ac0d694dd1b7a53bd182b9555048eaa3fb0bf512 braney Sun Jun 2 14:31:20 2019 -0700 sort myHub list alphabetically by shortLabel diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c index 72dd40b..f89faa8 100644 --- src/hg/hgHubConnect/hgHubConnect.c +++ src/hg/hgHubConnect/hgHubConnect.c @@ -1,1743 +1,1756 @@ /* hgHubConnect - the CGI web-based program to select track data hubs to connect with. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "errAbort.h" #include "errCatch.h" #include "hCommon.h" #include "dystring.h" #include "jksql.h" #include "cheapcgi.h" #include "htmshell.h" #include "hdb.h" #include "hui.h" #include "cart.h" #include "dbDb.h" #include "web.h" #include "trackHub.h" #include "hubConnect.h" #include "dystring.h" #include "hPrint.h" #include "jsHelper.h" #include "obscure.h" #include "hgConfig.h" #include "trix.h" #include "net.h" #include "hubSearchText.h" struct cart *cart; /* The user's ui state. */ struct hash *oldVars = NULL; static char *pageTitle = "Track Data Hubs"; char *database = NULL; char *organism = NULL; struct hubOutputStructure { struct hubOutputStructure *next; struct dyString *metaTags; struct dyString *descriptionMatch; struct genomeOutputStructure *genomes; int genomeCount; struct hash *genomeOutHash; }; struct genomeOutputStructure { struct genomeOutputStructure *next; struct dyString *shortLabel; struct dyString *metaTags; struct dyString *descriptionMatch; struct tdbOutputStructure *tracks; struct dyString *assemblyLink; char *genomeName; char *positionString; int trackCount; struct hash *tdbOutHash; int hitCount; }; struct tdbOutputStructure { struct tdbOutputStructure *next; struct dyString *shortLabel; struct dyString *metaTags; struct dyString *descriptionMatch; struct dyString *configUrl; struct tdbOutputStructure *children; int childCount; }; struct hubEntry // for entries pulled from hubPublic { struct hubEntry *next; char *hubUrl; char *shortLabel; char *longLabel; char *dbList; char *errorMessage; int id; char *descriptionUrl; bool tableHasDescriptionField; }; struct hubEntry *hubEntryTextLoad(char **row, bool hasDescription) { struct hubEntry *ret; AllocVar(ret); ret->hubUrl = cloneString(row[0]); ret->shortLabel = cloneString(row[1]); ret->longLabel = cloneString(row[2]); ret->dbList = cloneString(row[3]); ret->errorMessage = cloneString(row[4]); ret->id = sqlUnsigned(row[5]); if (hasDescription) ret->descriptionUrl = cloneString(row[6]); else ret->descriptionUrl = NULL; return ret; } static void ourCellStart() { fputs("<TD>", stdout); // do not add a newline } static void ourCellEnd() { puts("</TD>"); } static void ourPrintCellLink(char *str, char *url) { ourCellStart(); printf("<A class=\"cv\" HREF=\"%s\" TARGET=_BLANK>\n", url); if (str != NULL) fputs(str, stdout); // do not add a newline -- was causing trailing blanks get copied in cut and paste puts("</A>"); ourCellEnd(); } static void ourPrintCell(char *str) { ourCellStart(); if (str != NULL) fputs(str, stdout); // do not add a newline -- was causing trailing blanks get copied in cut and paste ourCellEnd(); } static char *removeLastComma(char *string) { if (string != NULL) { int len = strlen(string); if ( string[len - 1] == ',') string[len - 1] = 0; else if (len > 2 && endsWith(string,", ")) string[len - 2] = 0; } return string; } #define GENLISTWIDTH 40 static void printGenomeList(char *hubUrl, struct slName *genomes, int row, boolean withLink) /* print supported assembly names from sl list */ { struct dyString *dyHtml = newDyString(1024); struct dyString *dyShortHtml = newDyString(1024); // create two strings: one shortened to GENLISTWIDTH characters // and another one with all genomes int charCount = 0; struct slName *genome = genomes; for(; genome; genome = genome->next) { char *trimmedName = trackHubSkipHubName(genome->name); char *shortName = cloneString(trimmedName); // If even the first element is too long, truncate its short name. if (genome==genomes && strlen(trimmedName) > GENLISTWIDTH) shortName[GENLISTWIDTH] = 0; // append to dyShortHtml if necessary if (charCount == 0 || (charCount+strlen(trimmedName)<=GENLISTWIDTH)) { if (withLink) dyStringPrintf(dyShortHtml,"<a title='Connect hub and open the %s assembly' href='hgTracks?hubUrl=%s&genome=%s'>%s</a>" , genome->name, hubUrl, genome->name, shortName); else dyStringPrintf(dyShortHtml,"%s" , shortName); dyStringPrintf(dyShortHtml,", "); } freeMem(shortName); charCount += strlen(trimmedName); // always append to dyHtml if (withLink) dyStringPrintf(dyHtml,"<a title='Connect hub and open the %s assembly' href='hgTracks?hubUrl=%s&genome=%s'>%s</a>" , genome->name, hubUrl, genome->name, trimmedName); else dyStringPrintf(dyHtml,"%s" , trimmedName); if (genome->next) { dyStringPrintf(dyHtml,", "); } } char *longHtml = dyStringCannibalize(&dyHtml); char *shortHtml = dyStringCannibalize(&dyShortHtml); shortHtml = removeLastComma(shortHtml); if (charCount < GENLISTWIDTH) ourPrintCell(shortHtml); else { char id[256]; char tempHtml[1024+strlen(longHtml)+strlen(shortHtml)]; safef(tempHtml, sizeof tempHtml, "<span id=Short%d><span style='cursor:default' id='Short%dPlus'>[+] </span>%s...</span>" "<span id=Full%d style=\"display:none\"><span style='cursor:default' id='Full%dMinus'>[-]<br></span>%s</span>" , row, row, shortHtml , row, row, longHtml); safef(id, sizeof id, "Short%dPlus", row); jsOnEventByIdF("click", id, "document.getElementById('Short%d').style.display='none';" "document.getElementById('Full%d').style.display='inline';" "return false;" , row, row); safef(id, sizeof id, "Full%dMinus", row); jsOnEventByIdF("click", id, "document.getElementById('Full%d').style.display='none';" "document.getElementById('Short%d').style.display='inline';" "return false;" , row, row); ourPrintCell(tempHtml); } freeMem(longHtml); freeMem(shortHtml); } static void printGenomes(struct trackHub *thub, int row, boolean withLink) /* print supported assembly names from trackHub */ { /* List of associated genomes. */ struct trackHubGenome *genomes = thub->genomeList; struct slName *list = NULL, *el; for(; genomes; genomes = genomes->next) { el = slNameNew(genomes->name); slAddHead(&list, el); } slReverse(&list); printGenomeList(thub->url, list, row, withLink); } static void hgHubConnectUnlisted(struct hubConnectStatus *hubList, struct hash *publicHash) /* Put up the list of unlisted hubs and other controls for the page. */ /* uses publicHash to distingusih public hubs from unlisted ones */ /* NOTE: Destroys hubList */ { // put out the top of our page printf("<div id=\"unlistedHubs\" class=\"hubList\"> \n" "<table id=\"unlistedHubsTable\"> \n" "<thead><tr> \n" "<th colspan=\"6\" id=\"addHubBar\"><label for=\"hubUrl\">URL:</label> \n" "<input name=\"hubText\" id=\"hubUrl\" class=\"hubField\" " "type=\"text\" size=\"65\"> \n" "<input name=\"hubAddButton\" id='hubAddButton' " "class=\"hubField\" type=\"button\" value=\"Add Hub\">\n" "</th> \n" "</tr> \n"); jsOnEventById("click", "hubAddButton", "var hubText = document.getElementById('hubUrl');" "hubText.value=$.trim(hubText.value);" "if(validateUrl($('#hubUrl').val())) { " " document.addHubForm.elements['hubUrl'].value=hubText.value;" " document.addHubForm.submit(); return true; } " "else { return false; }" ); // 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("<tr><td>No Unlisted Track Hubs</td></tr>"); printf("</thead></table></div>"); return; } // time to output the big table. First the header printf( "<tr> " "<th>Display</th> " "<th>Hub Name</th> " "<th>Description</th> " "<th>Assemblies</th> " "</tr>\n" "</thead>\n"); // start first row printf("<tbody>"); char id[256]; int count = 0; for(hub = unlistedHubList; hub; hub = hub->next) { char hubName[64]; safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, hub->id); if (!cartUsualBoolean(cart, hubName, FALSE)) continue; if (count) webPrintLinkTableNewRow(); // ends last row and starts a new one count++; puts("<tr>"); ourCellStart(); safef(id, sizeof id, "hubDisconnectButtonU%d", count); printf("<input name=\"hubDisconnectButton\" id='%s' " "class=\"hubDisconnectButton\" type=\"button\" value=\"Disconnect\">\n", id); jsOnEventByIdF("click", id, "document.disconnectHubForm.elements['hubId'].value='%d';" "document.disconnectHubForm.submit(); return true;", hub->id); ourCellEnd(); if (hub->trackHub != NULL) { ourPrintCellLink(hub->trackHub->shortLabel, hub->hubUrl); } else ourPrintCell(""); boolean hubHasError = (!isEmpty(hub->errorMessage)); if (hubHasError) { ourCellStart(); printf("<span class=\"hubError\">ERROR: %s </span>" "<a TARGET=_BLANK href=\"../goldenPath/help/hgTrackHubHelp.html#Debug\">Debug Help</a>\n", hub->errorMessage); safef(id, sizeof id, "hubClearButton%d", count); // give people a chance to clear the error printf("<input name=\"hubClearButton\" id='%s' " "class=\"hubButton\" type=\"button\" value=\"Retry Hub\">" , id); jsOnEventByIdF("click", id, "document.resetHubForm.elements['hubCheckUrl'].value='%s';" "document.resetHubForm.submit(); return true;", hub->hubUrl); ourCellEnd(); } else if (hub->trackHub != NULL) { if (hub->trackHub->descriptionUrl != NULL) ourPrintCellLink(hub->trackHub->longLabel, hub->trackHub->descriptionUrl); else ourPrintCell(hub->trackHub->longLabel); } else ourPrintCell(""); if (hub->trackHub != NULL) printGenomes(hub->trackHub, count, !hubHasError); else ourPrintCell(""); puts("</tr>"); } printf("</tbody></TABLE>\n"); printf("</div>"); } int doCheckTrackDb(struct dyString *errors, struct trackHub *hub, struct trackHubGenome *genome) /* Attempt to open a trackDb from a hub and report errors back. * Eventually will check every stanza and not die if there's an error with the first one*/ { int errorCount = 0; struct trackDb *tdb = NULL, *tdbList = NULL; struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { tdbList = trackHubTracksForGenome(hub, genome); tdbList = trackDbLinkUpGenerations(tdbList); tdbList = trackDbPolishAfterLinkup(tdbList, genome->name); trackHubPolishTrackNames(genome->trackHub, tdbList); for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { struct errCatch *trackFileCatch = errCatchNew(); if (errCatchStart(trackFileCatch)) hubCheckBigDataUrl(hub, genome, tdb); errCatchEnd(trackFileCatch); if (trackFileCatch->gotError) { errorCount += 1; dyStringPrintf(errors, "<ul>\n<li>track name: %s\n", tdb->track); dyStringPrintf(errors, "<ul>\n<li><span class=\"hubError\"><b>bigDataUrl error</b>: %s</span></li></ul></ul>\n", trackFileCatch->message->string); } errCatchFree(&trackFileCatch); } if (tdbList != NULL && errorCount == 0) { dyStringPrintf(errors, "<ul>\n<li>No errors found</li>\n</ul></ul>"); } } errCatchEnd(errCatch); if (errCatch->gotError) { errorCount += 1; dyStringPrintf(errors, "<ul><li><span class=\"hubError\">Error: %s</span></li></ul>\n", errCatch->message->string); } errCatchFree(&errCatch); return errorCount; } int doCheckGenomesFile(struct dyString *errors, struct trackHub *hub) /* Mostly just calls doCheckTrackDb() but applies correct styling to error messages */ { struct trackHubGenome *genome = NULL; int errorCount = 0; int trackDbErrorCount = 0; struct dyString *trackDbErrorString = dyStringNew(0); for (genome = hub->genomeList; genome != NULL; genome = genome->next) { trackDbErrorCount = 0; dyStringPrintf(errors, "<ul>\n<li>genome %s", genome->name); // check each track for this genome trackDbErrorCount = doCheckTrackDb(trackDbErrorString, hub, genome); errorCount += trackDbErrorCount; if (trackDbErrorCount > 0) { if (trackDbErrorCount == 1) dyStringPrintf(errors, " (%d error)\n%s</ul>\n", trackDbErrorCount, trackDbErrorString->string); else dyStringPrintf(errors, " (%d errors)\n%s</ul>\n", trackDbErrorCount, trackDbErrorString->string); } else dyStringPrintf(errors, "<ul><li>No trackDb errors</ul></ul>"); dyStringClear(trackDbErrorString); } dyStringFree(&trackDbErrorString); return errorCount; } struct trackHub *trackHubCheckHubFile(struct dyString *errors, char *hubUrl) /* Wrap trackHubOpen in an errCatch, HTML style the error message */ { struct trackHub *hub = NULL; struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) hub = trackHubOpen(hubUrl, ""); errCatchEnd(errCatch); if (errCatch->gotError) dyStringPrintf(errors, "<span class=\"hubError\">Error: %s", errCatch->message->string); errCatchFree(&errCatch); return hub; } void doValidateNewHub(char *hubUrl) /* Open up a track hub and report errors to user. */ { struct trackHub *hub = NULL; struct dyString *errors = dyStringNew(0); // string with HTML of all the errors udcSetCacheTimeout(1); printf("<tr><td>"); hub = trackHubCheckHubFile(errors, hubUrl); if (hub) { // go through each genome and check each trackDb stanza, building up errors string int errorCount = doCheckGenomesFile(errors, hub); if (errorCount > 0) { printf("<div style=\"text-align: left\" class=\"hubTdbTree\">"); if (errorCount == 1) printf("<ul>\n<li>Found %d error in %s<ul><li>hub name: \"%s\"\n", errorCount, hub->url, hub->shortLabel); else printf("<ul>\n<li>Found %d errors in %s<ul><li>hub name: \"%s\"\n", errorCount, hub->url, hub->shortLabel); printf("%s", errors->string); printf("</ul>\n"); } else printf("<div>No configuration errors for hub: %s</div>", hub->shortLabel); } else { printf("<div>%s</div>", errors->string); } dyStringFree(&errors); printf("</div></td></tr>"); } void hgHubConnectValidateNewHub() { // put out the top of our page char *hubUrl = cartOptionalString(cart, "validateHubUrl"); printf("<div id=\"validateHub\" class=\"hubList\"> \n" "<table id=\"validateHub\"> \n" "<thead><tr> \n"); printf("<th colspan=\"6\" id=\"addHubBar\"><label for=\"validateHubUrl\">URL:</label> \n"); if (hubUrl != NULL) { printf("<input name=\"validateText\" id=\"validateHubUrl\" class=\"hubField\" " "type=\"text\" size=\"65\" value=\"%s\"> \n", hubUrl); } else { printf("<input name=\"validateText\" id=\"validateHubUrl\" class=\"hubField\" " "type=\"text\" size=\"65\"> \n"); } printf("<input name=\"hubValidateButton\" id='hubValidateButton' " "class=\"hubField\" type=\"button\" value=\"Validate Hub\">\n" "</th> \n" "</tr> \n"); if (hubUrl == NULL) printf("<tr><td>Enter URL to hub to check settings</td></tr> \n"); else doValidateNewHub(hubUrl); printf("</table>"); 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; i<strlen(cloneTerms); i++) { // allowed punctuation is underscore and apostrophe, and we'll do special handling for hyphen if (!isalnum(cloneTerms[i]) && cloneTerms[i] != '_' && cloneTerms[i] != '\'' && cloneTerms[i] != '-') cloneTerms[i] = ' '; } char *splitTerms[1024]; int termCount = chopByWhite(cloneTerms, splitTerms, sizeof(splitTerms)); for (i=0; i<termCount; i++) { char *hyphenatedTerms[1024]; int hyphenTerms = chopString(splitTerms[i], "-", hyphenatedTerms, sizeof(hyphenatedTerms)); int j; for (j=0; j<hyphenTerms-1; j++) { dyStringPrintf(modifiedTerms, "+%s ", hyphenatedTerms[j]); } if (isStrictSearch) dyStringPrintf(modifiedTerms, "+%s ", hyphenatedTerms[j]); else { dyStringPrintf(modifiedTerms, "+%s* ", hyphenatedTerms[j]); } } } return dyStringCannibalize(&modifiedTerms); } struct hubSearchText *getHubSearchResults(struct sqlConnection *conn, char *hubSearchTableName, char *hubSearchTerms, bool checkLongText, char *dbFilter, struct hash *hubLookup) /* Find hubs, genomes, and tracks that match the provided search terms. * Return all hits that satisfy the (optional) supplied assembly filter. * if checkLongText is FALSE, skip searching within the long description text entries */ { char *cleanSearchTerms = cloneString(hubSearchTerms); if (isNotEmpty(cleanSearchTerms)) tolowers(cleanSearchTerms); bool isStrictSearch = FALSE; char *modifiedSearchTerms = modifyTermsForHubSearch(cleanSearchTerms, isStrictSearch); struct hubSearchText *hubSearchResultsList = NULL; struct dyString *query = dyStringNew(100); char *noLongText = NULL; if (!checkLongText) noLongText = cloneString("textLength = 'Short' and"); else noLongText = cloneString(""); sqlDyStringPrintf(query, "select * from %s where %s match(text) against ('%s' in boolean mode)" " order by match(text) against ('%s' in boolean mode)", hubSearchTableName, noLongText, modifiedSearchTerms, modifiedSearchTerms); struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query)); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct hubSearchText *hst = hubSearchTextLoadWithNullGiveContext(row, cleanSearchTerms); // Skip rows where the long text matched the more lax MySQL search (punctuation just // splits terms into two words, so "rna-seq" finds "rna" and "seq" separately, but // not the more strict rules used to find context for the search terms. if ((hst->textLength == 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:<BR>" "<input name=\"hubSearchTerms\" id=\"hubSearchTerms\" class=\"hubField\" " "type=\"text\" size=\"65\" value=\"%s\"> \n", hubSearchTerms!=NULL?hubSearchTerms:""); printf("<br>\n"); } else { safef(event, sizeof(event), "document.searchHubForm.elements['hubDbFilter'].value=$('#hubDbFilter').val();" "document.searchHubForm.submit();return true;"); } printf("Filter hubs by assembly: " "<input name=\"%s\" id=\"hubDbFilter\" class=\"hubField\" " "type=\"text\" size=\"10\" value=\"%s\"> \n" "<input name=\"hubSearchButton\" id='hubSearchButton' " "class=\"hubField\" type=\"button\" value=\"Search Public Hubs\">\n", hgHubDbFilter, dbFilter!=NULL?dbFilter:""); jsOnEventById("click", "hubSearchButton", event); puts("<br><br>\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 <B>restricted by search terms:</B> %s\n", hubSearchTerms); puts("<input name=\"hubDeleteSearchButton\" id='hubDeleteSearchButton' " "class=\"hubField\" type=\"button\" value=\"Show All Hubs\">\n"); jsOnEventById("click", "hubDeleteSearchButton", "document.searchHubForm.elements['hubSearchTerms'].value='';" "document.searchHubForm.elements['hubDbFilter'].value='';" "document.searchHubForm.submit();return true;"); puts("<BR><BR>\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("<BR><BR>\n"); } void printHubListHeader() /* Write out the header for a list of hubs in its own table */ { puts("<I>Clicking Connect redirects to the gateway page of the selected hub's default assembly.</I><BR>"); printf("<table id=\"publicHubsTable\" class=\"hubList\"> " "<thead><tr> " "<th>Display</th> " "<th>Hub Name</th> " "<th>Description</th> " "<th>Assemblies</th> " "</tr></thead></table>\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("<tr>\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("<input name=\"hubDisconnectButton\" id='%s' " "class=\"hubDisconnectButton\" type=\"button\" value=\"Disconnect\">\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("<input name=\"hubConnectButton\" id='%s' " "class=\"hubButton\" type=\"button\" value=\"Connect\">\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("<span class=\"hubError\">ERROR: %s </span>" "<a href=\"../goldenPath/help/hgTrackHubHelp.html#Debug\">Debug Help</a>", hubInfo->errorMessage); safef(jsId, sizeof jsId, "hubClearButton%d", count); printf( "<input name=\"hubClearButton\" id='%s' " "class=\"hubButton\" type=\"button\" value=\"Retry Hub\">" , 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("</tr>\n"); } void printSearchOutputForTrack(struct tdbOutputStructure *tdbOut) /* Write out a <li> entry for a search hit on a track, along with a nested * <ul> for any included hits to subtracks */ { printf("<li configLink='%s' nodeType='track'>\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("<br><span class='descriptionMatch'><em>Metadata: %s</em></span>\n", dyStringContents(tdbOut->metaTags)); } if (isNotEmpty(dyStringContents(tdbOut->descriptionMatch))) { printf("<br><span class='descriptionMatch'><em>Description: %s</em></span>\n", dyStringContents(tdbOut->descriptionMatch)); } if (tdbOut->children != NULL) { struct tdbOutputStructure *child = tdbOut->children; printf("<ul>\n"); while (child != NULL) { printSearchOutputForTrack(child); child = child->next; } printf("</ul>\n"); } printf("</li>\n"); } void printSearchOutputForGenome(struct genomeOutputStructure *genomeOut) /* Write out a chunk of search results for a genome as a <li>, with a nested ul * element for hits to tracks within that genome */ { printf("<li assemblyLink='%s' nodeType='assembly'>%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("<br><span class='descriptionMatch'><em>%s</em></span>\n", dyStringContents(genomeOut->metaTags)); } if (isNotEmpty(dyStringContents(genomeOut->descriptionMatch))) { printf("<br>\n<em>Assembly Description:</em> %s\n", dyStringContents(genomeOut->descriptionMatch)); } if (genomeOut->tracks != NULL) { printf("<ul>\n"); struct tdbOutputStructure *tdbOut = genomeOut->tracks; while (tdbOut != NULL) { printSearchOutputForTrack(tdbOut); tdbOut = tdbOut->next; } printf("</ul>\n"); } printf("</li>\n"); } struct trackHub *fetchTrackHub(struct hubEntry *hubInfo) /* Fetch the hub structure for a public hub, trapping the error * if the hub cannot be reached */ { struct errCatch *errCatch = errCatchNew(); struct trackHub *hub = NULL; if (errCatchStart(errCatch)) { char hubName[4096]; safef(hubName, sizeof(hubName), "hub_%d", hubInfo->id); hub = trackHubOpen(hubInfo->hubUrl, hubName); } errCatchEnd(errCatch); if (errCatch->gotError) { fprintf(stderr, "%s\n", errCatch->message->string); } errCatchFree(&errCatch); return hub; } struct tdbOutputStructure *addOrUpdateTrackOut(char *track, struct genomeOutputStructure *genomeOut, struct hash *tdbHash, struct trackHub *hub) /* If an output structure already exists for the track within genomeOut, return that. Otherwise, * create one for it and add it to genomeOut. Any missing parent tracks are also added at * the same time. * tdbHash takes track names to the struct trackDb * for that track */ { struct tdbOutputStructure *tdbOut = hashFindVal(genomeOut->tdbOutHash, track); if (tdbOut == NULL) { genomeOut->trackCount++; AllocVar(tdbOut); tdbOut->shortLabel = dyStringNew(0); tdbOut->metaTags = dyStringNew(0); tdbOut->descriptionMatch = dyStringNew(0); tdbOut->configUrl = dyStringNew(0); struct trackDb *trackInfo = (struct trackDb *) hashFindVal(tdbHash, track); if (trackInfo == NULL) { // Some tracks are prefixed with the hub name; try that char withHubName[4096]; safef(withHubName, sizeof(withHubName), "%s_%s", hub->name, track); trackInfo = hashFindVal(tdbHash, withHubName); if (trackInfo == NULL) { warn("Error: Unable to locate info for matching track '%s'. Skipping ...\n", withHubName); return NULL; } } if (isNotEmpty(trackInfo->longLabel)) dyStringPrintf(tdbOut->shortLabel, "%s", trackInfo->longLabel); else if (isNotEmpty(trackInfo->shortLabel)) dyStringPrintf(tdbOut->shortLabel, "%s", trackInfo->shortLabel); else dyStringPrintf(tdbOut->shortLabel, "%s", trackHubSkipHubName(trackInfo->track)); if (tdbIsCompositeView(trackInfo) || tdbIsCompositeChild(trackInfo)) { struct trackDb *parentTdb = tdbGetComposite(trackInfo); dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s", hub->url, genomeOut->genomeName, parentTdb->track, cartSessionId(cart), genomeOut->positionString); } else { dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s", hub->url, genomeOut->genomeName, trackInfo->track, cartSessionId(cart), genomeOut->positionString); } if (trackInfo->parent != NULL) { struct trackDb *parent = trackInfo->parent; struct tdbOutputStructure *parentOut = addOrUpdateTrackOut(parent->track, genomeOut, tdbHash, hub); if (parentOut != NULL) { // addOrUpdateTrackOut only returns NULL if it can't find the parent here. // This probably means the trackDb is corrupted, which should have already // generated a fatal error. All the same ... slAddTail(&(parentOut->children), tdbOut); parentOut->childCount++; } else { // If we can't find the track's rightful parent, we can't report its position // in the track hierarchy accurately. Time to abort. A warning will already // have been generated by addOrUpdateTrackOut(parent) failing. return NULL; } } else // No parent track, so add it to the root level track list for output slAddTail(&(genomeOut->tracks), tdbOut); hashAdd(genomeOut->tdbOutHash, track, tdbOut); } return tdbOut; } void buildTdbHash(struct hash *tdbHash, struct trackDb *tdbList) /* Recursively add all tracks from tdbList to the hash (indexed by track), * along with all parents and children of those tracks */ { struct trackDb *tdb = tdbList; while (tdb != NULL) { hashAdd(tdbHash, tdb->track, tdb); if (tdb->subtracks != NULL) buildTdbHash(tdbHash, tdb->subtracks); if (tdb->parent != NULL) { // supertracks might be omitted from tdbList, but are still referred to by parent links if (hashFindVal(tdbHash, tdb->parent->track) == NULL) hashAdd(tdbHash, tdb->parent->track, tdb->parent); } tdb = tdb->next; } } char *getPositionStringForDb(struct trackHubGenome *genome) { char positionVar[1024]; safef(positionVar, sizeof(positionVar), "position.%s", genome->name); char *position = cartOptionalString(cart, positionVar); if (position == NULL) { struct dyString *tmp = dyStringCreate("position="); if (genome->defaultPos != NULL) dyStringAppend(tmp, genome->defaultPos); else dyStringAppend(tmp, hDefaultPos(genome->name)); // memory leak from hDefaultPos return value position = dyStringCannibalize(&tmp); } return position; } struct hubOutputStructure *buildHubSearchOutputStructure(struct trackHub *hub, struct hubSearchText *searchResults) /* Build a structure that contains the data for writing out the hub search results for this hub */ { struct hash *missingGenomes = hashNew(0); struct hubOutputStructure *hubOut = NULL; AllocVar(hubOut); hubOut->metaTags = dyStringNew(0); hubOut->descriptionMatch = dyStringNew(0); hubOut->genomeOutHash = newHash(5); struct hash *tdbHashHash = newHash(5); // takes genome names to trackDb hashes struct hubSearchText *hst = NULL; for (hst = searchResults; hst != NULL; hst = hst->next) { if (isEmpty(hst->db)) { // must be a hit to the hub itself, not an assembly or track within it if (hst->textLength == hubSearchTextLong) { dyStringPrintf(hubOut->descriptionMatch, "%s", hst->text); } else if (hst->textLength == hubSearchTextMeta) { if (isNotEmpty(dyStringContents(hubOut->metaTags))) dyStringPrintf(hubOut->metaTags, ", %s", hst->text); else dyStringPrintf(hubOut->metaTags, "%s", hst->text); } continue; } char *db = cloneString(hst->db); if (hashLookup(missingGenomes, db) != NULL) continue; struct trackHubGenome *genome = hashFindVal(hub->genomeHash, db); if (genome == NULL) { // assembly hub genomes are stored with a prefix; try that char withHubName[4096]; safef(withHubName, sizeof(withHubName), "%s_%s", hub->name, db); genome = hashFindVal(hub->genomeHash, withHubName); if (genome == NULL) { hashStoreName(missingGenomes, db); warn("Error: Unable to find info for matching assembly '%s'. Skipping ...\n", withHubName); continue; } } struct genomeOutputStructure *genomeOut = hashFindVal(hubOut->genomeOutHash, db); if (genomeOut == NULL) { AllocVar(genomeOut); genomeOut->tdbOutHash = newHash(5); genomeOut->metaTags = dyStringNew(0); genomeOut->descriptionMatch = dyStringNew(0); genomeOut->shortLabel = dyStringNew(0); genomeOut->assemblyLink = dyStringNew(0); genomeOut->positionString = getPositionStringForDb(genome); dyStringPrintf(genomeOut->assemblyLink, "../cgi-bin/hgTracks?hubUrl=%s&db=%s&hgsid=%s&%s", hub->url, genome->name, cartSessionId(cart), genomeOut->positionString); char *name = trackHubSkipHubName(genome->name); if (isNotEmpty(genome->description)) dyStringPrintf(genomeOut->shortLabel, "%s (%s)", genome->description, name); else if (isNotEmpty(genome->organism)) dyStringPrintf(genomeOut->shortLabel, "%s %s", genome->organism, name); else dyStringPrintf(genomeOut->shortLabel, "%s", name); genomeOut->genomeName = cloneString(genome->name); hashAdd(hubOut->genomeOutHash, db, genomeOut); slAddTail(&(hubOut->genomes), genomeOut); hubOut->genomeCount++; } if (isEmpty(hst->track)) { if (hst->textLength == hubSearchTextLong) // Genome description match dyStringPrintf(genomeOut->descriptionMatch, "%s", hst->text); else if (hst->textLength == hubSearchTextMeta) { if (isNotEmpty(dyStringContents(genomeOut->metaTags))) dyStringPrintf(genomeOut->metaTags, ", %s", hst->text); else dyStringPrintf(genomeOut->metaTags, "%s", hst->text); } } if (isNotEmpty(hst->track)) { // Time to add a track! (or add info to one, maybe) struct hash *tdbHash = (struct hash *) hashFindVal(tdbHashHash, db); if (tdbHash == NULL) { tdbHash = newHash(5); hashAdd(tdbHashHash, db, tdbHash); struct trackDb *tdbList = trackHubTracksForGenome(hub, genome); tdbList = trackDbLinkUpGenerations(tdbList); tdbList = trackDbPolishAfterLinkup(tdbList, db); trackHubPolishTrackNames(hub, tdbList); buildTdbHash(tdbHash, tdbList); } struct tdbOutputStructure *tdbOut = addOrUpdateTrackOut(hst->track, genomeOut, tdbHash, hub); if (tdbOut != NULL) { if (hst->textLength == hubSearchTextLong) dyStringPrintf(tdbOut->descriptionMatch, "%s", hst->text); else if (hst->textLength == hubSearchTextMeta) { if (isNotEmpty(dyStringContents(tdbOut->metaTags))) dyStringPrintf(tdbOut->metaTags, ", %s", hst->text); else dyStringPrintf(tdbOut->metaTags, "%s", hst->text); } } } } return hubOut; } static void printOutputForHub(struct hubEntry *hubInfo, struct hubSearchText *hubSearchResult, int count) /* Given a hub's info and a structure listing the search hits within the hub, first print * a basic line of hub information with a "connect" button. Then, if the search results * are non-NULL, write out information about the genomes and tracks from the search hits that * match the db filter. * If there are no search results to print, the basic hub lines are combined into a single HTML table * that is defined outside this function. * Otherwise, each hub line is printed in its own table followed by a <ul> containing details * about the search results. */ { if (hubSearchResult != NULL) printf("<table class='hubList'><tbody>\n"); outputPublicTableRow(hubInfo, count); if (hubSearchResult != NULL) { printf("</tbody></table>\n"); struct trackHub *hub = fetchTrackHub(hubInfo); struct hubOutputStructure *hubOut = buildHubSearchOutputStructure(hub, hubSearchResult); if (dyStringIsEmpty(hubOut->descriptionMatch) && (hubOut->genomes == NULL)) return; // no detailed search results; hit must have been to hub short label or something printf("<div class=\"hubTdbTree\">\n"); printf("<ul>\n"); printf("<li>Search details ...\n<ul>\n"); if (isNotEmpty(dyStringContents(hubOut->descriptionMatch))) printf("<li>Hub Description: <span class='descriptionMatch'><em>%s</em></span></li>\n", dyStringContents(hubOut->descriptionMatch)); struct genomeOutputStructure *genomeOut = hubOut->genomes; if (genomeOut != NULL) { printf("<li>%d Matching Assembl%s\n<ul>\n", hubOut->genomeCount, hubOut->genomeCount==1?"y":"ies"); while (genomeOut != NULL) { printSearchOutputForGenome(genomeOut); genomeOut = genomeOut->next; } printf("</ul></li>\n"); } printf("</ul></li></ul></div>\n"); } } void printHubList(struct slName *hubsToPrint, struct hash *hubLookup, struct hash *searchResultHash) /* Print out a list of hubs, possibly along with search hits to those hubs. * hubLookup takes hub URLs to struct hubEntry * searchResultHash takes hub URLs to struct hubSearchText * (list of hits on that hub) */ { int count = 0; int udcTimeoutVal = udcCacheTimeout(); char *udcOldDir = cloneString(udcDefaultDir()); char *searchUdcDir = cfgOptionDefault("hgHubConnect.cacheDir", udcOldDir); udcSetDefaultDir(searchUdcDir); udcSetCacheTimeout(1<<30); if (hubsToPrint != NULL) { printHubListHeader(); if (searchResultHash == NULL) // if not displaying search results, join the hub <tr>s into one table printf("<table class='hubList'><tbody>\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) { /* This shouldn't happen often, but maybe the search hits list was built from an outdated * search text file that includes hubs for which no info is available. * Skip this hub. */ continue; } struct hubSearchText *searchResult = NULL; if (searchResultHash != NULL) { searchResult = (struct hubSearchText *) hashMustFindVal(searchResultHash, thisHubName->name); } printOutputForHub(hubInfo, searchResult, count); count++; } if (searchResultHash == NULL) printf("</tbody></table>\n"); } udcSetCacheTimeout(udcTimeoutVal); udcSetDefaultDir(udcOldDir); if (hubsToPrint != NULL) { /* Write out the list of hubs in a single table inside a div that will be hidden by * javascript. This table is used (before being hidden) to set common column widths for * the individual hub tables when they're split by detailed search results. */ printf("<div id='hideThisDiv'>\n"); printf("<table class='hubList' id='hideThisTable'><tbody>\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("</tbody></table>\n"); printf("</div>\n"); } jsInline( "function lineUpCols()\n" " {\n" " var tableList = $('table.hubList');\n" " if (tableList.length == 0)\n" " return;\n" " var colWidths = new Array();\n" " var combinedTrackTable = $('#hideThisTable');\n" " for (i=0; i<combinedTrackTable[0].rows[0].cells.length; i++)\n" " colWidths[i] = combinedTrackTable[0].rows[0].cells[i].clientWidth;\n" " $('#hideThisDiv')[0].style.display = 'none';\n" " for(i=0; i<tableList.length; i++)\n" " {\n" " for(j=0; j<tableList[i].rows[0].cells.length; j++)\n" " tableList[i].rows[0].cells[j].style.width = colWidths[j]+'px';\n" " }\n" " }\n" "window.onload = lineUpCols();\n" ); } static bool outputPublicTable(struct sqlConnection *conn, char *publicTable, char *statusTable, struct hash **pHash) /* Put up the list of public hubs and other controls for the page. */ { char *hubSearchTerms = cartOptionalString(cart, hgHubSearchTerms); char *dbFilter = cartOptionalString(cart, hgHubDbFilter); char *lcDbFilter = cloneString(dbFilter); if (isNotEmpty(lcDbFilter)) tolowers(lcDbFilter); // make sure all the public hubs are in the hubStatus table. addPublicHubsToHubStatus(conn, publicTable, statusTable); // build full public hub lookup hash, taking each URL to struct hubEntry * for that hub struct hash *hubLookup = buildPublicLookupHash(conn, publicTable, statusTable, pHash); printf("<div id=\"publicHubs\" class=\"hubList\"> \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("</div>"); return (hubsToPrint != NULL); } struct hash *hgHubConnectPublic() /* Put up the list of public hubs and other controls for the page. */ { struct hash *retHash = NULL; struct sqlConnection *conn = hConnectCentral(); char *publicTable = cfgOptionEnvDefault("HGDB_HUB_PUBLIC_TABLE", hubPublicTableConfVariable, defaultHubPublicTableName); char *statusTable = cfgOptionEnvDefault("HGDB_HUB_STATUS_TABLE", hubStatusTableConfVariable, defaultHubStatusTableName); if (!(sqlTableExists(conn, publicTable) && outputPublicTable(conn, publicTable,statusTable, &retHash)) ) { printf("<div id=\"publicHubs\" class=\"hubList\"> \n"); printf("No Public Track Hubs found that match search criteria.<BR>"); printf("</div>"); } hDisconnectCentral(&conn); return retHash; } static void tryHubOpen(unsigned id) /* try to open hub, leaks trackHub structure */ { /* try opening this again to reset error */ struct sqlConnection *conn = hConnectCentral(); struct errCatch *errCatch = errCatchNew(); struct hubConnectStatus *hub = NULL; if (errCatchStart(errCatch)) hub = hubConnectStatusForId(conn, id); errCatchEnd(errCatch); if (errCatch->gotError) hubUpdateStatus( errCatch->message->string, NULL); else hubUpdateStatus(NULL, hub); errCatchFree(&errCatch); hDisconnectCentral(&conn); } static int doRedirect(struct cart *theCart) { struct hubConnectStatus *hub = hubConnectNewHub(); if (hub == NULL) return 0; char headerText[1024]; char *errorMessage; hubFindOrAddUrlInStatusTable(database, cart, hub->hubUrl, &errorMessage); // if there is an error message, we stay in hgHubConnect if (errorMessage != NULL) return 0; getDbAndGenome(cart, &database, &organism, oldVars); int redirDelay = 3; printf( "<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s?%s\">", redirDelay,"../cgi-bin/hgGateway",cartSidUrlString(cart)); safef(headerText, sizeof(headerText), "Hub Connect Successful"); cartWebStart(cart, NULL, "%s", headerText); hPrintf("You will be automatically redirected to the gateway page for this hub's default database " "(<A HREF=\"../cgi-bin/hgGateway?%s\">%s</A>) in %d seconds.<BR><BR>", cartSidUrlString(cart),trackHubSkipHubName(database),redirDelay); struct trackHub *tHub = hub->trackHub; if (tHub->email != NULL) { hPrintf("<B>This hub is provided courtesy of <A HREF=\"mailto:%s\">%s</A>.</B> Please contact them with any questions.", tHub->email, tHub->email); } hPrintf("<BR><BR>"); hPrintf("Hub: %s<BR><BR>", tHub->longLabel); hPrintf("Hub Genomes: "); struct trackHubGenome *genomeList = tHub->genomeList; bool firstTime = TRUE; for(; genomeList; genomeList = genomeList->next) { if (!firstTime) hPrintf(","); firstTime = FALSE; hPrintf("<A href=\"../cgi-bin/hgTracks?db=%s&%s\">%s</A>",genomeList->name, cartSidUrlString(cart),trackHubSkipHubName(genomeList->name)); } hPrintf("<BR><BR>"); return 1; } static void doResetHub(struct cart *theCart) { char *url = cartOptionalString(cart, hgHubCheckUrl); if (url != NULL) { udcSetCacheTimeout(1); unsigned id = hubResetError(url); tryHubOpen(id); } else errAbort("must specify url in %s\n", hgHubDataText); } static void doClearHub(struct cart *theCart) { char *url = cartOptionalString(cart, hgHubDataText); printf("<pre>clearing hub %s\n",url); if (url != NULL) hubClearStatus(url); else errAbort("must specify url in %s\n", hgHubDataText); printf("<pre>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; + +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( "<link rel=\"stylesheet\" href=\"https://cdnjs.cloudflare.com/ajax/libs/jstree/3.3.7/themes/default/style.min.css\" />\n" "<script src=\"https://cdnjs.cloudflare.com/ajax/libs/jquery/1.12.1/jquery.min.js\"></script>\n" "<script src=\"https://cdnjs.cloudflare.com/ajax/libs/jstree/3.3.7/jstree.min.js\"></script>\n" "<style>.jstree-default .jstree-anchor { height: initial; } </style>\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); printf("<div id=\"hgHubConnectUI\"> <div id=\"description\"> \n"); printf( "<P>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 " "<A HREF=\"../goldenPath/help/hgTrackHubHelp.html#Hosting\">host</A> your track hub, see the " "<A HREF=\"../goldenPath/help/hgTrackHubHelp.html\" TARGET=_blank>" "User's Guide</A>." "To import a public hub click its \"Connect\" button below.</P>" "<P><B>NOTE: Because Track Hubs are created and maintained by external sources," " UCSC is not responsible for their content.</B></P>" ); printf("</div>\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("<span style='background-color:yellow;'><A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\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("<FORM ACTION=\"%s\" NAME=\"addHubForm\">\n", "../cgi-bin/hgHubConnect"); cgiMakeHiddenVar("hubUrl", ""); cgiMakeHiddenVar( hgHubDoFirstDb, "on"); cgiMakeHiddenVar( hgHubDoRedirect, "on"); cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on"); cartSaveSession(cart); puts("</FORM>"); // this is the form for the connect hub button printf("<FORM ACTION=\"%s\" NAME=\"connectHubForm\">\n", "../cgi-bin/hgHubConnect"); cgiMakeHiddenVar("hubUrl", ""); cgiMakeHiddenVar("db", ""); cgiMakeHiddenVar( hgHubDoRedirect, "on"); cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on"); cartSaveSession(cart); puts("</FORM>"); // this is the form for the disconnect hub button printf("<FORM ACTION=\"%s\" NAME=\"disconnectHubForm\">\n", "../cgi-bin/hgHubConnect"); cgiMakeHiddenVar("hubId", ""); cgiMakeHiddenVar(hgHubDoDisconnect, "on"); cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on"); cartSaveSession(cart); puts("</FORM>"); // this is the form for the reset hub button printf("<FORM ACTION=\"%s\" NAME=\"resetHubForm\">\n", "../cgi-bin/hgHubConnect"); cgiMakeHiddenVar(hgHubCheckUrl, ""); cartSaveSession(cart); puts("</FORM>"); // this is the form for the search hub button printf("<FORM ACTION=\"%s\" NAME=\"searchHubForm\">\n", "../cgi-bin/hgHubConnect"); cgiMakeHiddenVar(hgHubSearchTerms, ""); cgiMakeHiddenVar(hgHubDoSearch, "on"); cgiMakeHiddenVar(hgHubDbFilter, ""); cartSaveSession(cart); puts("</FORM>"); // this is the form for the validate button boolean doValidate = cfgOptionBooleanDefault("hgHubConnect.validateHub", FALSE); if (doValidate) { printf("<FORM ACTION=\"%s\" NAME=\"validateHubForm\">\n", "../cgi-bin/hgHubConnect"); cgiMakeHiddenVar("validateHubUrl", ""); cartSaveSession(cart); puts("</FORM>"); } // ... and now the main form printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", "../cgi-bin/hgGateway"); cartSaveSession(cart); // we have two tabs for the public and unlisted hubs printf("<div id=\"tabs\">" "<ul> <li><a href=\"#publicHubs\">Public Hubs</a></li>" "<li><a href=\"#unlistedHubs\">My Hubs</a></li> "); if (doValidate) // put up the validate tab if hg.conf statement present printf("<li><a href=\"#validateHub\">Validate Hub</a></li>"); printf("</ul> "); struct hash *publicHash = hgHubConnectPublic(); hgHubConnectUnlisted(hubList, publicHash); if (doValidate) hgHubConnectValidateNewHub(); printf("</div>"); printf("<div class=\"tabFooter\">"); printf("<span class=\"small\">" "Contact <a href=\"../contacts.html\">us</A> to add a public hub." "</span>\n"); printf("</div>"); cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on"); puts("</FORM>"); printf("</div>\n"); jsInline( "var hubSearchTree = (function() {\n" " // Effectively global vars set by init\n" " var treeDiv; // Points to div we live in\n" "\n" " function hubSearchTreeContextMenuHandler (node, callback) {\n" " var nodeType = node.li_attr.nodetype;\n" " if (nodeType == 'track') {\n" " callback({\n" " 'openConfig': {\n" " 'label' : 'Configure this track',\n" " 'action' : function () {window.open(node.li_attr.configlink, '_blank'); }\n" " }\n" " });\n" " }\n" " else if (nodeType == 'assembly') {\n" " callback({\n" " 'openConfig': {\n" " 'label' : 'Open this assembly',\n" " 'action' : function () {window.open(node.li_attr.assemblylink, '_blank'); }\n" " }\n" " });\n" " }\n" " }\n" " function toggleExpansion(node, event) {\n" " var ident = '#' + node.id;\n" " if (event.type != 'contextmenu')\n" " $(ident).jstree(true).toggle_node(node);\n" " return false;\n" " }\n" " function init() {\n" " $.jstree.defaults.core.themes.icons = false;\n" " $.jstree.defaults.core.themes.dots = true;\n" " $.jstree.defaults.contextmenu.show_at_node = false;\n" " $.jstree.defaults.contextmenu.items = hubSearchTreeContextMenuHandler\n" " treeDiv=$('.hubTdbTree');\n" " treeDiv.jstree({\n" " 'conditionalselect' : function (node, event) { toggleExpansion(node, event); },\n" " 'plugins' : ['conditionalselect', 'contextmenu'],\n" " 'core' : { dblclick_toggle: false }\n" " });\n" " }\n\n" " return { init: init};\n\n" "}());\n" "\n" "$(function () {\n" " hubSearchTree.init();\n" "});\n" ); 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); cgiSpoof(&argc, argv); cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars); cgiExitTime("hgHubConnect", enteredMainTime); return 0; }