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/near/hgNear/search.c src/hg/near/hgNear/search.c index ee70a8b..9f44f79 100644 --- src/hg/near/hgNear/search.c +++ src/hg/near/hgNear/search.c @@ -1,292 +1,292 @@ /* search - manage simple searches - ones based on just a single name. */ /* 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 "hash.h" #include "jksql.h" #include "hdb.h" #include "obscure.h" #include "hgNear.h" int searchResultCmpShortLabel(const void *va, const void *vb) /* Compare to sort based on short label. */ { const struct searchResult *a = *((struct searchResult **)va); const struct searchResult *b = *((struct searchResult **)vb); return strcmp(a->shortLabel, b->shortLabel); } static struct genePos *findGenePredPos(struct sqlConnection *conn, char *table, char *search) /* Find out gene ID from search term. */ { char query[256]; struct sqlResult *sr; char **row; struct genePos *gpList = NULL, *gp; if (search != NULL) { sqlSafef(query, sizeof(query), "select name,chrom,txStart,txEnd from %s where name = '%s'", table, search); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(gp); gp->name = cloneString(row[0]); gp->chrom = cloneString(row[1]); gp->start = sqlUnsigned(row[2]); gp->end = sqlUnsigned(row[3]); slAddHead(&gpList, gp); } sqlFreeResult(&sr); } slReverse(&gpList); return gpList; } struct columnSearchResults /* Search results for one column. */ { struct columnSearchResults *next; /* next in list. */ char *label; /* Description of column - not allocated here. */ struct searchResult *results; /* List of results. */ }; static void transformToCanonical(struct searchResult *list, struct sqlConnection *conn) /* Transform search results to canonical versions. */ { -struct dyString *dy = newDyString(1024); +struct dyString *dy = dyStringNew(1024); char *cannon = genomeSetting("canonicalTable"); char *isoform = genomeSetting("isoformTable"); struct sqlResult *sr; char **row; struct searchResult *el; for (el = list; el != NULL; el = el->next) { dyStringClear(dy); sqlDyStringPrintf(dy, "select %s.transcript,%s.chrom,%s.chromStart,%s.chromEnd,%s.protein ", cannon, cannon, cannon, cannon, cannon); sqlDyStringPrintf(dy, "from %s,%s ", isoform, cannon); sqlDyStringPrintf(dy, "where %s.transcript = '%s' ", isoform, el->gp.name); sqlDyStringPrintf(dy, "and %s.clusterId = %s.clusterId", isoform, cannon); sr = sqlGetResult(conn, dy->string); if ((row = sqlNextRow(sr)) != NULL) genePosFillFrom5(&el->gp, row); sqlFreeResult(&sr); } dyStringFree(&dy); } static struct searchResult *removeDupes(struct searchResult *list) /* Remove duplicates from list. Return weeded list. */ { struct searchResult *el, *next, *newList = NULL; struct hash *dupHash = newHash(0); for (el = list; el != NULL; el = next) { next = el->next; if (!hashLookup(dupHash, el->gp.name)) { hashAdd(dupHash, el->gp.name, NULL); slAddHead(&newList, el); } } hashFree(&dupHash); slReverse(&newList); return newList; } static void fillInMissingLabels(struct sqlConnection *conn, struct column *colList, struct searchResult *srList) /* Fill in missing columns by looking up name and description * if possible. */ { struct column *nameColumn = findNamedColumn("name"); struct column *desColumn = findNamedColumn("description"); struct searchResult *sr; for (sr = srList; sr != NULL; sr = sr->next) { if (sr->shortLabel == NULL) { if (nameColumn != NULL) sr->shortLabel = nameColumn->cellVal(nameColumn, &sr->gp, conn); if (sr->shortLabel == NULL) sr->shortLabel = cloneString(sr->gp.name); } if (sr->longLabel == NULL) { if (desColumn != NULL) sr->longLabel = desColumn->cellVal(desColumn, &sr->gp, conn); else sr->longLabel = cloneString(""); } } } static boolean allSame(struct columnSearchResults *csrList) /* Return TRUE if all search results point to the same place. */ { struct hash *dupeHash = newHash(0); char hashName[512]; int sepCount = 0; struct columnSearchResults *csr; struct searchResult *sr; for (csr = csrList; csr != NULL && sepCount < 2; csr = csr->next) { for (sr = csr->results; sr != NULL && sepCount < 2; sr = sr->next) { char *chrom = sr->gp.chrom; if (chrom == NULL) chrom = "n/a"; safef(hashName, sizeof(hashName), "%s %s:%d-%d", sr->gp.name, chrom, sr->gp.start, sr->gp.end); if (!hashLookup(dupeHash, hashName)) { hashAdd(dupeHash, hashName, NULL); ++sepCount; } } } hashFree(&dupeHash); return sepCount <= 1; } static void searchAllColumns(struct sqlConnection *conn, struct column *colList, char *search) /* Call search on each column. */ { struct column *col; struct searchResult *srList, *sr; struct columnSearchResults *csrList = NULL, *csr; int totalCount = 0; struct searchResult *srOne = NULL; for (col = colList; col != NULL; col = col->next) { if (col->simpleSearch) { srList = col->simpleSearch(col, conn, search); if (showOnlyCanonical() && srList != NULL) { transformToCanonical(srList, conn); srList = removeDupes(srList); } if (srList != NULL) { srOne = srList; fillInMissingLabels(conn, colList, srList); AllocVar(csr); csr->label = columnSetting(col, "searchLabel", col->longLabel); csr->results = srList; slAddTail(&csrList, csr); totalCount += slCount(srList); } } } if (totalCount == 0) { displayData(conn, colList, NULL); if (anyWild(search)) warn("Sorry, the search box doesn't take wildcards, " "though in most cases it will find things without " "them. Try entering your search without * or ? " "characters."); else warn("Sorry, couldn't find '%s'", search); } else if (totalCount == 1 || allSame(csrList)) // else if (totalCount == 1) displayData(conn, colList, &srOne->gp); else { makeTitle("Simple Search Results", NULL); for (csr = csrList; csr != NULL; csr = csr->next) { hPrintf("<H2>%s</H2>\n", csr->label); slSort(&csr->results, searchResultCmpShortLabel); for (sr = csr->results; sr != NULL; sr = sr->next) { selfAnchorSearch(&sr->gp); if (sr->matchingId != NULL) hPrintf("%s (%s)", sr->matchingId, sr->shortLabel); else hPrintf("%s", sr->shortLabel); hPrintf("</A> - %s<BR>\n", sr->longLabel); } } } } static char *transcriptToCanonical(struct sqlConnection *conn, char *transcript) /* Translate transcript to canonical ID if possible, otherwise just return * a copy of transcript. */ { -struct dyString *dy = newDyString(1024); +struct dyString *dy = dyStringNew(1024); char *cannon = genomeSetting("canonicalTable"); char *isoform = genomeSetting("isoformTable"); char buf[128]; char *result = NULL; sqlDyStringPrintf(dy, "select %s.transcript from %s,%s where %s.transcript = '%s'", cannon, isoform, cannon, isoform, transcript); sqlDyStringPrintf(dy, " and %s.clusterId = %s.clusterId", isoform, cannon); result = sqlQuickQuery(conn, dy->string, buf, sizeof(buf)); if (result != NULL) return(cloneString(result)); else return(cloneString(transcript)); } static struct genePos *findKnownAccessions(struct sqlConnection *conn, char *search) /* Return list of known accessions. */ { search = transcriptToCanonical(conn, search); return findGenePredPos(conn, genomeSetting("geneTable"), search); } void doSearch(struct sqlConnection *conn, struct column *colList) /* Search. If result is unambiguous call displayData, otherwise * put up a page of choices. */ { char *search = cartString(cart, searchVarName); char *escSearch = makeEscapedString(trimSpaces(search), '\''); struct genePos *accList; accList = findKnownAccessions(conn, escSearch); if (accList != NULL) { if (slCount(accList) == 1 || !sameString(groupOn, "position")) displayData(conn, colList, accList); else { struct genePos *acc; hPrintf("%s maps to %d positions, please pick one below:<BR>\n", search, slCount(accList)); for (acc = accList; acc != NULL; acc = acc->next) { hPrintf(" "); selfAnchorSearch(acc); hPrintf("%s:%d-%d</A><BR>\n", acc->chrom, acc->start+1, acc->end); } } } else { searchAllColumns(conn, colList, escSearch); } freez(&escSearch); }