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/hgTracks/rmskTrack.c src/hg/hgTracks/rmskTrack.c index 33ccd1c..21a7530 100644 --- src/hg/hgTracks/rmskTrack.c +++ src/hg/hgTracks/rmskTrack.c @@ -1,200 +1,200 @@ /* rmskTrack - Handle RepeatMasker track. */ /* Copyright (C) 2014 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 "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "rmskOut.h" /* Repeat items. Since there are so many of these, to avoid * memory problems we don't query the database and store the results * during repeatLoad, but rather query the database during the * actual drawing. */ static struct repeatItem *otherRepeatItem = NULL; static char *repeatClassNames[] = { "SINE", "LINE", "LTR", "DNA", "Simple", "Low Complexity", "Satellite", "RNA", "Other", "Unknown", }; static char *repeatClasses[] = { "SINE", "LINE", "LTR", "DNA", "Simple_repeat", "Low_complexity", "Satellite", "RNA", "Other", "Unknown", }; static struct repeatItem *riList = NULL; // can be re-used by all windows static struct repeatItem *makeRepeatItems() /* Make the stereotypical repeat masker tracks. */ { if (!riList) { struct repeatItem *ri; int i; int numClasses = ArraySize(repeatClasses); for (i=0; i<numClasses; ++i) { AllocVar(ri); ri->class = repeatClasses[i]; ri->className = repeatClassNames[i]; slAddHead(&riList, ri); if (sameString(repeatClassNames[i], "Other")) otherRepeatItem = ri; } slReverse(&riList); } return riList; } static void repeatLoad(struct track *tg) /* Load up repeat tracks. (Will query database during drawing for a change.) */ { tg->items = makeRepeatItems(); } static void repeatFree(struct track *tg) /* Free up repeatMasker items. */ { slFreeList(&tg->items); } static char *repeatName(struct track *tg, void *item) /* Return name of repeat item track. */ { struct repeatItem *ri = item; return ri->className; } static void repeatDraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) { int baseWidth = seqEnd - seqStart; struct repeatItem *ri; int y = yOff; int heightPer = tg->heightPer; int lineHeight = tg->lineHeight; int x1,x2,w; boolean isFull = (vis == tvFull); Color col; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int rowOffset; if (isFull) { /* Do gray scale representation spread out among tracks. */ struct hash *hash = newHash(6); struct rmskOut ro; int percId; int grayLevel; char statusLine[128]; for (ri = tg->items; ri != NULL; ri = ri->next) { ri->yOffset = y; y += lineHeight; hashAdd(hash, ri->class, ri); } sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { rmskOutStaticLoad(row+rowOffset, &ro); char class[256]; // Simplify repClass for lookup: strip trailing '?', simplify *RNA to RNA: safecpy(class, sizeof(class), ro.repClass); char *p = &(class[strlen(class)-1]); if (*p == '?') *p = '\0'; if (endsWith(class, "RNA")) safecpy(class, sizeof(class), "RNA"); ri = hashFindVal(hash, class); if (ri == NULL) ri = otherRepeatItem; percId = 1000 - ro.milliDiv - ro.milliDel - ro.milliIns; grayLevel = grayInRange(percId, 500, 1000); col = shadesOfGray[grayLevel]; x1 = roundingScale(ro.genoStart-winStart, width, baseWidth)+xOff; x1 = max(x1, 0); x2 = roundingScale(ro.genoEnd-winStart, width, baseWidth)+xOff; if (x1 < insideX) x1 = insideX; if (x2 > insideX+width) x2 = insideX+width; w = x2-x1; if (w <= 0) w = 1; hvGfxBox(hvg, x1, ri->yOffset, w, heightPer, col); if (baseWidth <= 100000) { if (ri == otherRepeatItem) { sprintf(statusLine, "Repeat %s, family %s, class %s", ro.repName, ro.repFamily, ro.repClass); } else { sprintf(statusLine, "Repeat %s, family %s", ro.repName, ro.repFamily); } mapBoxHc(hvg, ro.genoStart, ro.genoEnd, x1, ri->yOffset, w, heightPer, tg->track, ro.repName, statusLine); } } freeHash(&hash); } else { char table[HDB_MAX_TABLE_STRING]; boolean hasBin; - struct dyString *query = newDyString(1024); + struct dyString *query = dyStringNew(1024); /* Do black and white on single track. Fetch less than we need from database. */ if (hFindSplitTable(database, chromName, tg->table, table, sizeof table, &hasBin)) { sqlDyStringPrintf(query, "select genoStart,genoEnd from %s where ", table); if (hasBin) hAddBinToQuery(winStart, winEnd, query); - dyStringPrintf(query, "genoStart<%u and genoEnd>%u ", winEnd, winStart); + sqlDyStringPrintf(query, "genoStart<%u and genoEnd>%u ", winEnd, winStart); /* if we're using a single rmsk table, add genoName to the where clause */ if (startsWith("rmsk", table)) sqlDyStringPrintf(query, " and genoName = '%s' ", chromName); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { int start = sqlUnsigned(row[0]); int end = sqlUnsigned(row[1]); x1 = roundingScale(start-winStart, width, baseWidth)+xOff; x2 = roundingScale(end-winStart, width, baseWidth)+xOff; w = x2-x1; if (w <= 0) w = 1; hvGfxBox(hvg, x1, yOff, w, heightPer, MG_BLACK); } } dyStringFree(&query); } sqlFreeResult(&sr); hFreeConn(&conn); } void repeatMethods(struct track *tg) /* Make track for repeats. */ { tg->loadItems = repeatLoad; tg->freeItems = repeatFree; tg->drawItems = repeatDraw; tg->colorShades = shadesOfGray; tg->itemName = repeatName; tg->mapItemName = repeatName; tg->totalHeight = tgFixedTotalHeightNoOverflow; tg->itemHeight = tgFixedItemHeight; tg->itemStart = tgItemNoStart; tg->itemEnd = tgItemNoEnd; tg->mapsSelf = TRUE; }