3f06ffc10df40e72dfa18a150eeca23fda6b41df angie Thu Feb 8 13:42:04 2018 -0800 annoStreamDbPslPlus internally used a json config to join in CDS and sequence with the underlying PSL -- so annoStreamDbPslPlusNew did not accept an incoming config, so hgVai's RefSeq Status option was ignored. Add jsonObjectMerge so that the config from hgVai can be merged with the internal config, and make sure that the extra columns from the internal annoStreamDb are added to annoStreamDbPslPlusNew's asObj. We can't just use the internal annoStreamDb's asObj because the field names for CDS etc. fields would differ for refSeqAli vs ncbiRefSeq and column-matching to recognize annoStreamDbPslPlus would fail. refs #20948 diff --git src/inc/jsonParse.h src/inc/jsonParse.h index ae6acd9..2af3706 100644 --- src/inc/jsonParse.h +++ src/inc/jsonParse.h @@ -1,137 +1,143 @@ /* jsonParse - routines to parse JSON strings and traverse and pick things out of the * resulting object tree. */ #ifndef JSONPARSE_H #define JSONPARSE_H /* JSON Element code let's you build up a DOM like data structure in memory and then serialize it into html for communication with client side code. */ // supported types typedef enum _jsonElementType { jsonList = 0, jsonObject = 1, jsonNumber = 2, jsonDouble = 3, jsonBoolean = 4, jsonString = 5, jsonNull = 6 } jsonElementType; union jsonElementVal { struct slRef *jeList; struct hash *jeHash; long jeNumber; double jeDouble; boolean jeBoolean; char *jeString; void *jeNull; }; struct jsonElement { jsonElementType type; union jsonElementVal val; }; // constructors for each jsonElementType struct jsonElement *newJsonString(char *str); struct jsonElement *newJsonBoolean(boolean val); struct jsonElement *newJsonNumber(long val); struct jsonElement *newJsonDouble(double val); struct jsonElement *newJsonObject(struct hash *h); struct jsonElement *newJsonList(struct slRef *list); struct jsonElement *newJsonNull(); void jsonObjectAdd(struct jsonElement *h, char *name, struct jsonElement *ele); // Add a new element to a jsonObject; existing values are replaced. +void jsonObjectMerge(struct jsonElement *objA, struct jsonElement *objB); +/* Recursively merge fields of objB into objA. If objA and objB each have a list child with + * the same key then concatenate the lists. If objA and objB each have an object child with + * the same key then merge the object children. If objA and objB each have a child of some + * other type then objB's child replaces objA's child. */ + void jsonListAdd(struct jsonElement *list, struct jsonElement *ele); // Add a new element to a jsonList struct jsonElement *jsonParse(char *str); // parse string into an in-memory json representation char *jsonStringEscape(char *inString); /* backslash escape a string for use in a double quoted json string. * More conservative than javaScriptLiteralEncode because * some json parsers complain if you escape & or ' */ void jsonFindNameRecurse(struct jsonElement *ele, char *jName, struct slName **pList); // Search the JSON tree recursively to find all the values associated to // the name, and add them to head of the list. struct slName *jsonFindName(struct jsonElement *json, char *jName); // Search the JSON tree to find all the values associated to the name // and add them to head of the list. struct slName *jsonFindNameUniq(struct jsonElement *json, char *jName); // Search the JSON tree to find all the values associated to the name // and add them to head of the list. void jsonElementRecurse(struct jsonElement *ele, char *name, boolean isLast, void (*startCallback)(struct jsonElement *ele, char *name, boolean isLast, void *context), // Called at element start void (*endCallback)(struct jsonElement *ele, char *name, boolean isLast, void *context), // Called at element end void *context); /* Recurse through JSON tree calling callback functions with element and context. * Either startCallback or endCallback may be NULL, as can be name. */ void jsonPrintOneStart(struct jsonElement *ele, char *name, boolean isLast, int indent, FILE *f); /* Print the start of one json element - just name and maybe an opening brace or bracket. * Recursion is handled elsewhere. */ void jsonPrintOneEnd(struct jsonElement *ele, char *name, boolean isLast, boolean indent, FILE *f); /* Print object end */ void jsonPrintToFile(struct jsonElement *root, char *name, FILE *f, int indentPer); /* Print out JSON object and all children nicely indented to f as JSON objects. * Name may be NULL. Implemented via jsonPrintOneStart/jsonPrintOneEnd. */ /** Routines that check json type and return corresponding value. **/ struct slRef *jsonListVal(struct jsonElement *ele, char *name); /* Enforce element is type jsonList or jsonNull. Return list value, which may be NULL. */ struct hash *jsonObjectVal(struct jsonElement *ele, char *name); /* Enforce object is type jsonObject or jsonNull. Return object hash, which may be NULL. */ long jsonNumberVal(struct jsonElement *ele, char *name); /* Enforce element is type jsonNumber and return value. */ double jsonDoubleVal(struct jsonElement *ele, char *name); /* Enforce element is type jsonDouble and return value. */ boolean jsonBooleanVal(struct jsonElement *ele, char *name); /* Enforce element is type jsonBoolean and return value. */ char *jsonStringVal(struct jsonElement *ele, char *eleName); /* Enforce element is type jsonString or jsonNull. Return value, which may be NULL. */ /** Routines that help work with json objects (bracket enclosed key/val pairs **/ struct jsonElement *jsonFindNamedField(struct jsonElement *object, char *objectName, char *field); /* Find named field of object or return NULL if not found. Abort if object * is not actually an object. */ struct jsonElement *jsonMustFindNamedField(struct jsonElement *object, char *objectName, char *field); /* Find named field of object or die trying. */ char *jsonOptionalStringField(struct jsonElement *object, char *field, char *defaultVal); /* Return string valued field of object, or defaultVal if it doesn't exist. */ char *jsonStringField(struct jsonElement *object, char *field); /* Return string valued field of object or abort if field doesn't exist. */ boolean jsonOptionalBooleanField(struct jsonElement *object, char *field, boolean defaultVal); /* Return boolean valued field of object, or defaultVal if it doesn't exist. */ #endif /* JSONPARSE_H */