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/snpCheckCluster.c src/hg/snp/snpLoad/snpCheckCluster.c index 722f6fa..5c2794c 100644 --- src/hg/snp/snpLoad/snpCheckCluster.c +++ src/hg/snp/snpLoad/snpCheckCluster.c @@ -1,232 +1,232 @@ /* snpCheckCluster -- check for clustering errors. */ /* First version checks insertions only. */ /* assuming input already filtered on locType = 'between' and class = 'insertion' */ /* assert insertions in sorted order */ /* assert end == start */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* SKIPPING chrY because of those damned PAR SNPs */ #include "common.h" #include "dystring.h" #include "hdb.h" static char *database = NULL; static char *snpTable = NULL; static FILE *exceptionFileHandle = NULL; void usage() /* Explain usage and exit. */ { errAbort( "snpCheckCluster - check for clustering errors\n" "usage:\n" " snpCheckCluster database snpTable\n"); } boolean isValidObserved(char *observed) { int slashCount = 0; if (strlen(observed) < 2) return FALSE; if (observed[0] != '-') return FALSE; if (observed[1] != '/') return FALSE; slashCount = chopString(observed, "/", NULL, 0); if (slashCount > 2) return FALSE; return TRUE; } char *reverseComplementObserved(char *observed) { char *subString = NULL; struct dyString *myDy = NULL; subString = cloneString(observed); subString = subString + 2; reverseComplement(subString, strlen(subString)); -myDy = newDyString(1024); +myDy = dyStringNew(1024); dyStringAppend(myDy, "-/"); dyStringAppend(myDy, subString); return myDy->string; } boolean listAllEqual(struct slName *list) /* return TRUE if all elements in the list are the same */ /* list must have at least 2 elements */ { struct slName *element = NULL; char *example = NULL; assert (list != NULL); assert (list->next != NULL); example = cloneString(list->name); list = list->next; for (element = list; element !=NULL; element = element->next) if (!sameString(element->name, example)) return FALSE; return TRUE; } void printException(char *chromName, int pos, struct slName *observedList, struct slName *nameList) { char exception[32]; struct slName *element = NULL; if (listAllEqual(observedList)) safef(exception, sizeof(exception), "DuplicateObserved"); else safef(exception, sizeof(exception), "MixedObserved"); for (element = nameList; element !=NULL; element = element->next) fprintf(exceptionFileHandle, "%s\t%d\t%d\t%s\t%s\n", chromName, pos, pos, element->name, exception); } int checkCluster(char *chromName) /* detect if more than one insertion at the same location */ /* detect if all the observed strings match or not */ /* return error count */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; boolean clusterFound = FALSE; int pos = 0; int posPrevious = 0; int start = 0; int end = 0; int errors = 0; char *rsId = NULL; char *rsIdPrevious = NULL; char *strand = NULL; char *observed = NULL; char *observedPrevious = NULL; struct slName *observedList = NULL; struct slName *nameList = NULL; struct slName *element = NULL; sqlSafef(query, sizeof(query), "select chromStart, chromEnd, name, strand, observed from %s where chrom = '%s'", snpTable, chromName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { start = sqlUnsigned(row[0]); end = sqlUnsigned(row[1]); rsId = cloneString(row[2]); strand = cloneString(row[3]); observed = cloneString(row[4]); if (!isValidObserved(observed)) continue; if (sameString(strand, "-")) observed = reverseComplementObserved(observed); /* end must equal start */ assert (end == start); /* SNPs per chrom must be sorted */ if (start < pos) verbose(1, "out of order at %d (pos = %d)\n", start, pos); assert (start >= pos); if (start > pos) { if (clusterFound) { errors++; clusterFound = FALSE; printException(chromName, posPrevious, observedList, nameList); } pos = start; observedPrevious = cloneString(observed); rsIdPrevious = cloneString(rsId); slFreeList(&observedList); slFreeList(&nameList); continue; } /* are we in a cluster? */ if (start == pos) { /* if first time through, pick up previous values */ if (!clusterFound) { posPrevious = pos; clusterFound = TRUE; element = slNameNew(observedPrevious); slAddHead(&observedList, element); element = slNameNew(rsIdPrevious); slAddHead(&nameList, element); } element = slNameNew(observed); slAddHead(&observedList, element); element = slNameNew(rsId); slAddHead(&nameList, element); } } if (clusterFound) { errors++; printException(chromName, posPrevious, observedList, nameList); } sqlFreeResult(&sr); hFreeConn(&conn); if (errors > 0) verbose(1, " %d clustered positions detected\n", errors); return errors; } int main(int argc, char *argv[]) /* read snpTable, report positions with more than one insertion */ { if (argc != 3) usage(); database = argv[1]; hSetDb(database); snpTable = argv[2]; if (!hTableExists(snpTable)) errAbort("no %s table\n", snpTable); // chromList = hAllChromNames(); // exceptionFileHandle = mustOpen("snpCheckCluster.tab", "w"); // for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) // { // if (sameString(chromPtr->name, "chrY")) continue; // verbose(1, "chrom = %s\n", chromPtr->name); // totalErrors = totalErrors + checkCluster(chromPtr->name); // } exceptionFileHandle = mustOpen("snpCheckClusterChrY.tab", "w"); checkCluster("chrY"); carefulClose(&exceptionFileHandle); // verbose(1, "TOTAL errors = %d\n", totalErrors); return 0; }