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/hgLoadOut/hgLoadOut.c src/hg/makeDb/hgLoadOut/hgLoadOut.c index 1f0c59b..fabd504 100644 --- src/hg/makeDb/hgLoadOut/hgLoadOut.c +++ src/hg/makeDb/hgLoadOut/hgLoadOut.c @@ -1,391 +1,392 @@ /* hgLoadOut - load RepeatMasker .out files into database. */ /* 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 "rmskOut.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 (if strand is +) or -#bases after match (if strand is -) in repeat sequence\n" -" repEnd int not null, # End in repeat sequence\n" -" repLeft int not null, # -#bases after match (if strand is +) or start (if strand is -) in repeat sequence\n" -" id char(1) not null, # First digit of id field in RepeatMasker .out file. Best ignored.\n" -" #Indices\n"; boolean noBin = FALSE; boolean split = FALSE; boolean noSplit = FALSE; char *tabFileName = NULL; char *suffix = NULL; int badRepCnt = 0; /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"tabFile", OPTION_STRING}, {"tabfile", OPTION_STRING}, {"nosplit", OPTION_BOOLEAN}, {"noSplit", OPTION_BOOLEAN}, {"split", OPTION_BOOLEAN}, {"table", OPTION_STRING}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "hgLoadOut - load RepeatMasker .out files into database\n" "usage:\n" " hgLoadOut database file(s).out\n" "For multiple files chrN.out this will create the single table 'rmsk'\n" "in the database, use the -split argument to obtain separate chrN_rmsk tables.\n" "options:\n" " -tabFile=text.tab - don't actually load database, just create tab file\n" " -split - load chrN_rmsk separate tables even if a single file is given\n" " -table=name - use a different suffix other than the default (rmsk)"); } 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)); } int parenSignInt(char *s, struct lineFile *lf) /* Convert from ascii notation where a parenthesized integer is negative * to straight int. */ { if (s[0] == '(') return -atoi(s+1); else return atoi(s); } boolean checkRepeat(struct rmskOut *r, struct lineFile *lf) /* check for bogus repeat */ { /* this is bogus on both strands */ if (r->repEnd < 0 || r->repStart > r->repEnd) { badRepCnt++; if (verboseLevel() > 1) { verbose(2, "bad rep range [%d, %d] line %d of %s \n", r->repStart, r->repEnd, lf->lineIx, lf->fileName); } return FALSE; } return TRUE; } FILE *theFile = NULL; struct hash *chromFpHash = NULL; char *defaultTempName = "rmsk.tab"; FILE *getFileForChrom(char *chrom) /* Return the appropriate file pointer for the given chrom if -split. * If not using -split, then there is only one file pointer in action. */ { static int chromCount = 0; char *tempName = tabFileName ? tabFileName : defaultTempName; if (split) { if (chromFpHash == NULL) chromFpHash = hashNew(10); theFile = (FILE *)hashFindVal(chromFpHash, chrom); if (theFile == NULL) { char fName[512]; if (chromCount > 1000) { /* We will probably run into the operating system limit on open * files well before this point, but just in case... */ errAbort("-split should not be used when there are >1000 sequences" " -- too many split tables."); } safef(fName, sizeof(fName), "%s_%s", chrom, tempName); theFile = mustOpen(fName, "w"); hashAdd(chromFpHash, chrom, theFile); chromCount++; } } else { 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() /* If split, close each file pointer in chromFpHash. Otherwise close the * single file pointer that we've been using. */ { if (split) { hashTraverseEls(chromFpHash, helCarefulClose); } else 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) || startsWith(" SW perc perc", line) || startsWith(" SW perc perc", line) || startsWith(" bit 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 rmskOut 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 = parenSignInt(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 = parenSignInt(words[11-wordOffset], lf); r.repEnd = atoi(words[12-wordOffset]); r.repLeft = parenSignInt(words[13-wordOffset], lf); r.id[0] = ((wordCount > (14-wordOffset)) ? words[14-wordOffset][0] : ' '); if (checkRepeat(&r, lf)) { FILE *f = getFileForChrom(r.genoName); if (!noBin) fprintf(f, "%u\t", hFindBin(r.genoStart, r.genoEnd)); rmskOutTabOut(&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); +sqlDyStringPrintf(query, +"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 (if strand is +) or -#bases after match (if strand is -) in repeat sequence\n" +" repEnd int not null, # End in repeat sequence\n" +" repLeft int not null, # -#bases after match (if strand is +) or start (if strand is -) in repeat sequence\n" +" id char(1) not null, # First digit of id field in RepeatMasker .out file. Best ignored.\n" +" #Indices\n" +, tableName); /* Create the indexes */ if (!noSplit) { - dyStringAppend(query, " INDEX(bin))\n"); + sqlDyStringPrintf(query, " INDEX(bin))\n"); } else { 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); if (split || noSplit) errAbort("program error: processOneOut doesn't do -split or -nosplit."); 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 loadOneSplitTable(struct hashEl *hel) /* Load the table for the given chrom. */ { char tempName[512]; char tableName[256]; char *chrom = hel->name; safef(tempName, sizeof(tempName), "%s_%s", chrom, defaultTempName); safef(tableName, sizeof(tableName), "%s_%s", chrom, suffix); loadOneTable(sqlGetDatabase(theConn), theConn, tempName, tableName); } void loadSplitTables(char *database, struct sqlConnection *conn) /* For each chrom in chromHash, load its tempfile into table chrom_suffix. */ { theConn = conn; hashTraverseEls(chromFpHash, loadOneSplitTable); } void hgLoadOut(char *database, int rmskCount, char *rmskFileNames[], char *suffix) /* hgLoadOut - load RepeatMasker .out files into database. */ { struct sqlConnection *conn = NULL; int i; if (tabFileName == NULL) { conn = hAllocConn(database); verbose(2,"#\thgLoadOut: connected to database: %s\n", database); } for (i=0; i<rmskCount; ++i) { if (split || noSplit) readOneOut(rmskFileNames[i]); else processOneOut(database, conn, rmskFileNames[i], suffix); } closeFiles(); if (tabFileName == NULL) { if (split) loadSplitTables(database, conn); else if (noSplit) 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(); // default changed to noSplit Jan 2014 , ignore noSplit arguments split = optionExists("split"); noSplit = ! split; suffix = optionVal("table", "rmsk"); tabFileName = optionVal("tabFile", tabFileName); if (tabFileName == NULL) tabFileName = optionVal("tabfile", tabFileName); if (split && noSplit) errAbort("-split and -nosplit cannot be used together."); hgLoadOut(argv[1], argc-2, argv+2, suffix) ; return 0; }