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/snp/snpLoad/snpExpandAllele.c src/hg/snp/snpLoad/snpExpandAllele.c index 5dae698..942e7a2 100644 --- src/hg/snp/snpLoad/snpExpandAllele.c +++ src/hg/snp/snpLoad/snpExpandAllele.c @@ -1,350 +1,350 @@ /* snpExpandAllele - fourth step in dbSNP processing. * Read the chrN_snpTmp tables created by snpLocType and expand allele. * Rewrite to new chrN_snpTmp tables. Get chromInfo from ContigInfo. * Write syntax errors to snpExpandAllele.errors. * Write exceptions to snpExpandAllele.exceptions: RefAlleleWrongSize */ /* 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 "dystring.h" #include "hdb.h" static char *snpDb = NULL; static char *contigGroup = NULL; FILE *errorFileHandle = NULL; FILE *tabFileHandle = NULL; FILE *exceptionFileHandle = NULL; void usage() /* Explain usage and exit. */ { errAbort( "snpExpandAllele - expand allele in chrN_snpTmp\n" "usage:\n" " snpExpandAllele snpDb contigGroup\n"); } struct slName *getChromListFromContigInfo(char *contigGroup) /* get all chromNames that match contigGroup */ { struct slName *ret = NULL; struct slName *el = NULL; char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; char chromName[64]; sqlSafef(query, sizeof(query), "select distinct(contig_chr) from ContigInfo where group_term = '%s' and contig_end != 0", contigGroup); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { safef(chromName, sizeof(chromName), "%s", row[0]); el = slNameNew(chromName); slAddHead(&ret, el); } sqlFreeResult(&sr); sqlSafef(query, sizeof(query), "select distinct(contig_chr) from ContigInfo where group_term = '%s' and contig_end = 0", contigGroup); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { safef(chromName, sizeof(chromName), "%s_random", row[0]); el = slNameNew(chromName); slAddHead(&ret, el); } sqlFreeResult(&sr); hFreeConn(&conn); return ret; } void writeToExceptionFile(char *chrom, int start, int end, char *name, char *exception) { fprintf(exceptionFileHandle, "chr%s\t%d\t%d\trs%s\t%s\n", chrom, start, end, name, exception); } boolean needToSplit(char *allele) /* return true if allele contains open paren */ { char *openParen = NULL; openParen = strchr(allele, '('); if (openParen == NULL) return FALSE; return TRUE; } char *getLeftFlank(char *allele) /* We know allele has an open paren (could assert that). */ /* The flank will contain all ACGT. */ /* We may or may not have any flank. */ { int splitPos = 0; char *leftFlank = NULL; splitPos = strcspn(allele, "("); leftFlank = cloneString(allele); leftFlank[splitPos] = '\0'; return leftFlank; } int getRepeatCount(char *allele) /* We believe allele starts with one or two digit number. */ { char *localAllele = cloneString(allele); int size = strspn(localAllele, "0123456789"); if (size != 1 && size != 2) return 0; localAllele[size] = '\0'; return (sqlUnsigned(localAllele)); } char *generateRepeatString(char nucleotide, int count) /* create a string with count nucleotides */ { int pos; char *repeatString = needMem(count+1); for (pos = 0; pos < count; pos++) repeatString[pos] = nucleotide; repeatString[count] = '\0'; return repeatString; } char *expandAllele(char *startAllele) /* look for substrings such as (A)2, (C)3, (G)4, (T)5 etc. */ /* expand to AA, CCC, GGGG, TTTTT etc. */ /* can handle multiple substitutions in one string */ /* if syntax error detected, log to errorFile and return startAllele */ /* only called if at least one expansion is required */ { -struct dyString *newAllele = newDyString(1024); +struct dyString *newAllele = dyStringNew(1024); /* copy startAllele into oldAllele, which we consume as we go */ char *oldAllele = cloneString(startAllele); char *leftFlank = NULL; char nucleotide; int repeatCount = 0; char *repeatString = NULL; while (oldAllele != NULL) { if (!needToSplit(oldAllele)) { dyStringAppend(newAllele, oldAllele); if (!sameString(oldAllele, startAllele)) { verbose(5, "expandAllele started with %s\n", startAllele); verbose(5, "expandAllele returning %s\n", newAllele->string); verbose(5, "---------------------\n"); } return (newAllele->string); } leftFlank = getLeftFlank(oldAllele); verbose(5, "leftFlank = %s\n", leftFlank); // perhaps dyStringAppend can handle NULL input? if (leftFlank != NULL) { dyStringAppend(newAllele, leftFlank); } oldAllele = strpbrk(oldAllele, "("); verbose(5, "oldAllele = %s\n", oldAllele); /* if syntax error, give up */ if (strlen(oldAllele) < 3) return startAllele; nucleotide = oldAllele[1]; oldAllele = oldAllele + 3; /* if syntax error, give up */ if (strlen(oldAllele) < 1) return startAllele; repeatCount = getRepeatCount(oldAllele); /* if syntax error, give up */ if (repeatCount == 0) return startAllele; verbose(5, "repeatCount = %d\n", repeatCount); if (repeatCount <= 9) oldAllele = oldAllele + 1; else if (repeatCount <= 99) oldAllele = oldAllele + 2; else oldAllele = oldAllele + 3; repeatString = generateRepeatString(nucleotide, repeatCount); verbose(5, "repeatString = %s\n", repeatString); dyStringAppend(newAllele, repeatString); } return newAllele->string; } void writeToTabFile(char *snp_id, char *ctg_id, char *start, char *end, char *loc_type, char *orientation, char *allele, char *weight) { fprintf(tabFileHandle, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", snp_id, ctg_id, start, end, loc_type, orientation, allele, weight); } void writeToErrorFile(char *snp_id, char *ctg_id, char *start, char *end, char *loc_type, char *orientation, char *allele, char *weight) { fprintf(errorFileHandle, "snp_id = %s\nctg=%s\nchromStart = %s\nchromEnd = %s\nloc_type = %s\norientation=%s\nallele = %s\nweight=%s\n", snp_id, ctg_id, start, end, loc_type, orientation, allele, weight); fprintf(errorFileHandle, "---------------------------------------\n"); } void doExpandAllele(char *chromName) /* call expandAllele for all rows for this chrom */ /* don't do for loc_type 2 (exact) and loc_type 3 (between) */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; char tableName[64]; char fileName[64]; char *allele = NULL; int count = 0; int errorCount = 0; int start = 0; int end = 0; int size = 0; char newEndString[64]; safef(tableName, ArraySize(tableName), "chr%s_snpTmp", chromName); safef(fileName, ArraySize(fileName), "chr%s_snpTmp.tab", chromName); tabFileHandle = mustOpen(fileName, "w"); sqlSafef(query, sizeof(query), "select snp_id, ctg_id, chromStart, chromEnd, loc_type, orientation, allele, weight from %s ", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { /* no possible candidates in exact and between */ if (sameString(row[4], "2") || sameString(row[4], "3")) { writeToTabFile(row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7]); continue; } /* pass through alleles with no parens */ if (!needToSplit(row[6])) { writeToTabFile(row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7]); continue; } allele = expandAllele(row[6]); /* expandAllele returns original allele if syntax error detected */ /* detect errors but not removing from data set */ if (sameString(allele, row[6])) { errorCount++; writeToErrorFile(row[0], row[1], row[2], row[3], row[4], row[5], row[6], row[7]); } /* calculate end for locType 4, 5, 6 */ if (sameString(row[4], "4") || sameString(row[4], "5") || sameString(row[4], "6")) { start = sqlUnsigned(row[2]); end = start + strlen(allele); verbose(5, "setting end coord for %s, locType = %s, startAllele = %s\n", row[0], row[4], row[6]); sprintf(newEndString, "%d", end); writeToTabFile(row[0], row[1], row[2], newEndString, row[4], row[5], allele, row[7]); continue; } /* check for exceptions in locType 1 */ if (sameString(row[4], "1")) { start = sqlUnsigned(row[2]); end = sqlUnsigned(row[3]); size = end - start; if (size != strlen(allele)) writeToExceptionFile(chromName, start, end, row[0], "RefAlleleWrongSize"); } writeToTabFile(row[0], row[1], row[2], row[3], row[4], row[5], allele, row[7]); count++; } sqlFreeResult(&sr); hFreeConn(&conn); carefulClose(&tabFileHandle); verbose(2, "%d alleles expanded\n", count); verbose(2, "%d errors found\n", errorCount); } void cleanDatabaseTable(char *chromName) /* do a 'delete from tableName' */ { struct sqlConnection *conn = hAllocConn(); char query[256]; sqlSafef(query, ArraySize(query), "delete from chr%s_snpTmp", chromName); sqlUpdate(conn, query); hFreeConn(&conn); } void loadDatabase(char *chromName) /* load one table into database */ { FILE *f; struct sqlConnection *conn = hAllocConn(); char tableName[64], fileName[64]; safef(tableName, ArraySize(tableName), "chr%s_snpTmp", chromName); safef(fileName, ArraySize(fileName), "chr%s_snpTmp.tab", chromName); f = mustOpen(fileName, "r"); /* hgLoadTabFile closes the file handle */ hgLoadTabFile(conn, ".", tableName, &f); hFreeConn(&conn); } int main(int argc, char *argv[]) /* read chrN_snpTmp, handle allele, rewrite to individual chrom tables */ { struct slName *chromList, *chromPtr; if (argc != 3) usage(); snpDb = argv[1]; contigGroup = argv[2]; hSetDb(snpDb); chromList = getChromListFromContigInfo(contigGroup); if (chromList == NULL) { verbose(1, "couldn't get chrom info\n"); return 1; } errorFileHandle = mustOpen("snpExpandAllele.errors", "w"); exceptionFileHandle = mustOpen("snpExpandAllele.exceptions", "w"); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { verbose(1, "chrom = %s\n", chromPtr->name); doExpandAllele(chromPtr->name); /* snpExpandAllele doesn't change the table format, so just delete old rows */ cleanDatabaseTable(chromPtr->name); loadDatabase(chromPtr->name); verbose(2, "------------------------------\n"); } carefulClose(&errorFileHandle); carefulClose(&exceptionFileHandle); return 0; }