static void startSeqQuery(int conn, bioSeq *seq, char *type)
/* Send a query that involves some sequence. */
{
char buf[256];
sprintf(buf, "%s%s %d", gfSignature(), type, seq->size);
mustWriteFd(conn, buf, strlen(buf));
if (read(conn, buf, 1) < 0)
errAbort("startSeqQuery: read failed: %s", strerror(errno));
if (buf[0] != 'Y')
errAbort("Expecting 'Y' from server, got %c", buf[0]);
mustWriteFd(conn, seq->dna, seq->size);
}
void cpFile(int s, int d)
/* Copy from source file to dest until reach end of file. */
{
int bufSize = 64*1024, readSize;
char *buf = needMem(bufSize);
for (;;)
{
readSize = read(s, buf, bufSize);
if (readSize > 0)
mustWriteFd(d, buf, readSize);
if (readSize <= 0)
break;
}
freeMem(buf);
}
struct htmlPage *htmlPageFromForm(struct htmlPage *origPage, struct htmlForm *form,
char *buttonName, char *buttonVal)
/* Return a new htmlPage based on response to pressing indicated button
* on indicated form in origPage. */
{
struct htmlPage *newPage = NULL;
struct dyString *dyUrl = dyStringNew(0);
struct dyString *dyHeader = dyStringNew(0);
struct dyString *dyText = NULL;
char *url = htmlExpandUrl(origPage->url, form->action);
char *cgiVars = NULL;
int contentLength = 0;
int sd = -1;
dyStringAppend(dyUrl, url);
cookieOutput(dyHeader, origPage->cookies);
if (sameWord(form->method, "GET"))
{
cgiVars = htmlFormCgiVars(origPage, form, buttonName, buttonVal, dyHeader);
dyStringAppend(dyUrl, "?");
dyStringAppend(dyUrl, cgiVars);
verbose(3, "GET %s\n", dyUrl->string);
sd = netOpenHttpExt(dyUrl->string, form->method, dyHeader->string);
}
else if (sameWord(form->method, "POST"))
{
cgiVars = htmlFormCgiVars(origPage, form, buttonName, buttonVal, dyHeader);
contentLength = strlen(cgiVars);
verbose(3, "POST %s\n", dyUrl->string);
dyStringPrintf(dyHeader, "Content-length: %d\r\n", contentLength);
sd = netOpenHttpExt(dyUrl->string, form->method, dyHeader->string);
mustWriteFd(sd, cgiVars, contentLength);
}
dyText = netSlurpFile(sd);
close(sd);
newPage = htmlPageParse(url, dyStringCannibalize(&dyText));
freez(&url);
dyStringFree(&dyUrl);
dyStringFree(&dyHeader);
freez(&cgiVars);
return newPage;
}
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);
}
