\n" " \n" " \n" " \n" " \n"); // count up the number of unlisted hubs we currently have int unlistedHubCount = 0; struct hubConnectStatus *unlistedHubList = NULL; struct hubConnectStatus *hub, *nextHub; for(hub = hubList; hub; hub = nextHub) { nextHub = hub->next; // if url is not in publicHash, it's unlisted */ if (!((publicHash != NULL) && hashLookup(publicHash, hub->hubUrl))) { unlistedHubCount++; slAddHead(&unlistedHubList, hub); } } hubList = NULL; // hubList no longer valid if (unlistedHubCount == 0) { // nothing to see here printf(""); printf("

URL: \n" " \n" "\n" "
No Unlisted Track Hubs

\n"); // if we have a trix file, draw the search box if (haveTrixFile) { puts("Enter search terms to find in public track hub description pages:
" " \n" "\n"); puts("

\n"); } // if we have search terms, put out the line telling the user so if (haveTrixFile && !isEmpty(hubSearchTerms)) { printf("Displayed list restricted by search terms: %s\n", hubSearchTerms); puts("\n"); puts("

\n"); strLower(cleanSearchTerms); urlSearchHash = getUrlSearchHash(trixFile, cleanSearchTerms); } // make sure all the public hubs are in the hubStatus table. addPublicHubsToHubStatus(conn, publicTable, statusTable); struct hash *publicHash = newHash(5); char query[512]; bool hasDescription = sqlColumnExists(conn, publicTable, "descriptionUrl"); if (hasDescription) sqlSafef(query, sizeof(query), "select p.hubUrl,p.shortLabel,p.longLabel,p.dbList,s.errorMessage,s.id,p.descriptionUrl from %s p,%s s where p.hubUrl = s.hubUrl", publicTable, statusTable); else sqlSafef(query, sizeof(query), "select p.hubUrl,p.shortLabel,p.longLabel,p.dbList,s.errorMessage,s.id from %s p,%s s where p.hubUrl = s.hubUrl", publicTable, statusTable); struct sqlResult *sr = sqlGetResult(conn, query); char **row; int count = 0; boolean gotAnyRows = FALSE; while ((row = sqlNextRow(sr)) != NULL) { ++count; char *url = row[0], *shortLabel = row[1], *longLabel = row[2], *dbList = row[3], *errorMessage = row[4], *descriptionUrl = row[6]; int id = atoi(row[5]); hashStore(publicHash, url); if ((urlSearchHash != NULL) && (hashLookup(urlSearchHash, url) == NULL)) continue; struct slName *dbListNames = slNameListFromComma(dbList); if (gotAnyRows) webPrintLinkTableNewRow(); else { /* output header */ puts("Clicking Connect redirects to the gateway page of the selected hub's default assembly.
"); printf(" " " " " " " " " " " " "\n"); // start first row printf(""); gotAnyRows = TRUE; } if (id != 0) { ourCellStart(); char hubName[32]; safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id); if (cartUsualBoolean(cart, hubName, FALSE)) printf("\n", id); else { // get first name off of list of supported databases char * name = dbListNames->name; // if the name isn't currently loaded, we assume it's a hub if (!hDbExists(name)) { char buffer[512]; safef(buffer, sizeof buffer, "hub_%d_%s", id, name); name = cloneString(buffer); } printf("\n", url,name); } ourCellEnd(); } else errAbort("cannot get id for hub with url %s\n", url); ourPrintCellLink(shortLabel, url); if (isEmpty(errorMessage)) { if (hasDescription && !isEmpty(descriptionUrl)) ourPrintCellLink(longLabel, descriptionUrl); else ourPrintCell(longLabel); } else { ourCellStart(); printf("ERROR: %s " "Debug Help", errorMessage); printf( "" , url); ourCellEnd(); } printGenomeList(dbListNames, count); } sqlFreeResult(&sr); if (gotAnyRows) printf("

Display	Hub Name	Description	Assemblies

\n"); printf("

clearing hub %s\n",url); if (url != NULL) hubClearStatus(url); else errAbort("must specify url in %s\n", hgHubDataText); printf("

Completed\n");
 }
 
 
 static void checkTrackDbs(struct hubConnectStatus *hubList)
 {
 struct hubConnectStatus *hub = hubList;
 
 for(; hub; hub = hub->next)
     {
     struct errCatch *errCatch = errCatchNew();
     if (errCatchStart(errCatch))
 	{
 	hubAddTracks(hub, database);
 	}
     errCatchEnd(errCatch);
     if (errCatch->gotError)
 	{
 	hub->errorMessage = cloneString(errCatch->message->string);
 	hubUpdateStatus( errCatch->message->string, hub);
 	}
     else
 	hubUpdateStatus(NULL, hub);
     }
 }
 
 void doMiddle(struct cart *theCart)
 /* Write header and body of html page. */
 {
 cart = theCart;
 
 if(cgiIsOnWeb())
     checkForGeoMirrorRedirect(cart);
 
 if (cartVarExists(cart, hgHubDoClear))
     {
     doClearHub(cart);
     cartWebEnd();
     return;
     }
 
 if (cartVarExists(cart, hgHubCheckUrl))
     {
     doResetHub(cart);
     }
 
 if (cartVarExists(cart, hgHubDoRedirect))
     {
     if (doRedirect(cart))
 	{
 	cartWebEnd();
 	return;
 	}
     }
 
 cartWebStart(cart, NULL, "%s", pageTitle);
 jsIncludeFile("jquery.js", NULL);
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("jquery-ui.js", NULL);
 
 webIncludeResourceFile("jquery-ui.css");
 
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("hgHubConnect.js", NULL);
 jsIncludeFile("jquery.cookie.js", NULL);
 
 printf("  \n");
 printf(
     "Track data hubs are collections of external tracks that can be imported into the UCSC Genome Browser. "
     "Hub tracks show up under the hub's own blue label bar on the main browser page, "
     "as well as on the configure page. For more information, see the "
     ""
     "User's Guide."
     "To import a public hub click its \"Connect\" button below."
     "NOTE: Because Track Hubs are created and maintained by external sources,"
     " UCSC is not responsible for their content."
    );
 printf("\n");
 
 getDbAndGenome(cart, &database, &organism, oldVars);
 
 char *survey = cfgOptionEnv("HGDB_HUB_SURVEY", "hubSurvey");
 char *surveyLabel = cfgOptionEnv("HGDB_HUB_SURVEY_LABEL", "hubSurveyLabel");
 
 if (survey && differentWord(survey, "off"))
     hPrintf("%s\n", survey, surveyLabel ? surveyLabel : "Take survey");
 hPutc('\n');
 
 // grab all the hubs that are listed in the cart
 struct hubConnectStatus *hubList =  hubConnectStatusListFromCartAll(cart);
 
 checkTrackDbs(hubList);
 
 // here's a little form for the add new hub button
 printf("\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar("hubUrl", "");
 cgiMakeHiddenVar( hgHubDoFirstDb, "on");
 cgiMakeHiddenVar( hgHubDoRedirect, "on");
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 cartSaveSession(cart);
 puts("");
 
 // this is the form for the connect hub button
 printf("\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar("hubUrl", "");
 cgiMakeHiddenVar("db", "");
 cgiMakeHiddenVar( hgHubDoRedirect, "on");
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 cartSaveSession(cart);
 puts("");
 
 // this is the form for the disconnect hub button
 printf("\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar("hubId", "");
 cgiMakeHiddenVar(hgHubDoDisconnect, "on");
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 cartSaveSession(cart);
 puts("");
 
 // this is the form for the reset hub button
 printf("\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar(hgHubCheckUrl, "");
 cartSaveSession(cart);
 puts("");
 
 // this is the form for the search hub button
 printf("\n",  "../cgi-bin/hgHubConnect");
 cgiMakeHiddenVar(hgHubSearchTerms, "");
 cgiMakeHiddenVar(hgHubDoSearch, "on");
 cartSaveSession(cart);
 puts("");
 
 // ... and now the main form
 printf("\n", "../cgi-bin/hgGateway");
 cartSaveSession(cart);
 
 // we have two tabs for the public and unlisted hubs
 printf(""
        " Public Hubs"
        "My Hubs "
        " ");
 
 struct hash *publicHash = hgHubConnectPublic();
 hgHubConnectUnlisted(hubList, publicHash);
 printf("");
 
 printf("");
 
 char *emailAddress = cfgOptionDefault("hub.emailAddress","genome@soe.ucsc.edu");
 printf(""
     "Contact %s to add a public hub."
     "\n", emailAddress,emailAddress);
 printf("");
 
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 
 printf("\n");
 puts("");
 cartWebEnd();
 }
 
 char *excludeVars[] = {"Submit", "submit", "hc_one_url", 
     hgHubCheckUrl, hgHubDoClear, hgHubDoDisconnect,hgHubDoRedirect, hgHubDataText, 
     hgHubConnectRemakeTrackHub, NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 long enteredMainTime = clock1000();
 oldVars = hashNew(10);
-setUdcCacheDir();
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 cgiExitTime("hgHubConnect", enteredMainTime);
 return 0;
 }