URL: \n" " \n" "\n" "
No Unlisted Track Hubs
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);
     }
 }
 
 int hubConnectStatusCmp(const void *va, const void *vb)
 /* Compare to sort based on shortLabel */
 {
 const struct hubConnectStatus *a = *((struct hubConnectStatus **)va);
 const struct hubConnectStatus *b = *((struct hubConnectStatus **)vb);
 struct trackHub *ta = a->trackHub;
 struct trackHub *tb = b->trackHub;
 
 if ((ta == NULL) || (tb == NULL))
     return 0;
 
 return strcasecmp(tb->shortLabel, ta->shortLabel);
 }
 
 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);
 
 printf(
 "\n"
 "\n"
 "\n"
 "\n"
 );
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("jquery-ui.js", NULL);
 webIncludeResourceFile("jquery-ui.css");
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("hgHubConnect.js", NULL);
 webIncludeResourceFile("hgHubConnect.css");
 jsIncludeFile("jquery.cookie.js", NULL);
 jsIncludeFile("spectrum.min.js", NULL);
 
 boolean doHubDevMode = cfgOptionBooleanDefault("hgHubConnect.validateHub", FALSE);
 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, including where to "
     "host your track hub, 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");
 if (doHubDevMode)
     {
     printf(" \n");
     printf("Check the configuration settings for a hub, including the settings "
         "in the hub.txt, genomes.txt, and trackDb.txt files. If there are errors in the hub "
         "setup, a heirarchal tree of tracks is presented with the errors in red text. A hub "
         "with no errors still has the tree present but needs to be clicked to be expanded to "
         " explore the track heirarchy.\n"
         "Also present are buttons to load the hub with track timing measuring turned on "
         "in order to profile slow loading tracks, and an option to disable the track caching "
         "mechanism so the Genome Browser picks up changes to the configuration files or "
         "track data files. For more information on making track hubs, please see the following links: \n "
         "
\n"
         "Track Hub Settings \n"
         "Where to host your track hub \n"
         " \n"
         "\n "
         );
     }
 
 // this variable is used by hub search and hub validate, initialize here so we don't
 // overwrite it unintentionally depending on which path the CGI takes
 jsInline("trackData = [];\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);
 
 slSort(&hubList, hubConnectStatusCmp);
 
 // 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");
 cgiMakeHiddenVar(hgHubDbFilter, "");
 cartSaveSession(cart);
 puts("");
 
 // this is the form for the validate button
 if (doHubDevMode)
     {
     printf("\n",  "../cgi-bin/hgHubConnect");
     cgiMakeHiddenVar("validateHubUrl", "");
     cgiMakeHiddenVar("measureTiming", "");
     cgiMakeHiddenVar("udcTimeout", "");
     // allows saving the old url in the search bar but not run hubCheck on it right away
     // mostly for when you come back to hgHubConnect after just looking at hgTracks
     cgiMakeHiddenVar(hgHubDoHubCheck, "off");
     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 ");
 if (doHubDevMode) // put up the validate tab if hg.conf statement present
     printf("Hub Development");
 printf(" ");
 
 struct hash *publicHash = hgHubConnectPublic();
 hgHubConnectUnlisted(hubList, publicHash);
 if (doHubDevMode)
     hgHubConnectDeveloperMode();
 // add the event listener for toggling the right description text
 jsInline(
     "var oldDesc = document.getElementById('description');\n"
     "var newDesc = document.getElementById('developerModeDescription');\n"
     "if (location.hash === \"#hubDeveloper\") {\n"
     "   toggleTwoDivs(newDesc, oldDesc);\n"
     "}\n"
     "window.addEventListener('hashchange', function() {\n"
     "   if (location.hash === \"#hubDeveloper\") {"
     "       toggleTwoDivs(newDesc, oldDesc);\n"
     "   } else {\n"
     "       toggleTwoDivs(oldDesc, newDesc);\n"
     "   }\n"
     "});\n"
     "var plusButton = document.getElementById('advancedSettingsButton');\n"
     "plusButton.addEventListener('click', function() {\n"
     "   var advancedSettingsDiv = document.getElementById('extraSettingsContainer');\n"
     "   var extraSettingsList = document.getElementById('extraSettingsList');\n"
     "   if (extraSettingsList.style.display != 'none') {\n"
     "       extraSettingsList.style.display = 'none';\n"
     "       imgTag = advancedSettingsDiv.getElementsByTagName('img')[0];\n"
     "       imgTag.src = \"../images/add_sm.gif\";\n"
     "   } else {\n"
     "       extraSettingsList.style.display = 'block';\n"
     "       imgTag = advancedSettingsDiv.getElementsByTagName('img')[0];\n"
     "       imgTag.src = \"../images/remove_sm.gif\";\n"
     "   }\n"
     "});"
     );
 printf("");
 
 printf("");
 
 printf(""
     "Contact us to add a public hub."
     "\n");
 printf("");
 
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 
 puts("");
 printf("\n");
 
 cartWebEnd();
 }
 
 char *excludeVars[] = {"Submit", "submit", "hc_one_url", hgHubDoHubCheck,
     hgHubCheckUrl, hgHubDoClear, hgHubDoDisconnect,hgHubDoRedirect, hgHubDataText, 
     hgHubConnectRemakeTrackHub, NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 long enteredMainTime = clock1000();
 oldVars = hashNew(10);
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 cgiExitTime("hgHubConnect", enteredMainTime);
 return 0;
 }