44ccfacbe3a3d4b300f80d48651c77837a4b571e galt Tue Apr 26 11:12:02 2022 -0700 SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix. diff --git src/hg/lib/hgFindSpecCustom.c src/hg/lib/hgFindSpecCustom.c index b38f68e..0ef3beb 100644 --- src/hg/lib/hgFindSpecCustom.c +++ src/hg/lib/hgFindSpecCustom.c @@ -1,539 +1,539 @@ /* hgFindSpecCustom - custom (not autoSQL generated) code for working * with hgFindSpec. This code is concerned with making the hgFindSpec * MySQL table out of the trackDb.ra files. */ /* 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 "jksql.h" #include "hgFindSpec.h" #include "hdb.h" #include "hui.h" #include "ra.h" #include "hash.h" #include "obscure.h" #include "regexHelper.h" #include "trackDb.h" /* ----------- End of AutoSQL generated code --------------------- */ static void anchorTermRegex(struct hgFindSpec *hfs) /* termRegex must match the whole term. If it doesn't already start with * ^ and end in $, add those (no need to make the trackDb.ra file even * harder to read with those extra magic chars :). */ { if (isNotEmpty(hfs->termRegex)) { char *orig = hfs->termRegex; char first = orig[0]; char last = orig[strlen(orig)-1]; char buf[512]; safef(buf, sizeof(buf), "%s%s%s", (first == '^') ? "" : "^", orig, (last == '$') ? "" : "$"); freeMem(hfs->termRegex); hfs->termRegex = cloneString(buf); } else if (hfs->termRegex == NULL) hfs->termRegex = ""; } static void checkTermRegex(struct hgFindSpec *hfs) /* Make sure termRegex compiles OK. */ { if (isNotEmpty(hfs->termRegex)) { char buf[256]; safef(buf, sizeof(buf), "hfsPolish: search %s: termRegex", hfs->searchName); // Discard returned compiled expression (void) regexCompile(hfs->termRegex, buf, (REG_EXTENDED | REG_ICASE | REG_NOSUB)); } } static void escapeTermRegex(struct hgFindSpec *hfs) /* Escape any '\' characters in termRegex for sql storage. */ { if (isNotEmpty(hfs->termRegex)) { char *orig = hfs->termRegex; hfs->termRegex = makeEscapedString(orig, '\\'); freeMem(orig); } } static char *genePredDefaultFormat = "select chrom,txStart,txEnd,name from %s where name like "; static char *bedDefaultFormat = "select chrom,chromStart,chromEnd,name from %s where name like "; static char *pslDefaultFormat = "select tName,tStart,tEnd,qName from %s where qName like "; static char *exactTermFormat = "'%s'"; static char *prefixTermFormat = "'%s%%'"; static char *fuzzyTermFormat = "'%%%s%%'"; static char *getQueryFormat(struct hgFindSpec *hfs) /* Fill in query format from searchType if necessary. */ { char *queryFormat = hfs->query; char buf[256]; if (isEmpty(queryFormat)) { char *baseFmt = ""; char *termFmt = ""; buf[0] = 0; if (sameString(hfs->searchType, "genePred")) baseFmt = genePredDefaultFormat; else if (sameString(hfs->searchType, "bed")) baseFmt = bedDefaultFormat; else if (sameString(hfs->searchType, "psl")) baseFmt = pslDefaultFormat; if (isNotEmpty(baseFmt)) { if (isNotEmpty(hfs->xrefQuery)) termFmt = exactTermFormat; else if (sameString(hfs->searchMethod, "fuzzy")) termFmt = fuzzyTermFormat; else if (sameString(hfs->searchMethod, "prefix")) termFmt = prefixTermFormat; else termFmt = exactTermFormat; } safef(buf, sizeof(buf), "%s%s", baseFmt, termFmt); queryFormat = cloneString(buf); } return(queryFormat); } static char *queryFormatRegex = "^select [[:alnum:]]+, ?[[:alnum:]]+, ?[[:alnum:]]+, ?[[:alnum:]]+ " "from %s where [[:alnum:]]+ (r?like|=) ['\"]?.*%s.*['\"]?$"; static char *exactTermFormatRegex = "['\"]?.*%s.*['\"]?$"; static char *prefixTermFormatRegex = "['\"]?%s.*%%['\"]?$"; static void checkQueryFormat(struct hgFindSpec *hfs) /* Make sure query looks right and jives with searchMethod. */ { if (isNotEmpty(hfs->query) && !hgFindSpecSetting(hfs, "dontCheckQueryFormat")) { if (! regexMatchNoCase(hfs->query, queryFormatRegex)) errAbort("hfsPolish: search %s: query needs to be of the format " "\"select field1,field2,field3,field4 from %%s " "where field4 like '%%s'\" " "(for prefix, '%%s%%%%'; for fuzzy, '%%%%%%s%%%%'), " "but instead is this:\n%s", hfs->searchName, hfs->query); if (isNotEmpty(hfs->xrefQuery)) { if (!regexMatchNoCase(hfs->query, exactTermFormatRegex)) errAbort("hfsPolish: search %s: there is an xrefQuery so query " "needs to end with %s (exact match to xref results).", hfs->searchName, exactTermFormat); } else { if (sameString(hfs->searchMethod, "fuzzy") && !endsWith(hfs->query, fuzzyTermFormat)) errAbort("hfsPolish: search %s: searchMethod is fuzzy so query " "needs to end with %s.", hfs->searchName, fuzzyTermFormat); else if (sameString(hfs->searchMethod, "prefix") && !regexMatchNoCase(hfs->query, prefixTermFormatRegex)) errAbort("hfsPolish: search %s: searchMethod is prefix so query " "needs to end with %s.", hfs->searchName, prefixTermFormat); else if (sameString(hfs->searchMethod, "exact") && !regexMatchNoCase(hfs->query, exactTermFormatRegex)) errAbort("hfsPolish: search %s: searchMethod is exact so query " "needs to end with %s.", hfs->searchName, exactTermFormat); } } } static char *xrefQueryFormatRegex = "select [[:alnum:]]+, ?[[:alnum:]]+(\\([^)]+\\))? from %s where [[:alnum:]]+ (like|=) ['\"]?[%s]+['\"]?"; static void checkXrefQueryFormat(struct hgFindSpec *hfs) /* Make sure xrefQuery looks right and jives with searchMethod. */ { if (isNotEmpty(hfs->xrefQuery) && !hgFindSpecSetting(hfs, "dontCheckXrefQueryFormat")) { if (! regexMatchNoCase(hfs->xrefQuery, xrefQueryFormatRegex)) errAbort("hfsPolish: search %s: xrefQuery needs to be of the format " "\"select field1,field2 from %%s where field2 like '%%s'\" " "(for prefix, '%%s%%%%'; for exact, '%%%%%%s%%%%'), " "but instead is this:\n%s", hfs->searchName, hfs->xrefQuery); if (sameString(hfs->searchMethod, "fuzzy") && !endsWith(hfs->xrefQuery, fuzzyTermFormat)) errAbort("hfsPolish: search %s: searchMethod is fuzzy so xrefQuery " "needs to end with %s.", hfs->searchName, fuzzyTermFormat); else if (sameString(hfs->searchMethod, "prefix") && !regexMatchNoCase(hfs->xrefQuery, prefixTermFormatRegex)) errAbort("hfsPolish: search %s: searchMethod is prefix so xrefQuery " "needs to end with %s.", hfs->searchName, prefixTermFormat); else if (sameString(hfs->searchMethod, "exact") && !regexMatchNoCase(hfs->xrefQuery, exactTermFormatRegex)) errAbort("hfsPolish: search %s: searchMethod is exact so xrefQuery " " needs to end with %s.", hfs->searchName, exactTermFormat); } } static void hgFindSpecPolish(char *db, struct hgFindSpec *hfs) /* Fill in missing values with defaults, check for consistency. */ { /* At least one of {searchName, searchTable} must be defined. */ if ((hfs->searchName == NULL) && (hfs->searchTable == NULL)) errAbort("hfsPolish: searchName or searchTable must be defined.\n"); if (hfs->searchName == NULL) hfs->searchName = cloneString(hfs->searchTable); if (hfs->searchTable == NULL) hfs->searchTable = cloneString(hfs->searchName); /* If searchType is not defined, query must be defined. */ if (hfs->searchType == NULL && hfs->query == NULL) errAbort("hfsPolish: search %s: if searchType is not defined, " "then query must be defined.\n", hfs->searchName); /* If one of {xrefTable,xrefQuery} is defined, both must be. */ if ((hfs->xrefTable == NULL) ^ (hfs->xrefQuery == NULL)) errAbort("hfsPolish: search %s: can't define xrefTable without xrefQuery " "or vice versa.\n", hfs->searchName); if (hfs->searchMethod == NULL) hfs->searchMethod = cloneString("exact"); if (hfs->searchType == NULL) hfs->searchType = ""; anchorTermRegex(hfs); checkTermRegex(hfs); escapeTermRegex(hfs); if (hfs->query == NULL) hfs->query = getQueryFormat(hfs); checkQueryFormat(hfs); checkXrefQueryFormat(hfs); if (hfs->xrefTable == NULL) hfs->xrefTable = ""; if (hfs->xrefQuery == NULL) hfs->xrefQuery = ""; if (hfs->searchPriority == 0.0) hfs->searchPriority = 1000.0; if (hfs->searchDescription == NULL) { char buf[512]; struct sqlConnection *conn = hAllocConn(db); struct trackDb *tdb = hMaybeTrackInfo(conn, hfs->searchTable); hFreeConn(&conn); if (tdb != NULL) safecpy(buf, sizeof(buf), tdb->longLabel); else safef(buf, sizeof(buf), "%s", hfs->searchTable); hfs->searchDescription = cloneString(buf); } if (hfs->searchSettings == NULL) hfs->searchSettings = cloneString(""); } int hgFindSpecCmp(const void *va, const void *vb) /* Compare to sort based on searchPriority. */ { const struct hgFindSpec *a = *((struct hgFindSpec **)va); const struct hgFindSpec *b = *((struct hgFindSpec **)vb); float dif = a->searchPriority - b->searchPriority; if (dif < 0) return -1; else if (dif == 0.0) return 0; else return 1; } static void hgFindSpecAddInfo(struct hgFindSpec *hfs, char *var, char *value) /* Add info from a variable/value pair to hgFindSpec. */ { if (sameString(var, "searchName")) hfs->searchName = cloneString(value); else if (sameString(var, "searchTable")) hfs->searchTable = cloneString(value); else if (sameString(var, "searchMethod")) hfs->searchMethod = cloneString(value); else if (sameString(var, "searchType")) hfs->searchType = cloneString(value); else if (sameWord(var, "shortCircuit")) hfs->shortCircuit = TRUE; else if (sameString(var, "termRegex")) hfs->termRegex = cloneString(value); else if (sameString(var, "query")) hfs->query = cloneString(value); else if (sameString(var, "xrefTable")) hfs->xrefTable = cloneString(value); else if (sameString(var, "xrefQuery")) hfs->xrefQuery = cloneString(value); else if (sameString(var, "searchPriority")) hfs->searchPriority = atof(value); else if (sameString(var, "searchDescription")) hfs->searchDescription = cloneString(value); else /* Add to settings. */ { if (hfs->settingsHash == NULL) hfs->settingsHash = hashNew(7); hashAdd(hfs->settingsHash, var, cloneString(value)); if (sameWord(var, "semiShortCircuit")) hfs->shortCircuit = TRUE; } } static void hgFindSpecAddRelease(struct hgFindSpec *hfs, char *releaseTag) /* Add release tag */ { hgFindSpecAddInfo(hfs, "release", cloneString(releaseTag)); } struct hgFindSpec *hgFindSpecFromRa(char *db, char *raFile, char *releaseTag) /* Load track info from ra file into list. */ { static boolean reEntered = FALSE; struct lineFile *lf = lineFileOpen(raFile, TRUE); char *line, *word; struct hgFindSpec *hfsList = NULL, *hfs; boolean done = FALSE; char *incFile; for (;;) { /* Seek to next line that starts with 'searchName' or 'searchTable' */ for (;;) { char *subRelease; if (!lineFileNext(lf, &line, NULL)) { done = TRUE; break; } if (startsWith("searchName", line) || startsWith("searchTable", line)) { lineFileReuse(lf); break; } else if ((incFile = trackDbInclude(raFile, line, &subRelease)) != NULL) { if (subRelease) trackDbCheckValidRelease(subRelease); if (releaseTag && subRelease && !sameString(subRelease, releaseTag)) errAbort("Include with release %s inside include with release %s line %d of %s", subRelease, releaseTag, lf->lineIx, lf->fileName); /* Set reEntered=TRUE whenever we recurse, so we don't polish * multiple times and get too many backslash-escapes. */ boolean reBak = reEntered; reEntered = TRUE; struct hgFindSpec *incHfs = hgFindSpecFromRa(db, incFile, subRelease); reEntered = reBak; hfsList = slCat(hfsList, incHfs); } } if (done) break; /* Allocate track structure and fill it in until next blank line. */ AllocVar(hfs); slAddHead(&hfsList, hfs); for (;;) { /* Break at blank line or EOF. */ if (!lineFileNext(lf, &line, NULL)) break; line = skipLeadingSpaces(line); if (line == NULL || line[0] == 0) break; /* Skip comments. */ if (line[0] == '#') continue; /* Parse out first word and decide what to do. */ word = nextWord(&line); if (line == NULL) errAbort("No value for %s line %d of %s", word, lf->lineIx, lf->fileName); line = trimSpaces(line); hgFindSpecAddInfo(hfs, word, line); } if (releaseTag) hgFindSpecAddRelease(hfs, releaseTag); } lineFileClose(&lf); if (! reEntered) { for (hfs = hfsList; hfs != NULL; hfs = hfs->next) { hgFindSpecPolish(db, hfs); } } slReverse(&hfsList); return hfsList; } char *hgFindSpecSetting(struct hgFindSpec *hfs, char *name) /* Return setting string or NULL if none exists. */ { if (hfs == NULL) errAbort("Program error: null hfs passed to hgFindSpecSetting."); if (hfs->settingsHash == NULL) hfs->settingsHash = raFromString(hfs->searchSettings); return hashFindVal(hfs->settingsHash, name); } char *hgFindSpecRequiredSetting(struct hgFindSpec *hfs, char *name) /* Return setting string or squawk and die. */ { char *ret = hgFindSpecSetting(hfs, name); if (ret == NULL) errAbort("Missing required %s setting in %s (%s) search spec", name, hfs->searchTable, hfs->searchName); return ret; } char *hgFindSpecSettingOrDefault(struct hgFindSpec *hfs, char *name, char *defaultVal) /* Return setting string, or defaultVal if none exists */ { char *val = hgFindSpecSetting(hfs, name); return (val == NULL ? defaultVal : val); } static struct slName *hgFindSpecNameList(char *db) /* Return the hgFindSpec table name(s) to use (based on trackDb name). */ { struct slName *trackDbList = hTrackDbList(); struct slName *specNameList = NULL; struct slName *tdbName; for (tdbName = trackDbList; tdbName != NULL; tdbName = tdbName->next) { char *subbed = replaceChars(tdbName->name, "trackDb", "hgFindSpec"); if (hTableExists(db, subbed)) slNameAddHead(&specNameList, subbed); freez(&subbed); } if (!specNameList) specNameList = slNameNew("hgFindSpec"); else slReverse(&specNameList); return specNameList; } static boolean haveSpecAlready(struct hgFindSpec *list, struct hgFindSpec *spec) /* Simply check to see if we have this search in our list already. */ { struct hgFindSpec *cur = list; while ((cur != NULL) && (!sameString(cur->searchName, spec->searchName))) cur = cur->next; return (cur) ? TRUE : FALSE; } static int hgFindSpecPriCmp(const void *va, const void *vb) /* Compare to sort by assending searchPriority. */ { const struct hgFindSpec *a = *((struct hgFindSpec **)va); const struct hgFindSpec *b = *((struct hgFindSpec **)vb); float diff = a->searchPriority - b->searchPriority; if (diff < 0) return -1; else if (diff > 0) return 1; else return 0; } static struct hgFindSpec *loadFindSpecsTbl(char *db, char *tblSpec, char *where) /* Load find specs for the given where and a given tblSpec. where can be * NULL. */ { struct hgFindSpec *hfsList = NULL; char *tbl; struct sqlConnection *conn = hAllocConnProfileTbl(db, tblSpec, &tbl); char query[512]; if (where != NULL) sqlSafef(query, sizeof(query), "select * from %s where %s", tbl, where); else sqlSafef(query, sizeof(query), "select * from %s", tbl); struct sqlResult *sr = sqlGetResult(conn, query); char **row = NULL; while ((row = sqlNextRow(sr)) != NULL) { struct hgFindSpec *hfs = hgFindSpecLoad(row); if (!haveSpecAlready(hfsList, hfs)) slAddHead(&hfsList, hfs); } sqlFreeResult(&sr); hFreeConn(&conn); return(hfsList); } static struct hgFindSpec *loadFindSpecs(char *db, char *where) /* Load find specs for the given where. */ { struct hgFindSpec *hfsList = NULL; struct slName *hgFindSpecList = hgFindSpecNameList(db); struct slName *oneSpec; for (oneSpec = hgFindSpecList; oneSpec != NULL; oneSpec = oneSpec->next) hfsList = slCat(hfsList, loadFindSpecsTbl(db, oneSpec->name, where)); slSort(&hfsList, hgFindSpecPriCmp); return(hfsList); } struct hgFindSpec *hgFindSpecGetSpecs(char *db, boolean shortCircuit) /* Load all short-circuit (or not) search specs from the current db, sorted by * searchPriority. */ { char where[64]; -sqlSafefFrag(where, sizeof(where), "shortCircuit = %d", shortCircuit); +sqlSafef(where, sizeof(where), "shortCircuit = %d", shortCircuit); struct hgFindSpec *hfsList = loadFindSpecs(db, where); slSort(&hfsList, hgFindSpecPriCmp); return(hfsList); } void hgFindSpecGetAllSpecs(char *db, struct hgFindSpec **retShortCircuitList, struct hgFindSpec **retAdditiveList) /* Load all search specs from the current db, separated according to * shortCircuit and sorted by searchPriority. */ { struct hgFindSpec *hfs, *hfsList = loadFindSpecs(db, NULL); struct hgFindSpec *shortList = NULL, *longList = NULL; while ((hfs = slPopHead(&hfsList)) != NULL) { if (hfs->shortCircuit) slAddHead(&shortList, hfs); else slAddHead(&longList, hfs); } if (retShortCircuitList != NULL) { slSort(&shortList, hgFindSpecPriCmp); *retShortCircuitList = shortList; } else hgFindSpecFreeList(&shortList); if (retAdditiveList != NULL) { slSort(&longList, hgFindSpecPriCmp); *retAdditiveList = longList; } else hgFindSpecFreeList(&longList); }