e81403a315a24af601884b8a19e89bcecc92f267 galt Sat Dec 8 20:04:28 2018 -0800 Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596. diff --git src/hg/hgTracks/rmskTrack.c src/hg/hgTracks/rmskTrack.c index 65ed288..be49e0b 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 README in this or parent directory 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[64]; + char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct dyString *query = newDyString(1024); /* Do black and white on single track. Fetch less than we need from database. */ - if (hFindSplitTable(database, chromName, tg->table, table, &hasBin)) + 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); /* 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; }