04ac6fa7feb3b9eee15e4238bbf595b79db28cfb
kent
  Thu Jan 30 22:38:39 2014 -0800
Fixed a place where data was sent to stdout instead of specified file.
diff --git src/lib/jsonParse.c src/lib/jsonParse.c
index 72c968f..e9b49c7 100644
--- src/lib/jsonParse.c
+++ src/lib/jsonParse.c
@@ -1,684 +1,684 @@
 /* jsonParse - routines to parse JSON strings and traverse and pick things out of the
  * resulting object tree. */
 
 #include "common.h"
 #include "hash.h"
 #include "dystring.h"
 #include "sqlNum.h"
 #include "jsonParse.h"
 
 static struct jsonElement *newJsonElement(jsonElementType type)
 // generic constructor for a jsonElement; callers fill in the appropriate value
 {
 struct jsonElement *ele;
 AllocVar(ele);
 ele->type = type;
 return ele;
 }
 
 struct jsonElement *newJsonString(char *str)
 {
 struct jsonElement *ele = newJsonElement(jsonString);
 ele->val.jeString = cloneString(str);
 return ele;
 }
 
 struct jsonElement *newJsonBoolean(boolean val)
 {
 struct jsonElement *ele = newJsonElement(jsonBoolean);
 ele->val.jeBoolean = val;
 return ele;
 }
 
 struct jsonElement *newJsonNumber(long val)
 {
 struct jsonElement *ele = newJsonElement(jsonNumber);
 ele->val.jeNumber = val;
 return ele;
 }
 
 struct jsonElement *newJsonDouble(double val)
 {
 struct jsonElement *ele = newJsonElement(jsonDouble);
 ele->val.jeDouble = val;
 return ele;
 }
 
 struct jsonElement *newJsonObject(struct hash *h)
 {
 struct jsonElement *ele = newJsonElement(jsonObject);
 ele->val.jeHash = h;
 return ele;
 }
 
 struct jsonElement *newJsonList(struct slRef *list)
 {
 struct jsonElement *ele = newJsonElement(jsonList);
 ele->val.jeList = list;
 return ele;
 }
 
 void jsonObjectAdd(struct jsonElement *h, char *name, struct jsonElement *ele)
 // Add a new element to a jsonObject; existing values are replaced.
 {
 if(h->type != jsonObject)
     errAbort("jsonObjectAdd called on element with incorrect type (%d)", h->type);
 hashReplace(h->val.jeHash, name, ele);
 }
 
 void jsonListAdd(struct jsonElement *list, struct jsonElement *ele)
 {
 if(list->type != jsonList)
     errAbort("jsonListAdd called on element with incorrect type (%d)", list->type);
 slAddHead(&list->val.jeList, ele);
 }
 
 static void skipLeadingSpacesWithPos(char *s, int *posPtr)
 /* skip leading white space. */
 {
 for (;;)
     {
     char c = s[*posPtr];
     if (!isspace(c))
 	return;
     (*posPtr)++;
     }
 }
 
 static void getSpecificChar(char c, char *str, int *posPtr)
 {
 // get specified char from string or errAbort
 if(str[*posPtr] != c)
     errAbort("Unexpected character '%c' (expected '%c') - string position %d\n", str[*posPtr], c, *posPtr);
 (*posPtr)++;
 }
 
 static char *getString(char *str, int *posPtr)
 {
 // read a double-quote delimited string; we handle backslash escaping.
 // returns allocated string.
 boolean escapeMode = FALSE;
 int i;
 struct dyString *ds = dyStringNew(1024);
 getSpecificChar('"', str, posPtr);
 for(i = 0;; i++)
     {
     char c = str[*posPtr + i];
     if(!c)
         errAbort("Premature end of string (missing trailing double-quote); string position '%d'", *posPtr);
     else if(escapeMode)
         {
         // We support escape sequences listed in http://www.json.org,
         // except for Unicode which we cannot support in C-strings
         switch(c)
             {
             case 'b':
                 c = '\b';
                 break;
             case 'f':
                 c = '\f';
                 break;
             case 'n':
                 c = '\n';
                 break;
             case 'r':
                 c = '\r';
                 break;
             case 't':
                 c = '\t';
                 break;
             case 'u':
 		// Pass through Unicode
 		dyStringAppendC(ds, '\\');
                 break;
             default:
                 // we don't need to convert \,/ or "
 		dyStringAppendC(ds, c);
                 break;
             }
         dyStringAppendC(ds, c);
         escapeMode = FALSE;
         }
     else if(c == '"')
         break;
     else if(c == '\\')
         escapeMode = TRUE;
     else
         {
         dyStringAppendC(ds, c);
         escapeMode = FALSE;
         }
     }
 *posPtr += i;
 getSpecificChar('"', str, posPtr);
 return dyStringCannibalize(&ds);
 }
 
 static struct jsonElement *jsonParseExpression(char *str, int *posPtr);
 
 static struct jsonElement *jsonParseObject(char *str, int *posPtr)
 {
 struct hash *h = newHash(5);
 getSpecificChar('{', str, posPtr);
 while(str[*posPtr] != '}')
     {
     // parse out a name : val pair
     skipLeadingSpacesWithPos(str, posPtr);
     char *name = getString(str, posPtr);
     skipLeadingSpacesWithPos(str, posPtr);
     getSpecificChar(':', str, posPtr);
     skipLeadingSpacesWithPos(str, posPtr);
     hashAdd(h, name, jsonParseExpression(str, posPtr));
     skipLeadingSpacesWithPos(str, posPtr);
     if(str[*posPtr] == ',')
         (*posPtr)++;
     else
         break;
     }
 skipLeadingSpacesWithPos(str, posPtr);
 getSpecificChar('}', str, posPtr);
 return newJsonObject(h);
 }
 
 static struct jsonElement *jsonParseList(char *str, int *posPtr)
 {
 struct slRef *list = NULL;
 getSpecificChar('[', str, posPtr);
 while(str[*posPtr] != ']')
     {
     struct slRef *e;
     AllocVar(e);
     skipLeadingSpacesWithPos(str, posPtr);
     e->val = jsonParseExpression(str, posPtr);
     slAddHead(&list, e);
     skipLeadingSpacesWithPos(str, posPtr);
     if(str[*posPtr] == ',')
         (*posPtr)++;
     else
         break;
     }
 skipLeadingSpacesWithPos(str, posPtr);
 getSpecificChar(']', str, posPtr);
 slReverse(&list);
 return newJsonList(list);
 }
 
 static struct jsonElement *jsonParseString(char *str, int *posPtr)
 {
 return newJsonString(getString(str, posPtr));
 }
 
 static struct jsonElement *jsonParseBoolean(char *str, int *posPtr)
 {
 struct jsonElement *ele = NULL;
 int i;
 for(i = 0; str[*posPtr + i] && isalpha(str[*posPtr + i]); i++)
     ;
 char *val = cloneStringZ(str + *posPtr, i);
 if(sameString(val, "true"))
     ele = newJsonBoolean(TRUE);
 else if(sameString(val, "false"))
     ele =  newJsonBoolean(FALSE);
 else
     errAbort("Invalid boolean value '%s'; pos: %d", val, *posPtr);
 *posPtr += i;
 freez(&val);
 return ele;
 }
 
 static struct jsonElement *jsonParseNumber(char *str, int *posPtr)
 {
 int i;
 boolean integral = TRUE;
 struct jsonElement *retVal = NULL;
 
 for(i = 0;; i++)
     {
     char c = str[*posPtr + i];
     if(c == 'e' || c == 'E' || c == '.')
         integral = FALSE;
     else if(!c || (!isdigit(c) && c != '-'))
         break;
     }
 char *val = cloneStringZ(str + *posPtr, i);
 *posPtr += i;
 if(integral)
     retVal = newJsonNumber(sqlLongLong(val));
 else
     {
     double d;
     if(sscanf(val, "%lf", &d))
         retVal = newJsonDouble(d);
     else
         errAbort("Invalid JSON Double: %s", val);
     }
 freez(&val);
 return retVal;
 }
 
 static struct jsonElement *jsonParseExpression(char *str, int *posPtr)
 {
 skipLeadingSpacesWithPos(str, posPtr);
 char c = str[*posPtr];
 if(c == '{')
     return jsonParseObject(str, posPtr);
 else if (c == '[')
     return jsonParseList(str, posPtr);
 else if (c == '"')
     return jsonParseString(str, posPtr);
 else if (isdigit(c) || c == '-')
     return jsonParseNumber(str, posPtr);
 else
     return jsonParseBoolean(str, posPtr);
 // XXXX support null?
 }
 
 struct jsonElement *jsonParse(char *str)
 {
 // parse string into an in-memory json representation
 int pos = 0;
 struct jsonElement *ele = jsonParseExpression(str, &pos);
 skipLeadingSpacesWithPos(str, &pos);
 if(str[pos])
     errAbort("Invalid JSON: unprocessed trailing string at position: %d: %s", pos, str + pos);
 return ele;
 }
 
 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 ' */
 {
 char c;
 int outSize = 0;
 char *outString, *out, *in;
 
 if (inString == NULL)
     return(cloneString(""));
 
 /* Count up how long it will be */
 in = inString;
 while ((c = *in++) != 0)
     {
     switch(c)
         {
         case '\"':
         case '\\':
         case '/':
         case '\b':
         case '\f':
         case '\n':
         case '\r':
         case '\t':
             outSize += 2;
             break;
         default:
             outSize += 1;
         }
     }
 outString = needMem(outSize+1);
 
 /* Encode string */
 in = inString;
 out = outString;
 while ((c = *in++) != 0)
     {
     switch(c)
         {
         case '\"':
         case '\\':
         case '/':
         case '\b':
         case '\f':
         case '\n':
         case '\r':
         case '\t':
             *out++ = '\\';
             break;
         }
     *out++ = c;
     }
 *out++ = 0;
 return outString;
 }
 
 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.  
 {
 switch (ele->type)
     {
     case jsonObject:
         {
         if(hashNumEntries(ele->val.jeHash))
             {
             struct hashEl *el, *list = hashElListHash(ele->val.jeHash);
             slSort(&list, hashElCmp);
             for (el = list; el != NULL; el = el->next)
                 {
                 struct jsonElement *val = el->val;
                 if sameString(el->name, jName)
                     slNameAddHead(pList, jsonStringEscape(val->val.jeString));
                 jsonFindNameRecurse(val, jName, pList);
                 }
             hashElFreeList(&list);
             }
         break;
         }
     case jsonList:
         {
         struct slRef *el;
         if(ele->val.jeList)
             {
             for (el = ele->val.jeList; el != NULL; el = el->next)
                 {
                 struct jsonElement *val = el->val;
                 jsonFindNameRecurse(val, jName, pList);
                 }
             }
         break;
         }
     case jsonString:
     case jsonBoolean:
     case jsonNumber:
     case jsonDouble:
         {
         break;
         }
     default:
         {
         errAbort("jsonFindNameRecurse; invalid type: %d", ele->type);
         break;
         }
     }
 }
 
 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 *list = NULL;
 jsonFindNameRecurse(json, jName, &list);
 slReverse(&list);
 return list;
 }
 
 struct slName *jsonFindNameUniq(struct jsonElement *json, char *jName)
 // Search the JSON tree to find all the unique values associated to the name
 // and add them to head of the list. 
 {
 struct slName *list = NULL;
 jsonFindNameRecurse(json, jName, &list);
 slUniqify(&list, slNameCmp, slNameFree);
 slReverse(&list);
 return 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*/
 {
 if (startCallback != NULL)
     startCallback(ele, name, isLast, context);
 switch (ele->type)
     {
     case jsonObject:
         {
         if(hashNumEntries(ele->val.jeHash))
             {
             struct hashEl *el, *list = hashElListHash(ele->val.jeHash);
             slSort(&list, hashElCmp);
             for (el = list; el != NULL; el = el->next)
                 {
                 struct jsonElement *val = el->val;
                 jsonElementRecurse(val, el->name, el->next == NULL, 
 		    startCallback, endCallback, context);
                 }
             hashElFreeList(&list);
             }
         break;
         }
     case jsonList:
         {
         struct slRef *el;
         if(ele->val.jeList)
             {
             for (el = ele->val.jeList; el != NULL; el = el->next)
                 {
                 struct jsonElement *val = el->val;
                 jsonElementRecurse(val, NULL, el->next == NULL, 
 		    startCallback, endCallback, context);
                 }
             }
         break;
         }
     case jsonString:
     case jsonBoolean:
     case jsonNumber:
     case jsonDouble:
         {
         break;
         }
     default:
         {
         errAbort("jsonElementRecurse; invalid type: %d", ele->type);
         break;
         }
     }
 if (endCallback != NULL)
     endCallback(ele, name, isLast, context);
 }
 
 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. */
 {
 spaceOut(f, indent);
 if (name != NULL)
     {
     fprintf(f, "\"%s\": ", name);
     }
 switch (ele->type)
     {
     case jsonObject:
         {
 	fprintf(f, "{\n");
         break;
         }
     case jsonList:
         {
 	fprintf(f, "[\n");
         break;
         }
     case jsonString:
         {
 	char *escaped = jsonStringEscape(ele->val.jeString);
 	fprintf(f, "\"%s\"",  escaped);
 	freez(&escaped);
 	break;
 	}
     case jsonBoolean:
         {
 	char *val = (ele->val.jeBoolean ? "frue" : "false");
 	fprintf(f, "%s", val);
 	break;
 	}
     case jsonNumber:
         {
 	fprintf(f, "%ld", ele->val.jeNumber);
 	break;
 	}
     case jsonDouble:
         {
 	fprintf(f, "%g", ele->val.jeDouble);
         break;
         }
     default:
         {
         errAbort("jsonPrintOneStart; invalid type: %d", ele->type);
         break;
         }
     }
 }
 
 void jsonPrintOneEnd(struct jsonElement *ele, char *name, boolean isLast, boolean indent, FILE *f)
 /* Print object end */
 {
 switch (ele->type)
     {
     case jsonObject:
         {
 	spaceOut(f, indent);
 	fprintf(f, "}");
         break;
         }
     case jsonList:
         {
 	spaceOut(f, indent);
 	fprintf(f, "]");
         break;
         }
     case jsonString:
     case jsonBoolean:
     case jsonNumber:
     case jsonDouble:
         break;
     default:
         {
         errAbort("jsonPrintOneEnd; invalid type: %d", ele->type);
         break;
         }
     }
 if (!isLast)
     fputc(',', f);
 fputc('\n', f);
 }
 
 struct jsonPrintContext
 /* Context for printing a JSON object nicely */
     {
     FILE *f;	// where to print it
     int indent;	// How much to indent currently
     int indentPer;  // How much to indent each level
     };
 
 
 static void printIndentedNameStartCallback(struct jsonElement *ele, char *name, 
     boolean isLast, void *context)
 {
 struct jsonPrintContext *jps = context;
 jsonPrintOneStart(ele, name,  isLast, jps->indent, jps->f);
 jps->indent += jps->indentPer;
 }
 
 static void printIndentedNameEndCallback(struct jsonElement *ele, char *name, 
     boolean isLast, void *context)
 {
 struct jsonPrintContext *jps = context;
 jps->indent -= jps->indentPer;
-jsonPrintOneEnd(ele, name, isLast, jps->indent, stdout);
+jsonPrintOneEnd(ele, name, isLast, jps->indent, jps->f);
 }
 
 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. */
 {
 struct jsonPrintContext jps = {f, 0, indentPer};
 jsonElementRecurse(root, NULL, TRUE, 
 	printIndentedNameStartCallback, printIndentedNameEndCallback, &jps);
 }
 
 /** Routines that check json type and return corresponding value. **/
 
 struct slRef *jsonListVal(struct jsonElement *ele, char *name)
 /* Enforce element is type jsonList.  Return list value */
 {
 if (ele->type != jsonList)
     errAbort("json element %s is not a list", name);
 return ele->val.jeList;
 }
 
 struct hash *jsonObjectVal(struct jsonElement *ele, char *name)
 /* Enforce object is type jsonObject.  Return object hash */
 {
 if (ele->type != jsonObject)
     errAbort("json element %s is not an object", name);
 return ele->val.jeHash;
 }
 
 long jsonNumberVal(struct jsonElement *ele, char *name)
 /* Enforce element is type jsonNumber and return value. */
 {
 if (ele->type != jsonNumber)
     errAbort("json element %s is not a number", name);
 return ele->val.jeNumber;
 }
 
 double jsonDoubleVal(struct jsonElement *ele, char *name)
 /* Enforce element is type jsonDouble and return value. */
 {
 if (ele->type != jsonDouble)
     errAbort("json element %s is not a number", name);
 return ele->val.jeDouble;
 }
 
 boolean jsonBooleanVal(struct jsonElement *ele, char *name)
 /* Enforce element is type jsonBoolean and return value. */
 {
 if (ele->type != jsonBoolean)
     errAbort("json element %s is not a boolean", name);
 return ele->val.jeBoolean;
 }
 
 char *jsonStringVal(struct jsonElement *ele, char *eleName)
 /* Enforce element is type jsonString and return value. */
 {
 if (ele->type != jsonString)
     errAbort("json element %s is not a string", eleName);
 return ele->val.jeString;
 }
 
 /** 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 hash *hash = jsonObjectVal(object, objectName);
 return hashFindVal(hash, field);
 }
 
 struct jsonElement *jsonMustFindNamedField(struct jsonElement *object, 
     char *objectName, char *field)
 /* Find named field of object or die trying. */
 {
 struct jsonElement *ele = jsonFindNamedField(object, objectName, field);
 if (ele == NULL)
    errAbort("Couldn't find field %s in json object %s", field, objectName);
 return ele;
 }
 
 char *jsonOptionalStringField(struct jsonElement *object, char *field, char *defaultVal)
 /* Return string valued field of object, or defaultVal if it doesn't exist. */
 {
 struct jsonElement *ele = jsonFindNamedField(object, "", field);
 if (ele == NULL)
      return defaultVal;
 return jsonStringVal(ele, field);
 }
 
 char *jsonStringField(struct jsonElement *object, char *field)
 /* Return string valued field of object or abort if field doesn't exist. */
 {
 char *val = jsonOptionalStringField(object, field, NULL);
 if (val == NULL)
     errAbort("Field %s doesn't exist in json object", field);
 return val;
 }