a8273be9da3b7a87a8d829d3efb79bce66e22039 angie Wed Jan 23 17:42:02 2019 -0800 New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf diff --git src/hg/inc/cart.h src/hg/inc/cart.h index 755958c..9b2c11b 100644 --- src/hg/inc/cart.h +++ src/hg/inc/cart.h @@ -1,656 +1,660 @@ /* cart - stuff to manage variables that persist from * one invocation of a cgi script to another (variables * that are carted around). */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #ifndef CART_H #define CART_H struct cart; // forward definition for use in trackDb.h #include "jksql.h" #include "errAbort.h" #include "dystring.h" #include "linefile.h" #include "trackDb.h" // If cgi set as CART_VAR_EMPTY, then removed from cart // If If cgi created new and oldVars are stored, then will be CART_VAR_EMPTY in old vars #define CART_VAR_EMPTY "[]" #define IS_CART_VAR_EMPTY(var) ((var) == NULL || sameString(var,CART_VAR_EMPTY)) typedef struct sqlConnection *(*DbConnector)(); /* funtion type used to get a connection to database */ typedef void (*DbDisconnect)(struct sqlConnection **pConn); /* function type used to cleanup a connection from database */ struct cart /* A cart of settings that persist. */ { struct cart *next; /* Next in list. */ char *userId; /* User ID in database. */ char *sessionId; /* Session ID in database. */ struct hash *hash; /* String valued hash. */ struct hash *exclude; /* Null valued hash of variables not to save. */ struct cartDb *userInfo; /* Info on user. */ struct cartDb *sessionInfo; /* Info on session. */ }; INLINE char *_cartVarDbName(const char *db, const 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; } boolean cartTablesOk(struct sqlConnection *conn); /* Return TRUE if cart tables are accessible (otherwise, the connection * doesn't do us any good). */ 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 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. oldVars is an optional hash to put in values * that were just overwritten by cgi-variables. */ struct cart *cartOfNothing(); /* Create a new, empty, cart with no real connection to the database. */ struct cart *cartFromHash(struct hash *hash); /* Create a cart from hash */ 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, and no way to write back to database either. */ void cartCheckout(struct cart **pCart); /* Save cart to database and free it up. */ void cartSaveState(struct cart *cart); /* Free up cart and save it to database. * Intended for updating cart before background CGI runs. * Use cartCheckout() instead. */ void cartEncodeState(struct cart *cart, struct dyString *dy); /* Add a CGI-encoded var=val&... string of all cart variables to dy. */ char *cartSessionVarName(); /* Return name of CGI session ID variable. */ char *cartSessionId(struct cart *cart); /* Return session id. */ unsigned cartSessionRawId(struct cart *cart); /* Return raw session id without security key. */ unsigned cartUserRawId(struct cart *cart); /* Return raw user id without security key. */ char *cartSidUrlString(struct cart *cart); /* Return session id string as in hgsid=N . */ char *cartUserId(struct cart *cart); /* Return session id. */ void cartRemove(struct cart *cart, char *var); /* Remove variable from cart. */ 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 slPair *cartVarsLike(struct cart *cart, char *wildCard); /* Return a slPair list of cart vars that match the wildcard */ struct slPair *cartVarsWithPrefix(struct cart *cart, char *prefix); /* Return a slPair list of cart vars that begin with prefix */ 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. */ void cartRemoveLike(struct cart *cart, char *wildCard); /* Remove all variable from cart that match wildCard. */ void cartRemovePrefix(struct cart *cart, char *prefix); /* Remove variables with given prefix from cart. */ boolean cartVarExists(struct cart *cart, char *var); /* Return TRUE if variable is in cart. */ boolean cartListVarExists(struct cart *cart, char *var); /* Return TRUE if a list variable is in cart (list may still be empty). */ INLINE boolean cartVarExistsDb(struct cart *cart, char *db, char *var) /* Return TRUE if variable_$db is in cart. */ { return cartVarExists(cart, _cartVarDbName(db, var)); } char *cartString(struct cart *cart, char *var); /* Return string valued cart variable. */ INLINE char *cartStringDb(struct cart *cart, char *db, char *var) /* Return string valued cart var_$db. */ { return cartString(cart, _cartVarDbName(db, var)); } char *cartOptionalString(struct cart *cart, char *var); /* Return string valued cart variable or NULL if it doesn't exist. */ INLINE char *cartOptionalStringDb(struct cart *cart, char *db, char *var) /* Return string valued cart variable_$db or NULL if it doesn't exist. */ { return cartOptionalString(cart, _cartVarDbName(db, 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. */ INLINE char *cartNonemptyStringDb(struct cart *cart, char *db, char *name) /* Return string value associated with name_$db. Return NULL * if value doesn't exist or if it is pure white space. */ { return cartNonemptyString(cart, _cartVarDbName(db, name)); } char *cartUsualString(struct cart *cart, char *var, char *usual); /* Return variable value if it exists or usual if not. */ INLINE char *cartUsualStringDb(struct cart *cart, char *db, char *var, char *usual) /* Return var_$db value if it exists or usual if not. */ { return cartUsualString(cart, _cartVarDbName(db, var), usual); } char *cartCgiUsualString(struct cart *cart, char *var, char *usual); /* Look for var in CGI, then in cart, if not found then 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 hash *cartHashList(struct cart *cart, char *var); /* Return hash with multiple values for the same var or NULL if not found. */ 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. */ void cartSetString(struct cart *cart, char *var, char *val); /* Set string valued cart variable. */ INLINE void cartSetStringDb(struct cart *cart, char *db, char *var, char *val) /* Set string valued cart var_$db. */ { cartSetString(cart, _cartVarDbName(db, var), val); } int cartInt(struct cart *cart, char *var); /* Return int valued variable. */ INLINE int cartIntDb(struct cart *cart, char *db, char *var) /* Return int valued variable_$db. */ { return cartInt(cart, _cartVarDbName(db, var)); } int cartIntExp(struct cart *cart, char *var); /* Return integer valued expression in variable. */ int cartUsualInt(struct cart *cart, char *var, int usual); /* Return variable value if it exists or usual if not. */ INLINE int cartUsualIntDb(struct cart *cart, char *db, char *var, int usual) /* Return variable_$db value if it exists or usual if not. */ { return cartUsualInt(cart, _cartVarDbName(db, var), usual); } int cartUsualIntClipped(struct cart *cart, char *var, int usual, int minVal, int maxVal); /* Return integer variable clipped to lie between minVal/maxVal */ int cartCgiUsualInt(struct cart *cart, char *var, int usual); /* Look for var in CGI, then in cart, if not found then return usual. */ void cartSetInt(struct cart *cart, char *var, int val); /* Set integer value. */ INLINE void cartSetIntDb(struct cart *cart, char *db, char *var, int val) /* Set integer value for var_$db. */ { cartSetInt(cart, _cartVarDbName(db, var), val); } double cartDouble(struct cart *cart, char *var); /* Return double valued variable. */ INLINE double cartDoubleDb(struct cart *cart, char *db, char *var) /* Return double valued var_$db. */ { return cartDouble(cart, _cartVarDbName(db, var)); } double cartUsualDouble(struct cart *cart, char *var, double usual); /* Return variable value if it exists or usual if not. */ INLINE double cartUsualDoubleDb(struct cart *cart, char *db, char *var, double usual) /* Return var_$db value if it exists or usual if not. */ { return cartUsualDouble(cart, _cartVarDbName(db, var), usual); } double cartCgiUsualDouble(struct cart *cart, char *var, double usual); /* Look for var in CGI, then in cart, if not found then return usual. */ void cartSetDouble(struct cart *cart, char *var, double val); /* Set double value. */ INLINE void cartSetDoubleDb(struct cart *cart, char *db, char *var, double val) /* Set double value for var_$db. */ { cartSetDouble(cart, _cartVarDbName(db, var), val); } boolean cartBoolean(struct cart *cart, char *var); /* Retrieve cart boolean. */ INLINE boolean cartBooleanDb(struct cart *cart, char *db, char *var) /* Retrieve cart boolean for var_$db. */ { return cartBoolean(cart, _cartVarDbName(db, var)); } boolean cartUsualBoolean(struct cart *cart, char *var, boolean usual); /* Return variable value if it exists or usual if not. */ INLINE boolean cartUsualBooleanDb(struct cart *cart, char *db, char *var, boolean usual) /* Return var_$db value if it exists or usual if not. */ { return cartUsualBoolean(cart, _cartVarDbName(db, var), usual); } boolean cartCgiUsualBoolean(struct cart *cart, char *var, boolean usual); /* Look for var in CGI, then in cart, if not found then return usual. */ void cartSetBoolean(struct cart *cart, char *var, boolean val); /* Set boolean value. */ INLINE void cartSetBooleanDb(struct cart *cart, char *db, char *var, boolean val) /* Set boolean value for $var_db. */ { cartSetBoolean(cart, _cartVarDbName(db, var), val); } 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. */ 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. */ 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. */ 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. */ 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). */ 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. */ void cartDump(struct cart *cart); /* Dump contents of cart with anti-XSS HTML encoding. */ void cartDumpHgSession(struct cart *cart); /* Dump contents of cart with escaped newlines for hgSession output files. * Cart variable "cartDumpAsTable" is ignored. */ #define CART_DUMP_AS_TABLE "cartDumpAsTable" void cartDumpPrefix(struct cart *cart, char *prefix); /* Dump all cart variables with prefix */ void cartDumpLike(struct cart *cart, char *wildcard); /* Dump all cart variables matching wildcard */ 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. */ 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. */ char *cartFindFirstLike(struct cart *cart, char *wildCard); /* Find name of first variable that matches wildCard in cart. * Return NULL if none. */ void cartResetInDb(char *cookieName); /* Clear cart in database. */ void cartEarlyWarningHandler(char *format, va_list args); /* Write an error message so user can see it before page is really started */ void cartWarnCatcher(void (*doMiddle)(struct cart *cart), struct cart *cart, WarnHandler warner); /* Wrap error and warning handlers around doMiddl. */ 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. */ 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. */ void cartHtmlStart(char *title); /* Write HTML header and put in normal error handler. Needed with cartEmptyShell, * but not cartHtmlShell. */ void cartFooter(void); /* Write out HTML footer, possibly with googleAnalytics too */ void cartHtmlEnd(); /* Write out HTML footer and get rid or error handler. Needed with cartEmptyShell, * but not cartHtmlShell. */ void cartWebStart(struct cart *theCart, char *db, char *format, ...) /* Print out pretty wrapper around things when working * from cart. Balance this with cartWebEnd. */ #if defined(__GNUC__) __attribute__((format(printf, 3, 4))) #endif ; void cartVaWebStart(struct cart *cart, char *db, char *format, va_list args); /* Print out pretty wrapper around things when working * from cart. */ void cartWebStartHeader(struct cart *cart, char *db, char *format, ...); /* Print out Content-type header and then pretty wrapper around things when working * from cart. */ void cartWebEnd(); /* End out pretty wrapper around things when working * from cart. */ 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. */ 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. oldVars is an optional hash that will get values * of things in the cart that were overwritten by cgi-variables. */ void cartWriteCookie(struct cart *cart, char *cookieName); /* Write out HTTP Set-Cookie statement for 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. */ 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. */ 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. */ struct cart *cartForSession(char *cookieName, char **exclude, struct hash *oldVars); /* This gets the cart without writing any HTTP lines at all to stdout. */ void cartSetDbConnector(DbConnector connector); /* Set the connector that will be used by the cart to connect to the * database. Default connector is hConnectCart */ void cartSetDbDisconnector(DbDisconnect disconnector); /* Set the connector that will be used by the cart to disconnect from the * database. Default disconnector is hDisconnectCart */ /* Libified constants and code that originally belonged only to hgSession * (now hgTracks uses them too), plus a couple for DataTables in hgSession * and hgPublicSessions: */ #define hgSessionPrefix "hgS_" #define hgPublicSessionsPrefix "hgPS_" #define dataTableStateName "DataTableState" #define hgSessionTableState hgSessionPrefix dataTableStateName #define hgPublicSessionsTableState hgPublicSessionsPrefix dataTableStateName #define hgsOtherUserName hgSessionPrefix "otherUserName" #define hgsOtherUserSessionName hgSessionPrefix "otherUserSessionName" #define hgsDoOtherUser hgSessionPrefix "doOtherUser" #define hgsLoadUrlName hgSessionPrefix "loadUrlName" #define hgsDoLoadUrl hgSessionPrefix "doLoadUrl" #define namedSessionTable "namedSessionDb" void sessionTouchLastUse(struct sqlConnection *conn, char *encUserName, char *encSessionName); /* Increment namedSessionDb.useCount and update lastUse for this session. */ 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. */ boolean cartLoadSettingsFromUserInput(struct lineFile *lf, struct cart *cart, struct hash *oldVars, char *actionVar, struct dyString *dyMessage); /* Verify that the user data in lf looks like valid settings (hgSession saved file; * like cartDump output, but values may or may not be htmlEncoded). * Older session files may have unencoded newlines, causing bogus variables; * watch out for those after pasted input variables like hgta_pastedIdentifiers. * Users have uploaded custom tracks, DTC genotypes, hgTracks HTML, even * binary data files. Look for problematic patterns observed in the past. * Load settings 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. * If input contains suspect data, then add diagnostics to dyMessage. If input * contains so much garbage that we shouldn't even try to load what passes the filters, * return FALSE. */ 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 *cartGetOrderFromFileAndMsaTable(char *genomeDb, struct cart *cart, char *speciesUseFile, char *msaTable); /* Look in a cart variable that holds the filename that has a list of * species to show in a maf file */ 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: subtrackName.suffix, then compositeName.view.suffix, then compositeName.suffix Optionally fills the non NULL pVariable with the actual name of the variable in the cart */ #define cartOptionalStringClosestToHome(cart,tdb,parentLevel,suffix) \ cartLookUpVariableClosestToHome((cart),(tdb),(parentLevel),(suffix),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 *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 */ 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 */ 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). */ 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 */ 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 */ 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 */ 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 */ 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 */ 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 */ void cartRemoveAllForTdb(struct cart *cart, struct trackDb *tdb); /* Remove all variables from cart that are associated with this tdb. */ void cartRemoveAllForTdbAndChildren(struct cart *cart, struct trackDb *tdb); /* Remove all variables from cart that are associated with this tdb and it's children. */ 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. */ 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. */ 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. */ 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 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 */ 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 */ boolean cartTdbTreeReshapeIfNeeded(struct cart *cart,struct trackDb *tdbComposite); /* When subtrack vis is set via findTracks, and composite has no cart settings, then fashion composite to match found */ boolean cartTdbTreeCleanupOverrides(struct trackDb *tdb,struct cart *newCart,struct hash *oldVars, struct lm *lm); /* When composite/view settings changes, remove subtrack specific settings Returns TRUE if any cart vars are removed */ void cartCopyCustomComposites(struct cart *cart); /* Find any custom composite hubs and copy them so they can be modified. */ +void cartReplaceHubVars(struct cart *cart, char *hubFileVar, char *oldHubUrl, char *newHubUrl); +/* Replace all cart variables corresponding to oldHubUrl (and/or its hub ID) with + * equivalents for newHubUrl. */ + void cgiExitTime(char *cgiName, long enteredMainTime); /* single stderr print out called at end of CGI binaries to record run * time in apache error_log */ void cartHubWarn(char *format, va_list args); /* save up hub related warnings to put out later */ void cartFlushHubWarnings(); /* flush the hub errors (if any) */ void cartCheckForCustomTracks(struct cart *cart, struct dyString *dyMessage); /* Scan cart for ctfile_<db> 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. */ #define CART_HAS_DEFAULT_VISIBILITY "defaultsSet" extern 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 *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 * if no position set in cart nor as CGI var. * For virtual modes, returns the type and extraState. */ void cartSetDbPosition(struct cart *cart, char *database, struct cart *lastDbPosCart); /* Set the 'position.db' variable in the cart.*/ void cartSetLastPosition(struct cart *cart, char *position, struct hash *oldVars); /* If position and oldVars are non-NULL, and oldVars' position is different, add it to the cart * as lastPosition. This is called by cartHtmlShell{,WithHead} but not other cart openers; * it should be called after cartGetPosition or equivalent. */ void cartTdbFetchMinMaxPixels(struct cart *theCart, struct trackDb *tdb, int defaultMin, int defaultMax, int defaultDefault, int *retMin, int *retMax, int *retDefault, int *retCurrent); /* Configure maximum track height for variable height tracks (e.g. wiggle, barchart) * Initial height and limits may be defined in trackDb with the maxHeightPixels string, * Or user requested limits are defined in the cart. */ #endif /* CART_H */