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/snpException/snpException.c src/hg/snpException/snpException.c index 4507d1e..56e50aa 100644 --- src/hg/snpException/snpException.c +++ src/hg/snpException/snpException.c @@ -1,202 +1,208 @@ /* snpException.c - Get exceptions to snp invariant rules */ /* 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 "errAbort.h" #include "linefile.h" #include "obscure.h" #include "dystring.h" #include "cheapcgi.h" #include "dnaseq.h" #include "hdb.h" #include "memalloc.h" #include "hash.h" #include "jksql.h" #include "snp.h" #include "snpExceptions.h" void usage() /* Explain usage and exit. */ { errAbort("snpException - Get exceptions to a snp invariant rule.\n" "Usage: \tsnpException database exceptionId fileBase\n" "Example:\tsnpException hg17 1 hg17snpException\n" "where the exceptionId is the primary key from the snpExceptions table,\n" "\tand using exceptionId=0 will process all invariant rules. \n"); } struct slName *getChromList(char *db) /* Get list of all chromosomes. */ { struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; char **row = NULL; struct slName *list = NULL; struct slName *el = NULL; -char *query = NOSQLINJ "select chrom from chromInfo"; +char query[1024]; +sqlSafef(query, sizeof query, "select chrom from chromInfo"); sr = sqlGetResult(conn, query); while ((row=sqlNextRow(sr))!=NULL) { el = newSlName(row[0]); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); hFreeConn(&conn); return list; } struct slName *getGroupList(char *db, char *group) /* Get list of all rsIds from where clause. */ { struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; char **row = NULL; struct slName *list = NULL; struct slName *el = NULL; char query[256]; sqlSafef(query,sizeof(query),"select name from snp %s", group); sr = sqlGetResult(conn, query); while ((row=sqlNextRow(sr))!=NULL) { el = newSlName(row[0]); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); hFreeConn(&conn); return list; } struct snpExceptions *getExceptionList(char *db, int inputExceptionId) /* Get list of all exceptions to be tested. */ { struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; char **row = NULL; struct snpExceptions *list = NULL; struct snpExceptions *el = NULL; -char query[256] = NOSQLINJ "select * from snpExceptions"; +char query[256]; if (inputExceptionId>0) sqlSafef(query, sizeof(query), "select * from snpExceptions where exceptionId=%d", inputExceptionId); +else + sqlSafef(query, sizeof(query), "select * from snpExceptions"); sr = sqlGetResult(conn, query); while ((row=sqlNextRow(sr))!=NULL) { el = snpExceptionsLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); hFreeConn(&conn); return list; } void getInvariants(char *db, struct snpExceptions *exceptionList, struct slName *chromList, char *fileBase) /* write list of invariants to output file */ { struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; struct snpExceptions *el = NULL; struct slName *chrom = NULL; char **row = NULL; char query[1024]; unsigned long int invariantCount; char thisFile[64]; FILE *outFile; int colCount, i; char idString[3]; for (el=exceptionList; el!=NULL; el=el->next) { if (el->exceptionId<10) safef(idString,sizeof(idString), "0%d", el->exceptionId); else safef(idString,sizeof(idString), "%d", el->exceptionId); invariantCount = 0; if (startsWith("select",el->query)) { safef(thisFile, sizeof(thisFile), "%s.%s.bed", fileBase, idString); outFile = mustOpen(thisFile, "w"); fprintf(outFile, "# exceptionId:\t%d\n# query:\t%s;\n", el->exceptionId, el->query); for (chrom=chromList; chrom!=NULL; chrom=chrom->next) { fflush(outFile); /* to keep an eye on output progress */ - sqlSafef(query, sizeof(query), - "%-s and chrom='%s'", el->query, chrom->name); - sr = sqlGetResult(conn, query); + + // FYI el->query does not contain printf replace-able parameters, so dynamic format is not required. + struct dyString *query2 = sqlDyStringCreate(el->query,NULL); + sqlDyStringPrintf(query2, " and chrom='%s'", chrom->name); + sr = sqlGetResult(conn, dyStringContents(query2)); + dyStringFree(&query2); colCount = sqlCountColumns(sr); while ((row = sqlNextRow(sr))!=NULL) { invariantCount++; fprintf(outFile, "%s", row[0]); for (i=1; i<colCount; i++) fprintf(outFile, "\t%s", row[i]); fprintf(outFile, "\n"); } } } else if (startsWith("group",el->query)) { struct slName *nameList = NULL; struct slName *name = NULL; safef(thisFile, sizeof(thisFile), "%s.%s.bed", fileBase, idString); outFile = mustOpen(thisFile, "w"); fprintf(outFile, "# exceptionId:\t%d\n# query:\t%s;\n", el->exceptionId, el->query); nameList = getGroupList(db, el->query); for (name=nameList; name!=NULL; name=name->next) { sqlSafef(query, sizeof(query), "select chrom,chromStart,chromEnd,name,%d as score,class,locType,observed " "from snp where name='%s'", el->exceptionId, name->name); sr = sqlGetResult(conn, query); colCount = sqlCountColumns(sr); while ((row = sqlNextRow(sr))!=NULL) { invariantCount++; fprintf(outFile, "%s", row[0]); for (i=1; i<colCount; i++) fprintf(outFile, "\t%s", row[i]); fprintf(outFile, "\n"); } } } else { printf("Invariant %d has no query string\n", el->exceptionId); continue; } carefulClose(&outFile); printf("Invariant %d has %lu exceptions, written to this file: %s\n", el->exceptionId, invariantCount, thisFile); fflush(stdout); sqlSafef(query, sizeof(query), "update snpExceptions set num=%lu where exceptionId=%d", invariantCount, el->exceptionId); sr=sqlGetResult(conn, query); /* there's probably a better way to do this */ } } int main(int argc, char *argv[]) /* error check, process command line input, and call getInvariants */ { struct snpExceptions *exceptionList = NULL; struct slName *chromList = NULL; if (argc != 4) { usage(); return 1; } char *db= argv[1];; exceptionList=getExceptionList(db, atoi(argv[2])); chromList=getChromList(db); getInvariants(db, exceptionList, chromList, argv[3]); return 0; }