af55bf269d6309fff07030b42224634d9fee7e67 tdreszer Wed Sep 29 11:13:57 2010 -0700 Extended composite shaping to shape multiTracks as well. There are some differences, though. diff --git src/hg/lib/cart.c src/hg/lib/cart.c index 04da163..8d6a7c6 100644 --- src/hg/lib/cart.c +++ src/hg/lib/cart.c @@ -1,2502 +1,2512 @@ #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" static char const rcsid[] = "$Id: cart.c,v 1.120 2010/05/20 03:15:51 kent Exp $"; 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; } } 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. */ char query[1024]; safef(query, sizeof(query), "select length(contents) from userDb " "where id = %d", u->id); uLen = sqlQuickNum(conn, query); safef(query, sizeof(query), "select length(contents) from sessionDb " "where id = %d", s->id); sLen = sqlQuickNum(conn, 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()); if (cart->userId != 0 && u->id != cart->userId) fprintf(stderr, "ASH: bad userId %d --> %d! pid=%ld\n", cart->userId, u->id, (long)getpid()); if (cart->sessionId != 0 && s->id != cart->sessionId) fprintf(stderr, "ASH: bad sessionId %d --> %d! pid=%ld\n", cart->sessionId, s->id, (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, "userDb")) { fprintf(stderr, "ASH: cartTablesOk failed on %s.userDb! pid=%ld\n", sqlGetDatabase(conn), (long)getpid()); return FALSE; } if (!sqlTableExists(conn, "sessionDb")) { fprintf(stderr, "ASH: cartTablesOk failed on %s.sessionDb! pid=%ld\n", sqlGetDatabase(conn), (long)getpid()); return FALSE; } return TRUE; } static 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, int id) /* Load up cartDb entry for particular ID. Returns NULL if no such id. */ { if (id == 0) return NULL; else { struct cartDb *cdb = NULL; char where[64]; safef(where, sizeof(where), "id = %u", id); cdb = cartDbLoadWhere(conn, table, 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=%d looks corrupted -- starting over with new %s id.\n", table, id, table); cdb = NULL; } return cdb; } } struct cartDb *loadDb(struct sqlConnection *conn, char *table, int id, boolean *found) /* Load bits from database and save in hash. */ { struct cartDb *cdb; char query[256]; boolean result = TRUE; cdb = cartDbLoadFromId(conn, table, id); if (!cdb) { result = FALSE; safef(query, sizeof(query), "INSERT %s VALUES(0,\"\",0,now(),now(),0)", table); sqlUpdate(conn, query); id = sqlLastAutoId(conn); if ((cdb = cartDbLoadFromId(conn,table,id)) == NULL) errAbort("Couldn't get cartDb for id=%d right after loading. " "MySQL problem??", id); } *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; dyStringPrintf(dy, "SELECT useCount FROM %s " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encUserName, encSessionName); useCount = sqlQuickNum(conn, dy->string) + 1; dyStringClear(dy); dyStringPrintf(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 static void cartCopyCustomTracks(struct cart *cart, struct hash *oldVars) /* If cart contains any live custom tracks, save off a new copy of them, * to prevent clashes by multiple loaders of the same session. */ { struct hashEl *el, *elList = hashElListHash(cart->hash); char *db=NULL, *ignored; getDbAndGenome(cart, &db, &ignored, oldVars); for (el = elList; el != NULL; el = el->next) { if (startsWith(CT_FILE_VAR_PREFIX, el->name)) { 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); #define CART_DIFFS_INCLUDE_EMPTIES #ifdef CART_DIFFS_INCLUDE_EMPTIES // 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)); #endif///def CART_DIFFS_INCLUDE_EMPTIES 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) { - int suffixOffset = strlen(el->name) - strlen(POSITION_SUFFIX); - if(suffixOffset>0) - { - char *suffix = el->name + suffixOffset; - if(sameString(suffix,POSITION_SUFFIX)) + 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 //warn("Removing imgOrd for %s",name); 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); cartRemove(cart, multVar); } } } /* Handle non-boolean vars. */ for (cv = cgiVarList(); cv != NULL; cv = cv->next) { if (! (startsWith(booShadow, cv->name) || hashLookup(booHash, cv->name) || startsWith(multShadow, 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 or multiShad 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; 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."); safef(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(); unsigned hgsid = cartSessionId(cart); struct sqlConnection *conn2 = hConnectCentral(); sessionTouchLastUse(conn2, encSessionOwner, encSessionName); cartRemoveLike(cart, "*"); cartParseOverHash(cart, row[1]); cartSetInt(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); #ifndef GBROWSE cartCopyCustomTracks(cart, oldVars); #endif /* GBROWSE */ 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(); unsigned hgsid = cartSessionId(cart); cartRemoveLike(cart, "*"); cartSetInt(cart, sessionVar, hgsid); while (lineFileNext(lf, &line, &size)) { char *var = nextWord(&line); 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); #ifndef GBROWSE cartCopyCustomTracks(cart, oldVars); #endif /* GBROWSE */ if (isNotEmpty(actionVar)) cartRemove(cart, actionVar); } char *_cartVarDbName(char *db, char *var) /* generate cart variable name that is local to an assembly database. * Only for use inside of cart.h. WARNING: static return */ { static char buf[PATH_LEN]; // something rather big safef(buf, sizeof(buf), "%s_%s", var, db); return buf; } 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; 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(unsigned int userId, unsigned int 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; } struct cart *cartNew(unsigned int userId, unsigned int 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 */ { 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, "userDb", userId, &userIdFound); cart->sessionInfo = loadDb(conn, "sessionDb", 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 %d %d", 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.) */ if (! (cgiScriptName() && endsWith(cgiScriptName(), "hgSession"))) { if (cartVarExists(cart, hgsDoOtherUser)) { 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); } else if (cartVarExists(cart, hgsDoLoadUrl)) { char *url = cartString(cart, hgsLoadUrlName); struct lineFile *lf = netLineFileOpen(url); cartLoadSettings(lf, cart, oldVars, hgsDoLoadUrl); lineFileClose(&lf); cartTrace(cart, "after cartLS", conn); } } #endif /* GBROWSE */ if (exclude != NULL) { while ((ex = *exclude++)) cartExclude(cart, ex); } cartDefaultDisconnector(&conn); 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); dyStringPrintf(dy, "UPDATE %s SET contents='", table); dyStringAppendN(dy, contents, contentSize); dyStringPrintf(dy, "',lastUse=now(),useCount=%d ", cdb->useCount+1); dyStringPrintf(dy, " where id=%u", cdb->id); 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, "userDb", cart->userInfo, encoded->string, encoded->stringSize); updateOne(conn, "sessionDb", 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, "userDb", 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; } unsigned int cartSessionId(struct cart *cart) /* Return session id. */ { return cart->sessionInfo->id; } char *cartSidUrlString(struct cart *cart) /* Return session id string as in hgsid=N . */ { static char buf[64]; safef(buf, sizeof(buf), "%s=%u", cartSessionVarName(), cartSessionId(cart)); return buf; } unsigned int cartUserId(struct cart *cart) /* Return session id. */ { return cart->userInfo->id; } static int cartRemoveAndCount(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; } void cartRemove(struct cart *cart, char *var) /* Remove variable from cart. */ { struct hashEl *hel = hashLookup(cart->hash, var); while (hel != NULL) { struct hashEl *nextHel = hashLookupNext(hel); freez(&hel->val); hashRemove(cart->hash, var); hel = nextHel; } } 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; } 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; } 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 (sameString(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 (sameString(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. */ { cartSetInt(cart,var,(val?1:0)); // Be explicit because some cartBools overloaded with negative "disabled" values } 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. */ { char buf[64]; safef(buf, sizeof(buf), "%u", cart->sessionInfo->id); cgiMakeHiddenVar(sessionVar, buf); } 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 int getCookieId(char *cookieName) /* Get id value from cookie. */ { char *hguidString = findCookieData(cookieName); return (hguidString == NULL ? 0 : atoi(hguidString)); } static int getSessionId() /* Get session id if any from CGI. */ { return cgiUsualInt("hgsid", 0); } static void clearDbContents(struct sqlConnection *conn, char *table, unsigned id) /* Clear out contents field of row in table that matches id. */ { char query[256]; if (id == 0) return; safef(query, sizeof(query), "update %s set contents='' where id=%u", table, id); sqlUpdate(conn, query); } void cartResetInDb(char *cookieName) /* Clear cart in database. */ { int hguid = getCookieId(cookieName); int hgsid = getSessionId(); struct sqlConnection *conn = cartDefaultConnector(); clearDbContents(conn, "userDb", hguid); clearDbContents(conn, "sessionDb", hgsid); cartDefaultDisconnector(&conn); } void cartWriteCookie(struct cart *cart, char *cookieName) /* Write out HTTP Set-Cookie statement for cart. */ { printf("Set-Cookie: %s=%u; path=/; domain=%s; expires=%s\r\n", cookieName, cart->userInfo->id, cfgVal("central.domain"), cookieDate()); } struct cart *cartForSession(char *cookieName, char **exclude, struct hash *oldVars) /* This gets the cart without writing any HTTP lines at all to stdout. */ { int hguid = getCookieId(cookieName); int 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; void cartHtmlStart(char *title) /* Write HTML header and put in normal error handler. */ { pushWarnHandler(htmlVaWarn); htmStart(stdout, title); } 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, 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); cgiMakeHiddenVar("db", db); } void cartWebEnd() /* Write out HTML footer and get rid or error handler. */ { webEnd(); popWarnHandler(); } 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 cartFooter(); popWarnHandler(); } 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. */ { struct cart *cart = cartAndCookie(cookieName, exclude, oldVars); cartWarnCatcher(doMiddle, cart, cartEarlyWarningHandler); cartCheckout(&cart); } void cartHtmlShellPB(char *title, void (*doMiddle)(struct cart *cart), char *cookieName, char **exclude, struct hash *oldVars) /* For Proteome Browser, 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. */ { struct cart *cart; char *db, *org; char titlePlus[128]; char *proteinID; pushWarnHandler(cartEarlyWarningHandler); cart = cartAndCookie(cookieName, exclude, oldVars); getDbAndGenome(cart, &db, &org, oldVars); proteinID = cartOptionalString(cart, "proteinID"); safef(titlePlus, sizeof(titlePlus), "%s protein %s - %s", org, proteinID, title); popWarnHandler(); htmStart(stdout, titlePlus); cartWarnCatcher(doMiddle, cart, htmlVaWarn); cartCheckout(&cart); cartFooter(); } void cartHtmlShellPbGlobal(char *title, void (*doMiddle)(struct cart *cart), char *cookieName, char **exclude, struct hash *oldVars) /* For Proteome Browser, 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. */ /* cartHtmlShellPbGloabl differs from cartHtmlShellPB that it does not call getDbAndGenome */ { struct cart *cart; char titlePlus[128]; char *proteinID; pushWarnHandler(cartEarlyWarningHandler); cart = cartAndCookie(cookieName, exclude, oldVars); proteinID = cartOptionalString(cart, "proteinID"); safef(titlePlus, sizeof(titlePlus), "Protein %s - %s", proteinID, title); popWarnHandler(); htmStart(stdout, titlePlus); cartWarnCatcher(doMiddle, cart, htmlVaWarn); cartCheckout(&cart); cartFooter(); } 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, *clade=NULL; char titlePlus[128]; char extra[128]; pushWarnHandler(cartEarlyWarningHandler); cart = cartAndCookie(cookieName, exclude, oldVars); getDbAndGenome(cart, &db, &org, oldVars); clade = hClade(org); pos = cartOptionalString(cart, positionCgiName); 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",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",org, extra,pos, title ); popWarnHandler(); htmStartWithHead(stdout, head, titlePlus); cartWarnCatcher(doMiddle, cart, htmlVaWarn); cartCheckout(&cart); cartFooter(); } 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"); safef(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]); safef(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 *)) )) { safef(query, sizeof(query), "select id from %s where id like '%s%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 compositeLevel, 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 (compositeLevel) tdb = tdb->parent; for ( ; tdb != NULL; tdb = tdb->parent) { char buf[512]; 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; } // NEVER CHECKED IN. //#define NORMALIZE_CLOSEST_TO_HOME #ifdef NORMALIZE_CLOSEST_TO_HOME static void cartPairNormalize(struct cart *cart,struct cart *oldCart,char **lowestVar,char **lowestVal,char *parentVar,char *parentVal) /* Removes the lower level variable if it is the same as parent OR if the parent just changed */ { if(parentVal) { if(*lowestVal) { if(sameString(*lowestVal,parentVal)) // same so don't need lowest { cartRemove(cart,*lowestVar); *lowestVal = NULL; } else // Is parent newer? { char *oldVal = hashFindVal(oldCart->hash, parentVar); if(oldVal == NULL || differentString(oldVal,parentVal)) // parent updated { oldVal = hashFindVal(oldCart->hash, *lowestVar); if(oldVal && sameString(oldVal,*lowestVal)) // lowest not updated { cartRemove(cart,*lowestVar); // parent newer *lowestVal = NULL; } } } } if(*lowestVal == NULL) { *lowestVal = parentVal; //safecpy(*lowestVar, sizeof *lowestVar, parentVar); strcpy(*lowestVar, parentVar); // NOTE: these two must be same size! } } } char *cartNormalizeVariableClosestToHome(struct cart *cart,struct cart *oldCart,struct trackDb *tdb,boolean oneLevel, char *suffix) /* returns the ClosestToHome cart variable, but will remove any cart variable most recently superceded */ { char childVar[512]; safef(childVar, sizeof childVar, "%s.%s", tdb->track,suffix); char *lowestVar = childVar; char *lowestVal = hashFindVal(cart->hash, childVar); if(!tdbIsCompositeChild(tdb)) return lowestVal; char *oldVal = cartOptionalString(oldCart, childVar); if(oldVal && differentString(oldVal,lowestVal)) return lowestVal; // It is newest and nothing needs to be removed // Find the closest to home parent char parentVar[512]; char *parentVal = NULL; char *stView; if (tdbIsView(viewTdb,&stView)) { safef(parentVar,sizeof parentVar,"%s.%s.%s",tdb->parent->track,stView,suffix); parentVal = hashFindVal(cart->hash, parentVar); cartPairNormalize(cart,oldCart,&lowestVar,&lowestVal,parentVar,parentVal); } if(!oneLevel) { safef(parentVar,sizeof parentVar,"%s.%s",tdb->parent->track,suffix); parentVal = hashFindVal(cart->hash, parentVar); cartPairNormalize(cart,oldCart,&lowestVar,&lowestVal,parentVar,parentVal); } return lowestVal?lowestVal:parentVal; } #endif//def NORMALIZE_CLOSEST_TO_HOME void cartRemoveVariableClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix,&var); if(var != NULL) { cartRemove(cart,var); freeMem(var); } } char *cartStringClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix); if(setting == NULL) errAbort("cartStringClosestToHome: '%s' not found", suffix); return setting; } boolean cartVarExistsAnyLevel(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix)); } char *cartUsualStringClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix); if(setting == NULL) setting = usual; return setting; } boolean cartBooleanClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix); return (sameString(setting, "on") || atoi(setting) > 0); } boolean cartUsualBooleanClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix); if(setting == NULL) return usual; return (sameString(setting, "on") || atoi(setting) > 0); } int cartUsualIntClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix); if (setting == NULL) return usual; return atoi(setting); } double cartUsualDoubleClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,suffix); if (setting == NULL) return usual; return atof(setting); } struct slName *cartOptionalSlNameListClosestToHome(struct cart *cart, struct trackDb *tdb, boolean compositeLevel, 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,compositeLevel,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 compositeLevel = isNameAtCompositeLevel(tdb, var); return cartUsualStringClosestToHome(cart, tdb, compositeLevel, 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); } // 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) #ifdef CART_DIFFS_INCLUDE_EMPTIES return FALSE; // All vars changed by cgi will be found in old vars #else///ifndef CART_DIFFS_INCLUDE_EMPTIES return (!ignoreCreated); #endif///ndef CART_DIFFS_INCLUDE_EMPTIES char *newValue = cartOptionalString(newCart,setting); if (newValue == NULL) return (!ignoreRemoved); #ifdef CART_DIFFS_INCLUDE_EMPTIES if (sameString(oldValue,CART_VAR_EMPTY)) { if (sameString(newValue,"hide") || sameString(newValue,"off") || sameString(newValue,"0")) // Special cases DANGER! return FALSE; } #endif///def CART_DIFFS_INCLUDE_EMPTIES return (differentString(newValue,oldValue)); } 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 { freeMem(oneName); 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 settingName[512]; // wgEncodeOpenChromChip.Peaks.vis if (vis) safef(settingName,sizeof(settingName),"%s",descendentTdb->track); else safef(settingName,sizeof(settingName),"%s.%s",descendentTdb->track,suffix); removed += cartRemoveAndCount(cart,settingName); } 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 the "_sel" setting only for detecting this moment continue; } // 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; } // Shaping composite vis by subtrack specific vis comes in 3 flavors: // Simple) No shaping. Subtrack specific vis overrides composite/view level but does not alter it // Plan A) When composite is in default settings only, then composite/vis is shaped to reflect current subtrack vis // Plan B) Whenever there is subtrack level vis, the composite and view vis are shaped to show maximum subtrack vis, // while subtracks with inherited vis may be given subtrack specific vis to return them to that state #define COMPOSITE_VIS_SHAPING_PLAN_A #define COMPOSITE_VIS_SHAPING_PLAN_B +#ifndef COMPOSITE_VIS_SHAPING_PLAN_B +static boolean cartVarsNoneFoundForTdb(struct cart *cart,struct hash *subVisHash,struct trackDb *tdb) +{ +struct slPair *cartVar,*cartVars = cartVarsWithPrefix(cart,tdb->track); +if (cartVars != NULL) + { + for (cartVar = cartVars; cartVar != NULL; cartVar = cartVar->next) + { + if (tdbIsCompositeView(tdb) || !hashFindVal(subVisHash, cartVar->name)) // subVisHash does not contain anything prefixed by view! + { + // If composite vis changed but it is the same as trackDb default then ignore it + if (tdbIsContainer(tdb) + && sameString(cartVar->name,tdb->track) + && sameString((char *)cartVar->val,hStringFromTv(tdb->visibility)) ) + continue; + + // If view vis changed but it is the same as trackDb default then ignore it + if (tdbIsContainer(tdb) + && endsWith((char *)cartVar->val,".vis")) + { + // find out view + char *val = skipBeyondDelimit(cartVar->name,'.'); + char *viewFound = cloneFirstWordByDelimiter(val,'.'); + if (viewFound) + { + // find tdb for View + struct trackDb *viewTdb; + for (viewTdb=tdb->subtracks; viewTdb!=NULL; viewTdb=viewTdb->next) + { + char *viewOfTdb = NULL; + if (tdbIsView(viewTdb,&viewOfTdb) && sameString(viewOfTdb,viewFound)) + { + if(sameString((char *)cartVar->val,hStringFromTv(viewTdb->visibility)) ) + continue; + break; + } + } + } + } + WARN("cartVarsNoneFoundForTdb: %s=%s",cartVar->name,(char *)cartVar->val); + slFreeList(&cartVars); + return FALSE; // Any view cart vars means non-default so do not "shape" composite + } + } + slFreeList(&cartVars); + } +return TRUE; +} +#endif///ndef COMPOSITE_VIS_SHAPING_PLAN_B + #if defined(COMPOSITE_VIS_SHAPING_PLAN_A) || defined(COMPOSITE_VIS_SHAPING_PLAN_B) static int cartTdbParentShapeVis(struct cart *cart,struct trackDb *parent,char *view,struct hash *subVisHash,boolean reshapeFully) -// This shapes one level of vis (view or composite) based upon subtrack specific visibility. Returns count of subtracks affected +// This shapes one level of vis (view or container) based upon subtrack specific visibility. Returns count of subtracks affected { -ASSERT(view || (tdbIsComposite(parent) && tdbIsCompositeChild(parent->subtracks))); +ASSERT(view || (tdbIsContainer(parent) && tdbIsContainerChild(parent->subtracks))); struct trackDb *subtrack = NULL; char setting[512]; if (view != NULL) safef(setting,sizeof(setting),"%s.%s.vis",parent->parent->track,view); else safef(setting,sizeof(setting),"%s",parent->track); enum trackVisibility visMax = tvHide; -//enum trackVisibility visOrig = hTvFromString(cartUsualString(cart,setting,hStringFromTv(parent->visibility))); 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 individual vis AND... if (foundVis != NULL) { 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 countExplicitVis=0; if (visMax != visOrig || reshapeFully) { cartSetString(cart,setting,hStringFromTv(visMax)); // Set this explicitly. The visOrig may be inherited! 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)) // subtrack is checked (should include subtrack level vis) + if (!fourStateChecked(fourState)) + cartRemove(cart,subtrack->track); // Remove subtrack level vis if it isn't even checked just in case + else // subtrack is checked (should include subtrack level vis) { if (!hashFindVal(subVisHash, subtrack->track)) // if the subtrack doesn't have individual vis AND... { if (reshapeFully || visMax == tvHide) { subtrackFourStateCheckedSet(subtrack, cart,FALSE,fourStateEnabled(fourState)); // uncheck cartRemove(cart,subtrack->track); // Remove it if it exists, just in case countUnchecked++; } else if (visOrig != tvHide) { + if (tdbIsMultiTrack(parent)) + cartRemove(cart,subtrack->track); // MultiTrack vis is ALWAYS inherited + else cartSetString(cart,subtrack->track,hStringFromTv(visOrig)); countExplicitVis++; } } - } - else if (reshapeFully) - { - cartRemove(cart,subtrack->track); // Remove it if it exists, just in case - countUnchecked++; + else if (tdbIsMultiTrack(parent)) + cartRemove(cart,subtrack->track); // MultiTrack vis is ALWAYS inherited vis and non-selected should not have vis } } if (tdbIsCompositeView(parent)) { visOrig = tdbVisLimitedByAncestry(cart, parent->parent, FALSE); cartSetString(cart,parent->parent->track,"full"); // Now set composite to full. if (visOrig == tvHide && tdbIsSuperTrackChild(parent->parent)) cartTdbOverrideSuperTracks(cart,parent->parent,FALSE); // deal with superTrack vis! cleanup } - WARN("%s visOrig:%d visMax:%d unchecked:%d explicitVis:%d",parent->track,visOrig,visMax,countUnchecked,countExplicitVis); - } -return (countUnchecked + countExplicitVis); + WARN("%s visOrig:%s visMax:%s unchecked:%d explicitVis:%d",parent->track,hStringFromTv(visOrig),hStringFromTv(visMax),countUnchecked,countExplicitVis); } -#endif/// defined(COMPOSITE_VIS_SHAPING_PLAN_A) || defined(COMPOSITE_VIS_SHAPING_PLAN_B) - -#ifndef COMPOSITE_VIS_SHAPING_PLAN_B -static boolean cartVarsNoneFoundForTdb(struct cart *cart,struct hash *subVisHash,struct trackDb *tdb) -{ -struct slPair *cartVar,*cartVars = cartVarsWithPrefix(cart,tdb->track); -if (cartVars != NULL) - { - for (cartVar = cartVars; cartVar != NULL; cartVar = cartVar->next) - { - if (tdbIsCompositeView(tdb) || !hashFindVal(subVisHash, cartVar->name)) // subVisHash does not contain anything prefixed by view! - { - // If composite vis changed but it is the same as trackDb default then ignore it - if (tdbIsComposite(tdb) - && sameString(cartVar->name,tdb->track) - && sameString((char *)cartVar->val,hStringFromTv(tdb->visibility)) ) - continue; - - // If view vis changed but it is the same as trackDb default then ignore it - if (tdbIsComposite(tdb) - && endsWith((char *)cartVar->val,".vis")) - { - // find out view - char *val = skipBeyondDelimit(cartVar->name,'.'); - char *viewFound = cloneFirstWordByDelimiter(val,'.'); - if (viewFound) +else if (tdbIsMultiTrack(parent)) { - // find tdb for View - struct trackDb *viewTdb; - for (viewTdb=tdb->subtracks; viewTdb!=NULL; viewTdb=viewTdb->next) + // 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) { - char *viewOfTdb = NULL; - if (tdbIsView(viewTdb,&viewOfTdb) && sameString(viewOfTdb,viewFound)) - { - if(sameString((char *)cartVar->val,hStringFromTv(viewTdb->visibility)) ) - continue; - break; - } - } - } - } - WARN("cartVarsNoneFoundForTdb: %s=%s",cartVar->name,(char *)cartVar->val); - slFreeList(&cartVars); - return FALSE; // Any view cart vars means non-default so do not "shape" composite + if (!endsWith(cartVar->name,"_sel")) + cartRemove(cart,cartVar->name); } } - slFreeList(&cartVars); - } -return TRUE; + +return (countUnchecked + countExplicitVis); } -#endif///ndef COMPOSITE_VIS_SHAPING_PLAN_B +#endif/// defined(COMPOSITE_VIS_SHAPING_PLAN_A) || defined(COMPOSITE_VIS_SHAPING_PLAN_B) -boolean cartTdbTreeMatchSubtrackVis(struct cart *cart,struct trackDb *tdbComposite) +boolean cartTdbTreeMatchSubtrackVis(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 !defined(COMPOSITE_VIS_SHAPING_PLAN_A) && !defined(COMPOSITE_VIS_SHAPING_PLAN_B) return FALSE; // Don't do any shaping #else/// if defined(COMPOSITE_VIS_SHAPING_PLAN_A) || defined(COMPOSITE_VIS_SHAPING_PLAN_B) +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(tdbComposite->subtracks); +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 (cartUsualInt(cart,setting,0) != 0) // FIXME: sub level vis is not getting cleared out!!!! 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"); + WARN("No subtrack level vis for %s",tdbContainer->track); return FALSE; } // Next look for any cart settings other than subtrack vis/sel - // FIXME: New directive means that if composite is hidden, then ignore previous and don't bother checking cart. #ifdef COMPOSITE_VIS_SHAPING_PLAN_B -boolean reshapeFully = (tdbVisLimitedByAncestry(cart, tdbComposite, FALSE) == tvHide); -#else///ifndef COMPOSITE_VIS_SHAPING_PLAN_B -boolean reshapeFully = cartVarsNoneFoundForTdb(cart,subVisHash,tdbComposite); -#endif///ndef COMPOSITE_VIS_SHAPING_PLAN_B +// New directive means that 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); -// What about view level settings? -#ifdef COMPOSITE_VIS_SHAPING_PLAN_B -boolean hasViews = tdbIsCompositeView(tdbComposite->subtracks); #else///ifndef COMPOSITE_VIS_SHAPING_PLAN_B +boolean reshapeFully = cartVarsNoneFoundForTdb(cart,subVisHash,tdbContainer); boolean hasViews = FALSE; -tdbView = tdbComposite->subtracks; +tdbView = tdbContainer->subtracks; if (tdbIsCompositeView(tdbView)) { hasViews = TRUE; if (reshapeFully) { for( ;tdbView != NULL; tdbView = tdbView->next ) { if(!cartVarsNoneFoundForTdb(cart,subVisHash,tdbView)) { reshapeFully = FALSE; break; } } } } // How about subtrack level settings? Assume that compositePrefix caught them? If views then YES if (reshapeFully && !hasViews) { - for(subtrack = tdbComposite->subtracks;subtrack != NULL; subtrack = subtrack->next ) + for(subtrack = tdbContainer->subtracks;subtrack != NULL; subtrack = subtrack->next ) { if (!cartVarsNoneFoundForTdb(cart,subVisHash,subtrack)); { reshapeFully = FALSE; break; } } } if (!reshapeFully) { hashFree(&subVisHash); return FALSE; // Any view cart vars means non-default so do not "shape" composite } #endif///ndef COMPOSITE_VIS_SHAPING_PLAN_B -WARN("reshapeFully:%s",reshapeFully?"TRUE":"FALSE"); +WARN("reshape: %s",reshapeFully?"Fully":"Incrementally"); // Now shape views and composite to match subtrack specific visibility int count = 0; if (hasViews) { - for(tdbView = tdbComposite->subtracks;tdbView != NULL; tdbView = tdbView->next ) + for(tdbView = tdbContainer->subtracks;tdbView != NULL; tdbView = tdbView->next ) { char *view = NULL; if (tdbIsView(tdbView,&view) ) count += cartTdbParentShapeVis(cart,tdbView,view,subVisHash,reshapeFully); } } else // If no views then composite is not set to fuul but to max of subtracks - count = cartTdbParentShapeVis(cart,tdbComposite,NULL,subVisHash,reshapeFully); + count = cartTdbParentShapeVis(cart,tdbContainer,NULL,subVisHash,reshapeFully); hashFree(&subVisHash); return TRUE; #endif/// defined(COMPOSITE_VIS_SHAPING_PLAN_A) || defined(COMPOSITE_VIS_SHAPING_PLAN_B) } boolean cartTdbTreeCleanupOverrides(struct trackDb *tdb,struct cart *newCart,struct hash *oldVars) -/* When composite/view settings changes, remove subtrack specific settings +/* 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 (!tdbIsComposite(tdb)) +if (!tdbIsContainer(tdb)) return anythingChanged; // vis is a special additive case! composite or view level changes then remove subtrack vis -boolean compositeVisChanged = cartValueHasChanged(newCart,oldVars,tdb->track,TRUE,FALSE); -if (compositeVisChanged) +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) - compositeVisChanged = FALSE; + containerVisChanged = FALSE; } struct trackDb *tdbView = NULL; struct slPair *oneName = NULL; char *suffix = NULL; int clensed = 0; -// Build list of current settings for composite and views +// 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 = cartVarsWithPrefix(newCart, setting); for (tdbView = tdb->subtracks;tdbView != NULL; tdbView = tdbView->next) { if (!tdbIsView(tdbView,&view)) break; hasViews = TRUE; - safef(setting,sizeof(setting),"%s.",tdbView->track); // unfortunatly setting name could be wgEncodeBroadHistoneViewSig.??? - //safef(setting, sizeof(setting),"%s.%s.",tdb->track,view); // or wgEncodeBroadHistone.Sig.??? HOWEVER: this are picked up by composite prefix + safef(setting,sizeof(setting),"%s.",tdbView->track); // unfortunatly setting name could be viewTrackName.??? + //safef(setting, sizeof(setting),"%s.%s.",tdb->track,view); // or containerName.Sig.??? HOWEVER: this are picked up by containerName prefix struct slPair *changeViewSettings = cartVarsWithPrefix(newCart, setting); changedSettings = slCat(changedSettings, changeViewSettings); } -if (changedSettings == NULL && !compositeVisChanged) +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 && !compositeVisChanged) + if (changedSettings == NULL && !containerVisChanged) return anythingChanged; } // Walk through views if (hasViews) { for (tdbView = tdb->subtracks;tdbView != NULL; tdbView = tdbView->next) { boolean viewVisChanged = FALSE; if (!tdbIsView(tdbView,&view)) break; // If just created and if vis is the same as tdb default then vis has not changed safef(setting,sizeof(setting),"%s.%s.vis",tdb->track,view); char *cartVis = cartOptionalString(newCart,setting); char *oldValue = hashFindVal(oldVars,setting); if (cartVis && oldValue == NULL && hTvFromString(cartVis) != tdbView->visibility) viewVisChanged = FALSE; - safef(setting, sizeof(setting),"%s.%s.",tdb->track,view); // unfortunatly setting name could be wgEncodeBroadHistone.Sig.???r + safef(setting, sizeof(setting),"%s.%s.",tdb->track,view); // unfortunatly setting name could be containerName.View.??? char settingAlt[512]; - safef(settingAlt,sizeof(settingAlt),"%s.",tdbView->track); // or wgEncodeBroadHistoneViewSig.??? + safef(settingAlt,sizeof(settingAlt),"%s.",tdbView->track); // or viewTrackName.??? struct slPair *leftOvers = NULL; // Walk through settings that match this view while ((oneName = slPopHead(&changedSettings)) != NULL) { if(startsWith(setting,oneName->name)) suffix = oneName->name + strlen(setting); else if(startsWith(settingAlt,oneName->name)) suffix = oneName->name + strlen(settingAlt); else { slAddHead(&leftOvers,oneName); continue; } if (sameString(suffix,"vis")) { viewVisChanged = TRUE; } else if (cartRemoveFromTdbTree(newCart,tdbView,suffix,TRUE) > 0) clensed++; freeMem(oneName); } - if (compositeVisChanged || viewVisChanged) + if (containerVisChanged || viewVisChanged) { // vis is a special additive case! WARN("Removing subtrack vis for %s.%s",tdb->track,view); if (cartRemoveFromTdbTree(newCart,tdbView,NULL,TRUE) > 0) clensed++; } changedSettings = leftOvers; } } -// Now deal with anything remaining at the composite level +// Now deal with anything remaining at the container level while ((oneName = slPopHead(&changedSettings)) != NULL) { suffix = oneName->name + strlen(tdb->track) + 1; if(cartRemoveFromTdbTree(newCart,tdb,suffix,TRUE) > 0) clensed++; freeMem(oneName); } -if (compositeVisChanged || !hasViews) +if (containerVisChanged || !hasViews) { // vis is a special additive case! if (cartRemoveFromTdbTree(newCart,tdb,NULL,TRUE) > 0) clensed++; } anythingChanged = (anythingChanged || (clensed > 0)); return anythingChanged; }