\n" " \n" " \n"); printf(" \n" " \n"); if (hubUrl == NULL) printf(" \n"); else doValidateNewHub(hubUrl); printf("

URL: \n"); if (hubUrl != NULL) { printf(" \n", hubUrl); } else { printf(" \n"); } printf("\n" "
Enter URL to hub to check settings

"); jsOnEventById("click", "hubValidateButton", "var validateText = document.getElementById('validateHubUrl');" "validateText.value=$.trim(validateText.value);" "if(validateUrl($('#validateHubUrl').val())) { " " document.validateHubForm.elements['validateHubUrl'].value=validateText.value;" " document.validateHubForm.submit(); return true; }" "else { return false; }" ); } static void addPublicHubsToHubStatus(struct sqlConnection *conn, char *publicTable, char *statusTable) /* Add urls in the hubPublic table to the hubStatus table if they aren't there already */ { char query[1024]; sqlSafef(query, sizeof(query), "select %s.hubUrl from %s left join %s on %s.hubUrl = %s.hubUrl where %s.hubUrl is NULL", publicTable, publicTable, statusTable, publicTable, statusTable, statusTable); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { char *errorMessage = NULL; char *url = row[0]; // add this url to the hubStatus table hubFindOrAddUrlInStatusTable(database, cart, url, &errorMessage); } } char *modifyTermsForHubSearch(char *hubSearchTerms, bool isStrictSearch) /* This won't exactly be pretty. MySQL treats any sequence of alphanumerics and underscores * as a word, and single apostrophes are allowed as long as they don't come back-to-back. * Cut down to those characters, then add initial + (for requiring word) and * (for word * expansion) as appropriate. */ { char *cloneTerms = cloneString(hubSearchTerms); struct dyString *modifiedTerms = dyStringNew(0); if (isNotEmpty(cloneTerms)) { int i; for (i=0; itextLength == hubSearchTextLong) && isEmpty(hst->text)) continue; char *hubUrl = hst->hubUrl; struct hubEntry *hubInfo = hashFindVal(hubLookup, hubUrl); if (hubInfo == NULL) continue; // Search table evidently includes a hub that's not on this server. Skip it. char *db = cloneString(hst->db); tolowers(db); if (isNotEmpty(dbFilter)) { if (isNotEmpty(db)) { if (stringIn(dbFilter, db) == NULL) continue; } else { // no db in the hubSearchText means this is a top-level hub hit. // filter by the db list associated with the hub instead char *dbList = cloneString(hubInfo->dbList); tolowers(dbList); if (stringIn(dbFilter, dbList) == NULL) continue; } } // Add hst to the list to be returned slAddHead(&hubSearchResultsList, hst); } slReverse(&hubSearchResultsList); return hubSearchResultsList; } void printSearchAndFilterBoxes(int searchEnabled, char *hubSearchTerms, char *dbFilter) /* Create the text boxes for search and database filtering along with the required * javscript */ { char event[4096]; if (searchEnabled) { safef(event, sizeof(event), "document.searchHubForm.elements['hubSearchTerms'].value=$('#hubSearchTerms').val();" "document.searchHubForm.elements['hubDbFilter'].value=$('#hubDbFilter').val();" "document.searchHubForm.submit();return true;"); printf("Enter search terms to find in public track hub description pages:
" " \n", hubSearchTerms!=NULL?hubSearchTerms:""); printf("
\n"); } else { safef(event, sizeof(event), "document.searchHubForm.elements['hubDbFilter'].value=$('#hubDbFilter').val();" "document.searchHubForm.submit();return true;"); } printf("Filter hubs by assembly: " " \n" "\n", hgHubDbFilter, dbFilter!=NULL?dbFilter:""); jsOnEventById("click", "hubSearchButton", event); puts("

\n"); } void printSearchTerms(char *hubSearchTerms) /* Write out a reminder about the current search terms and a note about * how to navigate detailed search results */ { printf("Displayed list restricted by search terms: %s\n", hubSearchTerms); puts("\n"); jsOnEventById("click", "hubDeleteSearchButton", "document.searchHubForm.elements['hubSearchTerms'].value='';" "document.searchHubForm.elements['hubDbFilter'].value='';" "document.searchHubForm.submit();return true;"); puts("

\n"); printf("When exploring the detailed search results for a hub, you may right-click " "on an assembly or track line to open it in a new window.\n"); puts("

\n"); } void printHubListHeader() /* Write out the header for a list of hubs in its own table */ { puts("Clicking Connect redirects to the gateway page of the selected hub's default assembly.
"); printf(" " " " " " " " " " " " "

Display	Hub Name	Description	Assemblies

\n"); } struct hash *buildPublicLookupHash(struct sqlConnection *conn, char *publicTable, char *statusTable, struct hash **pHash) /* Return a hash linking hub URLs to struct hubEntries. Also make pHash point to a hash that just stores * the names of the public hubs (for use later when determining if hubs were added by the user) */ { struct hash *hubLookup = newHash(5); struct hash *publicLookup = 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; while ((row = sqlNextRow(sr)) != NULL) { struct hubEntry *hubInfo = hubEntryTextLoad(row, hasDescription); hubInfo->tableHasDescriptionField = hasDescription; hashAddUnique(hubLookup, hubInfo->hubUrl, hubInfo); hashStore(publicLookup, hubInfo->hubUrl); } sqlFreeResult(&sr); *pHash = publicLookup; return hubLookup; } void outputPublicTableRow(struct hubEntry *hubInfo, int count) /* Prints out a table row with basic information about a hub and a button * to connect to that hub */ { int id = hubInfo->id; char jsId[256]; struct slName *dbListNames = slNameListFromComma(hubInfo->dbList); printf("\n"); if (id != 0) { ourCellStart(); char hubName[32]; safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id); if (cartUsualBoolean(cart, hubName, FALSE)) { safef(jsId, sizeof jsId, "hubDisconnectButtonP%d", count); printf("\n", jsId); jsOnEventByIdF("click", jsId, "document.disconnectHubForm.elements['hubId'].value= '%d';" "document.disconnectHubForm.submit();return true;", 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); } safef(jsId, sizeof jsId, "hubConnectButton%d", count); printf("\n", jsId); jsOnEventByIdF("click", jsId, "document.connectHubForm.elements['hubUrl'].value= '%s';" "document.connectHubForm.elements['db'].value= '%s';" "document.connectHubForm.submit();return true;", hubInfo->hubUrl,name); } ourCellEnd(); } else errAbort("cannot get id for hub with url %s\n", hubInfo->hubUrl); ourPrintCellLink(hubInfo->shortLabel, hubInfo->hubUrl); boolean hubHasNoError = isEmpty(hubInfo->errorMessage); if (hubHasNoError) { if (hubInfo->tableHasDescriptionField && !isEmpty(hubInfo->descriptionUrl)) ourPrintCellLink(hubInfo->longLabel, hubInfo->descriptionUrl); else ourPrintCell(hubInfo->longLabel); } else { ourCellStart(); printf("ERROR: %s " "Debug Help", hubInfo->errorMessage); safef(jsId, sizeof jsId, "hubClearButton%d", count); printf( "" , jsId); jsOnEventByIdF("click", jsId, "document.resetHubForm.elements['hubCheckUrl'].value='%s';" "document.resetHubForm.submit();return true;", hubInfo->hubUrl); ourCellEnd(); } printGenomeList(hubInfo->hubUrl, dbListNames, count, hubHasNoError); printf("\n"); } void printSearchOutputForTrack(struct tdbOutputStructure *tdbOut) /* Write out a

entry for a search hit on a track, along with a nested *

\n", dyStringContents(tdbOut->configUrl)); printf("%s", dyStringContents(tdbOut->shortLabel)); if (tdbOut->childCount > 0) printf(" (%d subtrack%s)", tdbOut->childCount, tdbOut->childCount==1?"":"s"); if (isNotEmpty(dyStringContents(tdbOut->metaTags))) { printf("
Metadata: %s\n", dyStringContents(tdbOut->metaTags)); } if (isNotEmpty(dyStringContents(tdbOut->descriptionMatch))) { printf("
Description: %s\n", dyStringContents(tdbOut->descriptionMatch)); } if (tdbOut->children != NULL) { struct tdbOutputStructure *child = tdbOut->children; printf("
\n"); } printf("
, with a nested ul * element for hits to tracks within that genome */ { printf("
%s", dyStringContents(genomeOut->assemblyLink), dyStringContents(genomeOut->shortLabel)); if (genomeOut->trackCount > 0) printf(" (%d track%s)", genomeOut->trackCount, genomeOut->trackCount==1?"":"s"); if (isNotEmpty(dyStringContents(genomeOut->metaTags))) { printf("
%s\n", dyStringContents(genomeOut->metaTags)); } if (isNotEmpty(dyStringContents(genomeOut->descriptionMatch))) { printf("
\nAssembly Description: %s\n", dyStringContents(genomeOut->descriptionMatch)); } if (genomeOut->tracks != NULL) { printf("
\n"); } printf("

\n"); printf("

Search details ...\n
- Hub Description: %s
- %d Matching Assembl%s\n

\n"); printf("\n"); struct slName *thisHubName = NULL; for (thisHubName = hubsToPrint; thisHubName != NULL; thisHubName = thisHubName->next) { struct hubEntry *hubInfo = (struct hubEntry *) hashFindVal(hubLookup, thisHubName->name); if (hubInfo == NULL) { continue; } printOutputForHub(hubInfo, NULL, count); count++; } printf("

\n"); printf("

\n"); char *hubSearchTableName = cfgOptionDefault("hubSearchTextTable", "hubSearchText"); int searchEnabled = sqlTableExists(conn, hubSearchTableName); printSearchAndFilterBoxes(searchEnabled, hubSearchTerms, dbFilter); struct hash *searchResultHash = NULL; struct slName *hubsToPrint = NULL; if (searchEnabled && !isEmpty(hubSearchTerms)) { printSearchTerms(hubSearchTerms); // Forcing checkDescriptions to TRUE right now, but we might want to add this as a // checkbox option for users in the near future. bool checkDescriptions = TRUE; struct hubSearchText *hubSearchResults = getHubSearchResults(conn, hubSearchTableName, hubSearchTerms, checkDescriptions, lcDbFilter, hubLookup); searchResultHash = newHash(5); struct hubSearchText *hst = hubSearchResults; while (hst != NULL) { struct hubSearchText *nextHst = hst->next; hst->next = NULL; struct hashEl *hubHashEnt = hashLookup(searchResultHash, hst->hubUrl); if (hubHashEnt == NULL) { slNameAddHead(&hubsToPrint, hst->hubUrl); hashAdd(searchResultHash, hst->hubUrl, hst); } else slAddHead(&(hubHashEnt->val), hst); hst = nextHst; } struct hashEl *hel; struct hashCookie cookie = hashFirst(searchResultHash); while ((hel = hashNext(&cookie)) != NULL) slReverse(&(hel->val)); } else { // There is no active search, so just add all hubs to the list struct hashEl *hel; struct hashEl *helList; helList = hashElListHash(hubLookup); for (hel = helList; hel != NULL; hel = hel->next) { if (isNotEmpty(lcDbFilter)) { struct hubEntry *hubEnt = (struct hubEntry *) hel->val; char *lcDbList = cloneString(hubEnt->dbList); if (isNotEmpty(lcDbList)) tolowers(lcDbList); if ((lcDbList == NULL) || (stringIn(lcDbFilter, lcDbList) == NULL)) continue; } slNameAddHead(&hubsToPrint, hel->name); } } slReverse(&hubsToPrint); printHubList(hubsToPrint, hubLookup, searchResultHash); printf("