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);
}
void syncOneRecord(struct sqlConnection *conn, char *type, struct jsonWrite *json,
char *table, long long id)
/* Send over one record and save UUID result to row of table defined by id in idField. */
{
/* Construct dyString for URL */
struct dyString *dyUrl = dyStringNew(0);
dyStringPrintf(dyUrl, "http://%s:%s@%s/%s/", gUserId, gPassword, gHost, type);
verbose(2, "%s\n", dyUrl->string);
/* Construct dyString for http header */
struct dyString *dyHeader = dyStringNew(0);
dyStringPrintf(dyHeader, "Content-length: %d\r\n", json->dy->stringSize);
dyStringPrintf(dyHeader, "Content-type: text/javascript\r\n");
/* Send header and then JSON */
int sd = netOpenHttpExt(dyUrl->string, "POST", dyHeader->string);
mustWriteFd(sd, json->dy->string, json->dy->stringSize);
/* Grab response */
struct dyString *dyText = netSlurpFile(sd);
close(sd);
uglyf("%s\n", dyText->string);
/* Turn it into htmlPage structure - this will also parse out http header */
struct htmlPage *response = htmlPageParse(dyUrl->string, dyText->string);
uglyf("status %s %d\n", response->status->version, response->status->status);
/* If we got bad status abort with hopefully very informative message. */
int status = response->status->status;
if (status != 200 && status != 201) // HTTP codes
{
errAbort("ERROR - Metadatabase returns %d to our post request\n"
"POSTED JSON: %s\n"
"URL: %s\n"
"FULL RESPONSE: %s\n", status, json->dy->string, dyUrl->string, dyText->string);
}
/* Parse uuid out of json response. It should look something like
{
"status": "success",
"@graph": [
{
"description": "The macs2 peak calling software from Tao Liu.",
"name": "macs2", "title": "macs2", "url": "https://github.com/taoliu/MACS/",
"uuid": "9bda84fd-9872-49e3-9aa0-b71adbf9f31d",
"schema_version": "1",
"source_url": "https://github.com/taoliu/MACS/",
"references": [],
"@id": "/software/9bda84fd-9872-49e3-9aa0-b71adbf9f31d/",
"@type": ["software", "item"],
"aliases": []
}
],
"@type": ["result"]
}
*/
struct jsonElement *jsonRoot = jsonParse(response->htmlText);
struct jsonElement *graph = jsonMustFindNamedField(jsonRoot, "", "@graph");
struct slRef *ref = jsonListVal(graph, "@graph");
assert(slCount(ref) == 1);
struct jsonElement *graphEl = ref->val;
char *uuid = jsonStringField(graphEl, "uuid");
uglyf("Got uuid %s\n", uuid);
/* Save uuid to table */
char query[256];
sqlSafef(query, sizeof(query),
"update %s set metaUuid='%s' where id=%lld", table, uuid, id);
sqlUpdate(conn, query);
/* Clean up */
dyStringFree(&dyUrl);
dyStringFree(&dyHeader);
dyStringFree(&dyText);
response->fullText = NULL; // avoid double free of this
htmlPageFree(&response);
}
