void rsyncEdwExpDataType(char *url, char *userId, char *password, char *outTab)
/* rsyncEdwExpDataType - Get experiment and data types from ENCODED via json.. */
{
char *jsonText = NULL;
if (jsonIn)
readInGulp(jsonIn, &jsonText, NULL);
else
jsonText = getJsonViaHttps(url, userId, password);
if (jsonOut)
writeGulp(jsonOut, jsonText, strlen(jsonText));
struct jsonElement *jsonRoot = jsonParse(jsonText);
char *expListName = "@graph";
struct jsonElement *jsonExpList = jsonMustFindNamedField(jsonRoot, "", expListName);
verbose(1, "Got @graph %p\n", jsonExpList);
struct slRef *ref, *refList = jsonListVal(jsonExpList, expListName);
verbose(1, "Got %d experiments\n", slCount(refList));
FILE *f = mustOpen(outTab, "w");
int realExpCount = 0;
for (ref = refList; ref != NULL; ref = ref->next)
{
struct jsonElement *el = ref->val;
char *acc = jsonStringField(el, "accession");
char *dataType = jsonStringField(el, "assay_term_name");
if (dataType != NULL)
{
fprintf(f, "%s\t%s\t%s\t%s\t%s\n", acc, dataType,
jsonOptionalStringField(el, "lab.title", ""),
jsonOptionalStringField(el, "biosample_term_name", ""),
jsonOptionalStringField(el, "award.rfa", ""));
++realExpCount;
}
}
verbose(1, "Got %d experiments with dataType\n", realExpCount);
carefulClose(&f);
}
static void writeAutoUpgradeTableResult(char *tableName, char *result)
/* Write table upgrade result */
{
char path[AUTOUPGRPATHSIZE];
makeResultName(tableName, path);
writeGulp(path, result, strlen(result));
}
