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); }