int main(int argc, char *argv[], char* envp[]) {
char options[] = "pisuU:dvV:cC:";
int c, dflg = 0, fflg = 0, gflg = 0;
char *f_ptr, *g_ptr;
while ((c = getopt(argc, argv, options)) != EOF) {
switch (c) {
case 'i':
printRealAndEffectiveId();
break;
case 's':
makeMeLeader();
break;
case 'p':
printProcessId();
break;
case 'u':
printUlimit();
break;
case 'U':
setUlimit(optarg);
break;
case 'd':
printCurrentDirectory();
break;
case 'v':
printEviron();
break;
case 'V':
setEnviron(optarg);
break;
case 'c':
printCore();
break;
case 'C':
setCore(optarg);
break;
case '?':
printf("invalid option is %c\n", optopt);
}
}
}
void rWriteJson(FILE *f, struct tagStorm *storm, struct tagStanza *stanza,
struct ttjSubObj *obj, struct ttjSubObj *labeledObj, struct hash *schemaHash,
struct dyString *scratch)
/* Write out json object recursively */
{
boolean isArray = allDigitNames(obj->children);
struct ttjSubObj *field;
if (isArray)
{
fprintf(f, "[");
for (field = obj->children; field != NULL; field = field->next)
{
if (field != obj->children) // Only write comma separators after the first one
fprintf(f, ",");
rWriteJson(f, storm, stanza, field, labeledObj, schemaHash, scratch);
}
fprintf(f, "]");
}
else
{
fprintf(f, "{");
boolean firstOut = TRUE;
/* Figure out if we need to attach a core object and do so. The figuring bit is
* frankly clunky. */
char *objType = labeledObj->name;
if (sameString(objType, "submitter") || sameString(objType, "contributors"))
objType = "contact";
else if (sameString(objType, "publications"))
objType = "publication";
else if (sameString(objType, "protocol")) // protocol is actually just protocol_id
objType = "string";
else if (sameString(objType, "protocols")) // but protocols array is protocol
objType = "protocol";
else if (sameString(objType, "umi_barcode"))
objType = "barcode";
if (objNeedsCore(objType))
printCore(f, objType, &firstOut);
for (field = obj->children; field != NULL; field = field->next)
{
char *fieldName = field->name;
if (field->children != NULL)
{
/* Look for funny characteristics_ as these are largely up to user. */
if (startsWith("characteristics_", field->name))
errAbort("No '.' allowed in field name after characteristics_ in %s",
field->children->fullName);
/* If actually have data in this stanza write our field. */
if (prefixDotInStanza(field->fullName, stanza, scratch))
{
writeJsonTag(f, fieldName, &firstOut);
rWriteJson(f, storm, stanza, field, field, schemaHash, scratch);
}
}
else
{
char *val = tagFindVal(stanza, field->fullName);
if (val != NULL)
{
boolean isNum = FALSE;
char *schemaName = tagSchemaFigureArrayName(field->fullName, scratch);
struct tagSchema *schema = hashFindVal(schemaHash, schemaName);
if (schema != NULL)
isNum = (schema->type == '#' || schema->type == '%');
if (sameString(fieldName, "files"))
{
writeJsonTag(f, "lanes", &firstOut);
writeLaneArray(f, stanza, val);
}
else
{
boolean isArray = FALSE;
writeJsonTag(f, fieldName, &firstOut);
if (schema != NULL)
isArray = schema->isArray;
struct slName *list = csvParse(val);
if (isArray)
fputc('[', f);
else
{
if (list->next != NULL) // more than one element
errAbort("Multiple vals for scalar tag %s in stanza starting line %d of %s",
field->fullName, stanza->startLineIx, storm->fileName);
}
struct slName *el;
for (el = list; el != NULL; el = el->next)
{
writeJsonVal(f, el->name, isNum);
if (el->next != NULL)
fputc(',', f);
}
if (isArray)
fputc(']', f);
slFreeList(&list);
}
}
}
}
fprintf(f, "}");
}
}