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/association.c src/hg/near/hgNear/association.c index 54c1b2d..aebab90 100644 --- src/hg/near/hgNear/association.c +++ src/hg/near/hgNear/association.c @@ -1,540 +1,540 @@ /* association - handle association type columns. * An association is a two column table (or query) * with one column corresponding to a key, and the other * to a value. It is very similar to a lookup type. * However where there is only one value per key in a lookup * there can be multiple values per keyin an association. * * Originally the pfam column was an association. Unfortunately * mySQL was just too slow with the join that it required. */ /* 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 "linefile.h" #include "localmem.h" #include "dystring.h" #include "obscure.h" #include "jksql.h" #include "hdb.h" #include "hgNear.h" boolean associationExists(struct column *col, struct sqlConnection *conn) /* This returns true if all tables this depends on exists. */ { char *dupe = cloneString(col->tablesUsed); char *s = dupe; char *table; boolean ok = TRUE; while ((table = nextWord(&s)) != NULL) { if (!sqlTableExists(conn, table)) { ok = FALSE; break; } } freez(&dupe); return ok; } struct assocList /* A gene and a list of strings associated with it. */ { struct slRef *list; /* References to strings. */ }; struct assocGroup /* Structure to help group an association table into * something a little easier to handle. */ { struct hash *listHash; /* assocList valued hash keyed by keyField. */ struct hash *valStringHash; /* String values to save some space. */ struct lm *lm; /* Local memory pool for speed. Parasites off * of valStringHash. */ }; void assocGroupFree(struct assocGroup **pAg) /* Free up resources of assocGroup. */ { struct assocGroup *ag = *pAg; if (ag != NULL) { hashFree(&ag->listHash); hashFree(&ag->valStringHash); freez(pAg); } } struct assocGroup *assocGroupNew(int hashSize) /* Create new assocGroup. HashSize should be roughly * the log base 2 of the number of items. */ { struct assocGroup *ag; AllocVar(ag); ag->listHash = hashNew(hashSize); ag->valStringHash = hashNew(hashSize); ag->lm = ag->valStringHash->lm; return ag; } void assocGroupAdd(struct assocGroup *ag, char *key, char *val) /* Add key/val pair to assocGroup. */ { struct assocList *al = hashFindVal(ag->listHash, key); struct slRef *ref; if (al == NULL) { lmAllocVar(ag->lm, al); hashAdd(ag->listHash, key, al); } val = hashStoreName(ag->valStringHash, val); lmAllocVar(ag->lm, ref); ref->val = val; slAddHead(&al->list, ref); } static boolean wildAnyRefMatch(char *wild, struct slRef *refList) /* Return true if any string-valued reference on list matches * wildcard. */ { struct slRef *ref; for (ref = refList; ref != NULL; ref = ref->next) { if (wildMatch(wild, ref->val)) return TRUE; } return FALSE; } static boolean wildMatchRefs(struct slName *wildList, struct slRef *refList, boolean orLogic) /* If using orLogic return true if any element of refList * matches any element of wildList. * If using andLogic return true all elements of wildList have * at least one match in refList. */ { struct slName *wildEl; if (orLogic) { for (wildEl = wildList; wildEl != NULL; wildEl = wildEl->next) { if (wildAnyRefMatch(wildEl->name, refList)) return TRUE; } return FALSE; } else { for (wildEl = wildList; wildEl != NULL; wildEl = wildEl->next) { if (!wildAnyRefMatch(wildEl->name, refList)) return FALSE; } return TRUE; } } static struct genePos *wildAssociationFilter( struct slName *wildList, boolean orLogic, struct column *col, struct sqlConnection *conn, struct genePos *list) /* Handle relatively slow filtering when there is a wildcard present. */ { struct assocGroup *ag = assocGroupNew(16); struct genePos *gp; struct hash *passHash = newHash(16); /* Hash of items passing filter. */ int assocCount = 0; struct sqlResult *sr; char **row; char query[1024]; -sqlSafef(query, sizeof query, "%-s", col->queryFull); // purely for side-effect of adding NOSQLINJ prefix +sqlSafef(query, sizeof query, col->queryFull, NULL); // trust /* Build up associations. */ sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { ++assocCount; assocGroupAdd(ag, row[0],row[1]); } sqlFreeResult(&sr); /* Look for matching associations and put them on newList. */ for (gp = list; gp != NULL; gp = gp->next) { char *key = (col->protKey ? (kgVersion == KG_III ? lookupProtein(conn, gp->name) : gp->protein) : gp->name); struct assocList *al = hashFindVal(ag->listHash, key); if (al != NULL) { if (wildList == NULL || wildMatchRefs(wildList, al->list, orLogic)) hashAdd(passHash, gp->name, gp); } } list = weedUnlessInHash(list, passHash); hashFree(&passHash); assocGroupFree(&ag); return list; } static struct genePos *tameAssociationFilter( struct slName *termList, boolean orLogic, struct column *col, struct sqlConnection *conn, struct genePos *list) /* Handle filtering when there are no wildcards present. */ { struct sqlResult *sr; char **row; struct slName *term; struct hash *passHash = newHash(17); struct hash *protHash = NULL; struct hash *prevHash = NULL; struct genePos *gp; int protCount = 0, termCount = 0, matchRow = 0, keyRow = 0; /* Make up protein-keyed hash if need be. */ if (col->protKey) { protHash = newHash(17); for (gp = list; gp != NULL; gp = gp->next) { hashAdd(protHash, gp->protein, gp->name); ++protCount; } } for (term = termList; term != NULL; term = term->next) { char query[1024]; sqlSafef(query, sizeof(query), col->invQueryOne, term->name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *key = row[0]; ++matchRow; if (protHash != NULL) key = hashFindVal(protHash, key); if (key != NULL) { ++keyRow; if (prevHash == NULL || hashLookup(prevHash, key) != NULL) { hashStore(passHash, key); } } } if (!orLogic) { hashFree(&prevHash); if (term->next != NULL) { prevHash = passHash; passHash = newHash(17); } } sqlFreeResult(&sr); ++termCount; } list = weedUnlessInHash(list, passHash); hashFree(&prevHash); freeHash(&protHash); freeHash(&passHash); return list; } static struct genePos *associationAdvFilter(struct column *col, struct sqlConnection *conn, struct genePos *list) /* Do advanced filter on position. */ { char *terms = advFilterVal(col, "terms"); if (terms != NULL) { boolean orLogic = advFilterOrLogic(col, "logic", TRUE); struct slName *termList = stringToSlNames(terms); if (anyWild(terms)) list = wildAssociationFilter(termList, orLogic, col, conn, list); else list = tameAssociationFilter(termList, orLogic, col, conn, list); } return list; } char *associationCellVal(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Make comma separated list of matches to association table. */ { char query[1024]; struct sqlResult *sr; char **row; boolean gotOne = FALSE; -struct dyString *dy = newDyString(512); +struct dyString *dy = dyStringNew(512); char *result = NULL; char *key = (col->protKey ? (kgVersion == KG_III ? lookupProtein(conn, gp->name) : gp->protein) : gp->name); struct hash *uniqHash = NULL; if (col->weedDupes) uniqHash = newHash(8); sqlSafef(query, sizeof(query), col->queryOne, key); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *s = row[0]; boolean needQuote; if (uniqHash != NULL) { if (hashLookup(uniqHash, s)) continue; else hashAdd(uniqHash, s, NULL); } needQuote = hasWhiteSpace(s); if (needQuote) dyStringAppendC(dy, '\''); dyStringAppend(dy, s); if (needQuote) dyStringAppendC(dy, '\''); dyStringAppend(dy, ","); gotOne = TRUE; } sqlFreeResult(&sr); if (gotOne) result = cloneString(dy->string); dyStringFree(&dy); freeHash(&uniqHash); return result; } static void associationCellPrint(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Print cell in association table. */ { char query[1024]; struct sqlResult *sr; char **row; boolean gotOne = FALSE; char *key = (col->protKey ? (kgVersion == KG_III ? lookupProtein(conn, gp->name) : gp->protein) : gp->name); struct hash *uniqHash = NULL; if (col->weedDupes) uniqHash = newHash(8); hPrintf("<TD>"); sqlSafef(query, sizeof(query), col->queryOne, key); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *s = row[0]; boolean needQuote; if (uniqHash != NULL) { if (hashLookup(uniqHash, s)) continue; else hashAdd(uniqHash, s, NULL); } needQuote = hasWhiteSpace(s); if (!gotOne) gotOne = TRUE; else hPrintf(" "); if (needQuote) hPrintf("'"); if (col->itemUrl) { hPrintf("<A HREF=\""); hPrintf(col->itemUrl, row[1]); hPrintf("\" TARGET=_blank>"); } hPrintEncodedNonBreak(s); if (col->itemUrl) { hPrintf("</A>"); } if (needQuote) hPrintf("'"); } sqlFreeResult(&sr); if (!gotOne) { hPrintf("n/a"); } hPrintf("</TD>"); freeHash(&uniqHash); } static void associationFilterControls(struct column *col, struct sqlConnection *conn) /* Print out controls for advanced filter. */ { hPrintf("Enclose term in single quotes if it " "contains multiple words. You may include " "* and ? wildcards.<BR>\n"); hPrintf("Term(s): "); advFilterRemakeTextVar(col, "terms", 35); hPrintf(" Include if "); advFilterAnyAllMenu(col, "logic", FALSE); hPrintf("terms match"); } struct searchResult *associationSimpleSearch(struct column *col, struct sqlConnection *conn, char *search) /* Search lookup type column. */ { struct dyString *query = dyStringNew(512); struct sqlResult *sr; char **row; struct searchResult *resList = NULL, *res; struct sqlConnection *conn2 = hAllocConn(database); sqlDyStringPrintf(query, col->invQueryOne, search); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { char *name = NULL; if (col->protKey) name = protToGeneId(conn2, row[0]); else name = cloneString(row[0]); if (name != NULL) { AllocVar(res); res->gp.name = name; slAddHead(&resList, res); } } /* Clean up and go home. */ sqlFreeResult(&sr); hFreeConn(&conn2); dyStringFree(&query); slReverse(&resList); return resList; } void setupColumnAssociation(struct column *col, char *parameters) /* Set up a column that looks for an association table * keyed by the geneId. */ { if ((col->queryFull = columnSetting(col, "queryFull", NULL)) == NULL) errAbort("Missing required queryFull field in column %s", col->name); if ((col->queryOne = columnSetting(col, "queryOne", NULL)) == NULL) errAbort("Missing required queryOne field in column %s", col->name); if ((col->invQueryOne = columnSetting(col, "invQueryOne", NULL)) == NULL) errAbort("Missing required invQueryOne field in column %s", col->name); col->protKey = (columnSetting(col, "protKey", NULL) != NULL); col->weedDupes = (columnSetting(col, "weedDupes", NULL) != NULL); col->tablesUsed = cloneString(parameters); col->exists = associationExists; col->filterControls = associationFilterControls; col->advFilter = associationAdvFilter; col->cellVal = associationCellVal; col->cellPrint = associationCellPrint; if (columnSetting(col, "search", NULL)) col->simpleSearch = associationSimpleSearch; } /* ----- Ordering by association. ----- */ static boolean associationOrderExists(struct order *ord, struct sqlConnection *conn) /* This returns true if needed tables exist. */ { return sqlTablesExist(conn, ord->tables); } static void associationCalcDistances(struct order *ord, struct sqlConnection *conn, /* connection to main database. */ struct genePos **pGeneList, struct hash *geneHash, int maxCount) /* Fill in distance fields in geneList. */ { struct sqlResult *sr; char **row; struct hash *curTerms = newHash(8); struct hash *protHash = NULL; struct hash *lookupHash = geneHash; char query[512]; struct genePos *gp; char *geneId = curGeneId->name; if (ord->protKey) { /* Build up hash of genes keyed by protein names. (The geneHash * passed in is keyed by the mrna name. */ protHash = newHash(17); for (gp = *pGeneList; gp != NULL; gp = gp->next) { char *id = (ord->protKey ? (kgVersion == KG_III ? lookupProtein(conn, gp->name) : gp->protein) : gp->name); hashAdd(protHash, id, gp); } /* Also switch current gene id and lookup hash to protein. */ geneId = curGeneId->protein; lookupHash = protHash; } /* Build up hash full of all go IDs associated with gene. */ if (geneId != NULL) { sqlSafef(query, sizeof(query), ord->queryOne, geneId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hashAdd(curTerms, row[0], NULL); } sqlFreeResult(&sr); } /* Stream through association table counting matches. */ -sqlSafef(query, sizeof(query), "%-s", ord->queryAll); // purely for side-effect of adding NOSQLINJ prefix +sqlSafef(query, sizeof(query), ord->queryAll, NULL); // trust sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (hashLookup(curTerms, row[1])) { struct hashEl *hel = hashLookup(lookupHash, row[0]); while (hel != NULL) { gp = hel->val; gp->count += 1; hel = hashLookupNext(hel); } } } sqlFreeResult(&sr); /* Go through list translating non-zero counts to distances. */ for (gp = *pGeneList; gp != NULL; gp = gp->next) { if (gp->count > 0) { gp->distance = 1.0/gp->count; gp->count = 0; } if (sameString(gp->name, curGeneId->name)) /* Force self to top of list. */ gp->distance = 0; } hashFree(&protHash); hashFree(&curTerms); } void associationSimilarityMethods(struct order *ord, char *parameters) /* Fill in associationSimilarity methods. */ { ord->exists = associationOrderExists; ord->calcDistances = associationCalcDistances; ord->tables = cloneString(parameters); ord->protKey = orderSettingExists(ord, "protKey"); ord->queryOne = orderRequiredSetting(ord, "queryOne"); ord->queryAll = orderRequiredSetting(ord, "queryAll"); }