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/rnaFoldTrack.c src/hg/hgTracks/rnaFoldTrack.c index 988cec1..00a009e 100644 --- src/hg/hgTracks/rnaFoldTrack.c +++ src/hg/hgTracks/rnaFoldTrack.c @@ -1,239 +1,239 @@ /* rnaStructure - stuff to handle loading and coloring of rna secondary structure predictions. */ /* Copyright (C) 2012 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "bed.h" #include "rnaSecStr.h" #include "rnautil.h" void bedLoadItemBySqlResult(struct track *tg, struct sqlResult *sr, int rowOffset, ItemLoader loader) /* Generic tg->item loader. */ { char **row = NULL; struct slList *itemList = NULL, *item = NULL; if (NULL == sr) errAbort("While loading track %s, bedLoadItemSqlResult was given empty sqlResult", tg->track); while ((row = sqlNextRow(sr)) != NULL) { item = loader(row + rowOffset); slAddHead(&itemList, item); } slSort(&itemList, bedCmp); tg->items = itemList; } void scoreFilterSqlClause(struct track *tg, char *extraWhere, size_t size, int defaultFilterScore) /* Make a 'where' clause for the sql query if the scoreFilter has been set. */ { char option[128]; /* Option - score filter */ char *optionScoreVal; int optionScore = defaultFilterScore; safef(option, sizeof(option), "%s.scoreFilter", tg->track); optionScoreVal = trackDbSetting(tg->tdb, "scoreFilter"); if (optionScoreVal != NULL) optionScore = atoi(optionScoreVal); optionScore = cartUsualInt(cart, option, optionScore); -safef(extraWhere, size, "score >= %d",optionScore); +sqlSafef(extraWhere, size, "score >= %d",optionScore); } void loadRnaSecStr(struct track *tg) /* Load up rnaSecStr from database table to track items. */ { struct sqlConnection *conn = hAllocConn(database); int rowOffset = 0; struct sqlResult *sr = NULL; char extraWhere[128]; scoreFilterSqlClause(tg, extraWhere, sizeof(extraWhere), 0); sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, extraWhere, &rowOffset); bedLoadItemBySqlResult(tg, sr, rowOffset, (ItemLoader)rnaSecStrLoad); sqlFreeResult(&sr); hFreeConn(&conn); } void freeRnaSecStr(struct track *tg) /* Free up rnaSecStr items. */ { rnaSecStrFreeList((struct rnaSecStr**)&tg->items); } void spreadAndColorString(struct hvGfx *hvg, int x, int y, int width, int height, Color *colorIxs, int maxShade, MgFont *font, char *text, int count, double *scores, double minScore, double maxScore) /* Draw evenly spaced letters in string. The scores array contains a * score for each letter in the text string. The score will determine * which color in the colorIxs will be used for a given * letter. ColorIxs is an array of size maxShade+1. The count param is * the number of bases to print, not length of the input line * (text) */ { char c[2] = ""; int i; int x1, x2; Color clr; for (i=0; i<count; i++, text++) { x1 = i * width / count; x2 = (i+1) * width/count; if (scores) clr = colorIxs[assignBin(*scores, minScore, maxScore, maxShade+1)]; else clr = colorIxs[maxShade]; c[0] = *text; hvGfxTextCentered(hvg, x1+x, y, x2-x1, height, clr, font, c); if (scores) scores++; } } void spreadAndGrayShadeString(struct hvGfx *hvg, int x, int y, int width, int height, MgFont *font, char *text, int count, double *scores, double minScore, double maxScore) /* Draw evenly spaced letters in string and gray shade letters according to scores. */ { spreadAndColorString(hvg, x, y, width, height, shadesOfGray+2, maxShade-2, font, text, count, scores, minScore, maxScore); } void spreadRnaFoldAnno(struct hvGfx *hvg, int x, int y, int width, int height, Color color, MgFont *font, struct rnaSecStr *item) /* Draw parenthesis structure which defines rna secondary structure. */ { char *fold = cloneString(item->secStr); double *scores = NULL; if (item->conf != NULL) scores = CloneArray(item->conf, item->size); if (*item->strand == '-') { reverseFold(fold); if (scores) reverseDoubles(scores, item->size); } spreadAndGrayShadeString(hvg, x, y, width, height, font, fold, item->size, scores, 0.0, 1.0); freeMem(fold); if (scores) freeMem(scores); } void drawCharBox(struct hvGfx *hvg, int x, int y, int width, int height, Color color, char *s, char c) /* s defines a string which spans width. Draw a box in intervals * corresponding to positions where s has letter c */ { double charWidth = ((double)width)/strlen(s); int i = 0, begin = 0, length = 0; for (;*s;s++,i++) { if (*s == c) { if (!length) begin = i; length++; } /* Draw box if at end of interval or at end of string */ if (*s != c || !*(s+1) ) if (length) { int x1 = x + (int) begin *charWidth; int w = (int) length*charWidth; hvGfxBox(hvg, x1, y, w, height, color); length = 0; } } } void colorSingleStranded(struct hvGfx *hvg, int x, int y, int width, int height, Color color, struct rnaSecStr *item) { char *fold = cloneString(item->secStr); if (*item->strand == '-') reverseFold(fold); drawCharBox(hvg, x, y, width, height, color, fold, '.'); freeMem(fold); } void rnaSecStrDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw a single simple rnaSecStr item at position. */ { struct rnaSecStr *rnaSecStr = item; int heightPer = tg->heightPer; int x1 = round((double)((int)rnaSecStr->chromStart-winStart)*scale) + xOff; int x2 = round((double)((int)rnaSecStr->chromEnd-winStart)*scale) + xOff; int w; struct trackDb *tdb = tg->tdb; int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0")); int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000")); if (tg->itemColor != NULL) color = tg->itemColor(tg, rnaSecStr, hvg); else { if (tg->colorShades) color = tg->colorShades[grayInRange(rnaSecStr->score, scoreMin, scoreMax)]; } w = x2-x1; if (w < 1) w = 1; if (color) { if (zoomedToBaseLevel) spreadRnaFoldAnno(hvg, x1, y, w, heightPer, color, font, rnaSecStr); else { hvGfxBox(hvg, x1, y, w, heightPer, color); colorSingleStranded(hvg, x1, y, w, heightPer, lighterColor(hvg, color), rnaSecStr); if (tg->subType == lfWithBarbs || tg->exonArrows) { int dir = 0; if (rnaSecStr->strand[0] == '+') dir = 1; else if (rnaSecStr->strand[0] == '-') dir = -1; if (dir != 0 && w > 2) { int midY = y + (heightPer>>1); Color textColor = hvGfxContrastingColor(hvg, color); clippedBarbs(hvg, x1, midY, w, 2, 5, dir, textColor, TRUE); } } } if (tg->drawName && vis != tvSquish) { char *s = tg->itemName(tg, rnaSecStr); w = x2-x1; if (w > mgFontStringWidth(font, s)) { Color textColor = hvGfxContrastingColor(hvg, color); hvGfxTextCentered(hvg, x1, y, w, heightPer, textColor, font, s); } mapBoxHc(hvg, rnaSecStr->chromStart, rnaSecStr->chromEnd, x1, y, x2 - x1, heightPer, tg->track, tg->mapItemName(tg, rnaSecStr), NULL); } } } void rnaSecStrMethods(struct track *tg) /* Make track which visualizes RNA secondary structure annotation. */ { tg->loadItems = loadRnaSecStr; tg->freeItems = freeRnaSecStr; tg->drawItemAt = rnaSecStrDrawAt; }