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/gtexEqtlClusterTrack.c src/hg/hgTracks/gtexEqtlClusterTrack.c index aef459c..6034c79 100644 --- src/hg/hgTracks/gtexEqtlClusterTrack.c +++ src/hg/hgTracks/gtexEqtlClusterTrack.c @@ -1,337 +1,337 @@ /* gtexEqtlClusterTrack - Track of clustered expression QTL's from GTEx */ /* Copyright (C) 2017 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "dystring.h" #include "hgTracks.h" #include "gtexInfo.h" #include "gtexTissue.h" #include "gtexUi.h" #include "gtexEqtlCluster.h" struct gtexEqtlClusterTrack /* Track info for filtering (maybe later for draw, map) */ { struct gtexTissue *tissues; /* Tissue names, descriptions */ struct hash *tissueHash; /* Tissue info, keyed by UCSC name, filtered by UI */ boolean doTissueColor; /* Display tissue color (for single-tissue eQTL's) */ double minEffect; /* Effect size filter (abs value) */ double minProb; /* Probability filter */ }; /* Utility functions */ static struct gtexEqtlCluster *loadOne(char **row) /* Load up gtexEqtlCluster from array of strings. */ { return gtexEqtlClusterLoad(row); } static boolean filterTissuesFromCart(struct track *track, struct gtexEqtlClusterTrack *extras) /* Check cart for tissue selection. Populate track tissues hash */ { char *version = gtexVersionSuffix(track->table); extras->tissues = gtexGetTissues(version); extras->tissueHash = hashNew(0); struct gtexTissue *tis = NULL; for (tis = extras->tissues; tis != NULL; tis = tis->next) hashAdd(extras->tissueHash, tis->name, tis); // if all tissues included, return full hash if (!cartListVarExistsAnyLevel(cart, track->tdb, FALSE, GTEX_TISSUE_SELECT)) return FALSE; struct slName *selectedValues = cartOptionalSlNameListClosestToHome(cart, track->tdb, FALSE, GTEX_TISSUE_SELECT); if (selectedValues == NULL || slCount(selectedValues) == slCount(extras->tissues)) return FALSE; // create tissue hash with only included tissues struct hash *tisHash = hashNew(0); struct slName *name; for (name = selectedValues; name != NULL; name = name->next) { tis = (struct gtexTissue *)hashFindVal(extras->tissueHash, name->name); if (tis != NULL) hashAdd(tisHash, name->name, tis); } extras->tissueHash = tisHash; return TRUE; } static void eqtlExcludeTissue(struct gtexEqtlCluster *eqtl, int i) /* Mark the tissue to exclude from display */ { eqtl->expScores[i] = 0.0; } static boolean eqtlIsExcludedTissue(struct gtexEqtlCluster *eqtl, int i) /* Check if eQTL is excluded */ { return (eqtl->expScores[i] == 0.0); } static boolean eqtlIncludeFilter(struct track *track, void *item) /* Apply all filters (except gene) to eQTL item. Invoked by filterTissues method */ { int i; int excluded = 0; double maxEffect = 0.0; double maxProb = 0.0; struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData; for (i=0; i<eqtl->expCount; i++) { if (hashFindVal(extras->tissueHash, eqtl->expNames[i])) { double effect = eqtl->expScores[i]; double prob = eqtl->expProbs[i]; maxEffect = fmax(maxEffect, fabs(effect)); maxProb = fmax(maxProb, fabs(prob)); if (effect < extras->minEffect || prob < extras->minProb) { eqtlExcludeTissue(eqtl, i); excluded++; } } else { eqtlExcludeTissue(eqtl, i); excluded++; } } // exclude if no tissues match selector if (excluded == eqtl->expCount || // or if variant has no selected tissue where effect size is above cutoff maxEffect < extras->minEffect || // or if variant has no selected tissue where probability is above cutoff maxProb < extras->minProb) return FALSE; return TRUE; } static int eqtlTissueCount(struct gtexEqtlCluster *eqtl) /* Return count of non-excluded tissues in the item */ { int included = 0; int i; for (i=0; i<eqtl->expCount; i++) if (!eqtlIsExcludedTissue(eqtl, i)) included++; return included; } static int eqtlTissueIndex(struct gtexEqtlCluster *eqtl) /* Return index of first non-excluded tissue in an eQTL cluster. Used for single-tissue items. */ { int i; for (i=0; i<eqtl->expCount; i++) if (!eqtlIsExcludedTissue(eqtl, i)) return i; return -1; } static struct rgbColor eqtlTissueColor(struct track *track, struct gtexEqtlCluster *eqtl) /* Return tissue color for single-tissue item, or NULL if none found */ { int i = eqtlTissueIndex(eqtl); assert(i>=0); struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData; struct gtexTissue *tis = (struct gtexTissue *)hashFindVal(extras->tissueHash, eqtl->expNames[i]); assert (tis); return (struct rgbColor){.r=COLOR_32_BLUE(tis->color), .g=COLOR_32_GREEN(tis->color), .b=COLOR_32_RED(tis->color)}; } static char *eqtlSourcesLabel(struct gtexEqtlCluster *eqtl) /* Right label is tissue (or number of tissues if >1) */ { int ct = eqtlTissueCount(eqtl); if (ct == 1) { int i = eqtlTissueIndex(eqtl); if (i<0) errAbort("GTEx eQTL %s/%s track tissue index is negative", eqtl->name, eqtl->target); return eqtl->expNames[i]; } struct dyString *ds = dyStringNew(0); dyStringPrintf(ds, "%d tissues", ct); return dyStringCannibalize(&ds); } /* Track methods */ static void gtexEqtlClusterLoadItems(struct track *track) /* Load items in window and prune those that don't pass filter */ { /* initialize track info */ struct gtexEqtlClusterTrack *extras; AllocVar(extras); track->extraUiData = extras; char cartVar[64]; // UI settings safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_TISSUE_COLOR); extras->doTissueColor = cartUsualBoolean(cart, cartVar, GTEX_EQTL_TISSUE_COLOR_DEFAULT); boolean isFiltered = FALSE; // filter by gene via SQL safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_GENE); char *gene = cartNonemptyString(cart, cartVar); char *where = NULL; if (gene) { struct dyString *ds = dyStringNew(0); - sqlDyStringPrintfFrag(ds, "%s = '%s'", GTEX_EQTL_GENE_FIELD, gene); + sqlDyStringPrintf(ds, "%s = '%s'", GTEX_EQTL_GENE_FIELD, gene); where = dyStringCannibalize(&ds); isFiltered = TRUE; } bedLoadItemWhere(track, track->table, where, (ItemLoader)loadOne); // more filtering safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_EFFECT); extras->minEffect = fabs(cartUsualDouble(cart, cartVar, GTEX_EQTL_EFFECT_DEFAULT)); safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_PROBABILITY); extras->minProb = cartUsualDouble(cart, cartVar, GTEX_EQTL_PROBABILITY_DEFAULT); boolean hasTissueFilter = filterTissuesFromCart(track, extras); if (hasTissueFilter || extras->minEffect != 0.0 || extras->minProb != 0.0) { isFiltered = TRUE; filterItems(track, eqtlIncludeFilter, "include"); } if (isFiltered) labelTrackAsFiltered(track); } static char *gtexEqtlClusterItemName(struct track *track, void *item) /* Left label is gene name */ { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; return eqtl->target; } // blues #define EQTL_COLOR_HIGH_NEGATIVE MAKECOLOR_32(0x0, 0x0, 0xff) #define EQTL_COLOR_LOW_NEGATIVE MAKECOLOR_32(0xa0, 0xa0, 0xff) // reds #define EQTL_COLOR_HIGH_POSITIVE MAKECOLOR_32(0xff, 0x0, 0x0) #define EQTL_COLOR_LOW_POSITIVE MAKECOLOR_32(0xff, 0xa0, 0xa0) // gray #define EQTL_COLOR_MIXED MAKECOLOR_32(0x69, 0x69, 0x69) static Color gtexEqtlClusterItemColor(struct track *track, void *item, struct hvGfx *hvg) /* Color by highest effect in list (blue -, red +), grayed for lower effect. Gray if mixed effect*/ { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; double maxEffect = 0.0; double minEffect = 0.0; int i; for (i=0; i<eqtl->expCount; i++) { if (eqtlIsExcludedTissue(eqtl, i)) continue; double effect = eqtl->expScores[i]; if (effect > maxEffect) maxEffect = effect; else if (effect < minEffect) minEffect = effect; } if (minEffect < 0.0 && maxEffect > 0.0) // mixed effect return EQTL_COLOR_MIXED; double cutoff = 2.0; if (minEffect < 0.0) { // down-regulation displayed as blue if (minEffect < 0.0 - cutoff) return EQTL_COLOR_HIGH_NEGATIVE; return EQTL_COLOR_LOW_NEGATIVE; } // up-regulation displayed as red if (maxEffect > cutoff) return EQTL_COLOR_HIGH_POSITIVE; return EQTL_COLOR_LOW_POSITIVE; } /* Helper macros */ #define tissueColorPatchSpacer (max(2, tl.nWidth/4)) #define tissueColorPatchWidth (tl.nWidth * .8) static int gtexEqtlClusterItemRightPixels(struct track *track, void *item) /* Return number of pixels we need to the right of an item (for sources label). */ { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; int ret = mgFontStringWidth(tl.font, eqtlSourcesLabel(eqtl)); if (eqtlTissueCount(eqtl) == 1) ret += tissueColorPatchWidth + tissueColorPatchSpacer; return ret; } static void gtexEqtlClusterDrawItemAt(struct track *track, void *item, struct hvGfx *hvg, int xOff, int y, double scale, MgFont *font, Color color, enum trackVisibility vis) /* Draw GTEx eQTL cluster with right label indicating source(s) */ { bedDrawSimpleAt(track, item, hvg, xOff, y, scale, font, color, vis); if (vis != tvFull && vis != tvPack) return; /* Draw text to the right */ struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData; int x2 = round((double)((int)eqtl->chromEnd-winStart)*scale) + xOff; int x = x2 + tl.mWidth/2; char *label = eqtlSourcesLabel(eqtl); int w = mgFontStringWidth(font, label); hvGfxTextCentered(hvg, x, y, w, track->heightPer, MG_BLACK, font, label); if (eqtlTissueCount(eqtl) == 1 && extras->doTissueColor) { // tissue color patch (box) x += w; int h = w = tissueColorPatchWidth; struct rgbColor tisColor = eqtlTissueColor(track, eqtl); int ix = hvGfxFindColorIx(hvg, tisColor.r, tisColor.g, tisColor.b); hvGfxBox(hvg, x + tissueColorPatchSpacer, y + (tl.fontHeight - h)/2 + tl.fontHeight/10, w, h, ix); } } static void gtexEqtlClusterMapItem(struct track *track, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) /* Create a map box on item and label with list of tissues with colors and effect size */ { char *title = itemName; if (track->limitedVis != tvDense) { struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item; struct dyString *ds = dyStringNew(0); dyStringPrintf(ds, "%s/%s: ", eqtl->name, eqtl->target); int i; for (i=0; i<eqtl->expCount; i++) { if (eqtlIsExcludedTissue(eqtl, i)) continue; double effect= eqtl->expScores[i]; dyStringPrintf(ds, "%s(%s%0.2f)%s", eqtl->expNames[i], effect < 0 ? "" : "+", effect, i < eqtl->expCount - 1 ? ", " : ""); } title = dyStringCannibalize(&ds); } int w = width + gtexEqtlClusterItemRightPixels(track, item); genericMapItem(track, hvg, item, title, itemName, start, end, x, y, w, height); } void gtexEqtlClusterMethods(struct track *track) /* BED5+5 with target, expNames,expScores, expProbs */ { track->loadItems = gtexEqtlClusterLoadItems; track->itemName = gtexEqtlClusterItemName; track->itemColor = gtexEqtlClusterItemColor; track->itemRightPixels = gtexEqtlClusterItemRightPixels; track->drawItemAt = gtexEqtlClusterDrawItemAt; track->mapItem = gtexEqtlClusterMapItem; }