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/hgTracks.c src/hg/hgTracks/hgTracks.c index ba6256a..7b451fc 100644 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@ -404,31 +404,31 @@ struct dyString *ui = uiStateUrlPart(toggleGroup); x = hvGfxAdjXW(hvg, x, width); if (theImgBox && curImgTrack) { char link[512]; safef(link,sizeof(link),"%s?complement_%s=%d&%s", hgTracksName(), database, !cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE),ui->string); imgTrackAddMapItem(curImgTrack,link,(char *)(message != NULL?message:NULL),x, y, x+width, y+height, NULL); } else { hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height); hPrintf("HREF=\"%s?complement_%s=%d", hgTracksName(), database, !cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE)); hPrintf("&%s\"", ui->string); - freeDyString(&ui); + dyStringFree(&ui); if (message != NULL) mapStatusMessage("%s", message); hPrintf(">\n"); } } char *trackUrl(char *mapName, char *chromName) /* Return hgTrackUi url; chromName is optional. */ { char *encodedMapName = cgiEncode(mapName); char buf[2048]; char *hgTrackUi = hTrackUiForTrack(mapName); if(chromName == NULL) safef(buf, sizeof(buf), "%s?%s=%s&db=%s&g=%s", hgTrackUi, cartSessionVarName(), cartSessionId(cart), database, encodedMapName); else @@ -2098,31 +2098,31 @@ { int vis = track->limitedVisSet ? track->limitedVis : track->visibility; if (vis) { logTrackList(dy, track->subtracks); if (dy->stringSize) dyStringAppendC(dy, ','); dyStringPrintf(dy,"%s:%d", track->track, vis); } } } static void logTrackVisibilities (char *hgsid, struct track *trackList, char *position) /* log visibile tracks and hgsid */ { -struct dyString *dy = newDyString(1024); +struct dyString *dy = dyStringNew(1024); // build up dyString logTrackList(dy, trackList); // put out ~1024 bye blocks to error_log because otherwise // Apache will chop up the lines char *begin = dy->string; char *ptr = begin; int count = 0; for(ptr=begin; ((ptr = strchr(ptr, ',')) != NULL); ptr++) { if (ptr - begin > 800) { *ptr = 0; fprintf(stderr, "trackLog %d %s %s %s\n", count++, database, hgsid, begin); @@ -3620,79 +3620,82 @@ // so that chr11 (not chr2) comes after chr1. Instead of trying to specify the sort order in the query, // which is slow, or trying to read one chrom at a time in the sorted order which is also slow, we can instead // just fetch them in their native order, and then create a duplicate array and copy the contents // to it in memory, one chunk per chrom, which would be very fast, but temporarily require duplicate vchrom array mem. // Not sure what to do about assemblies with many scaffolds. // // Adding support for extra options from Gencode hg38 so we can filter for // comprehensive, splice-variants, non-coding subsets. { struct sqlConnection *conn = hAllocConn(database); virtRegionList = NULL; struct sqlResult *sr; char **row; int rowOffset = 0; -char query[256]; +struct dyString *query = NULL; int padding = emPadding; if (sameString(virtModeType, "geneMostly")) padding = gmPadding; // knownCanonical Hash struct hash *kcHash = NULL; if (knownCanonical) // filter out alt splicing variants { // load up hash of canonical transcriptIds - sqlSafef(query, sizeof(query), "select transcript from %s" + query = sqlDyStringCreate("select transcript from %s" //" where chrom not like '%%_hap_%%' and chrom not like '%%_random'" , knownCanonical); if (virtualSingleChrom()) - sqlSafefAppend(query, sizeof(query), " where chrom='%s'", chromName); + sqlDyStringPrintf(query, " where chrom='%s'", chromName); kcHash = newHash(10); - sr = sqlGetResult(conn, query); + sr = sqlGetResult(conn, dyStringContents(query)); while ((row = sqlNextRow(sr)) != NULL) { hashAdd(kcHash, row[0], NULL); } sqlFreeResult(&sr); + dyStringFree(&query); } // knownToTag basic hash struct hash *ktHash = NULL; if (knownToTag) // filter out all but Basic { // load up hash of canonical transcriptIds - sqlSafef(query, sizeof(query), "select name from %s where value='basic'", knownToTag); + query = sqlDyStringCreate("select name from %s where value='basic'", knownToTag); ktHash = newHash(10); - sr = sqlGetResult(conn, query); + sr = sqlGetResult(conn, dyStringContents(query)); while ((row = sqlNextRow(sr)) != NULL) { hashAdd(ktHash, row[0], NULL); } sqlFreeResult(&sr); + dyStringFree(&query); } setEMGeneTrack(); if (!emGeneTable) errAbort("Unexpected error, emGeneTable=NULL in initVirtRegionsFromEMGeneTableExons"); if (hIsBinned(database, emGeneTable)) // skip first bin column if any ++rowOffset; -sqlSafef(query, sizeof(query), "select * from %s", emGeneTable); +query = sqlDyStringCreate("select * from %s", emGeneTable); if (virtualSingleChrom()) - sqlSafefAppend(query, sizeof(query), " where chrom='%s'", chromName); + sqlDyStringPrintf(query, " where chrom='%s'", chromName); // TODO GALT may have to change this to in-memory sorting? // refGene is out of order because of genbank continuous loading // also, using where chrom= causes it to use indexes which disturb order returned. -sqlSafefAppend(query, sizeof(query), " order by chrom, txStart"); -sr = sqlGetResult(conn, query); +sqlDyStringPrintf(query, " order by chrom, txStart"); +sr = sqlGetResult(conn, dyStringContents(query)); +dyStringFree(&query); char chrom[256] = ""; int start = -1; int end = -1; char lastChrom[256] = ""; int lastStart = -1; int lastEnd = -1; int chromSize = -1; char lastChromSizeChrom[256] = ""; boolean firstTime = TRUE; boolean isEOF = FALSE; struct kce *kceList = NULL, *bestKce = NULL, *prevKce = NULL; struct genePred *gene = NULL; while (1) { @@ -3925,35 +3928,37 @@ slAddHead(&virtRegionList, v); } slReverse(&virtRegionList); //if (winCount >= 2) // withNextExonArrows = FALSE; /* Display next exon navigation buttons near center labels? */ //warn("winCount=%d, exonSize=%d, intronSize=%d", winCount, exonSize, intronSize); } void initAllChroms() /* initialize virt region list for main chromosomes */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int winCount = 0; -char *query = -NOSQLINJ "select chrom, size from chromInfo" -" where chrom like 'chr%'" -" and chrom not like '%_random'" -" and chrom not like 'chrUn%'"; +char query[1024]; +sqlSafef(query, sizeof query, +"select chrom, size from chromInfo" +" where chrom like 'chr%%'" +" and chrom not like '%%_random'" +" and chrom not like 'chrUn%%'" +); // allow alternate haplotypes for now //" and chrom not like '%_hap%'" //" and chrom not like '%_alt'" //warn("%s",query); struct virtRegion *v; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { unsigned chromSize = sqlUnsigned(row[1]); AllocVar(v); v->chrom = cloneString(row[0]); v->start = 1 - 1; v->end = chromSize; slAddHead(&virtRegionList, v); ++winCount; @@ -7983,31 +7988,31 @@ struct sqlConnection *conn = hConnectCentral(); char query[1000]; sqlSafef(query, sizeof query, "SELECT contents FROM namedSessionDb where sessionName='%s'", replaceChars(sessionName, " ", "%20")); char *cartString = sqlQuickNonemptyString(conn, query); hDisconnectCentral(&conn); // TODO: use cheapcgi.cgiParsedVarsNew() to parse and get list ? #define MAX_SESSION_LEN 100000 char *curSessCart = (char *)needMem(MAX_SESSION_LEN); cgiDecodeFull(cartString, curSessCart, MAX_SESSION_LEN); char *curSessVisTracks = cgiTrackVisString(curSessCart); // get track-related vars from current cart -struct dyString *dsCgiVars = newDyString(0); +struct dyString *dsCgiVars = dyStringNew(0); cartEncodeState(cart, dsCgiVars); outDefaultTracks(cart, dsCgiVars); char *this = dyStringCannibalize(&dsCgiVars); // TODO: again, better parsing char *this2 = replaceChars(this, "%2D", "-"); char *thisSessVars = replaceChars(this2, "%2B", "+"); char *thisSessVisTracks = cgiTrackVisString(thisSessVars); //freeMem(curSessCart); boolean isSessChanged = FALSE; if (differentString(curSessVisTracks, thisSessVisTracks)) { isSessChanged = TRUE; } return isSessChanged; @@ -8189,31 +8194,31 @@ struct window *w; for (w = windows; w; w=w->next) { if (hTrackOnChrom(track->tdb, w->chromName)) hideIt = FALSE; } if (hideIt) { track->limitedVis = tvHide; track->limitedVisSet = TRUE; } } if (cartUsualBoolean(cart, "dumpTracks", FALSE)) { - struct dyString *dy = newDyString(1024); + struct dyString *dy = dyStringNew(1024); logTrackList(dy, trackList); printf("Content-type: text/html\n\n"); printf("%s\n", dy->string); exit(0); } if (sameString(cfgOptionDefault("trackLog", "off"), "on")) logTrackVisibilities(cartSessionId(cart), trackList, position); ///////////////// // NEED TO LOAD ALL WINDOWS NOW // @@ -8436,32 +8441,32 @@ setSharedErrorsAcrossWindows(sub); } } ////////////// END OF MULTI-WINDOW LOOP printTrackInitJavascript(trackList); /* Generate two lists of hidden variables for track group visibility. Kludgy, but required b/c we have two different navigation forms on this page, but we want open/close changes in the bottom form to be submitted even if the user submits via the top form. */ -struct dyString *trackGroupsHidden1 = newDyString(1000); -struct dyString *trackGroupsHidden2 = newDyString(1000); +struct dyString *trackGroupsHidden1 = dyStringNew(1000); +struct dyString *trackGroupsHidden2 = dyStringNew(1000); for (group = groupList; group != NULL; group = group->next) { if (group->trackList != NULL) { int looper; for (looper=1;looper<=2;looper++) { boolean isOpen = !isCollapsedGroup(group); char buf[1000]; safef(buf, sizeof(buf), "<input type='hidden' name=\"%s\" id=\"%s_%d\" value=\"%s\">\n", collapseGroupVar(group->name), collapseGroupVar(group->name), looper, isOpen ? "0" : "1"); dyStringAppend(looper == 1 ? trackGroupsHidden1 : trackGroupsHidden2, buf); } } } @@ -8724,32 +8729,32 @@ // This 'dirty' field is used to check if js/ajax changes to the page have occurred. // If so and it is reached by the back button, a page reload will occur instead. char buf[256]; if (virtualSingleChrom()) // DISGUISE VMODE safef(buf, sizeof buf, "%s", windowsSpanPosition()); else safef(buf, sizeof buf, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); hPrintf("<INPUT TYPE='text' style='display:none;' name='dirty' id='dirty' VALUE='false'>\n"); hPrintf("<INPUT TYPE=HIDDEN id='positionHidden' name='position' " "VALUE=\"%s\">", buf); hPrintf("\n%s", trackGroupsHidden1->string); hPrintf("</CENTER></FORM>\n"); hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" id=\"TrackForm\" METHOD=\"POST\">\n\n", hgTracksName()); hPrintf("%s", trackGroupsHidden2->string); - freeDyString(&trackGroupsHidden1); - freeDyString(&trackGroupsHidden2); + dyStringFree(&trackGroupsHidden1); + dyStringFree(&trackGroupsHidden2); if (!psOutput) cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ hPrintf("<CENTER>"); } /* Make line that says position. */ { char buf[256]; char *javascript = "document.location = '/cgi-bin/hgTracks?db=' + document.TrackForm.db.options[document.TrackForm.db.selectedIndex].value;"; if (containsStringNoCase(database, "zoo")) { hPuts("Organism "); printAssemblyListHtmlExtra(database, "change", javascript); } @@ -10302,36 +10307,38 @@ return; } struct sqlConnection *conn = hAllocConn(database); /* key is database sequence name, value is an alias name, can be multiple * entries for the same sequence name. NULL if no chromAlias available */ struct sqlResult *sr = NULL; char **row = NULL; long long total = 0; char query[512]; char msg1[512], msg2[512]; int seqCount = 0; boolean truncating; -seqCount = sqlQuickNum(conn, NOSQLINJ "select count(*) from chromInfo"); +sqlSafef(query, sizeof query, "select count(*) from chromInfo"); +seqCount = sqlQuickNum(conn, query); truncating = (limit > 0) && (seqCount > limit); if (!truncating) { - sr = sqlGetResult(conn, NOSQLINJ "select chrom,size from chromInfo order by size desc"); + sqlSafef(query, sizeof query, "select chrom,size from chromInfo order by size desc"); + sr = sqlGetResult(conn, query); } else { sqlSafef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit %d", limit); sr = sqlGetResult(conn, query); } while ((row = sqlNextRow(sr)) != NULL) { unsigned size = sqlUnsigned(row[1]); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); htmlPrintf("<A HREF=\"%s|none|?%s|url|=%s|url|&position=%s|url|\">%s</A>", hgTracksName(), cartSessionVarName(), cartSessionId(cart),