a1d7c07c50f1d895337de121680ea672b261c058 max Mon Aug 17 02:26:36 2026 -0700 escape reflected/echoed user input across several CGIs (XSS), refs #38057 Route user-, DB- and hub-derived values through htmlEncode (HTML/attribute text), cgiEncode (values composed into URLs), jsonStringEscape (values placed in a JS string literal inside an inline script) or, for hgMirror, the existing mustBeClean sanitizer. Covers hgHubConnect, hgUserSuggestion, hgLiftOver, hgBlat, hgc pubs, hgVisiGene, hgSession, hgTrackUi, hgGenome, phyloPng, hgFileSearch, hgLinkIn, hgPal, hui, hgPhyloPlace, hgMirror, hgCustom and hgSearch. diff --git src/hg/hgFileSearch/hgFileSearch.c src/hg/hgFileSearch/hgFileSearch.c index e59f0883f50..59d918f045e 100644 --- src/hg/hgFileSearch/hgFileSearch.c +++ src/hg/hgFileSearch/hgFileSearch.c @@ -1,494 +1,494 @@ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "obscure.h" #include "hash.h" #include "cheapcgi.h" #include "htmshell.h" #include "jsHelper.h" #include "trackDb.h" #include "hdb.h" #include "web.h" #include "mdb.h" #include "hCommon.h" #include "hui.h" #include "fileUi.h" #include "search.h" #include "cart.h" #include "grp.h" #include "botDelay.h" /* for earlyBotCheck() function at the beginning of main() */ #define delayFraction 1.0 /* standard penalty is 1.0 for most CGIs */ static boolean issueBotWarning = FALSE; #define FAKE_MDB_MULTI_SELECT_SUPPORT struct hash *trackHash = NULL; // Is this needed? boolean measureTiming = FALSE; /* DON'T EDIT THIS -- use CGI param "&measureTiming=." . */ #define FILE_SEARCH_WHAT "Downloadable ENCODE Files" #define FILE_SEARCH_NAME FILE_SEARCH_WHAT " Search" #define FILE_SEARCH "hgfs_Search" #define FILE_SEARCH_FORM "fileSearch" #define FILE_SEARCH_CURRENT_TAB "fsCurTab" #define FILE_SEARCH_ON_FILETYPE "fsFileType" // These are common with trackSearch. Should they be? #define TRACK_SEARCH_SIMPLE "tsSimple" #define TRACK_SEARCH_ON_NAME "tsName" #define TRACK_SEARCH_ON_GROUP "tsGroup" #define TRACK_SEARCH_ON_DESCR "tsDescr" #define TRACK_SEARCH_SORT "tsSort" //#define USE_TABS static struct trackDb *tdbFilterBy(struct trackDb **pTdbList, char *name, char *description, char *group) // returns tdbs that match supplied criterion, leaving unmatched in list passed in { // Set the word lists up once struct slName *nameList = NULL; if (name) nameList = slNameListOfUniqueWords(cloneString(name),TRUE); // TRUE means respect quotes struct slName *descList = NULL; if (description) descList = slNameListOfUniqueWords(cloneString(description),TRUE); struct trackDb *tdbList = *pTdbList; struct trackDb *tdbRejects = NULL; struct trackDb *tdbMatched = NULL; while (tdbList != NULL) { struct trackDb *tdb = slPopHead(&tdbList); if (!tdbIsComposite(tdb)) slAddHead(&tdbRejects,tdb); else if (group && differentString(tdb->grp,group)) slAddHead(&tdbRejects,tdb); else if (name && !searchNameMatches(tdb, nameList)) slAddHead(&tdbRejects,tdb); else if (description && !searchDescriptionMatches(tdb, descList)) slAddHead(&tdbRejects,tdb); else slAddHead(&tdbMatched,tdb); } *pTdbList = tdbRejects; //warn("matched %d tracks",slCount(tdbMatched)); return tdbMatched; } static boolean mdbSelectsAddFoundComposites(struct slPair **pMdbSelects,struct trackDb *tdbsFound) // Adds a composite mdbSelect (if found in tdbsFound) to the head of the pairs list. // If tdbsFound is NULL, then add dummy composite search criteria { // create comma separated list of composites struct dyString *dyComposites = dyStringNew(256); struct trackDb *tdb = tdbsFound; for (;tdb != NULL; tdb = tdb->next) { if (tdbIsComposite(tdb)) dyStringPrintf(dyComposites,"%s,",tdb->track); else if (tdbIsCompositeChild(tdb)) { struct trackDb *composite = tdbGetComposite(tdb); dyStringPrintf(dyComposites,"%s,",composite->track); } } if (dyStringLen(dyComposites) > 0) { char *composites = dyStringCannibalize(&dyComposites); composites[strlen(composites) - 1] = '\0'; // drop the last ',' slPairAdd(pMdbSelects,MDB_VAR_COMPOSITE,composites); // Composite should not already be in the list, because it is only indirectly sortable return TRUE; } //warn("No composites found"); dyStringFree(&dyComposites); return FALSE; } #ifdef USE_TABS static struct slRef *simpleSearchForTdbs(struct trix *trix,char **descWords,int descWordCount) // Performs the simple search and returns the found tracks. { struct slRef *foundTdbs = NULL; struct trixSearchResult *tsList; for (tsList = trixSearch(trix, descWordCount, descWords, tsmExpand); tsList != NULL; tsList = tsList->next) { struct trackDb *tdb = (struct track *) hashFindVal(trackHash, tsList->itemId); if (track != NULL) // It is expected that this is NULL { // (e.g. when the trix references trackDb tracks which have no tables) refAdd(&foundTdbs, tdb); } } return foundTdbs; } #endif///def USE_TABS struct slName *tdbListGetGroups(struct trackDb *tdbList) // Returns a list of groups found in the tdbList // FIXME: Should be moved to trackDbCustom and shared { struct slName *groupList = NULL; char *lastGroup = "[]"; struct trackDb *tdb = tdbList; for (;tdb!=NULL;tdb=tdb->next) { if (differentString(lastGroup,tdb->grp)) lastGroup = slNameStore(&groupList, tdb->grp); } return groupList; } struct grp *groupsFilterForTdbList(struct grp **grps,struct trackDb *tdbList) { struct grp *grpList = *grps; *grps = NULL; struct slName *tdbGroups = tdbListGetGroups(tdbList); if (tdbList == NULL) return *grps; while (grpList != NULL) { struct grp *grp = slPopHead(&grpList); if (slNameInList(tdbGroups,grp->name)) slAddHead(grps,grp); } slNameFreeList(&tdbGroups); slReverse(grps); return *grps; } static void doFileSearch(char *db,char *organism,struct cart *cart,struct trackDb *tdbList) { struct sqlConnection *conn = hAllocConn(db); boolean metaDbExists = sqlTableExists(conn, "metaDb"); if (!sqlTableExists(conn, "metaDb")) { warn("Assembly %s %s does not support Downloadable Files search.", organism, hFreezeFromDb(db)); hFreeConn(&conn); return; } char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME); char *descSearch=NULL; char *fileTypeSearch = cartOptionalString(cart, FILE_SEARCH_ON_FILETYPE); boolean doSearch = sameWord(cartUsualString(cart, FILE_SEARCH,"no"), "search"); #ifdef ONE_FUNC struct hash *parents = newHash(4); #endif///def ONE_FUNC int cols; #ifdef USE_TABS enum searchTab selectedTab = simpleTab; char *currentTab = cartUsualString(cart, FILE_SEARCH_CURRENT_TAB, "simpleTab"); if (sameString(currentTab, "simpleTab")) { selectedTab = simpleTab; descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE); freez(&nameSearch); } else if (sameString(currentTab, "filesTab")) { selectedTab = filesTab; descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR); } #else///ifndef USE_TABS descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR); #endif///ndef USE_TABS #ifdef USE_TABS struct trix *trix; char trixFile[HDB_MAX_PATH_STRING]; getSearchTrixFile(db, trixFile, sizeof(trixFile)); trix = trixOpen(trixFile); #endif///def USE_TABS printf("<div style='max-width:1080px;'>"); // FIXME: Do we need a form at all? printf("<form action='../cgi-bin/hgFileSearch' name='%s' id='%s' method='get'>\n\n", FILE_SEARCH_FORM,FILE_SEARCH_FORM); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo printf("<input type='hidden' name='db' value='%s'>\n", db); printf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW); printf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW); #ifdef USE_TABS printf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", FILE_SEARCH_CURRENT_TAB, currentTab); printf("<div id='tabs' style='display:none; %s'>\n" "<ul>\n" "<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, " "Helvetica, san-serif;'>Search</B></a></li>\n" "<li><a href='#filesTab'><B style='font-size:.9em;font-family: arial, Geneva, " "Helvetica, san-serif;'>Files</B></a></li>\n" "</ul>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;"); // Files tab printf("<div id='simpleTab' style='max-width:inherit;'>\n"); printf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>"); printf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' " "style='max-width:1000px; width:100%%;'>\n", - TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch); + TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : htmlEncode(descSearch)); // search string into attr, escape (XSS) jsOnEventById("keyup", "simpleSearch", "findTracks.searchButtonsEnable(true);"); printf("</td></tr><td style='max-height:4px;'></td></tr></table>"); printf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", FILE_SEARCH); printf("<input type='button' name='clear' id='clear' value='clear' class='clear' style='font-size:.8em;'>\n"); jsOnEventById("click","clear","findTracks.clear();"); printf("<input type='submit' name='submit' value='cancel' class='cancel' " "style='font-size:.8em;'>\n"); printf("</div>\n"); #endif///def USE_TABS // Files tab printf("<div id='filesTab' style='width:inherit;'>\n" "<table id='filesTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n"); cols = 8; // Track Name contains printf("<tr><td colspan=3></td>"); printf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>"); printf("<td align='right'>contains</td>\n"); printf("<td colspan='%d'>", cols - 4); printf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' " "style='min-width:326px; font-size:.9em;'>", TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch); jsOnEventById("keyup", "nameSearch", "findTracks.searchButtonsEnable(true);"); printf("</td></tr>\n"); // Description contains printf("<tr><td colspan=2></td><td align='right'>and </td>"); printf("<td><b style='max-width:100px;'>Description:</b></td>"); printf("<td align='right'>contains</td>\n"); printf("<td colspan='%d'>", cols - 4); printf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' " "style='max-width:536px; width:536px; font-size:.9em;'>", TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch); jsOnEventById("keyup", "descSearch", "findTracks.searchButtonsEnable(true);"); printf("</td></tr>\n"); // Set up Group dropdown struct grp *grps = hLoadGrps(db); grps = groupsFilterForTdbList(&grps,tdbList); int numGroups = slCount(grps) + 1; // Add Any char **groups = needMem(sizeof(char *) * numGroups); char **labels = needMem(sizeof(char *) * numGroups); groups[0] = ANYLABEL; labels[0] = ANYLABEL; int ix=1; struct grp *grp = grps; for (; grp != NULL; grp = grp->next,ix++) { groups[ix] = cloneString(grp->name); labels[ix] = cloneString(grp->label); } printf("<tr><td colspan=2></td><td align='right'>and </td>\n"); printf("<td><b style='max-width:100px;'>Group:</b></td>"); printf("<td align='right'>is</td>\n"); printf("<td colspan='%d'>", cols - 4); char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP); cgiMakeDropListFullExt(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, NULL, NULL, "min-width:40%; font-size:.9em;", "groupSearch"); printf("</td></tr>\n"); // Track Type is (drop down) printf("<tr><td colspan=2></td><td align='right'>and </td>\n"); printf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>"); printf("<td align='right'>is</td>\n"); printf("<td colspan='%d'>", cols - 4); char *dropDownHtml = fileFormatSelectHtml(FILE_SEARCH_ON_FILETYPE,fileTypeSearch, NULL, NULL, "min-width:40%; font-size:.9em;"); if (dropDownHtml) { puts(dropDownHtml); freeMem(dropDownHtml); } printf("</td></tr>\n"); // mdb selects struct slPair *mdbSelects = NULL; if (metaDbExists) { struct slPair *mdbVars = mdbVarsSearchable(conn,FALSE,TRUE); // Not tables, just files mdbSelects = mdbSelectPairs(cart, mdbVars); char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,TRUE); // just for fileSearch if (output) { puts(output); freeMem(output); } slPairFreeList(&mdbVars); } printf("</table>\n"); printf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", FILE_SEARCH); printf("<input type='button' name='clear' id='clear' value='clear' class='clear' style='font-size:.8em;'>\n"); jsOnEventById("click", "clear", "findTracks.clear();"); printf("<input type='submit' name='submit' value='cancel' class='cancel' " "style='font-size:.8em;'>\n"); printf("</div>\n"); #ifdef USE_TABS printf("</div>\n"); // End tabs div #endif///def USE_TABS if (nameSearch != NULL && !strlen(nameSearch)) nameSearch = NULL; if (descSearch != NULL && !strlen(descSearch)) descSearch = NULL; if (groupSearch != NULL && sameString(groupSearch, ANYLABEL)) groupSearch = NULL; printf("</form>\n"); printf("</div>"); // Restricts to max-width:1000px; cgiDown(0.8); if (measureTiming) uglyTime("Generated search controls"); #ifdef USE_TABS if (doSearch && selectedTab==simpleTab && isEmpty(descSearch)) doSearch = FALSE; #endif///def USE_TABS if (doSearch) { // Now search #ifdef USE_TABS struct slRef *foundTdbs = NULL; if (selectedTab==simpleTab) { foundTdbs = simpleSearchForTdbs(trix,descWords,descWordCount); // What to do now? if (measureTiming) uglyTime("Searched for tracks"); // Sort and Print results if (selectedTab!=filesTab) { enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance); int tracksFound = slCount(foundTdbs); if (tracksFound > 1) findTracksSort(&tracks,sortBy); displayFoundTracks(cart,tracks,tracksFound,sortBy); if (measureTiming) uglyTime("Displayed found files"); } } else if (selectedTab==filesTab && mdbPairs != NULL) #endif ///def USE_TABS { if (nameSearch || descSearch || groupSearch) { // Use nameSearch, descSearch and groupSearch to narrow down the list of composites. if (isNotEmpty(nameSearch) || isNotEmpty(descSearch) || isNotEmpty(groupSearch)) { struct trackDb *tdbList = hTrackDb(db); struct trackDb *tdbsMatch = tdbFilterBy(&tdbList, nameSearch, descSearch, groupSearch); // Now we have a list of tracks, so we need a unique list of composites to add doSearch = mdbSelectsAddFoundComposites(&mdbSelects,tdbsMatch); } } if (doSearch && mdbSelects != NULL && isNotEmpty(fileTypeSearch)) fileSearchResults(db, conn, cart, mdbSelects, fileTypeSearch); else printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n"); if (measureTiming) uglyTime("Searched for files"); } slPairFreeList(&mdbSelects); } hFreeConn(&conn); webNewSection("About " FILE_SEARCH_NAME); printf("Search for downloadable ENCODE files by entering search terms in " "the Track name or Description fields and/or by making selections with " "the group, data format, and/or ENCODE metadata drop-downs."); printf("<BR><a target='_blank' href='../goldenPath/help/fileSearch.html'>more help</a>\n"); } void doMiddle(struct cart *cart) /* Write body of web page. */ { /* Using earlyBotCheck() at the beginning of main() to output message here if in delay time */ if (issueBotWarning) { char *ip = getenv("REMOTE_ADDR"); botDelayMessage(ip, botDelayMillis); } struct trackDb *tdbList = NULL; char *organism = NULL; char *db = NULL; getDbAndGenome(cart, &db, &organism, NULL); char *chrom = cartUsualString(cart, "c", hDefaultChrom(db)); measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming")); // QUESTION: Do We need track list ??? trackHash ??? Can't we just get one track and no children trackHash = trackHashMakeWithComposites(db,chrom,&tdbList,FALSE); cartWebStart(cart, db, "Search for " FILE_SEARCH_WHAT " in the %s %s Assembly", organism, hFreezeFromDb(db)); webIncludeResourceFile("HGStyle.css"); webIncludeResourceFile("jquery-ui.css"); webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("jquery.js", NULL); jsIncludeFile("jquery-ui.js", NULL); jsIncludeFile("ui.dropdownchecklist.js",NULL); jsIncludeFile("utils.js",NULL); // This line is needed to get the multi-selects initialized jsIncludeFile("ddcl.js",NULL); jsInline("$(document).ready(function() " "{ findTracks.updateMdbHelp(0); });\n"); doFileSearch(db,organism,cart,tdbList); printf("<BR>\n"); webEnd(); } char *excludeVars[] = { "submit", "Submit", "g", "ajax", "clearCache", FILE_SEARCH,TRACK_SEARCH_ADD_ROW,TRACK_SEARCH_DEL_ROW}; int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); issueBotWarning = earlyBotCheck(enteredMainTime, "hgFileSearch", delayFraction, 0, 0, "html"); cgiSpoof(&argc, argv); cartEmptyShell(doMiddle, hUserCookie(), excludeVars, NULL); cgiExitTime("hgFileSearch", enteredMainTime); return 0; } // TODO: // 1) Done: Limit to first 1000 // 2) Work out simple verses advanced tabs // 3) work out support for non-encode downloads // 4) Make an hgTrackSearch to replace hgTracks track search ?? // Simpler code, but may not be good idea because of composite reshaping in cart vars