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/makeDb/hgFindSpec/hgFindSpec.c src/hg/makeDb/hgFindSpec/hgFindSpec.c index 03e2874..c876155 100644 --- src/hg/makeDb/hgFindSpec/hgFindSpec.c +++ src/hg/makeDb/hgFindSpec/hgFindSpec.c @@ -1,398 +1,400 @@ /* hgFindSpec - Create trackDb table from text files. */ /* Copyright (C) 2013 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 "sqlList.h" #include "jksql.h" #include "trackDb.h" #include "hgFindSpec.h" #include "hdb.h" #include "obscure.h" #include "portable.h" #include "dystring.h" #include "verbose.h" void usage() /* Explain usage and exit. */ { errAbort( "hgFindSpec - Create hgFindSpec table from trackDb.ra files.\n\n" "usage:\n" " hgFindSpec [options] orgDir database hgFindSpec hgFindSpec.sql hgRoot\n" "\n" "Options:\n" " -strict Add spec to hgFindSpec only if its table(s) exist.\n" " -raName=trackDb.ra - Specify a file name to use other than trackDb.ra\n" " for the ra files.\n" " -release=alpha|beta|public - Include trackDb entries with this release tag only.\n" ); } static struct optionSpec optionSpecs[] = { {"raName", OPTION_STRING}, {"strict", OPTION_BOOLEAN}, {"release", OPTION_STRING}, {NULL, 0} }; static char *raName = "trackDb.ra"; static char *release = "alpha"; // release tags #define RELEASE_ALPHA (1 << 0) #define RELEASE_BETA (1 << 1) #define RELEASE_PUBLIC (1 << 2) unsigned releaseBit = RELEASE_ALPHA; unsigned buildReleaseBits(char *rel) /* unpack the comma separated list of possible release tags */ { if (rel == NULL) return RELEASE_ALPHA | RELEASE_BETA | RELEASE_PUBLIC; char *oldString = cloneString(rel); unsigned bits = 0; while(rel) { char *end = strchr(rel, ','); if (end) *end++ = 0; rel = trimSpaces(rel); if (sameString(rel, "alpha")) bits |= RELEASE_ALPHA; else if (sameString(rel, "beta")) bits |= RELEASE_BETA; else if (sameString(rel, "public")) bits |= RELEASE_PUBLIC; else errAbort("track with release %s must have a release combination of alpha, beta, and public", oldString); rel = end; } return bits; } static struct hgFindSpec * pruneRelease(struct hgFindSpec *hfsList) /* Prune out alternate track entries for another release */ { /* Build up list that only includes things in this release. Release * can be inherited from parents. */ struct hgFindSpec *hfs; struct hgFindSpec *relList = NULL; struct hash *haveHash = hashNew(3); while ((hfs = slPopHead(&hfsList)) != NULL) { char *rel = hgFindSpecSetting(hfs, "release"); unsigned hfsRelBits = buildReleaseBits(rel); if (hfsRelBits & releaseBit) { /* we want to include this track, check to see if we already have it */ struct hashEl *hel; if ((hel = hashLookup(haveHash, hfs->searchName)) != NULL) { // TODO restore this warning to errAbort // This has been temporarily changed to a warning to avoid everybody being held up. char *one = (char *)hel->val; char *other = release; if (!one) one = "none"; if (!other) other = "none"; warn("ERROR: found two or more copies of %s: one with release %s, the other %s\n", hfs->searchName, one, other); } else { hashAdd(haveHash, hfs->searchName, rel); hashRemove(hfs->settingsHash, "release"); slAddHead(&relList, hfs); } } else verbose(3,"pruneRelease: removing '%s', release: '%s' != '%s'\n", hfs->searchName, rel, release); } freeHash(&haveHash); return relList; } void addVersion(boolean strict, char *database, char *dirName, char *raName, struct hash *uniqHash, struct hash *htmlHash, struct hgFindSpec **pSpecList) /* Read in specs from raName and add them to list/database if new. */ { struct hgFindSpec *hfsList = NULL, *hfs = NULL; struct hgFindSpec *hfsNext = NULL; hfsList = hgFindSpecFromRa(database, raName, NULL); /* prune records of the incorrect release */ hfsList = pruneRelease(hfsList); if (strict) { for (hfs = hfsList; hfs != NULL; hfs = hfsNext) { hfsNext = hfs->next; // for bigBed searchType's we don't check for the table because // it might not exist for bigDataUrl only tracks if (differentString(hfs->searchType, "bigBed") && ! hTableOrSplitExists(database, hfs->searchTable)) { if (verboseLevel() > 1) printf("%s missing\n", hfs->searchTable); slRemoveEl(&hfsList, hfs); } else if (hfs->xrefTable[0] != 0) { // Use sqlTableExists because xrefTable might be $db.$table, // not supported by hTableExists / hTableOrSplitExists // NOTE hfs->xrefTable can sometimes contain a comma-separated table list, // rather than just a single table. struct sqlConnection *conn = hAllocConn(database); char *tables = replaceChars(hfs->xrefTable, ",", " "); boolean exists = sqlTablesExist(conn, tables); hFreeConn(&conn); freeMem(tables); if (! exists) { if (verboseLevel() > 1) printf("%s (xref) missing\n", hfs->xrefTable); slRemoveEl(&hfsList, hfs); } } } } for (hfs = hfsList; hfs != NULL; hfs = hfsNext) { hfsNext = hfs->next; if (! hashLookup(uniqHash, hfs->searchName)) { hashAdd(uniqHash, hfs->searchName, hfs); slAddHead(pSpecList, hfs); } } } void updateBigTextField(struct sqlConnection *conn, char *table, char *whereField, char *whereVal, char *textField, char *textVal) /* Generate sql code to update a big text field that may include * newlines and stuff. */ { -struct dyString *dy = newDyString(4096); -sqlDyStringPrintf(dy, "update %s set %s=", table, textField); -dyStringQuoteString(dy, '"', textVal); -dyStringPrintf(dy, " where %s = '%s'", whereField, whereVal); +struct dyString *dy = dyStringNew(4096); +sqlDyStringPrintf(dy, "update %s set %s='%s'", table, textField, textVal); +sqlDyStringPrintf(dy, " where %s = '%s'", whereField, whereVal); sqlUpdate(conn, dy->string); -freeDyString(&dy); +dyStringFree(&dy); } char *subTrackName(char *create, char *tableName) /* Substitute tableName for whatever is between CREATE TABLE and first '(' freez()'s create passed in. */ { char newCreate[strlen(create) + strlen(tableName) + 10]; char *front = NULL; char *rear = NULL; int length = (strlen(create) + strlen(tableName) + 10); /* try to find "TABLE" or "table" in create */ front = strstr(create, "TABLE"); if(front == NULL) front = strstr(create, "table"); if(front == NULL) errAbort("hgFindSpec::subTrackName() - Can't find 'TABLE' in %s", create); /* try to find first "(" in string */ rear = strstr(create, "("); if(rear == NULL) errAbort("hgFindSpec::subTrackName() - Can't find '(' in %s", create); /* set to NULL character after "TABLE" */ front += 5; *front = '\0'; -sqlSafef(newCreate, length , "%-s %s %-s", create, tableName, rear); +// create argument from trusted source .sql file on disk +safef(newCreate, length, "%s %s %s", create, tableName, rear); return cloneString(newCreate); } void layerOn(boolean strict, char *database, char *dir, struct hash *uniqHash, struct hash *htmlHash, boolean mustExist, struct hgFindSpec **hfsList) /* Read search specs from trackDb.ra from directory, * and layer them on top of whatever is in hfsList. */ { char raFile[512]; if (raName[0] != '/') safef(raFile, sizeof(raFile), "%s/%s", dir, raName); else safef(raFile, sizeof(raFile), "%s", raName); if (fileExists(raFile)) { addVersion(strict, database, dir, raFile, uniqHash, htmlHash, hfsList); } else { if (mustExist) errAbort("%s doesn't exist!", raFile); } } static char *settingsFromHash(struct hash *hash) /* Create settings string from settings hash. */ { if (hash == NULL) return cloneString(""); else { struct dyString *dy = dyStringNew(1024); char *ret; struct hashEl *el, *list = hashElListHash(hash); slSort(&list, hashElCmp); for (el = list; el != NULL; el = el->next) dyStringPrintf(dy, "%s %s\n", el->name, (char *)el->val); slFreeList(&list); ret = cloneString(dy->string); dyStringFree(&dy); return ret; } } void hgFindSpec(char *org, char *database, char *hgFindSpecName, char *sqlFile, char *hgRoot, boolean strict) /* hgFindSpec - Create hgFindSpec table from text files. */ { struct hash *uniqHash = newHash(8); struct hash *htmlHash = newHash(8); struct hgFindSpec *hfsList = NULL, *hfs; char rootDir[512], orgDir[512], asmDir[512]; char *tab = rTempName(getTempDir(), hgFindSpecName, ".tab"); /* Create track list from hgRoot and hgRoot/org and hgRoot/org/assembly * ra format database. */ sprintf(rootDir, "%s", hgRoot); sprintf(orgDir, "%s/%s", hgRoot, org); sprintf(asmDir, "%s/%s/%s", hgRoot, org, database); layerOn(strict, database, asmDir, uniqHash, htmlHash, FALSE, &hfsList); layerOn(strict, database, orgDir, uniqHash, htmlHash, FALSE, &hfsList); layerOn(strict, database, rootDir, uniqHash, htmlHash, TRUE, &hfsList); slSort(&hfsList, hgFindSpecCmp); if (verboseLevel() > 0) printf("Loaded %d search specs total\n", slCount(hfsList)); /* Write to tab-separated file. */ { FILE *f = mustOpen(tab, "w"); for (hfs = hfsList; hfs != NULL; hfs = hfs->next) hgFindSpecTabOut(hfs, f); carefulClose(&f); } /* Update database */ { char *create, *end; - char query[256]; + char query[2048]; struct sqlConnection *conn = sqlConnect(database); /* Load in table definition. */ readInGulp(sqlFile, &create, NULL); create = trimSpaces(create); create = subTrackName(create, hgFindSpecName); end = create + strlen(create)-1; if (*end == ';') *end = 0; - sqlRemakeTable(conn, hgFindSpecName, create); + sqlSafef(query, sizeof query, create, NULL); + sqlRemakeTable(conn, hgFindSpecName, query); /* Load in regular fields. */ sqlSafef(query, sizeof query, "load data local infile '%s' into table %s", tab, hgFindSpecName); sqlUpdate(conn, query); /* Load in settings fields. */ for (hfs = hfsList; hfs != NULL; hfs = hfs->next) { if (hfs->settingsHash != NULL) { char *settings = settingsFromHash(hfs->settingsHash); updateBigTextField(conn, hgFindSpecName, "searchName", hfs->searchName, "searchSettings", settings); freeMem(settings); } } - sqlUpdate(conn, NOSQLINJ "flush tables"); + sqlSafef(query, sizeof query, "flush tables"); + sqlUpdate(conn, query); sqlDisconnect(&conn); if (verboseLevel() > 0) printf("Loaded database %s\n", database); } unlink(tab); } void adjustTrackDbName(char *hgFindSpecName) /* Some hgFindSpec info is pulled from the trackDb table. When the * hgFindSpec name is hgFindSpec_$USER and the user's ~/.hg.conf file * specifies trackDb_$USER, that works fine. However, when the * hgFindSpec name is just hgFindSpec (as for make alpha / make strict * invocations), but ~/hg.conf says trackDb_$USER, they're inconsistent. * So to make a long story short -- circumvent the ~/.hg.conf! */ { if (sameString(hgFindSpecName, "hgFindSpec")) hSetTrackDbName("trackDb"); else if (startsWith(hgFindSpecName, "hgFindSpec_")) { char trackDbName[256]; safef(trackDbName, sizeof(trackDbName), "trackDb_%s", hgFindSpecName + strlen("hgFindSpec_")); hSetTrackDbName(trackDbName); } } unsigned getReleaseBit(char *release) /* make sure that the tag is a legal release */ { if (sameString(release, "alpha")) return RELEASE_ALPHA; if (sameString(release, "beta")) return RELEASE_BETA; if (sameString(release, "public")) return RELEASE_PUBLIC; errAbort("release must be alpha, beta, or public"); return 0; /* make compiler happy */ } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 6) usage(); raName = optionVal("raName", raName); release = optionVal("release", release); releaseBit = getReleaseBit(release); adjustTrackDbName(argv[3]); hgFindSpec(argv[1], argv[2], argv[3], argv[4], argv[5], optionExists("strict")); return 0; }