if cartVar starts with "customComposite-". */ { return startsWith(customCompositeCartName "-", cartVar); } static char *dayOfMonthString() /* Return a two-character string with the current day of the month [01..31]. Do not free. * (Yeah, not [0..30]! See man 3 localtime.) */ { static char dayString[16]; time_t now = time(NULL); struct tm *tm = localtime(&now); safef(dayString, sizeof dayString, "%02u", tm->tm_mday); return dayString; } void saveSessionData(struct cart *cart, char *encUserName, char *encSessionName, char *dbSuffix) /* If hg.conf specifies safe places to store files and/or tables that belong to user sessions, * then scan cart for trashDir files and/or customTrash tables, store them in safe locations, * and update cart to point to the new locations. */ { char *sessionDataDbPrefix = cfgOption("sessionDataDbPrefix"); char *sessionDataDir = cfgOption("sessionDataDir"); // Use (URL-encoded) userName and sessionName to make directory hierarchy under sessionDataDir char *sessionDir = sessionDirFromNames(sessionDataDir, encUserName, encSessionName); if (isNotEmpty(sessionDataDbPrefix) || isNotEmpty(sessionDir)) { if (isNotEmpty(sessionDataDbPrefix) && dbSuffix == NULL) dbSuffix = dayOfMonthString(); struct slPair *allVars = cartVarsLike(cart, "*"); struct slPair *var; for (var = allVars; var != NULL; var = var->next) { if (startsWith(CT_FILE_VAR_PREFIX, var->name) || cartVarIsCustomComposite(var->name)) { // val is file that contains references to trash files and customTrash db tables; // replace with new file containing references to saved files and tables. char *oldTrackFile = cloneString(var->val); char *newTrackFile = saveTrackFile(cart, var->name, var->val, sessionDataDbPrefix, dbSuffix, sessionDir); if (newTrackFile && cartVarIsCustomComposite(var->name)) cartReplaceHubVars(cart, var->name, oldTrackFile, newTrackFile); freeMem(oldTrackFile); freeMem(newTrackFile); } else { // Regular cart var; save trash paths (possibly encoded) in value, if any are found. char *newVal = cloneString(var->val); saveTrashPaths(&newVal, sessionDir, FALSE); saveTrashPaths(&newVal, sessionDir, TRUE); - // Special case for lost hgPcr/blat result trash files: prevent errAbort in hgTracks - if ((startsWith("hgPcrResult_", var->name) || sameString("ss", var->name)) && - sameString(newVal, " ")) - cartRemove(cart, var->name); - else if (newVal != var->val && differentString(newVal, var->val)) + // If the variable would end up with an empty value, leave the old deleted trash file + // name in place because the CGIs know how to deal with that but may error out if the + // value is just empty. + if (newVal != var->val && isNotEmpty(skipLeadingSpaces(newVal)) && + differentString(newVal, var->val)) cartSetString(cart, var->name, newVal); freeMem(newVal); } } } }