c393b2f6fa265761873dc9222bc8ba83015b3d5d mspeir Fri Jun 3 13:04:17 2016 -0700 Custom tracks in sessions no longer expire. Changing cart message when session with custom tracks is saved. Reminds users to keep a local back-up of their session contents and custom tracks, refs #14724 diff --git src/hg/lib/cart.c src/hg/lib/cart.c index a16e65b..08aca5a 100644 --- src/hg/lib/cart.c +++ src/hg/lib/cart.c @@ -1,2915 +1,2916 @@ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hCommon.h" #include "obscure.h" #include "linefile.h" #include "errAbort.h" #include "hash.h" #include "cheapcgi.h" #include "cartDb.h" #include "htmshell.h" #include "hgConfig.h" #include "cart.h" #include "net.h" #include "web.h" #include "hdb.h" #include "jksql.h" #include "jsHelper.h" #include "trashDir.h" #ifndef GBROWSE #include "customFactory.h" #include "googleAnalytics.h" #include "wikiLink.h" #endif /* GBROWSE */ #include "hgMaf.h" #include "hui.h" #include "geoMirror.h" #include "hubConnect.h" #include "trackHub.h" #include "cgiApoptosis.h" static char *sessionVar = "hgsid"; /* Name of cgi variable session is stored in. */ static char *positionCgiName = "position"; DbConnector cartDefaultConnector = hConnectCart; DbDisconnect cartDefaultDisconnector = hDisconnectCart; static void hashUpdateDynamicVal(struct hash *hash, char *name, void *val) /* Val is a dynamically allocated (freeMem-able) entity to put * in hash. Override existing hash item with that name if any. * Otherwise make new hash item. */ { struct hashEl *hel = hashLookup(hash, name); if (hel == NULL) hashAdd(hash, name, val); else { freeMem(hel->val); hel->val = val; } } static struct dyString *hubWarnDy; void cartHubWarn(char *format, va_list args) /* save up hub related warnings to put out later */ { char warning[1024]; vsnprintf(warning,sizeof(warning),format, args); if (hubWarnDy == NULL) hubWarnDy = newDyString(100); dyStringPrintf(hubWarnDy, "%s\n", warning); } void cartFlushHubWarnings() /* flush the hub warning (if any) */ { if (hubWarnDy) warn("%s",hubWarnDy->string); } void cartTrace(struct cart *cart, char *when, struct sqlConnection *conn) /* Write some properties of the cart to stderr for debugging. */ { if (cfgOption("cart.trace") == NULL) return; struct cartDb *u = cart->userInfo, *s = cart->sessionInfo; char *pix = hashFindVal(cart->hash, "pix"); char *textSize = hashFindVal(cart->hash, "textSize"); char *trackControls = hashFindVal(cart->hash, "trackControlsOnMain"); int uLen, sLen; if (conn != NULL) { /* Since the content string is chopped, query for the actual length. */ struct dyString *query = dyStringNew(1024); sqlDyStringPrintf(query, "select length(contents) from %s" " where id = %d", userDbTable(), u->id); if (cartDbUseSessionKey()) sqlDyStringPrintf(query, " and sessionKey='%s'", u->sessionKey); uLen = sqlQuickNum(conn, query->string); dyStringClear(query); sqlDyStringPrintf(query, "select length(contents) from %s" " where id = %d", sessionDbTable(),s->id); if (cartDbUseSessionKey()) sqlDyStringPrintf(query, " and sessionKey='%s'", s->sessionKey); sLen = sqlQuickNum(conn, query->string); dyStringFree(&query); } else { uLen = strlen(u->contents); sLen = strlen(s->contents); } if (pix == NULL) pix = "-"; if (textSize == NULL) textSize = "-"; if (trackControls == NULL) trackControls = "-"; fprintf(stderr, "ASH: %22s: " "u.i=%d u.l=%d u.c=%d s.i=%d s.l=%d s.c=%d " "p=%s f=%s t=%s pid=%ld %s\n", when, u->id, uLen, u->useCount, s->id, sLen, s->useCount, pix, textSize, trackControls, (long)getpid(), cgiRemoteAddr()); char userIdKey[256]; cartDbSecureId(userIdKey, sizeof userIdKey, u); if (cart->userId && !sameString(userIdKey, cart->userId)) fprintf(stderr, "ASH: bad userId %s --> %d_%s! pid=%ld\n", cart->userId, u->id, u->sessionKey, (long)getpid()); char sessionIdKey[256]; cartDbSecureId(sessionIdKey, sizeof sessionIdKey, s); if (cart->sessionId && !sameString(sessionIdKey, cart->sessionId)) fprintf(stderr, "ASH: bad sessionId %s --> %d_%s! pid=%ld\n", cart->sessionId, s->id, s->sessionKey, (long)getpid()); } boolean cartTablesOk(struct sqlConnection *conn) /* Return TRUE if cart tables are accessible (otherwise, the connection * doesn't do us any good). */ { if (!sqlTableExists(conn, userDbTable())) { fprintf(stderr, "ASH: cartTablesOk failed on %s.%s! pid=%ld\n", sqlGetDatabase(conn), userDbTable(), (long)getpid()); return FALSE; } if (!sqlTableExists(conn, sessionDbTable())) { fprintf(stderr, "ASH: cartTablesOk failed on %s.%s! pid=%ld\n", sqlGetDatabase(conn), sessionDbTable(), (long)getpid()); return FALSE; } return TRUE; } void cartParseOverHash(struct cart *cart, char *contents) /* Parse cgi-style contents into a hash table. This will *not* * replace existing members of hash that have same name, so we can * support multi-select form inputs (same var name can have multiple * values which will be in separate hashEl's). */ { struct hash *hash = cart->hash; char *namePt, *dataPt, *nextNamePt; namePt = contents; while (namePt != NULL && namePt[0] != 0) { dataPt = strchr(namePt, '='); if (dataPt == NULL) errAbort("Mangled input string %s", namePt); *dataPt++ = 0; nextNamePt = strchr(dataPt, '&'); if (nextNamePt == NULL) nextNamePt = strchr(dataPt, ';'); /* Accomodate DAS. */ if (nextNamePt != NULL) *nextNamePt++ = 0; cgiDecode(dataPt,dataPt,strlen(dataPt)); hashAdd(hash, namePt, cloneString(dataPt)); namePt = nextNamePt; } } static boolean looksCorrupted(struct cartDb *cdb) /* Test for db corruption by checking format of firstUse field. */ { if (cdb == NULL) return FALSE; else { char *words[3]; int wordCount = 0; boolean isCorr = FALSE; char *fu = cloneString(cdb->firstUse); wordCount = chopByChar(fu, '-', words, ArraySize(words)); if (wordCount < 3) isCorr = TRUE; else { time_t theTime = time(NULL); struct tm *tm = localtime(&theTime); int year = atoi(words[0]); int month = atoi(words[1]); if ((year < 2000) || (year > (1900+tm->tm_year)) || (month < 1) || (month > 12)) isCorr = TRUE; } freez(&fu); return isCorr; } } struct cartDb *cartDbLoadFromId(struct sqlConnection *conn, char *table, char *secureId) /* Load up cartDb entry for particular ID. Returns NULL if no such id. */ { if (!secureId) return NULL; else { struct cartDb *cdb = NULL; struct dyString *where = dyStringNew(256); char *sessionKey = NULL; unsigned int id = cartDbParseId(secureId, &sessionKey); sqlDyStringPrintfFrag(where, "id = %u", id); if (cartDbUseSessionKey()) { if (!sessionKey) sessionKey = ""; sqlDyStringPrintfFrag(where, " and sessionKey='%s'", sessionKey); } cdb = cartDbLoadWhere(conn, table, where->string); dyStringFree(&where); if (looksCorrupted(cdb)) { /* Can't use warn here -- it interrupts the HTML header, causing an * err500 (and nothing useful in error_log) instead of a warning. */ fprintf(stderr, "%s id=%u looks corrupted -- starting over with new %s id.\n", table, id, table); cdb = NULL; } return cdb; } } struct cartDb *loadDb(struct sqlConnection *conn, char *table, char *secureId, boolean *found) /* Load bits from database and save in hash. */ { struct cartDb *cdb; boolean result = TRUE; cdb = cartDbLoadFromId(conn, table, secureId); if (!cdb) { result = FALSE; struct dyString *query = dyStringNew(256); sqlDyStringPrintf(query, "INSERT %s VALUES(0,'',0,now(),now(),0", table); char *sessionKey = ""; if (cartDbHasSessionKey(conn, table)) { if (cartDbUseSessionKey()) { sessionKey = cartDbMakeRandomKey(128+33); // at least 128 bits of protection, 33 for the world population size. } sqlDyStringPrintf(query, ",'%s'", sessionKey); } sqlDyStringPrintf(query, ")"); sqlUpdate(conn, query->string); dyStringFree(&query); unsigned int id = sqlLastAutoId(conn); char newSecureId[256]; if (cartDbUseSessionKey() && !sameString(sessionKey,"")) safef(newSecureId, sizeof newSecureId, "%u_%s", id, sessionKey); else safef(newSecureId, sizeof newSecureId, "%u", id); if ((cdb = cartDbLoadFromId(conn,table,newSecureId)) == NULL) errAbort("Couldn't get cartDb for id=%u right after loading. " "MySQL problem??", id); if (!sameString(sessionKey,"")) freeMem(sessionKey); } *found = result; return cdb; } void cartExclude(struct cart *cart, char *var) /* Exclude var from persistent storage. */ { hashAdd(cart->exclude, var, NULL); } void sessionTouchLastUse(struct sqlConnection *conn, char *encUserName, char *encSessionName) /* Increment namedSessionDb.useCount and update lastUse for this session. */ { struct dyString *dy = dyStringNew(1024); int useCount; sqlDyStringPrintf(dy, "SELECT useCount FROM %s " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encUserName, encSessionName); useCount = sqlQuickNum(conn, dy->string) + 1; dyStringClear(dy); sqlDyStringPrintf(dy, "UPDATE %s SET useCount = %d, lastUse=now() " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, useCount, encUserName, encSessionName); sqlUpdate(conn, dy->string); dyStringFree(&dy); } #ifndef GBROWSE void cartCopyCustomTracks(struct cart *cart) /* If cart contains any live custom tracks, save off a new copy of them, * to prevent clashes by multiple uses of the same session. */ { struct hashEl *el, *elList = hashElListHash(cart->hash); for (el = elList; el != NULL; el = el->next) { if (startsWith(CT_FILE_VAR_PREFIX, el->name)) { char *db = &el->name[strlen(CT_FILE_VAR_PREFIX)]; struct slName *browserLines = NULL; struct customTrack *ctList = NULL; char *ctFileName = (char *)(el->val); if (fileExists(ctFileName)) ctList = customFactoryParseAnyDb(db, ctFileName, TRUE, &browserLines); /* Save off only if the custom tracks are live -- if none are live, * leave cart variables in place so hgSession can detect and inform * the user. */ if (ctList) { struct customTrack *ct; static struct tempName tn; char *ctFileVar = el->name; char *ctFileName; for (ct = ctList; ct != NULL; ct = ct->next) { copyFileToTrash(&(ct->htmlFile), "ct", CT_PREFIX, ".html"); copyFileToTrash(&(ct->wibFile), "ct", CT_PREFIX, ".wib"); copyFileToTrash(&(ct->wigFile), "ct", CT_PREFIX, ".wig"); } trashDirFile(&tn, "ct", CT_PREFIX, ".bed"); ctFileName = tn.forCgi; cartSetString(cart, ctFileVar, ctFileName); customTracksSaveFile(db, ctList, ctFileName); } } } } #endif /* GBROWSE */ static void storeInOldVars(struct cart *cart, struct hash *oldVars, char *var) /* Store all cart hash elements for var into oldVars (if it exists). */ { if (oldVars == NULL) return; struct hashEl *hel = hashLookup(cart->hash, var); // NOTE: New cgi vars not in old cart cannot be distinguished from vars not newly set by cgi. // Solution: Add 'empty' var to old vars for cgi vars not already in cart if (hel == NULL) hashAdd(oldVars, var, cloneString(CART_VAR_EMPTY)); while (hel != NULL) { hashAdd(oldVars, var, cloneString(hel->val)); hel = hashLookupNext(hel); } } static void cartJustify(struct cart *cart, struct hash *oldVars) /* Handles rules for allowing some cart settings to override others. */ { // New priority (position) settings should erase imgOrd settings if (oldVars == NULL) return; #define POSITION_SUFFIX ".priority" #define IMGORD_SUFFIX "_imgOrd" struct hashEl *list = NULL, *el; list = hashElListHash(cart->hash); //warn("cartJustify() begins"); for (el = list; el != NULL; el = el->next) { if (endsWith(el->name,POSITION_SUFFIX)) { if (cartValueHasChanged(cart,oldVars,el->name,TRUE,TRUE)) { int suffixOffset = strlen(el->name) - strlen(POSITION_SUFFIX); if (suffixOffset>0) { char *name = cloneString(el->name); safecpy(name+suffixOffset,strlen(POSITION_SUFFIX),IMGORD_SUFFIX); // We know that POSITION_SUFFIX is longer than IMGORD_SUFFIX cartRemove(cart, name); // Removes if found freeMem(name); } } } } } static void loadCgiOverHash(struct cart *cart, struct hash *oldVars) /* Store CGI variables in cart. */ { struct cgiVar *cv, *cvList = cgiVarList(); char *booShadow = cgiBooleanShadowPrefix(); int booSize = strlen(booShadow); char *multShadow = cgiMultListShadowPrefix(); int multSize = strlen(multShadow); struct hash *booHash = newHash(8); struct hash *cgiHash = hashNew(11); /* First handle boolean variables and store in cgiHash. We store in a * separate hash in order to distinguish between a list-variable's old * values in the cart hash and new values from cgi. */ for (cv = cvList; cv != NULL; cv = cv->next) { if (startsWith(booShadow, cv->name)) { char *booVar = cv->name + booSize; // Support for 2 boolean CBs: checked/unchecked (1/0) and enabled/disabled:(-1/-2) char *val = (cgiVarExists(booVar) ? "1" : cv->val); storeInOldVars(cart, oldVars, booVar); cartRemove(cart, booVar); hashAdd(cgiHash, booVar, val); hashAdd(booHash, booVar, NULL); } else if (startsWith(multShadow, cv->name)) { /* This shadow variable enables us to detect when all inputs in * the multi-select box have been deselected. */ char *multVar = cv->name + multSize; if (! cgiVarExists(multVar)) { storeInOldVars(cart, oldVars, multVar); storeInOldVars(cart, oldVars, cv->name); cartRemove(cart, multVar); } } } /* Handle non-boolean vars. */ for (cv = cgiVarList(); cv != NULL; cv = cv->next) { if (! (startsWith(booShadow, cv->name) || hashLookup(booHash, cv->name))) { storeInOldVars(cart, oldVars, cv->name); cartRemove(cart, cv->name); if (differentString(cv->val, CART_VAR_EMPTY)) // NOTE: CART_VAR_EMPTY logic not implemented for boolShad hashAdd(cgiHash, cv->name, cv->val); } } /* Add new settings to cart (old values of these variables have been * removed above). */ struct hashEl *hel = hashElListHash(cgiHash); while (hel != NULL) { cartAddString(cart, hel->name, hel->val); hel = hel->next; } hashFree(&cgiHash); hashFree(&booHash); } static void hashEmpty(struct hash *hash) /* Remove everything from hash. */ { struct hashEl *hel, *helList = hashElListHash(hash); for (hel = helList; hel != NULL; hel = hel->next) { freez(&(hel->val)); hashRemove(hash, hel->name); } hashElFreeList(&helList); assert(hashNumEntries(hash) == 0); } #ifndef GBROWSE void cartLoadUserSession(struct sqlConnection *conn, char *sessionOwner, char *sessionName, struct cart *cart, struct hash *oldVars, char *actionVar) /* If permitted, load the contents of the given user's session, and then * reload the CGI settings (to support override of session settings). * If non-NULL, oldVars will contain values overloaded when reloading CGI. * If non-NULL, actionVar is a cartRemove wildcard string specifying the * CGI action variable that sent us here. */ { struct sqlResult *sr = NULL; char **row = NULL; /* Validate login cookies if login is enabled */ if (loginSystemEnabled()) { loginValidateCookies(cart); } char *userName = wikiLinkUserName(); char *encSessionName = cgiEncodeFull(sessionName); char *encSessionOwner = cgiEncodeFull(sessionOwner); char query[512]; if (isEmpty(sessionOwner)) errAbort("Please go back and enter a wiki user name for this session."); if (isEmpty(sessionName)) errAbort("Please go back and enter a session name to load."); sqlSafef(query, sizeof(query), "SELECT shared, contents FROM %s " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encSessionOwner, encSessionName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { boolean shared = atoi(row[0]); if (shared || (userName && sameString(sessionOwner, userName))) { char *sessionVar = cartSessionVarName(); char *hgsid = cartSessionId(cart); struct sqlConnection *conn2 = hConnectCentral(); sessionTouchLastUse(conn2, encSessionOwner, encSessionName); cartRemoveLike(cart, "*"); cartParseOverHash(cart, row[1]); cartSetString(cart, sessionVar, hgsid); if (oldVars) hashEmpty(oldVars); /* Overload settings explicitly passed in via CGI (except for the * command that sent us here): */ loadCgiOverHash(cart, oldVars); if (isNotEmpty(actionVar)) cartRemove(cart, actionVar); hDisconnectCentral(&conn2); } else errAbort("Sharing has not been enabled for user %s's session %s.", sessionOwner, sessionName); } else errAbort("Could not find session %s for user %s.", sessionName, sessionOwner); sqlFreeResult(&sr); freeMem(encSessionName); } #endif /* GBROWSE */ void cartLoadSettings(struct lineFile *lf, struct cart *cart, struct hash *oldVars, char *actionVar) /* Load settings (cartDump output) into current session, and then * reload the CGI settings (to support override of session settings). * If non-NULL, oldVars will contain values overloaded when reloading CGI. * If non-NULL, actionVar is a cartRemove wildcard string specifying the * CGI action variable that sent us here. */ { char *line = NULL; int size = 0; char *sessionVar = cartSessionVarName(); char *hgsid = cartSessionId(cart); cartRemoveLike(cart, "*"); cartSetString(cart, sessionVar, hgsid); while (lineFileNext(lf, &line, &size)) { char *var = nextWord(&line); if (isEmpty(var)) // blank line continue; char *val = line; if (sameString(var, sessionVar)) continue; else { if (val != NULL) { struct dyString *dy = dyStringSub(val, "\\n", "\n"); cartAddString(cart, var, dy->string); dyStringFree(&dy); } else if (var != NULL) { cartSetString(cart, var, ""); } } /* not hgsid */ } /* each line */ if (oldVars) hashEmpty(oldVars); /* Overload settings explicitly passed in via CGI (except for the * command that sent us here): */ loadCgiOverHash(cart, oldVars); if (isNotEmpty(actionVar)) cartRemove(cart, actionVar); } static char *now() /* Return a mysql-formatted time like "2008-05-19 15:33:34". */ { char nowBuf[256]; time_t seconds = clock1(); struct tm *theTime = localtime(&seconds); strftime(nowBuf, sizeof nowBuf, "%Y-%m-%d %H:%M:%S", theTime); return cloneString(nowBuf); } static struct cartDb *emptyCartDb() /* Create a new empty placeholder cartDb. */ { struct cartDb *cdb; AllocVar(cdb); cdb->contents = cloneString(""); cdb->firstUse = now(); cdb->lastUse = now(); cdb->useCount = 1; // TODO does anything need to go here for sessionKey? maybe not since id is not set here. return cdb; } struct cart *cartFromHash(struct hash *hash) /* Create a cart from hash */ { struct cart *cart; AllocVar(cart); cart->hash = hash; cart->exclude = newHash(7); cart->userInfo = emptyCartDb(); cart->sessionInfo = emptyCartDb(); return cart; } struct cart *cartOfNothing() /* Create a new, empty, cart with no real connection to the database. */ { return cartFromHash(newHash(0)); } struct cart *cartFromCgiOnly(char *userId, char *sessionId, char **exclude, struct hash *oldVars) /* Create a new cart that contains only CGI variables, nothing from the * database. */ { struct cart *cart = cartOfNothing(); cart->userId = userId; cart->sessionId = sessionId; loadCgiOverHash(cart, oldVars); if (exclude != NULL) { char *ex; while ((ex = *exclude++)) cartExclude(cart, ex); } return cart; } static void doDisconnectHub(struct cart *cart) { char *id = cartOptionalString(cart, "hubId"); if (id != NULL) { char buffer[1024]; safef(buffer, sizeof buffer, "hgHubConnect.hub.%s", id); cartRemove(cart, buffer); } cartRemove(cart, "hubId"); cartRemove(cart, hgHubDoDisconnect); } static void hideIfNotInCart(struct cart *cart, char *track) /* If this track is not mentioned in the cart, set it to hide */ { if (cartOptionalString(cart, track) == NULL) cartSetString(cart, track, "hide"); } void cartHideDefaultTracks(struct cart *cart) /* Hide all the tracks who have default visibilities in trackDb * that are something other than hide. Do this only if the * variable CART_HAS_DEFAULT_VISIBILITY is set in the cart. */ { char *defaultString = cartOptionalString(cart, CART_HAS_DEFAULT_VISIBILITY); boolean cartHasDefaults = (defaultString != NULL) && sameString(defaultString, "on"); if (!cartHasDefaults) return; char *db = cartString(cart, "db"); struct trackDb *tdb = hTrackDb(db); for(; tdb; tdb = tdb->next) { struct trackDb *parent = tdb->parent; if (parent && parent->isShow) hideIfNotInCart(cart, parent->track); if (tdb->visibility != tvHide) hideIfNotInCart(cart, tdb->track); } // Don't do this again until someone sets this variable, // presumably on session load. cartRemove(cart, CART_HAS_DEFAULT_VISIBILITY); } struct cart *cartNew(char *userId, char *sessionId, char **exclude, struct hash *oldVars) /* Load up cart from user & session id's. Exclude is a null-terminated list of * strings to not include */ { cgiApoptosisSetup(); if (cfgOptionBooleanDefault("showEarlyErrors", FALSE)) errAbortSetDoContentType(TRUE); if (cfgOptionBooleanDefault("suppressVeryEarlyErrors", FALSE)) htmlSuppressErrors(); struct cart *cart; struct sqlConnection *conn = cartDefaultConnector(); char *ex; boolean userIdFound = FALSE, sessionIdFound = FALSE; AllocVar(cart); cart->hash = newHash(12); cart->exclude = newHash(7); cart->userId = userId; cart->sessionId = sessionId; cart->userInfo = loadDb(conn, userDbTable(), userId, &userIdFound); cart->sessionInfo = loadDb(conn, sessionDbTable(), sessionId, &sessionIdFound); if (sessionIdFound) cartParseOverHash(cart, cart->sessionInfo->contents); else if (userIdFound) cartParseOverHash(cart, cart->userInfo->contents); char when[1024]; safef(when, sizeof(when), "open %s %s", userId, sessionId); cartTrace(cart, when, conn); loadCgiOverHash(cart, oldVars); // I think this is the place to justify old and new values cartJustify(cart, oldVars); #ifndef GBROWSE /* If some CGI other than hgSession been passed hgSession loading instructions, * apply those to cart before we do anything else. (If this is hgSession, * let it handle the settings so it can display feedback to the user.) */ boolean didSessionLoad = FALSE; if (! (cgiScriptName() && endsWith(cgiScriptName(), "hgSession"))) { if (cartVarExists(cart, hgsDoOtherUser)) { setUdcCacheDir(); char *otherUser = cartString(cart, hgsOtherUserName); char *sessionName = cartString(cart, hgsOtherUserSessionName); struct sqlConnection *conn2 = hConnectCentral(); cartLoadUserSession(conn2, otherUser, sessionName, cart, oldVars, hgsDoOtherUser); hDisconnectCentral(&conn2); cartTrace(cart, "after cartLUS", conn); didSessionLoad = TRUE; } else if (cartVarExists(cart, hgsDoLoadUrl)) { setUdcCacheDir(); char *url = cartString(cart, hgsLoadUrlName); struct lineFile *lf = netLineFileOpen(url); cartLoadSettings(lf, cart, oldVars, hgsDoLoadUrl); lineFileClose(&lf); cartTrace(cart, "after cartLS", conn); didSessionLoad = TRUE; } } #endif /* GBROWSE */ /* wire up the assembly hubs so we can operate without sql */ setUdcTimeout(cart); if (cartVarExists(cart, hgHubDoDisconnect)) doDisconnectHub(cart); pushWarnHandler(cartHubWarn); char *newDatabase = hubConnectLoadHubs(cart); popWarnHandler(); #ifndef GBROWSE if (didSessionLoad) cartCopyCustomTracks(cart); #endif /* GBROWSE */ if (newDatabase != NULL) { // this is some magic to use the defaultPosition and reset cart variables if (oldVars) { struct hashEl *hel; if ((hel = hashLookup(oldVars,"db")) != NULL) hel->val = "none"; else hashAdd(oldVars, "db", "none"); } cartSetString(cart,"db", newDatabase); } if (exclude != NULL) { while ((ex = *exclude++)) cartExclude(cart, ex); } cartDefaultDisconnector(&conn); if (didSessionLoad) cartHideDefaultTracks(cart); return cart; } static void updateOne(struct sqlConnection *conn, char *table, struct cartDb *cdb, char *contents, int contentSize) /* Update cdb in database. */ { struct dyString *dy = newDyString(4096); sqlDyStringPrintf(dy, "UPDATE %s SET contents='", table); sqlDyAppendEscaped(dy, contents); sqlDyStringPrintf(dy, "',lastUse=now(),useCount=%d ", cdb->useCount+1); sqlDyStringPrintf(dy, " where id=%u", cdb->id); if (cartDbUseSessionKey()) sqlDyStringPrintf(dy, " and sessionKey='%s'", cdb->sessionKey); sqlUpdate(conn, dy->string); dyStringFree(&dy); } void cartEncodeState(struct cart *cart, struct dyString *dy) /* Add a CGI-encoded var=val&... string of all cart variables to dy. */ { struct hashEl *el, *elList = hashElListHash(cart->hash); boolean firstTime = TRUE; char *s = NULL; for (el = elList; el != NULL; el = el->next) { if (!hashLookup(cart->exclude, el->name)) { if (firstTime) firstTime = FALSE; else dyStringAppendC(dy, '&'); dyStringAppend(dy, el->name); dyStringAppendC(dy, '='); s = cgiEncode(el->val); dyStringAppend(dy, s); freez(&s); } } hashElFreeList(&elList); } static void saveState(struct cart *cart) /* Save out state to permanent storage in both user and session db. */ { struct sqlConnection *conn = cartDefaultConnector(); struct dyString *encoded = newDyString(4096); /* Make up encoded string holding all variables. */ cartEncodeState(cart, encoded); /* Make up update statement unless it looks like a robot with * a great bunch of variables. */ if (encoded->stringSize < 16*1024 || cart->userInfo->useCount > 0) { updateOne(conn, userDbTable(), cart->userInfo, encoded->string, encoded->stringSize); updateOne(conn, sessionDbTable(), cart->sessionInfo, encoded->string, encoded->stringSize); } else { fprintf(stderr, "Cart stuffing bot? Not writing %d bytes to cart on first use of %d from IP=%s\n", encoded->stringSize, cart->userInfo->id, cgiRemoteAddr()); /* Do increment the useCount so that cookie-users don't get stuck here: */ updateOne(conn, userDbTable(), cart->userInfo, "", 0); } /* Cleanup */ cartDefaultDisconnector(&conn); dyStringFree(&encoded); } void cartCheckout(struct cart **pCart) /* Free up cart and save it to database. */ { struct cart *cart = *pCart; if (cart != NULL) { saveState(cart); struct sqlConnection *conn = cartDefaultConnector(); cartTrace(cart, "checkout", conn); cartDefaultDisconnector(&conn); cartDbFree(&cart->userInfo); cartDbFree(&cart->sessionInfo); freeHash(&cart->hash); freeHash(&cart->exclude); freez(pCart); } } char *cartSessionVarName() /* Return name of CGI session ID variable. */ { return sessionVar; } char *cartSessionId(struct cart *cart) /* Return session id. */ { static char buf[256]; cartDbSecureId(buf, sizeof buf, cart->sessionInfo); return buf; } char *cartSidUrlString(struct cart *cart) /* Return session id string as in hgsid=N . */ { static char buf[64]; safef(buf, sizeof(buf), "%s=%s", cartSessionVarName(), cartSessionId(cart)); return buf; } char *cartUserId(struct cart *cart) /* Return session id. */ { static char buf[256]; cartDbSecureId(buf, sizeof buf, cart->userInfo); return buf; } static char *cartMultShadowVar(struct cart *cart, char *var) /* Return a pointer to the list variable shadow variable name for var. * Don't modify or free result. */ { static char multShadowVar[PATH_LEN]; safef(multShadowVar, sizeof(multShadowVar), "%s%s", cgiMultListShadowPrefix(), var); return multShadowVar; } static int cartRemoveAndCountNoShadow(struct cart *cart, char *var) /* Remove variable from cart, returning count of removed vars. */ { int removed = 0; struct hashEl *hel = hashLookup(cart->hash, var); while (hel != NULL) { struct hashEl *nextHel = hashLookupNext(hel); freez(&hel->val); hashRemove(cart->hash, var); removed++; hel = nextHel; } return removed; } static int cartRemoveAndCount(struct cart *cart, char *var) /* Remove variable from cart, returning count of removed vars. */ { int removed = cartRemoveAndCountNoShadow(cart, var); (void)cartRemoveAndCountNoShadow(cart, cartMultShadowVar(cart, var)); return removed; } void cartRemove(struct cart *cart, char *var) /* Remove variable from cart. */ { (void)cartRemoveAndCount(cart, var); } void cartRemoveExcept(struct cart *cart, char **except) /* Remove variables except those in null terminated except array * from cart. Except array may be NULL in which case all * are removed. */ { struct hash *exceptHash = newHash(10); struct hashEl *list = NULL, *el; char *s; /* Build up hash of things to exclude. */ if (except != NULL) { while ((s = *except++) != NULL) hashAdd(exceptHash, s, NULL); } /* Get all cart variables and remove most of them. */ list = hashElListHash(cart->hash); for (el = list; el != NULL; el = el->next) { if (!hashLookup(exceptHash, el->name)) cartRemove(cart, el->name); } /* Clean up. */ hashFree(&exceptHash); hashElFreeList(&list); } struct slPair *cartVarsLike(struct cart *cart, char *wildCard) /* Return a slPair list of cart vars that match the wildcard */ { struct slPair *cartVars = NULL; struct hashEl *el, *elList = hashElListHash(cart->hash); slSort(&elList, hashElCmp); for (el = elList; el != NULL; el = el->next) { if (wildMatch(wildCard, el->name)) slAddHead(&cartVars,slPairNew(el->name,el->val)); } hashElFreeList(&elList); return cartVars; } struct slPair *cartVarsWithPrefix(struct cart *cart, char *prefix) /* Return a slPair list of cart vars that begin with prefix */ { struct slPair *cartVars = NULL; struct hashEl *el, *elList = hashElListHash(cart->hash); slSort(&elList, hashElCmp); for (el = elList; el != NULL; el = el->next) { if (startsWith(prefix, el->name)) slAddHead(&cartVars,slPairNew(el->name,el->val)); } hashElFreeList(&elList); return cartVars; } struct slPair *cartVarsWithPrefixLm(struct cart *cart, char *prefix, struct lm *lm) /* Return list of cart vars that begin with prefix allocated in local memory. * Quite a lot faster than cartVarsWithPrefix. */ { struct slPair *cartVars = NULL; struct hash *hash = cart->hash; int hashSize = hash->size; struct hashEl *hel; int i; for (i=0; itable[i]; hel != NULL; hel = hel->next) { if (startsWith(prefix, hel->name)) { struct slPair *pair; lmAllocVar(lm, pair); pair->name = lmCloneString(lm, hel->name); pair->val = lmCloneString(lm, hel->val); slAddHead(&cartVars, pair); } } } return cartVars; } void cartRemoveLike(struct cart *cart, char *wildCard) /* Remove all variable from cart that match wildCard. */ { struct slPair *cartVars = cartVarsLike(cart,wildCard); while (cartVars != NULL) { struct slPair *cartVar = slPopHead(&cartVars); cartRemove(cart, cartVar->name); freeMem(cartVar); } } void cartRemovePrefix(struct cart *cart, char *prefix) /* Remove variables with given prefix from cart. */ { struct slPair *cartVars = cartVarsWithPrefix(cart,prefix); while (cartVars != NULL) { struct slPair *cartVar = slPopHead(&cartVars); cartRemove(cart, cartVar->name); freeMem(cartVar); } } boolean cartVarExists(struct cart *cart, char *var) /* Return TRUE if variable is in cart. */ { return hashFindVal(cart->hash, var) != NULL; } boolean cartListVarExists(struct cart *cart, char *var) /* Return TRUE if a list variable is in cart (list may still be empty). */ { return cartVarExists(cart, cartMultShadowVar(cart, var)); } boolean cartListVarExistsAnyLevel(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix) /* Return TRUE if a list variable for tdb->track (or tdb->parent->track, * or tdb->parent->parent->track, etc.) is in cart (list itself may be NULL). */ { if (parentLevel) tdb = tdb->parent; for ( ; tdb != NULL; tdb = tdb->parent) { char var[PATH_LEN]; if (suffix[0] == '.' || suffix[0] == '_') safef(var, sizeof var, "%s%s%s", cgiMultListShadowPrefix(), tdb->track, suffix); else safef(var, sizeof var, "%s%s.%s", cgiMultListShadowPrefix(), tdb->track, suffix); char *cartSetting = hashFindVal(cart->hash, var); if (cartSetting != NULL) return TRUE; } return FALSE; } char *cartString(struct cart *cart, char *var) /* Return string valued cart variable. */ { return hashMustFindVal(cart->hash, var); } char *cartOptionalString(struct cart *cart, char *var) /* Return string valued cart variable or NULL if it doesn't exist. */ { return hashFindVal(cart->hash, var); } char *cartNonemptyString(struct cart *cart, char *name) /* Return string value associated with name. Return NULL * if value doesn't exist or if it is pure white space. */ { char *val = trimSpaces(cartOptionalString(cart, name)); if (val != NULL && val[0] == 0) val = NULL; return val; } char *cartUsualString(struct cart *cart, char *var, char *usual) /* Return variable value if it exists or usual if not. */ { char *s = cartOptionalString(cart, var); if (s == NULL) return usual; return s; } char *cartCgiUsualString(struct cart *cart, char *var, char *usual) /* Look for var in CGI, then in cart, if not found then return usual. */ { char *val = cgiOptionalString(var); if (val != NULL) return(val); if (cart != NULL) return cartUsualString(cart, var, usual); return(usual); } struct slName *cartOptionalSlNameList(struct cart *cart, char *var) /* Return slName list (possibly with multiple values for the same var) or * NULL if not found. */ { struct slName *slnList = NULL; struct hashEl *hel = hashLookup(cart->hash, var); while (hel != NULL) { if (hel->val != NULL) { struct slName *sln = slNameNew(hel->val); slAddHead(&slnList, sln); } hel = hashLookupNext(hel); } return slnList; } void cartAddString(struct cart *cart, char *var, char *val) /* Add string valued cart variable (if called multiple times on same var, * will create a list -- retrieve with cartOptionalSlNameList. */ { hashAdd(cart->hash, var, cloneString(val)); } void cartSetString(struct cart *cart, char *var, char *val) /* Set string valued cart variable. */ { hashUpdateDynamicVal(cart->hash, var, cloneString(val)); } int cartInt(struct cart *cart, char *var) /* Return int valued variable. */ { char *s = cartString(cart, var); return atoi(s); } int cartIntExp(struct cart *cart, char *var) /* Return integer valued expression in variable. */ { return intExp(cartString(cart, var)); } int cartUsualInt(struct cart *cart, char *var, int usual) /* Return variable value if it exists or usual if not. */ { char *s = cartOptionalString(cart, var); if (s == NULL) return usual; return atoi(s); } int cartUsualIntClipped(struct cart *cart, char *var, int usual, int minVal, int maxVal) /* Return integer variable clipped to lie between minVal/maxVal */ { int val = cartUsualInt(cart, var, usual); if (val < minVal) val = minVal; if (val > maxVal) val = maxVal; return val; } int cartCgiUsualInt(struct cart *cart, char *var, int usual) /* Look for var in CGI, then in cart, if not found then return usual. */ { char *val = cgiOptionalString(var); if (val != NULL) return atoi(val); if (cart != NULL) return cartUsualInt(cart, var, usual); return(usual); } void cartSetInt(struct cart *cart, char *var, int val) /* Set integer value. */ { char buf[32]; safef(buf, sizeof(buf), "%d", val); cartSetString(cart, var, buf); } double cartDouble(struct cart *cart, char *var) /* Return double valued variable. */ { char *s = cartString(cart, var); return atof(s); } double cartUsualDouble(struct cart *cart, char *var, double usual) /* Return variable value if it exists or usual if not. */ { char *s = cartOptionalString(cart, var); if (s == NULL) return usual; return atof(s); } double cartCgiUsualDouble(struct cart *cart, char *var, double usual) /* Look for var in CGI, then in cart, if not found then return usual. */ { char *val = cgiOptionalString(var); if (val != NULL) return atof(val); if (cart != NULL) return cartUsualDouble(cart, var, usual); return(usual); } void cartSetDouble(struct cart *cart, char *var, double val) /* Set double value. */ { char buf[32]; safef(buf, sizeof(buf), "%f", val); cartSetString(cart, var, buf); } boolean cartBoolean(struct cart *cart, char *var) /* Retrieve cart boolean. */ { char *s = cartString(cart, var); if (sameWord(s, "on") || atoi(s) > 0) return TRUE; else return FALSE; } boolean cartUsualBoolean(struct cart *cart, char *var, boolean usual) /* Return variable value if it exists or usual if not. */ { char *s = cartOptionalString(cart, var); if (s == NULL) return usual; return (sameWord(s, "on") || atoi(s) > 0); } boolean cartCgiUsualBoolean(struct cart *cart, char *var, boolean usual) /* Look for var in CGI, then in cart, if not found then return usual. */ { if (cgiBooleanDefined(var)) return cgiBoolean(var); if (cart != NULL) return cgiBoolean(var) || cartUsualBoolean(cart, var, usual); return(usual); } void cartSetBoolean(struct cart *cart, char *var, boolean val) /* Set boolean value. */ { // Be explicit because some cartBools overloaded with negative "disabled" values cartSetInt(cart,var,(val?1:0)); } void cartMakeTextVar(struct cart *cart, char *var, char *defaultVal, int charSize) /* Make a text control filled with value from cart if it exists or * default value otherwise. If charSize is zero it's calculated to fit * current value. Default value may be NULL. */ { cgiMakeTextVar(var, cartUsualString(cart, var, defaultVal), charSize); } void cartMakeIntVar(struct cart *cart, char *var, int defaultVal, int maxDigits) /* Make a text control filled with integer value - from cart if available * otherwise default. */ { cgiMakeIntVar(var, cartUsualInt(cart, var, defaultVal), maxDigits); } void cartMakeDoubleVar(struct cart *cart, char *var, double defaultVal, int maxDigits) /* Make a text control filled with integer value - from cart if available * otherwise default. */ { cgiMakeDoubleVar(var, cartUsualDouble(cart, var, defaultVal), maxDigits); } void cartMakeCheckBox(struct cart *cart, char *var, boolean defaultVal) /* Make a check box filled with value from cart if it exists or * default value otherwise. */ { cgiMakeCheckBox(var, cartUsualBoolean(cart, var, defaultVal)); } void cartMakeRadioButton(struct cart *cart, char *var, char *val, char *defaultVal) /* Make a radio button that is selected if cart variable exists and matches * value (or value matches default val if cart var doesn't exist). */ { boolean matches = sameString(val, cartUsualString(cart, var, defaultVal)); cgiMakeRadioButton(var, val, matches); } void cartSaveSession(struct cart *cart) /* Save session in a hidden variable. This needs to be called * somewhere inside of form or bad things will happen when user * has multiple windows open. */ { cgiMakeHiddenVar(sessionVar, cartSessionId(cart)); } static void cartDumpItem(struct hashEl *hel,boolean asTable) /* Dump one item in cart hash */ { char *var = htmlEncode(hel->name); char *val = htmlEncode((char *)(hel->val)); if (asTable) { printf("%s", var); int width=(strlen(val)+1)*8; if (width<100) width = 100; cgiMakeTextVarWithExtraHtml(hel->name, val, width, "onchange='setCartVar(this.name,this.value);'"); printf("\n"); } else printf("%s %s\n", var, val); freeMem(var); freeMem(val); } void cartDumpList(struct hashEl *elList,boolean asTable) /* Dump list of cart variables optionally as a table with ajax update support. */ { struct hashEl *el; if (elList == NULL) return; slSort(&elList, hashElCmp); if (asTable) printf("\n"); for (el = elList; el != NULL; el = el->next) cartDumpItem(el,asTable); if (asTable) { printf("\n",slCount(elList)); printf("
  count: %d
\n"); } hashElFreeList(&elList); } void cartDump(struct cart *cart) /* Dump contents of cart. */ { struct hashEl *elList = hashElListHash(cart->hash); cartDumpList(elList,cartVarExists(cart,CART_DUMP_AS_TABLE)); } void cartDumpPrefix(struct cart *cart, char *prefix) /* Dump all cart variables with prefix */ { struct hashEl *elList = cartFindPrefix(cart, prefix); cartDumpList(elList,cartVarExists(cart,CART_DUMP_AS_TABLE)); } void cartDumpLike(struct cart *cart, char *wildcard) /* Dump all cart variables matching wildcard */ { struct hashEl *elList = cartFindLike(cart, wildcard); cartDumpList(elList,cartVarExists(cart,CART_DUMP_AS_TABLE)); } char *cartFindFirstLike(struct cart *cart, char *wildCard) /* Find name of first variable that matches wildCard in cart. * Return NULL if none. */ { struct hashEl *el, *elList = hashElListHash(cart->hash); char *name = NULL; for (el = elList; el != NULL; el = el->next) { if (wildMatch(wildCard, el->name)) { name = el->name; break; } } hashElFreeList(&el); return name; } static struct hashEl *cartFindSome(struct cart *cart, char *pattern, boolean (*match)(const char *a, const char *b)) /* Return list of name/val pairs from cart where name matches * pattern. Free when done with hashElFreeList. */ { struct hashEl *el, *next, *elList = hashElListHash(cart->hash); struct hashEl *outList = NULL; for (el = elList; el != NULL; el = next) { next = el->next; if (match(pattern, el->name)) { slAddHead(&outList, el); } else { hashElFree(&el); } } return outList; } struct hashEl *cartFindLike(struct cart *cart, char *wildCard) /* Return list of name/val pairs from cart where name matches * wildcard. Free when done with hashElFreeList. */ { return cartFindSome(cart, wildCard, wildMatch); } struct hashEl *cartFindPrefix(struct cart *cart, char *prefix) /* Return list of name/val pairs from cart where name starts with * prefix. Free when done with hashElFreeList. */ { return cartFindSome(cart, prefix, startsWith); } static char *cookieDate() /* Return date string for cookie format. We'll have to * revisit this in 35 years.... */ { return "Thu, 31-Dec-2037 23:59:59 GMT"; } static char *getCookieId(char *cookieName) /* Get id value from cookie. */ { return findCookieData(cookieName); } static char *getSessionId() /* Get session id if any from CGI. */ { return cgiOptionalString("hgsid"); } static void clearDbContents(struct sqlConnection *conn, char *table, char * secureId) /* Clear out contents field of row in table that matches id. */ { if (!secureId) return; struct dyString *query = dyStringNew(256); char *sessionKey = NULL; unsigned int id = cartDbParseId(secureId, &sessionKey); sqlDyStringPrintf(query, "update %s set contents='' where id=%u", table, id); if (cartDbUseSessionKey()) { if (!sessionKey) sessionKey = ""; sqlDyStringPrintf(query, " and sessionKey='%s'", sessionKey); } sqlUpdate(conn, query->string); dyStringFree(&query); } void cartResetInDb(char *cookieName) /* Clear cart in database. */ { char *hguid = getCookieId(cookieName); char *hgsid = getSessionId(); struct sqlConnection *conn = cartDefaultConnector(); clearDbContents(conn, userDbTable(), hguid); clearDbContents(conn, sessionDbTable(), hgsid); cartDefaultDisconnector(&conn); } void cartWriteCookie(struct cart *cart, char *cookieName) /* Write out HTTP Set-Cookie statement for cart. */ { char *domain = cfgVal("central.domain"); if (sameWord("HTTPHOST", domain)) { // IE9 does not accept portnames in cookie domains char *hostWithPort = hHttpHost(); struct netParsedUrl npu; netParseUrl(hostWithPort, &npu); if (strchr(npu.host, '.') != NULL) // Domains without a . don't seem to be kept domain = cloneString(npu.host); else domain = NULL; } char userIdKey[256]; cartDbSecureId(userIdKey, sizeof userIdKey, cart->userInfo); // Some users reported blank cookie values. Do we see that here? if (sameString(userIdKey,"")) // make sure we do not write any blank cookies. { // Be sure we do not lose this message. // Because the error happens so early we cannot trust that the warn and error handlers // are setup correctly and working. verbose(1, "unexpected error in cartWriteCookie: userId string is empty."); dumpStack( "unexpected error in cartWriteCookie: userId string is empty."); warn( "unexpected error in cartWriteCookie: userId string is empty."); } else { if (!isEmpty(domain)) printf("Set-Cookie: %s=%s; path=/; domain=%s; expires=%s\r\n", cookieName, userIdKey, domain, cookieDate()); else printf("Set-Cookie: %s=%s; path=/; expires=%s\r\n", cookieName, userIdKey, cookieDate()); } if (geoMirrorEnabled()) { // This occurs after the user has manually choosen to go back to the original site; we store redirect value into a cookie so we // can use it in subsequent hgGateway requests before loading the user's cart char *redirect = cgiOptionalString("redirect"); if (redirect) { printf("Set-Cookie: redirect=%s; path=/; domain=%s; expires=%s\r\n", redirect, cgiServerName(), cookieDate()); } } /* Validate login cookies if login is enabled */ if (loginSystemEnabled()) { struct slName *newCookies = loginValidateCookies(cart), *sl; for (sl = newCookies; sl != NULL; sl = sl->next) printf("Set-Cookie: %s\r\n", sl->name); } } struct cart *cartForSession(char *cookieName, char **exclude, struct hash *oldVars) /* This gets the cart without writing any HTTP lines at all to stdout. */ { char *hguid = getCookieId(cookieName); char *hgsid = getSessionId(); struct cart *cart = cartNew(hguid, hgsid, exclude, oldVars); cartExclude(cart, sessionVar); if (sameOk(cfgOption("signalsHandler"), "on")) /* most cgis call this routine */ initSigHandlers(hDumpStackEnabled()); char *httpProxy = cfgOption("httpProxy"); /* most cgis call this routine */ if (httpProxy) setenv("http_proxy", httpProxy, TRUE); /* net.c cannot see the cart, pass the value through env var */ return cart; } struct cart *cartAndCookieWithHtml(char *cookieName, char **exclude, struct hash *oldVars, boolean doContentType) /* Load cart from cookie and session cgi variable. Write cookie * and optionally content-type part HTTP preamble to web page. Don't * write any HTML though. */ { if (doContentType) htmlPushEarlyHandlers(); else pushWarnHandler(cartEarlyWarningHandler); struct cart *cart = cartForSession(cookieName, exclude, oldVars); popWarnHandler(); cartWriteCookie(cart, cookieName); if (doContentType) { puts("Content-Type:text/html"); puts("\n"); } return cart; } struct cart *cartAndCookie(char *cookieName, char **exclude, struct hash *oldVars) /* Load cart from cookie and session cgi variable. Write cookie and * content-type part HTTP preamble to web page. Don't write any HTML though. */ { return cartAndCookieWithHtml(cookieName, exclude, oldVars, TRUE); } struct cart *cartAndCookieNoContent(char *cookieName, char **exclude, struct hash *oldVars) /* Load cart from cookie and session cgi variable. Don't write out * content type or any HTML. */ { return cartAndCookieWithHtml(cookieName, exclude, oldVars, FALSE); } static void cartErrorCatcher(void (*doMiddle)(struct cart *cart), struct cart *cart) /* Wrap error catcher around call to do middle. */ { int status = setjmp(htmlRecover); pushAbortHandler(htmlAbort); hDumpStackPushAbortHandler(); if (status == 0) doMiddle(cart); hDumpStackPopAbortHandler(); popAbortHandler(); } void cartEarlyWarningHandler(char *format, va_list args) /* Write an error message so user can see it before page is really started. */ { static boolean initted = FALSE; va_list argscp; va_copy(argscp, args); if (!initted) { htmStart(stdout, "Early Error"); initted = TRUE; } printf("%s", htmlWarnStartPattern()); htmlVaParagraph(format,args); printf("%s", htmlWarnEndPattern()); /* write warning/error message to stderr so they get logged. */ logCgiToStderr(); vfprintf(stderr, format, argscp); va_end(argscp); putc('\n', stderr); fflush(stderr); } void cartWarnCatcher(void (*doMiddle)(struct cart *cart), struct cart *cart, WarnHandler warner) /* Wrap error and warning handlers around doMiddle. */ { pushWarnHandler(warner); cartErrorCatcher(doMiddle, cart); popWarnHandler(); } static boolean inWeb = FALSE; static boolean didCartHtmlStart = FALSE; void cartHtmlStart(char *title) /* Write HTML header and put in normal error handler. */ { pushWarnHandler(htmlVaWarn); htmStart(stdout, title); didCartHtmlStart = TRUE; } void cartVaWebStart(struct cart *cart, char *db, char *format, va_list args) /* Print out pretty wrapper around things when working * from cart. */ { pushWarnHandler(htmlVaWarn); webStartWrapper(cart, trackHubSkipHubName(db), format, args, FALSE, FALSE); inWeb = TRUE; } void cartWebStart(struct cart *cart, char *db, char *format, ...) /* Print out pretty wrapper around things when working * from cart. */ { va_list args; va_start(args, format); cartVaWebStart(cart, db, format, args); va_end(args); jsIncludeFile("jquery.js", NULL); jsIncludeFile("utils.js", NULL); jsIncludeFile("ajax.js", NULL); // WTF - variable outside of a form on almost every page we make below? // Tim put this in. Talking with him it sounds like some pages might actually // depend on it. Not removing it until we have a chance to test. Best fix // might be to add it to cartSaveSession, though this would then no longer be // well named, and not all things have 'db.' Arrr. Probably best to remove // and test a bunch. cgiMakeHiddenVar("db", db); } void cartWebEnd() /* Write out HTML footer and get rid or error handler. */ { webEnd(); popWarnHandler(); inWeb = FALSE; } void cartFooter(void) /* Write out HTML footer, possibly with googleAnalytics too */ { #ifndef GBROWSE googleAnalytics(); /* can't do this in htmlEnd */ #endif /* GBROWSE */ htmlEnd(); /* because it is in a higher library */ } void cartHtmlEnd() /* Write out HTML footer and get rid or error handler. */ { if (inWeb) webEnd(); /* this does googleAnalytics for a lot of CGIs */ else if (didCartHtmlStart) cartFooter(); else return; popWarnHandler(); } void setThemeFromCart(struct cart *cart) /* If 'theme' variable is set in cart: overwrite background with the one from * defined for this theme Also set the "styleTheme", with additional styles * that can overwrite the main style settings */ { // Get theme from cart and use it to get background file from config; // format is browser.theme.=[,] char *cartTheme = cartOptionalString(cart, "theme"); // XXXX which setting should take precedence? Currently browser.theme does. char *styleFile = cfgOption("browser.style"); if(styleFile != NULL) { char buf[512]; safef(buf, sizeof(buf), "", styleFile); char *copy = cloneString(buf); htmlSetStyleTheme(copy); // for htmshell.c, used by hgTracks webSetStyle(copy); // for web.c, used by hgc } if(isNotEmpty(cartTheme)) { char *themeKey = catTwoStrings("browser.theme.", cartTheme); styleFile = cfgOption(themeKey); freeMem(themeKey); if (isEmpty(styleFile)) return; char * link = webTimeStampedLinkToResourceOnFirstCall(styleFile, TRUE); // resource file link wrapped in html if (link != NULL) { htmlSetStyleTheme(link); // for htmshell.c, used by hgTracks webSetStyle(link); // for web.c, used by hgc } } } void cartHtmlShellWithHead(char *head, char *title, void (*doMiddle)(struct cart *cart), char *cookieName, char **exclude, struct hash *oldVars) /* Load cart from cookie and session cgi variable. Write web-page * preamble including head and title, call doMiddle with cart, and write end of web-page. * Exclude may be NULL. If it exists it's a comma-separated list of * variables that you don't want to save in the cart between * invocations of the cgi-script. */ { struct cart *cart; char *db, *org, *pos; char titlePlus[2048]; char extra[2048]; pushWarnHandler(cartEarlyWarningHandler); cart = cartAndCookie(cookieName, exclude, oldVars); getDbAndGenome(cart, &db, &org, oldVars); pos = cartGetPosition(cart, db, NULL); pos = addCommasToPos(db, stripCommas(pos)); if(pos != NULL && oldVars != NULL) { struct hashEl *oldpos = hashLookup(oldVars, positionCgiName); if(oldpos != NULL && differentString(pos,oldpos->val)) cartSetString(cart,"lastPosition",oldpos->val); } *extra = 0; if (pos == NULL && org != NULL) safef(titlePlus,sizeof(titlePlus), "%s%s - %s",trackHubSkipHubName(org), extra, title ); else if (pos != NULL && org == NULL) safef(titlePlus,sizeof(titlePlus), "%s - %s",pos, title ); else if (pos == NULL && org == NULL) safef(titlePlus,sizeof(titlePlus), "%s", title ); else safef(titlePlus,sizeof(titlePlus), "%s%s %s - %s",trackHubSkipHubName(org), extra,pos, title ); popWarnHandler(); setThemeFromCart(cart); htmStartWithHead(stdout, head, titlePlus); cartWarnCatcher(doMiddle, cart, htmlVaWarn); cartCheckout(&cart); cartFooter(); } static void cartEmptyShellMaybeContent(void (*doMiddle)(struct cart *cart), char *cookieName, char **exclude, struct hash *oldVars, boolean doContentType) /* Get cart and cookies and set up error handling. * If doContentType, print out Content-type:text/html * but don't start writing any html yet. * The doMiddleFunction has to call cartHtmlStart(title), and * cartHtmlEnd(), as well as writing the body of the HTML. * oldVars - those in cart that are overlayed by cgi-vars are * put in optional hash oldVars. */ { struct cart *cart = cartAndCookieWithHtml(cookieName, exclude, oldVars, doContentType); setThemeFromCart(cart); cartWarnCatcher(doMiddle, cart, cartEarlyWarningHandler); cartCheckout(&cart); } void cartEmptyShell(void (*doMiddle)(struct cart *cart), char *cookieName, char **exclude, struct hash *oldVars) /* Get cart and cookies and set up error handling, but don't start writing any * html yet. The doMiddleFunction has to call cartHtmlStart(title), and * cartHtmlEnd(), as well as writing the body of the HTML. * oldVars - those in cart that are overlayed by cgi-vars are * put in optional hash oldVars. */ { cartEmptyShellMaybeContent(doMiddle, cookieName, exclude, oldVars, TRUE); } void cartEmptyShellNoContent(void (*doMiddle)(struct cart *cart), char *cookieName, char **exclude, struct hash *oldVars) /* Get cart and cookies and set up error handling. * The doMiddle function must write the Content-Type header line. * oldVars - those in cart that are overlayed by cgi-vars are * put in optional hash oldVars. */ { cartEmptyShellMaybeContent(doMiddle, cookieName, exclude, oldVars, FALSE); } void cartHtmlShell(char *title, void (*doMiddle)(struct cart *cart), char *cookieName, char **exclude, struct hash *oldVars) /* Load cart from cookie and session cgi variable. Write web-page * preamble, call doMiddle with cart, and write end of web-page. * Exclude may be NULL. If it exists it's a comma-separated list of * variables that you don't want to save in the cart between * invocations of the cgi-script. */ { cartHtmlShellWithHead("", title, doMiddle, cookieName, exclude, oldVars); } void cartSetDbConnector(DbConnector connector) /* Set the connector that will be used by the cart to connect to the * database. Default connector is hConnectCart */ { cartDefaultConnector = connector; } void cartSetDbDisconnector(DbDisconnect disconnector) /* Set the connector that will be used by the cart to disconnect from the * database. Default disconnector is hDisconnectCart */ { cartDefaultDisconnector = disconnector; } static void saveDefaultGsidLists(char *genomeDb, struct cart *cart) /* save the default lists of GSID subject and sequence IDs to 2 internal files under trash/ct for applications to use */ { char *outName = NULL; char *outName2= NULL; FILE *outF, *outF2; struct tempName tn; struct tempName tn2; struct sqlResult *sr=NULL, *sr2=NULL; char **row, **row2; char query[255], query2[255]; char *chp; struct sqlConnection *conn, *conn2; conn= hAllocConn(genomeDb); conn2= hAllocConn(genomeDb); trashDirFile(&tn, "ct", "gsidSubj", ".list"); outName = tn.forCgi; trashDirFile(&tn2, "ct", "gsidSeq", ".list"); outName2 = tn2.forCgi; outF = mustOpen(outName,"w"); outF2= mustOpen(outName2,"w"); sqlSafef(query, sizeof(query), "select distinct subjId from hgFixed.gsIdXref order by subjId"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { fprintf(outF, "%s\n", row[0]); sqlSafef(query2, sizeof(query2), "select dnaSeqId from hgFixed.gsIdXref where subjId='%s' order by dnaSeqId", row[0]); sr2 = sqlGetResult(conn2, query2); while ((row2 = sqlNextRow(sr2)) != NULL) { /* Remove "ss." from the front of the DNA sequence ID, so that they could be used both for DNA and protein MSA maf display */ chp = strstr(row2[0], "ss."); if (chp != NULL) { fprintf(outF2, "%s\t%s\n", chp+3L, row[0]); } else { fprintf(outF2, "%s\t%s\n", row2[0], row[0]); } } sqlFreeResult(&sr2); } sqlFreeResult(&sr); carefulClose(&outF); carefulClose(&outF2); hFreeConn(&conn); hFreeConn(&conn2); cartSetString(cart, gsidSubjList, outName); cartSetString(cart, gsidSeqList, outName2); } char *cartGetOrderFromFile(char *genomeDb, struct cart *cart, char *speciesUseFile) /* Look in a cart variable that holds the filename that has a list of * species to show in a maf file */ { char *val; struct dyString *orderDY = dyStringNew(256); char *words[16]; if ((val = cartUsualString(cart, speciesUseFile, NULL)) == NULL) { if (hIsGsidServer()) { saveDefaultGsidLists(genomeDb, cart); /* now it should be set */ val = cartUsualString(cart, speciesUseFile, NULL); if (val == NULL) errAbort("can't find species list file var '%s' in cart\n",speciesUseFile); } else { errAbort("can't find species list file var '%s' in cart\n",speciesUseFile); } } struct lineFile *lf = lineFileOpen(val, TRUE); if (lf == NULL) errAbort("can't open species list file %s",val); while( ( lineFileChopNext(lf, words, sizeof(words)/sizeof(char *)) )) dyStringPrintf(orderDY, "%s ",words[0]); return dyStringCannibalize(&orderDY); } char *cartGetOrderFromFileAndMsaTable(char *genomeDb, struct cart *cart, char *speciesUseFile, char *msaTable) /* This function is used for GSID server only. Look in a cart variable that holds the filename that has a list of * species to show in a maf file and also restrict the results by the IDs existing in an MSA table*/ { char *val; struct sqlResult *sr=NULL; char query[255]; struct sqlConnection *conn; struct dyString *orderDY = dyStringNew(256); char *words[16]; if ((val = cartUsualString(cart, speciesUseFile, NULL)) == NULL) { if (hIsGsidServer()) { saveDefaultGsidLists(genomeDb, cart); /* now it should be set */ val = cartUsualString(cart, speciesUseFile, NULL); if (val == NULL) errAbort("can't find species list file var '%s' in cart\n",speciesUseFile); } else { errAbort("can't find species list file var '%s' in cart\n",speciesUseFile); } } struct lineFile *lf = lineFileOpen(val, TRUE); if (lf == NULL) errAbort("can't open species list file %s",val); if (hIsGsidServer()) { conn= hAllocConn(genomeDb); while( ( lineFileChopNext(lf, words, sizeof(words)/sizeof(char *)) )) { sqlSafef(query, sizeof(query), "select id from %s where id like '%%%s'", msaTable, words[0]); sr = sqlGetResult(conn, query); if (sqlNextRow(sr) != NULL) { dyStringPrintf(orderDY, "%s ",words[0]); sqlFreeResult(&sr); } } hFreeConn(&conn); } else { while( ( lineFileChopNext(lf, words, sizeof(words)/sizeof(char *)) )) { dyStringPrintf(orderDY, "%s ",words[0]); } } return dyStringCannibalize(&orderDY); } char *cartLookUpVariableClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix,char **pVariable) /* Returns value or NULL for a cart variable from lowest level on up. Optionally * fills the non NULL pVariable with the actual name of the variable in the cart */ { if (parentLevel) tdb = tdb->parent; for ( ; tdb != NULL; tdb = tdb->parent) { char buf[512]; if (suffix[0] == '.' || suffix[0] == '_') safef(buf, sizeof buf, "%s%s", tdb->track,suffix); else safef(buf, sizeof buf, "%s.%s", tdb->track,suffix); char *cartSetting = hashFindVal(cart->hash, buf); if (cartSetting != NULL) { if(pVariable != NULL) *pVariable = cloneString(buf); return cartSetting; } } if (pVariable != NULL) *pVariable = NULL; return NULL; } void cartRemoveVariableClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix) /* Looks for then removes a cart variable from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *var = NULL; (void)cartLookUpVariableClosestToHome(cart,tdb,parentLevel,suffix,&var); if (var != NULL) { cartRemove(cart,var); freeMem(var); } } char *cartStringClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix) /* Returns value or Aborts for a cart string from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *setting = cartOptionalStringClosestToHome(cart,tdb,parentLevel,suffix); if (setting == NULL) errAbort("cartStringClosestToHome: '%s' not found", suffix); return setting; } boolean cartVarExistsAnyLevel(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix) /* Returns TRUE if variable exists anywhere, looking from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { return (NULL != cartOptionalStringClosestToHome(cart,tdb,parentLevel,suffix)); } char *cartUsualStringClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix, char *usual) /* Returns value or {usual} for a cart string from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *setting = cartOptionalStringClosestToHome(cart,tdb,parentLevel,suffix); if(setting == NULL) setting = usual; return setting; } boolean cartBooleanClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix) /* Returns value or Aborts for a cart boolean ('on' or != 0) from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *setting = cartStringClosestToHome(cart,tdb,parentLevel,suffix); return (sameString(setting, "on") || atoi(setting) > 0); } boolean cartUsualBooleanClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix,boolean usual) /* Returns value or {usual} for a cart boolean ('on' or != 0) from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *setting = cartOptionalStringClosestToHome(cart,tdb,parentLevel,suffix); if (setting == NULL) return usual; return (sameString(setting, "on") || atoi(setting) > 0); } int cartUsualIntClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix, int usual) /* Returns value or {usual} for a cart int from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *setting = cartOptionalStringClosestToHome(cart,tdb,parentLevel,suffix); if (setting == NULL) return usual; return atoi(setting); } double cartUsualDoubleClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix, double usual) /* Returns value or {usual} for a cart fp double from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *setting = cartOptionalStringClosestToHome(cart,tdb,parentLevel,suffix); if (setting == NULL) return usual; return atof(setting); } struct slName *cartOptionalSlNameListClosestToHome(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *suffix) /* Return slName list (possibly with multiple values for the same var) from lowest level on up: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix */ { char *var = NULL; cartLookUpVariableClosestToHome(cart,tdb,parentLevel,suffix,&var); if (var == NULL) return NULL; struct slName *slNames = cartOptionalSlNameList(cart,var); freeMem(var); return slNames; } void cartRemoveAllForTdb(struct cart *cart, struct trackDb *tdb) /* Remove all variables from cart that are associated with this tdb. */ { char setting[256]; safef(setting,sizeof(setting),"%s.",tdb->track); cartRemovePrefix(cart,setting); safef(setting,sizeof(setting),"%s_",tdb->track); // TODO: All should be {track}.{varName}... Fix {track}_sel cartRemovePrefix(cart,setting); cartRemove(cart,tdb->track); } void cartRemoveAllForTdbAndChildren(struct cart *cart, struct trackDb *tdb) /* Remove all variables from cart that are associated with this tdb and it's children. */ { struct trackDb *subTdb; for (subTdb=tdb->subtracks;subTdb!=NULL;subTdb=subTdb->next) cartRemoveAllForTdbAndChildren(cart,subTdb); cartRemoveAllForTdb(cart,tdb); saveState(cart); } char *cartOrTdbString(struct cart *cart, struct trackDb *tdb, char *var, char *defaultVal) /* Look first in cart, then in trackDb for var. Return defaultVal if not found. */ { char *tdbDefault = trackDbSettingClosestToHomeOrDefault(tdb, var, defaultVal); boolean parentLevel = isNameAtParentLevel(tdb, var); return cartUsualStringClosestToHome(cart, tdb, parentLevel, var, tdbDefault); } int cartOrTdbInt(struct cart *cart, struct trackDb *tdb, char *var, int defaultVal) /* Look first in cart, then in trackDb for var. Return defaultVal if not found. */ { char *a = cartOrTdbString(cart, tdb, var, NULL); if (a == NULL) return defaultVal; else return atoi(a); } double cartOrTdbDouble(struct cart *cart, struct trackDb *tdb, char *var, double defaultVal) /* Look first in cart, then in trackDb for var. Return defaultVal if not found. */ { char *a = cartOrTdbString(cart, tdb, var, NULL); if (a == NULL) return defaultVal; else return atof(a); } boolean cartOrTdbBoolean(struct cart *cart, struct trackDb *tdb, char *var, boolean defaultVal) /* Look first in cart, then in trackDb for var. Return defaultVal if not found. */ { boolean tdbVal = defaultVal; char *tdbSetting = trackDbSetting(tdb, var); if (tdbSetting != NULL) tdbVal = trackDbSettingClosestToHomeOn(tdb, var); return cartUsualBooleanClosestToHome(cart, tdb, isNameAtParentLevel(tdb, var), var, tdbVal); } // These macros allow toggling warn messages to NOOPS when no longer debugging //#define DEBUG_WITH_WARN #ifdef DEBUG_WITH_WARN #define WARN warn #define ASSERT assert #else///ifndef DEBUG_WITH_WARN #define WARN(...) #define ASSERT(...) #endif///ndef DEBUG_WITH_WARN boolean cartValueHasChanged(struct cart *newCart,struct hash *oldVars,char *setting, boolean ignoreRemoved,boolean ignoreCreated) /* Returns TRUE if new cart setting has changed from old cart setting */ { char *oldValue = hashFindVal(oldVars,setting); if (oldValue == NULL) return FALSE; // All vars changed by cgi will be found in old vars char *newValue = cartOptionalString(newCart,setting); if (newValue == NULL) return (!ignoreRemoved); if (sameString(oldValue,CART_VAR_EMPTY)) { if (sameString(newValue,"hide") || sameString(newValue,"off") || sameString(newValue,"0")) // Special cases DANGER! return FALSE; } return (differentString(newValue,oldValue)); } static int cartNamesPruneChanged(struct cart *newCart,struct hash *oldVars, struct slPair **cartNames,boolean ignoreRemoved,boolean unChanged) /* Prunes a list of cartNames if the settings have changed between new and old cart. Returns pruned count */ { int pruned = 0; struct slPair *oldList = *cartNames; struct slPair *newList = NULL; struct slPair *oneName = NULL; while ((oneName = slPopHead(&oldList)) != NULL) { boolean thisOneChanged = cartValueHasChanged(newCart,oldVars,oneName->name,ignoreRemoved,TRUE); if (unChanged != thisOneChanged) slAddHead(&newList,oneName); else { pruned++; } } *cartNames = newList; return pruned; } int cartRemoveFromTdbTree(struct cart *cart,struct trackDb *tdb,char *suffix,boolean skipParent) /* Removes a 'trackName.suffix' from all tdb descendents (but not parent). If suffix NULL then removes 'trackName' which holds visibility */ { int removed = 0; boolean vis = (suffix == NULL || *suffix == '\0'); struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(skipParent?tdb->subtracks:tdb); for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *descendentTdb = tdbRef->val; char setting[512]; if (vis) safef(setting,sizeof(setting),"%s",descendentTdb->track); else safef(setting,sizeof(setting),"%s.%s",descendentTdb->track,suffix); removed += cartRemoveAndCount(cart,setting); } return removed; } static int cartRemoveOldFromTdbTree(struct cart *newCart,struct hash *oldVars,struct trackDb *tdb, char *suffix,char *parentVal,boolean skipParent) // Removes a 'trackName.suffix' from all tdb descendents (but not parent), BUT ONLY // IF OLD or same as parentVal. If suffix NULL then removes 'trackName' which holds visibility { int removed = 0; boolean vis = (suffix == NULL || *suffix == '\0'); struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(skipParent?tdb->subtracks:tdb); for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *descendentTdb = tdbRef->val; char setting[512]; if (vis) safef(setting,sizeof(setting),"%s",descendentTdb->track); else safef(setting,sizeof(setting),"%s.%s",descendentTdb->track,suffix); char *newVal = cartOptionalString(newCart,setting); if ( newVal != NULL && ( (parentVal != NULL && sameString(newVal,parentVal)) || (FALSE == cartValueHasChanged(newCart,oldVars,setting,TRUE,FALSE)))) removed += cartRemoveAndCount(newCart,setting); } return removed; } static boolean cartTdbOverrideSuperTracks(struct cart *cart,struct trackDb *tdb, boolean ifJustSelected) // When when the child of a hidden supertrack is foudn and selected, then shape the // supertrack accordingly. Returns TRUE if any cart changes are made { // This is only pertinent to supertrack children just turned on if (!tdbIsSuperTrackChild(tdb)) return FALSE; char setting[512]; // Must be from having just selected the track in findTracks. // This will carry with it the "_sel" setting. if (ifJustSelected) { safef(setting,sizeof(setting),"%s_sel",tdb->track); if (!cartVarExists(cart,setting)) return FALSE; cartRemove(cart,setting); // Unlike composite subtracks, supertrack children keep } // the "_sel" setting only for detecting this moment // if parent is not hidden then nothing to do ASSERT(tdb->parent != NULL && tdbIsSuperTrack(tdb->parent)); enum trackVisibility vis = tdbVisLimitedByAncestry(cart, tdb->parent, FALSE); if (vis != tvHide) return FALSE; // Now turn all other supertrack children to hide and the supertrack to visible struct slRef *childRef; for (childRef = tdb->parent->children;childRef != NULL; childRef = childRef->next) { struct trackDb *child = childRef->val; if (child == tdb) continue; // Make sure this child hasn't also just been turned on! safef(setting,sizeof(setting),"%s_sel",child->track); if (cartVarExists(cart,setting)) { cartRemove(cart,setting); // Unlike composite subtracks, supertrack children keep continue; // the "_sel" setting only for detecting this moment } // hide this sibling if not already hidden char *cartVis = cartOptionalString(cart,child->track); if (cartVis != NULL) { if (child->visibility == tvHide) cartRemove(cart,child->track); else if (hTvFromString(cartVis) != tvHide) cartSetString(cart,child->track,"hide"); } else if (child->visibility != tvHide) cartSetString(cart,child->track,"hide"); } // and finally show the parent cartSetString(cart,tdb->parent->track,"show"); WARN("Set %s to 'show'",tdb->parent->track); return TRUE; } static int cartTdbParentShapeVis(struct cart *cart,struct trackDb *parent,char *view, struct hash *subVisHash,boolean reshapeFully) // This shapes one level of vis (view or container) based upon subtrack specific visibility. // Returns count of tracks affected { ASSERT(view || (tdbIsContainer(parent) && tdbIsContainerChild(parent->subtracks))); struct trackDb *subtrack = NULL; char setting[512]; safef(setting,sizeof(setting),"%s",parent->track); enum trackVisibility visMax = tvHide; enum trackVisibility visOrig = tdbVisLimitedByAncestry(cart, parent, FALSE); // Should walk through children to get max new vis for this parent for (subtrack = parent->subtracks;subtrack != NULL;subtrack = subtrack->next) { char *foundVis = hashFindVal(subVisHash, subtrack->track); // if the subtrack doesn't have if (foundVis != NULL) // individual vis AND... { enum trackVisibility visSub = hTvFromString(foundVis); if (tvCompare(visMax, visSub) >= 0) visMax = visSub; } else if (!reshapeFully && visOrig != tvHide) { int fourState = subtrackFourStateChecked(subtrack,cart); if (fourStateVisible(fourState)) // subtrack must be visible { enum trackVisibility visSub = tdbVisLimitedByAncestry(cart, subtrack, FALSE); if (tvCompare(visMax, visSub) >= 0) visMax = visSub; } } } // Now we need to update non-subtrack specific vis/sel in cart int countUnchecked=0; int countVisChanged=0; // If view, this should always be set, since if a single view needs // to be promoted, the composite will go to full. if (tdbIsCompositeView(parent)) { cartSetString(cart,setting,hStringFromTv(visMax)); // Set this explicitly. countVisChanged++; // The visOrig may be inherited! } if (visMax != visOrig || reshapeFully) { if (!tdbIsCompositeView(parent)) // view vis is always shaped, { // but composite vis is conditionally shaped. cartSetString(cart,setting,hStringFromTv(visMax)); // Set this explicitly. countVisChanged++; if (visOrig == tvHide && tdbIsSuperTrackChild(parent)) cartTdbOverrideSuperTracks(cart,parent,FALSE); // deal with superTrack vis! cleanup } // Now set all subtracks that inherit vis back to visOrig for (subtrack = parent->subtracks;subtrack != NULL;subtrack = subtrack->next) { int fourState = subtrackFourStateChecked(subtrack,cart); if (!fourStateChecked(fourState)) cartRemove(cart,subtrack->track); // Remove subtrack level vis if it isn't even checked else // subtrack is checked (should include subtrack level vis) { char *visFromHash = hashFindVal(subVisHash, subtrack->track); if (tdbIsMultiTrack(parent)) // MultiTrack vis is ALWAYS inherited vis cartRemove(cart,subtrack->track); // and non-selected should not have vis if (visFromHash == NULL) // if the subtrack doesn't have individual vis AND... { if (reshapeFully || visOrig == tvHide) { // uncheck subtrackFourStateCheckedSet(subtrack, cart,FALSE,fourStateEnabled(fourState)); cartRemove(cart,subtrack->track); // Remove it if it exists, just in case countUnchecked++; } else if (visOrig != tvHide) { cartSetString(cart,subtrack->track,hStringFromTv(visOrig)); countVisChanged++; } } else // This subtrack has explicit vis { enum trackVisibility vis = hTvFromString(visFromHash); if (vis == visMax) { cartRemove(cart,subtrack->track); // Remove vis which should now be inherited countVisChanged++; } } } } } else if (tdbIsMultiTrack(parent)) { // MultiTrack vis is ALWAYS inherited vis so remove any subtrack specific vis struct hashCookie brownie = hashFirst(subVisHash); struct hashEl* cartVar = NULL; while ((cartVar = hashNext(&brownie)) != NULL) { if (!endsWith(cartVar->name,"_sel")) cartRemove(cart,cartVar->name); } } if (countUnchecked + countVisChanged) { WARN("%s visOrig:%s visMax:%s unchecked:%d Vis changed:%d",parent->track, hStringFromTv(visOrig),hStringFromTv(visMax),countUnchecked,countVisChanged); } return (countUnchecked + countVisChanged); } boolean cartTdbTreeReshapeIfNeeded(struct cart *cart,struct trackDb *tdbContainer) /* When subtrack vis is set via findTracks, and composite has no cart settings, then "shape" composite to match found */ { if (!tdbIsContainer(tdbContainer)) return FALSE; // Don't do any shaping // First look for subtrack level vis char setting[512]; struct trackDb *subtrack = NULL; struct trackDb *tdbView = NULL; struct hash *subVisHash = newHash(0); struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdbContainer->subtracks); for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { subtrack = tdbRef->val; char *val=cartOptionalString(cart,subtrack->track); if (val && differentString(val,"hide")) // NOTE should we include hide? { int fourState = subtrackFourStateChecked(subtrack,cart); if (fourStateVisible(fourState)) // subtrack is checked too { WARN("Subtrack level vis %s=%s",subtrack->track,val); hashAdd(subVisHash,subtrack->track,val); safef(setting,sizeof(setting),"%s_sel",subtrack->track); hashAdd(subVisHash,setting,subtrack); // Add the "_sel" setting which should also exist. } // Point it to subtrack } } slFreeList(&tdbRefList); if (hashNumEntries(subVisHash) == 0) { //WARN("No subtrack level vis for %s",tdbContainer->track); return FALSE; } // Next look for any cart settings other than subtrack vis/sel // New directive means if composite is hidden, then ignore previous and don't bother checking cart. boolean reshapeFully = (tdbVisLimitedByAncestry(cart, tdbContainer, FALSE) == tvHide); boolean hasViews = tdbIsCompositeView(tdbContainer->subtracks); WARN("reshape: %s",reshapeFully?"Fully":"Incrementally"); // Now shape views and composite to match subtrack specific visibility int count = 0; if (hasViews) { for (tdbView = tdbContainer->subtracks;tdbView != NULL; tdbView = tdbView->next ) { char *view = NULL; if (tdbIsView(tdbView,&view) ) count += cartTdbParentShapeVis(cart,tdbView,view,subVisHash,reshapeFully); } if (count > 0) { // At least one view was shaped, so all views will get explicit vis. // This means composite must be set to full enum trackVisibility visOrig = tdbVisLimitedByAncestry(cart, tdbContainer, FALSE); cartSetString(cart,tdbContainer->track,"full"); // Now set composite to full. if (visOrig == tvHide && tdbIsSuperTrackChild(tdbContainer)) cartTdbOverrideSuperTracks(cart,tdbContainer,FALSE);// deal with superTrack vis cleanup } } else // If no views then composite is not set to fuul but to max of subtracks count = cartTdbParentShapeVis(cart,tdbContainer,NULL,subVisHash,reshapeFully); hashFree(&subVisHash); // If reshaped, be sure to set flag to stop composite cleanup if (count > 0) tdbExtrasReshapedCompositeSet(tdbContainer); return TRUE; } boolean cartTdbTreeCleanupOverrides(struct trackDb *tdb,struct cart *newCart,struct hash *oldVars, struct lm *lm) /* When container or composite/view settings changes, remove subtrack specific settings Returns TRUE if any cart vars are removed */ { boolean anythingChanged = cartTdbOverrideSuperTracks(newCart,tdb,TRUE); if (!tdbIsContainer(tdb)) return anythingChanged; // If composite has been reshaped then don't clean it up if (tdbExtrasReshapedComposite(tdb)) return anythingChanged; // vis is a special additive case! composite or view level changes then remove subtrack vis boolean containerVisChanged = cartValueHasChanged(newCart,oldVars,tdb->track,TRUE,FALSE); if (containerVisChanged) { // If just created and if vis is the same as tdb default then vis has not changed char *cartVis = cartOptionalString(newCart,tdb->track); char *oldValue = hashFindVal(oldVars,tdb->track); if (cartVis && oldValue == NULL && hTvFromString(cartVis) == tdb->visibility) containerVisChanged = FALSE; } struct trackDb *tdbView = NULL; struct slPair *oneName = NULL; char *suffix = NULL; int clensed = 0; // Build list of current settings for container or composite and views char setting[512]; safef(setting,sizeof(setting),"%s.",tdb->track); char * view = NULL; boolean hasViews = FALSE; struct slPair *changedSettings = cartVarsWithPrefixLm(newCart, setting, lm); for (tdbView = tdb->subtracks;tdbView != NULL; tdbView = tdbView->next) { if (!tdbIsView(tdbView,&view)) break; hasViews = TRUE; char *cartVis = cartOptionalString(newCart,tdbView->track); if (cartVis != NULL) // special to get viewVis in the list { lmAllocVar(lm, oneName); oneName->name = lmCloneString(lm, tdbView->track); oneName->val = lmCloneString(lm, cartVis); slAddHead(&changedSettings,oneName); } // Now the non-vis settings safef(setting,sizeof(setting),"%s.",tdbView->track); struct slPair *changeViewSettings = cartVarsWithPrefixLm(newCart, setting, lm); changedSettings = slCat(changedSettings, changeViewSettings); } if (changedSettings == NULL && !containerVisChanged) return anythingChanged; // Prune list to only those which have changed if (changedSettings != NULL) { (void)cartNamesPruneChanged(newCart,oldVars,&changedSettings,TRUE,FALSE); if (changedSettings == NULL && !containerVisChanged) return anythingChanged; } // Walk through views if (hasViews) { for (tdbView = tdb->subtracks;tdbView != NULL; tdbView = tdbView->next) { char *cartVis = NULL; boolean viewVisChanged = FALSE; if (!tdbIsView(tdbView,&view)) break; struct slPair *leftOvers = NULL; // Walk through settings that match this view while ((oneName = slPopHead(&changedSettings)) != NULL) { suffix = NULL; if (startsWith(tdbView->track,oneName->name)) { suffix = oneName->name + strlen(tdbView->track); if (*suffix == '.') // NOTE: standardize on '.' since its is so pervasive suffix++; else if (isalnum(*suffix)) // viewTrackName is subset of another track! suffix = NULL; // add back to list for next round } if (suffix == NULL) { slAddHead(&leftOvers,oneName); continue; } if (*suffix == '\0') { viewVisChanged = TRUE; cartVis = oneName->val; } else // be certain to exclude vis settings here if (cartRemoveOldFromTdbTree(newCart,oldVars,tdbView,suffix,oneName->val,TRUE) > 0) clensed++; //slPairFree(&oneName); // lm memory so free not needed } if (viewVisChanged) { // If just created and if vis is the same as tdb default then vis has not changed char *oldValue = hashFindVal(oldVars,tdbView->track); if (cartVis && oldValue == NULL && hTvFromString(cartVis) != tdbView->visibility) viewVisChanged = FALSE; } if (containerVisChanged || viewVisChanged) { // vis is a special additive case! WARN("Removing subtrack vis for %s.%s",tdb->track,view); char *viewVis = hStringFromTv(tdbVisLimitedByAncestry(newCart, tdbView, FALSE)); if (cartRemoveOldFromTdbTree(newCart,oldVars,tdbView,NULL,viewVis,TRUE) > 0) clensed++; } changedSettings = leftOvers; } } // Now deal with anything remaining at the container level while ((oneName = slPopHead(&changedSettings)) != NULL) { suffix = oneName->name + strlen(tdb->track) + 1; if (cartRemoveOldFromTdbTree(newCart,oldVars,tdb,suffix,oneName->val,TRUE) > 0) clensed++; } if (containerVisChanged && !hasViews) { // vis is a special additive case! char *vis = hStringFromTv(tdbVisLimitedByAncestry(newCart, tdb, FALSE)); if (cartRemoveOldFromTdbTree(newCart,oldVars,tdb,NULL,vis,TRUE) > 0) clensed++; } anythingChanged = (anythingChanged || (clensed > 0)); return anythingChanged; } void cgiExitTime(char *cgiName, long enteredMainTime) /* single stderr print out called at end of CGI binaries to record run * time in apache error_log */ { if (sameWord("yes", cfgOptionDefault("browser.cgiTime", "yes")) ) fprintf(stderr, "CGI_TIME: %s: Overall total time: %ld millis\n", cgiName, clock1000() - enteredMainTime); } void cartCheckForCustomTracks(struct cart *cart, struct dyString *dyMessage) /* Scan cart for ctfile_ variables. Tally up the databases that have * live custom tracks and those that have expired custom tracks. */ /* While we're at it, also look for saved blat results. */ { struct hashEl *helList = cartFindPrefix(cart, CT_FILE_VAR_PREFIX); if (helList != NULL) { struct hashEl *hel; boolean gotLiveCT = FALSE, gotExpiredCT = FALSE; struct slName *liveDbList = NULL, *expiredDbList = NULL, *sln = NULL; for (hel = helList; hel != NULL; hel = hel->next) { char *db = hel->name + strlen(CT_FILE_VAR_PREFIX); boolean thisGotLiveCT = FALSE, thisGotExpiredCT = FALSE; /* If the file doesn't exist, just remove the cart variable so it * doesn't get copied from session to session. If it does exist, * leave it up to customFactoryTestExistence to parse the file for * possible customTrash table references, some of which may exist * and some not. */ if (!fileExists(hel->val)) { cartRemove(cart, hel->name); thisGotExpiredCT = TRUE; } else { customFactoryTestExistence(db, hel->val, &thisGotLiveCT, &thisGotExpiredCT); } if (thisGotLiveCT) slNameAddHead(&liveDbList, db); if (thisGotExpiredCT) slNameAddHead(&expiredDbList, db); gotLiveCT |= thisGotLiveCT; gotExpiredCT |= thisGotExpiredCT; } if (gotLiveCT) { slSort(&liveDbList, slNameCmp); dyStringPrintf(dyMessage, "

Note: the session has at least one active custom " "track (in database "); for (sln = liveDbList; sln != NULL; sln = sln->next) dyStringPrintf(dyMessage, "%s%s", cartSidUrlString(cart), sln->name, sln->name, (sln->next ? sln->next->next ? ", " : " and " : "")); dyStringAppend(dyMessage, "; click on the database link " "to manage custom tracks). "); } if (gotExpiredCT) { slSort(&expiredDbList, slNameCmp); dyStringPrintf(dyMessage, "

Note: the session has at least one expired custom " "track (in database "); for (sln = expiredDbList; sln != NULL; sln = sln->next) dyStringPrintf(dyMessage, "%s%s", sln->name, (sln->next ? sln->next->next ? ", " : " and " : "")); dyStringPrintf(dyMessage, "), so it may not appear as originally intended. "); } dyStringPrintf(dyMessage, - "Custom tracks are subject to an expiration policy described in the " - "" - "Session documentation.

"); + "These custom tracks should not expire, however, " + "the UCSC Genome Browser is not a data storage service; " + "please keep a local backup of your sessions contents " + "and custom track data.

"); slNameFreeList(&liveDbList); slNameFreeList(&expiredDbList); } /* Check for saved blat results (quasi custom track). */ char *ss = cartOptionalString(cart, "ss"); if (isNotEmpty(ss)) { char buf[1024]; char *words[2]; int wordCount; boolean exists = FALSE; safecpy(buf, sizeof(buf), ss); wordCount = chopLine(buf, words); if (wordCount < 2) exists = FALSE; else exists = fileExists(words[0]) && fileExists(words[1]); if (exists) dyStringPrintf(dyMessage, "

Note: the session contains BLAT results. "); else dyStringPrintf(dyMessage, "

Note: the session contains an expired reference to " "previously saved BLAT results, so it may not appear as " "originally intended. "); dyStringPrintf(dyMessage, "BLAT results are subject to an " "" "expiration policy."); } } char *cartGetPosition(struct cart *cart, char *database, struct cart **pLastDbPosCart) /* get the current position in cart as a string chr:start-end. * This can handle the special CGI params 'default' and 'lastDbPos' * Returned value has to be freed. Returns * default position of assembly is no position set in cart nor as CGI var. * Returns NULL if no position set anywhere and no default position. * For virtual modes, returns the type and extraState. */ { // position=lastDbPos in URL? -> go back to the last browsed position for this db char *position = NULL; char *defaultPosition = hDefaultPos(database); struct cart *lastDbPosCart = cartOfNothing(); boolean gotCart = FALSE; char dbPosKey[256]; safef(dbPosKey, sizeof(dbPosKey), "position.%s", database); if (sameOk(cgiOptionalString("position"), "lastDbPos")) { char *dbLocalPosContent = cartUsualString(cart, dbPosKey, NULL); if (dbLocalPosContent) { //warn("dbLocalPosContent=%s",dbLocalPosContent); // DEBUG REMOVE if (strchr(dbLocalPosContent, '=')) { gotCart = TRUE; cartParseOverHash(lastDbPosCart, cloneString(dbLocalPosContent)); // this function chews up input position = cloneString(cartUsualString(lastDbPosCart, "position", NULL)); //warn("gotCart position=%s",position); // DEBUG REMOVE // DEBUG REMOVE: //struct dyString *dbPosValue = newDyString(4096); //cartEncodeState(lastDbPosCart, dbPosValue); //warn("gotCart dbPosValue->string=[%s]",dbPosValue->string); } else { position = dbLocalPosContent; // old style value } } else { position = defaultPosition; // no value was set } } if (position == NULL) { position = cloneString(cartUsualString(cart, "position", NULL)); } /* default if not set at all, as would happen if it came from a URL with no * position. Otherwise tell them to go back to the gateway. Also recognize * "default" as specifying the default position. */ if (((position == NULL) || sameString(position, "default")) && (defaultPosition != NULL)) position = cloneString(defaultPosition); if (!gotCart) { cartSetBoolean(lastDbPosCart, "virtMode", FALSE); cartSetString(lastDbPosCart, "virtModeType", "default"); cartSetString(lastDbPosCart, "lastVirtModeType", "default"); cartSetString(lastDbPosCart, "position", position); cartSetString(lastDbPosCart, "nonVirtPosition", position); cartSetString(lastDbPosCart, "lastVirtModeExtra", ""); } if (pLastDbPosCart) *pLastDbPosCart = lastDbPosCart; return position; } void cartSetDbPosition(struct cart *cart, char *database, struct cart *lastDbPosCart) /* Set the 'position.db' variable in the cart.*/ { char dbPosKey[256]; safef(dbPosKey, sizeof dbPosKey, "position.%s", database); struct dyString *dbPosValue = newDyString(4096); cartEncodeState(lastDbPosCart, dbPosValue); cartSetString(cart, dbPosKey, dbPosValue->string); }