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/hgLoadOutJoined/hgLoadOutJoined.c src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c index 82c6d5b..dfd187b 100644 --- src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c +++ src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c @@ -1,317 +1,317 @@ /* hgLoadOutJoined - fixed loading RepeatMasker .out files. */ /* correctly load the id field, and new meaning for repStart, repEnd, repLeft */ /* 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 "dystring.h" #include "options.h" #include "cheapcgi.h" #include "hCommon.h" #include "hdb.h" #include "jksql.h" #include "rmskOut2.h" char *createRmskOut = "CREATE TABLE %s (\n" " bin smallint unsigned not null, # bin index field for range queries\n" " swScore int unsigned not null, # Smith Waterman alignment score\n" " milliDiv int unsigned not null, # Base mismatches in parts per thousand\n" " milliDel int unsigned not null, # Bases deleted in parts per thousand\n" " milliIns int unsigned not null, # Bases inserted in parts per thousand\n" " genoName varchar(255) not null, # Genomic sequence name\n" " genoStart int unsigned not null, # Start in genomic sequence\n" " genoEnd int unsigned not null, # End in genomic sequence\n" " genoLeft int not null, # -#bases after match in genomic sequence\n" " strand char(1) not null, # Relative orientation + or -\n" " repName varchar(255) not null, # Name of repeat\n" " repClass varchar(255) not null, # Class of repeat\n" " repFamily varchar(255) not null, # Family of repeat\n" " repStart int not null, # Start in repeat sequence - regardless of orient\n" " repEnd int not null, # End in repeat sequence - regardless of orient\n" " repLeft int not null, # -#bases after match in repeat sequence - regardless of orient\n" " id int not null, # The ID of the hit. Used to link related fragments\n" " #Indices\n"; boolean noBin = FALSE; char *tabFileName = NULL; char *suffix = NULL; int badRepCnt = 0; /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"tabFile", OPTION_STRING}, {"tabfile", OPTION_STRING}, {"table", OPTION_STRING}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "hgLoadOutJoined - load new style (2014) RepeatMasker .out files into database\n" "usage:\n" " hgLoadOutJoined database file(s).out\n" "For multiple files chrN.out this will create the single table 'rmskOutBaseline'\n" "in the database.\n" "options:\n" " -tabFile=text.tab - don't actually load database, just create tab file\n" " -table=name - use a different suffix other than the default (rmskOutBaseline)"); } void badFormat(struct lineFile *lf, int id) /* Print generic bad format message. */ { errAbort("Badly formatted line %d in %s\n", lf->lineIx, lf->fileName); } int makeMilli(char *s, struct lineFile *lf) /* Convert ascii floating point to parts per thousand representation. */ { /* Cope with -0.0 and -0.2 etc.*/ if (s[0] == '-') { if (!sameString(s, "-0.0")) warn("Strange perc. field %s line %d of %s", s, lf->lineIx, lf->fileName); s = "0.0"; } if (!isdigit(s[0])) badFormat(lf,1); return round(10.0*atof(s)); } static int parenInt(char *s, struct lineFile *lf) /* Convert from ascii to int where a parenthesized integer is the same */ { if (s[0] == '(') return atoi(s+1); else return atoi(s); } boolean checkRepeat(struct rmskOut2 *r, struct lineFile *lf) /* check for bogus repeat */ { /* this is bogus on both strands */ if (r->repStart > r->repEnd) { badRepCnt++; if (verboseLevel() > 1) { verbose(2, "bad rep range [%d, %d] line %d of %s %s:%d-%d\n", r->repStart, r->repEnd, lf->lineIx, lf->fileName, r->genoName, r->genoStart, r->genoEnd); } return FALSE; } return TRUE; } FILE *theFile = NULL; struct hash *chromFpHash = NULL; char *defaultTempName = "rmskOutBaseline.tab"; FILE *getFileForChrom(char *chrom) /* Return the appropriate file pointer for the given chrom */ { char *tempName = tabFileName ? tabFileName : defaultTempName; if (theFile == NULL) theFile = mustOpen(tempName, "w"); return theFile; } void helCarefulClose(struct hashEl *hel) /* Call carefulClose on hashed file pointer. */ { FILE *f = (FILE *)(hel->val); carefulClose(&f); } void closeFiles() /* Close the * single file pointer that we've been using. */ { carefulClose(&theFile); } void readOneOut(char *rmskFile) /* Read .out file rmskFile, check each line, and print OK lines to .tab. */ { struct lineFile *lf; char *line, *words[24]; int lineSize, wordCount; /* Open .out file and process header. */ lf = lineFileOpen(rmskFile, TRUE); if (!lineFileNext(lf, &line, &lineSize)) errAbort("Empty %s", lf->fileName); if (!startsWith(" SW perc perc", line)) { if (!startsWith(" SW perc perc", line)) errAbort("%s doesn't seem to be a RepeatMasker .out file, first " "line seen:\n%s", lf->fileName, line); } lineFileNext(lf, &line, &lineSize); lineFileNext(lf, &line, &lineSize); /* Process line oriented records of .out file. */ while (lineFileNext(lf, &line, &lineSize)) { static struct rmskOut2 r; char *s; wordCount = chopLine(line, words); if (wordCount < 14) errAbort("Expecting 14 or 15 words line %d of %s", lf->lineIx, lf->fileName); r.swScore = atoi(words[0]); r.milliDiv = makeMilli(words[1], lf); r.milliDel = makeMilli(words[2], lf); r.milliIns = makeMilli(words[3], lf); r.genoName = words[4]; r.genoStart = atoi(words[5])-1; r.genoEnd = atoi(words[6]); r.genoLeft = parenInt(words[7], lf); r.strand[0] = (words[8][0] == '+' ? '+' : '-'); r.repName = words[9]; r.repClass = words[10]; char *repClassTest = cloneString(r.repClass); stripChar(repClassTest, '('); stripChar(repClassTest, ')'); int nonDigitCount = countLeadingNondigits(repClassTest); int wordOffset = 0; // this repClass is only digits, (or only (digits) with surrounding parens) // this is the sign of an empty field here // due to custom library in use that has no class/family indication if (0 == nonDigitCount) { wordOffset = 1; r.repClass = cloneString("Unspecified"); r.repFamily = cloneString("Unspecified"); } else { s = strchr(r.repClass, '/'); if (s == NULL) r.repFamily = r.repClass; else { *s++ = 0; r.repFamily = s; } } r.repStart = parenInt(words[11-wordOffset], lf); r.repEnd = atoi(words[12-wordOffset]); r.repLeft = parenInt(words[13-wordOffset], lf); r.id = atoi(words[14-wordOffset]); if (words[8][0] == 'C') { r.repLeft = parenInt(words[11-wordOffset], lf); r.repStart = parenInt(words[13-wordOffset], lf); } if (checkRepeat(&r, lf)) { FILE *f = getFileForChrom(r.genoName); if (!noBin) fprintf(f, "%u\t", hFindBin(r.genoStart, r.genoEnd)); rmskOut2TabOut(&r, f); } } } void loadOneTable(char *database, struct sqlConnection *conn, char *tempName, char *tableName) /* Load .tab file tempName into tableName and remove tempName. */ { -struct dyString *query = newDyString(1024); +struct dyString *query = dyStringNew(1024); verbose(1, "Loading up table %s\n", tableName); if (sqlTableExists(conn, tableName)) { sqlDyStringPrintf(query, "DROP table %s", tableName); sqlUpdate(conn, query->string); } /* Create first part of table definitions, the fields. */ dyStringClear(query); sqlDyStringPrintf(query, createRmskOut, tableName); /* Create the indexes */ int indexLen = hGetMinIndexLength(database); sqlDyStringPrintf(query, " INDEX(genoName(%d),bin))\n", indexLen); sqlUpdate(conn, query->string); /* Load database from tab-file. */ dyStringClear(query); sqlDyStringPrintf(query, "LOAD data local infile '%s' into table %s", tempName, tableName); sqlUpdate(conn, query->string); remove(tempName); } void processOneOut(char *database, struct sqlConnection *conn, char *rmskFile, char *suffix) /* Read one RepeatMasker .out file and load it into database. */ { verbose(1, "Processing %s\n", rmskFile); readOneOut(rmskFile); /* Create database table (if not -tabFile). */ if (tabFileName == NULL) { char dir[256], base[128], extension[64]; char tableName[256]; splitPath(rmskFile, dir, base, extension); chopSuffix(base); safef(tableName, sizeof(tableName), "%s_%s", base, suffix); closeFiles(); loadOneTable(database, conn, defaultTempName, tableName); } } struct sqlConnection *theConn = NULL; void hgLoadOutJoined(char *database, int rmskCount, char *rmskFileNames[], char *suffix) /* hgLoadOutJoined - load RepeatMasker .out files into database. */ { struct sqlConnection *conn = NULL; int i; if (tabFileName == NULL) { conn = hAllocConn(database); verbose(2,"#\thgLoadOutJoined: connected to database: %s\n", database); } for (i=0; i<rmskCount; ++i) { readOneOut(rmskFileNames[i]); } closeFiles(); if (tabFileName == NULL) { loadOneTable(database, conn, defaultTempName, suffix); } hFreeConn(&conn); if (badRepCnt > 0) { warn("note: %d records dropped due to repEnd < 0 or repStart > repEnd\n", badRepCnt); if (verboseLevel() < 2) warn(" run with -verbose=2 for details\n"); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc < 3) usage(); suffix = optionVal("table", "rmskOutBaseline"); tabFileName = optionVal("tabFile", tabFileName); if (tabFileName == NULL) tabFileName = optionVal("tabfile", tabFileName); hgLoadOutJoined(argv[1], argc-2, argv+2, suffix) ; return 0; }