c7211155cab4ec213239cf6979ee4b63a1d96374 max Tue Aug 11 03:07:18 2015 -0700 adding email display during redirect, GET urls, adding onlyDbs/notDbs tags to support hg38, refs #15113. diff --git src/hg/hgTracks/extTools.c src/hg/hgTracks/extTools.c index 50ec9cf..00f512f 100644 --- src/hg/hgTracks/extTools.c +++ src/hg/hgTracks/extTools.c @@ -8,38 +8,43 @@ * See README in this or parent directory for licensing information. */ #include "common.h" #include "dystring.h" #include "hCommon.h" #include "htmshell.h" #include "hash.h" #include "web.h" #include "ra.h" #include "hgTracks.h" #include "extTools.h" #include "hgFind.h" #include "obscure.h" #include "net.h" -static char *getRequiredRaSetting(struct hash *hash, char *name, struct lineFile *lf) -/* Grab a group setting out of the ra hash. errAbort if not found. */ +static char *cloneRaSetting(struct hash *hash, char *name, struct lineFile *lf, bool mustExist) +/* clone a setting out of the ra hash. errAbort if mustExit and not found, otherwise NULL. */ { char *str; if ((str = hashFindVal(hash, name)) == NULL) + { + if (mustExist) errAbort("missing required setting '%s' on line %d in file %s\n", name, lf->lineIx, lf->fileName); -return str; + else + return NULL; + } +return cloneString(str); } struct extTool *readExtToolRa(char *raFileName) /* parse the extTools.ra file. Inspired by trackHub.c:readGroupRa() */ { struct lineFile *lf = udcWrapShortLineFile(raFileName, NULL, 1*1024*1024); struct extTool *list = NULL; //struct hash *ra; struct slPair *raList; while ((raList = raNextStanzAsPairs(lf)) != NULL) { struct extTool *et; AllocVar(et); struct slPair *paramList = NULL; @@ -59,42 +64,53 @@ // hacky way to allow spaces in parameter names and values char *name = replaceChars(paramArr[0], "%20", " "); char *val; if (fCount==2) val = cloneString(paramArr[1]); else val = cloneString(""); val = replaceChars(val, "%20", " "); slPairAdd(¶mList, name, val); } else // add all other name/val pairs to the hash hashAdd(raHash, raPair->name, cloneString(raPair->val)); } - // pull out the normal fields from the hash - et->tool = cloneString(getRequiredRaSetting(raHash, "tool", lf)); - et->shortLabel = cloneString(getRequiredRaSetting(raHash, "shortLabel", lf)); + // pull out the required fields from the hash + et->tool = cloneRaSetting(raHash, "tool", lf, TRUE); + et->shortLabel = cloneRaSetting(raHash, "shortLabel", lf, TRUE); + et->longLabel = cloneRaSetting(raHash, "longLabel", lf, TRUE); + et->url = cloneRaSetting(raHash, "url", lf, TRUE); + et->dbs = NULL; + + // optional fields + et->email = cloneRaSetting(raHash, "email", lf, FALSE); + if (hashFindVal(raHash, "onlyDbs")) + et->dbs = commaSepToSlNames(hashFindVal(raHash, "onlyDbs")); + if (hashFindVal(raHash, "notDbs")) + et->notDbs = commaSepToSlNames(hashFindVal(raHash, "notDbs")); + + char *isHttpGet = hashFindVal(raHash, "isHttpGet"); + if (isHttpGet && \ + (sameString(isHttpGet, "yes") || sameString(isHttpGet, "on") || sameString(isHttpGet, "true"))) + et->isHttpGet = TRUE; + char *maxSize = hashFindVal(raHash, "maxSize"); if (maxSize!=NULL) et->maxSize = sqlUnsignedOrError(maxSize, "Error: maxSize %s for tool %s is not a number", \ maxSize, et->tool); - et->longLabel = cloneString(getRequiredRaSetting(raHash, "longLabel", lf)); - et->url = cloneString(getRequiredRaSetting(raHash, "url", lf)); - et->dbs = NULL; - if (hashFindVal(raHash, "dbs")) - et->dbs = commaSepToSlNames(hashFindVal(raHash, "dbs")); slReverse(¶mList); et->params = paramList; slAddHead(&list, et); freeHashAndVals(&raHash); slPairFree(&raList); } if (list) slReverse(&list); lineFileClose(&lf); return list; } @@ -105,104 +121,118 @@ struct extTool *extTools = readExtToolRa("extTools.ra"); struct extTool *et; for (et = extTools; et != NULL; et = et->next) if (sameWord(et->tool, tool)) break; if (et==NULL) errAbort("No configuration found for tool %s", tool); // construct an invisible CGI form with the given parameters printf("<html><body>\n"); if (debug) printf("Target URL: %s<p>", et->url); -printf("<form id=\"redirForm\" method=\"POST\" action=\"%s\">\n", et->url); - -struct slPair *slp; -char *db = cartString(cart, "db"); -char *pos = cartString(cart, "position"); - char *chromName; int winStart, winEnd; -findGenomePos(db, pos, &chromName, &winStart, &winEnd, cart); +char *db = cartString(cart, "db"); +char *pos = cartString(cart, "position"); int len = winEnd-winStart; +findGenomePos(db, pos, &chromName, &winStart, &winEnd, cart); + +char *url = replaceInUrl(et->url, "", cart, db, chromName, winStart, winEnd, NULL, TRUE); + +printf("You're being redirected from the UCSC Genome Browser to the site %s<br>\n", url); +if (et->email) + printf("Please contact %s for questions on this tool.<br>\n", et->email); + +char *method = "POST"; +if (et->isHttpGet) + method = "GET"; + +printf("<form id=\"redirForm\" method=\"%s\" action=\"%s\">\n", method, url); + +struct slPair *slp; if (et->maxSize!=0 && len > et->maxSize) { printf("Sorry, this tool accepts only a sequence with less than %d base pairs<p>\n" "Try to zoom in some more.<p>\n", et->maxSize); return; } boolean submitDone = FALSE; for (slp=et->params; slp!=NULL; slp=slp->next) { char* val = slp->val; if (sameWord(val, "$db")) val = db; if (sameWord(val, "$position")) val = pos; if (sameWord(val, "$returnUrl")) { + // get the full URL of this hgTracks page, so external page can construct a custom track + // and link back to us char* host = getenv("HTTP_HOST"); char* reqUrl = getenv("REQUEST_URI"); struct netParsedUrl npu; netParseUrl(reqUrl, &npu); safecpy(npu.protocol, sizeof(npu.protocol), "http"); safecpy(npu.host, sizeof(npu.host), host); // remove everything after ? in URL char *e = strchr(npu.file, '?'); if (e) *e = 0; val = urlFromNetParsedUrl(&npu); } // half the current window size if (stringIn("$halfLen", val)) { char buf[64]; safef(buf, sizeof(buf), "%d", len/2); val = replaceChars(val, "$halfLen", buf); } if (sameWord(val, "$seq")) { static struct dnaSeq *seq = NULL; seq = hDnaFromSeq(db, chromName, winStart, winEnd, dnaLower); val = seq->dna; } // any remaining $-expression might be one of the general ones if (stringIn("$", val)) + { val = replaceInUrl(val, "", cart, db, chromName, winStart, winEnd, NULL, TRUE); + } // output if (debug) { printf("%s: ", slp->name); - printf("<input name=\"%s\" value=\"%s\"><p>", slp->name, val); + printf("<input name=\"%s\" value=\"%s\"><p>\n", slp->name, val); } else { // parameter named submit is a special case if (sameWord(slp->name, "submit")) { submitDone = TRUE; printf("<input type=\"submit\" value=\"%s\" style=\"position: absolute; left: -9999px; " "width: 1px; height: 1px;\">\n", val); } else - printf("<input type=\"hidden\" name=\"%s\" value=\"%s\">", slp->name, val); + printf("<input type=\"hidden\" name=\"%s\" value=\"%s\">\n", slp->name, val); } } // a hidden submit button, see // http://stackoverflow.com/questions/477691/submitting-a-form-by-pressing-enter-without-a-submit-button if (debug) printf("<input type=\"submit\">\n"); else if (!submitDone) printf("<input type=\"submit\" style=\"position: absolute; left: -9999px; width: 1px; height: 1px;\">\n"); printf("</form>\n"); // a little javascript that clicks the submit button if (!debug) printf("<script>document.getElementById(\"redirForm\").submit();</script>\n"); printf("</body></html>\n"); }