d1bc57639309864bb2665bd46eddfe75863f76e4 braney Tue Apr 23 16:42:54 2024 -0700 rearrange how we're doing hub groups. diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c index 35784c3..2f7c769 100644 --- src/hg/hgHubConnect/hgHubConnect.c +++ src/hg/hgHubConnect/hgHubConnect.c @@ -1,1689 +1,1689 @@ /* 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 kent/LICENSE or http://genome.ucsc.edu/license/ 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" #include "pipeline.h" #include "hubPublic.h" static boolean measureTiming; 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; }; 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, boolean withPaste) /* print supported assembly names from sl list */ { struct dyString *dyLongHtml = dyStringNew(1024); struct dyString *dyShortHtml = dyStringNew(1024); char *linkHtml = "<input type='hidden' value='%s'><svg title='click to copy genome browser hub connection URL to clipboard, for sharing with others' class='pasteIcon' style='margin-left: 6px; cursor: pointer; vertical-align:baseline; width:0.8em' xmlns='http://www.w3.org/2000/svg' viewBox='0 0 512 512'><!-- Font Awesome Pro 5.15.4 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license (Commercial License) --><path d='M502.6 70.63l-61.25-61.25C435.4 3.371 427.2 0 418.7 0H255.1c-35.35 0-64 28.66-64 64l.0195 256C192 355.4 220.7 384 256 384h192c35.2 0 64-28.8 64-64V93.25C512 84.77 508.6 76.63 502.6 70.63zM464 320c0 8.836-7.164 16-16 16H255.1c-8.838 0-16-7.164-16-16L239.1 64.13c0-8.836 7.164-16 16-16h128L384 96c0 17.67 14.33 32 32 32h47.1V320zM272 448c0 8.836-7.164 16-16 16H63.1c-8.838 0-16-7.164-16-16L47.98 192.1c0-8.836 7.164-16 16-16H160V128H63.99c-35.35 0-64 28.65-64 64l.0098 256C.002 483.3 28.66 512 64 512h192c35.2 0 64-28.8 64-64v-32h-47.1L272 448z'/></svg>"; // 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 class='hgTracksLink' title='Connect hub and open the %s assembly' href='hgTracks?hubUrl=%s&genome=%s&position=lastDbPos'>%s</a>" , genome->name, hubUrl, genome->name, shortName); // https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt if (withPaste) dyStringPrintf(dyShortHtml, linkHtml, hubUrl); } else dyStringPrintf(dyShortHtml,"%s" , shortName); dyStringPrintf(dyShortHtml,", "); } freeMem(shortName); charCount += strlen(trimmedName); // always append to dyLongHtml if (withLink) { dyStringPrintf(dyLongHtml,"<a title='Connect hub and open the %s assembly' href='hgTracks?hubUrl=%s&genome=%s&position=lastDbPos'>%s</a>" , genome->name, hubUrl, genome->name, trimmedName); if (withPaste) dyStringPrintf(dyLongHtml, linkHtml, hubUrl); } else dyStringPrintf(dyLongHtml,"%s" , trimmedName); if (genome->next) { dyStringPrintf(dyLongHtml,", "); } } char *longHtml = dyStringCannibalize(&dyLongHtml); char *shortHtml = dyStringCannibalize(&dyShortHtml); shortHtml = removeLastComma(shortHtml); if (charCount < GENLISTWIDTH) ourPrintCell(shortHtml); else { char tempHtml[1024+strlen(longHtml)+strlen(shortHtml)]; safef(tempHtml, sizeof tempHtml, "<span class='short'><span style='cursor:default' class='shortPlus'>[+] </span>%s...</span>" "<span class='full' style=\"display:none\"><span style='cursor:default' class='fullMinus'>[-]<br></span>%s</span>", shortHtml, longHtml); 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, TRUE); } 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 puts("<div id=\"unlistedHubs\" class=\"hubList\"> \n" "<div class='tabSection' style='border-bottom:none'>"); printf("<FORM ACTION=\"%s\" id='unlistedHubForm' NAME=\"unlistedHubForm\">\n", "../cgi-bin/hgGateway"); cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on"); cartSaveSession(cart); puts("<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 (!startsWith("/gbdb", hub->hubUrl)) { unlistedHubCount++; slAddHead(&unlistedHubList, hub); } } hubList = NULL; // hubList no longer valid puts("<p>Enter hub URLs below to connect hubs. Hubs connected this way are not accessible to " "other users by default.</p><p>If you wish to share your hub you can create a " "<a href=\"/goldenPath/help/hgSessionHelp.html\" style='color:#121E9A' target=_blank>session link</a>. " "First, connect the hub and configure the tracks image as desired, then navigate to " "<a href=\"/cgi-bin/hgSession\" style='color:#121E9A' target=_blank>My Sessions</a> (<b>My Data</b> > <b>My Sessions</b>). " "The resulting stable link can be added to publications and shared freely. You, as the author, " "also have the power to update the session contents freely. " "Alternatively, you may <a href=\"/goldenPath/help/hgTrackHubHelp.html#Sharing\" " "style='color:#121E9A' target=_blank>build a link with the hub URL</a> to allow users to retain their browser " "configuration, connected hubs, and custom tracks.</p>" "</p>" "<p>See our <a href=\"/goldenPath/help/publicHubGuidelines.html\" style='color:#121E9A'>public " "hub guidelines</A> for information on submitting a new public hub.</p>\n" ); if (unlistedHubCount == 0) { // nothing to see here printf("<tr><td style='text-align:left'>No connected track or assembly hubs.<p>To connect a hub:" "<ul><li>Enter its URL into the input box above and click 'Add Hub'. </li>" "<li>Alternatively, you can go to the 'Public Hubs' tab on this page and connect one " "of the hubs that were submitted to us. </li>" "<li>Another way to connect to hubs is via a direct connection link copied using the copy icon, shown on this page, when a hub is connected. </li>" "<li>You can also connect to hub by following a short link to a saved session, created though the menu " "'My Data > My Sessions', if the Genome Browser had connected hubs when the session was saved.</li>" "</ul></td></tr>"); printf("</thead></table>\n"); puts("</FORM>"); // return from within DIV and FROM is probably not a good idea puts("</div></div>"); // tabSection and .unlistedHubs return; } // time to output the big table. First the header puts( "<tr> " "<th>Display</th> " "<th>Hub Name</th> " "<th>Description</th> " "<th>Assemblies<span class='assemblyClickNote'>Click to connect and browse directly. Click copy icon to copy URL to clipboard for sharing.</span></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"); puts("</FORM>"); printf("</div>"); // .tabSection printf("</div>"); // #unlistedHubs } int doValidateNewHub(char *hubUrl) /* Run hubCheck on a hub. */ { int ret = 0; udcSetCacheTimeout(1); char *expireTime = cfgOptionDefault("browser.cgiExpireMinutes", "20"); unsigned expireMinutes = sqlUnsigned(expireTime); int hubCheckTimeout = (expireMinutes - 1) * 60 > 0 ? (expireMinutes - 1) * 60 : 60; printf("<div id=\"validateHubResult\" class=\"hubTdbTree\" style=\"overflow: auto\"></div>"); char *cmd[] = {"loader/hubCheck", "-htmlOut", "-noTracks", hubUrl, NULL}; struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { struct pipeline *pl = pipelineOpen1(cmd, pipelineRead | pipelineNoAbort, NULL, NULL, hubCheckTimeout); struct lineFile *lf = pipelineLineFile(pl); char *line; while (lineFileNext(lf, &line, NULL)) jsInlineF("%s", line); pipelineClose(&pl); // the 'false' below prevents a few hub-search specific jstree configuration options jsInline("hubSearchTree.init(false);"); } errCatchEnd(errCatch); if (errCatch->gotError || errCatch->gotWarning) { printf("hubCheck timed out after running for %d minute%s. Please try on a Unix command line", hubCheckTimeout / 60, hubCheckTimeout/60 > 1 ? "s" : ""); ret = 1; } errCatchFree(&errCatch); return ret; } void hgHubConnectDeveloperMode() /* Put up the controls for the "Hub Development" Tab, which includes a button to run the * hubCheck utility on a hub and load a hub with the udcTimeout and measureTiming * variables turned on */ { // put out the top of our page char *hubUrl = cartOptionalString(cart, "validateHubUrl"); // the outer div for all the elements in the tab puts("<div id=\"hubDeveloper\" class=\"hubList\">"); char *hubUrlVal = ""; if (hubUrl != NULL) hubUrlVal = catThreeStrings(" value='", hubUrl, "'"); puts("<div class='tabSection'>"); puts("<h4>Create your own hub</h4>"); puts("For information on making track hubs, see the following pages: \n " "<ul>\n" "<li><a href='../goldenPath/help/hubQuickStart.html' style='color:#121E9A' target=_blank>Quick Start Guide</a></li>\n" "<li><a href=\"../goldenPath/help/hgTrackHubHelp.html\" style='color:#121E9A' TARGET=_blank>Track Hub User's Guide</a></li>\n" "<li><a href=\"../goldenPath/help/hgTrackHubHelp#Hosting\" style='color:#121E9A' target=_blank>Where to Host Your Track Hub</a></li>\n" "<li><a href=\"../goldenPath/help/trackDb/trackDbHub.html\" style='color:#121E9A' target=_blank>Track Hub Settings Reference</a></li>\n" "<li><a href=\"../goldenPath/help/publicHubGuidelines.html\" style='color:#121E9A' target=_blank>Guidelines for Submitting a Public Hub</a></li>\n" "</ul>\n" "<BR>You may also <a href='../contacts.html' style='color:#121E9A'>contact us</a> if you have any " "issues or questions on hub development."); puts("</div>"); // .tabSection puts("<div class='tabSection'>"); puts("<h4>Check a hub for errors</h4>"); printf("<label for=\"validateHubUrl\"><b>Hub URL:</b></label>"); printf("<input id='validateHubUrl' name='validateHubUrl' class='hubField' " "type='text' size='65'%s>\n", hubUrlVal); printf("<button type='button' id='hubValidateButton'>Check</button>\n"); printf("  <span style='font-size:90%%' class='link' id='loadSampleHub'>Load Example URL</span>\n"); puts("<div class='help'>Use the URL bar above to check a hub for errors. This will " "validate the hub's configuration files, including hub.txt, " "genomes.txt and trackDb.txt. " "It will also present a hierarchical tree of tracks with any errors in red. A hub " "with no errors still shows the tree which can be used to explore the track hierarchy. " "Hub error checking will always refresh the files and never use our remote file cache (see below)." "</div>\n " ); puts("</div>"); // .tabSection puts("<div class='tabSection'>"); puts("<h4>Enable Genome Browser debugging modes</h4>"); puts("<div class='help'>These apply to all connected hubs. By default, caching is activated and track load times are not shown, but you can change these settings while developing your hub:</div>"); puts("<div style='margin-left: 15px'>"); puts("<FORM ACTION='hgHubConnect#hubDeveloper' METHOD='POST' NAME='debugForm'>"); // output the udcTimeout button char *noCacheLabel = "Inactive, never cache"; char *timeout = "5"; char *cacheStatus = "ON"; char *description = "Always cache contents at UCSC. This means that data access is faster, but you cannot see the effect of changes to your files on the Genome Browser for at least 5 minutes."; if (cartNonemptyString(cart, "udcTimeout")) { noCacheLabel = "Active, always cache"; timeout = ""; cacheStatus = "OFF"; description = "Do not cache contents at UCSC and always load them from the source server. This means that data access is slower, but you can see the effect of changes to your files immediately on the Genome Browser."; } printf("<b style='font-size:90%%'>File caching: %s</b> ", cacheStatus); printf("<button type='submit' name='udcTimeout' value='%s'>Change to: %s</button>", timeout, noCacheLabel); printf("<div class='help'>Current setting: %s<br>", description); puts("For custom tracks, this affects only the remote formats (bigBed, bigWig, VCF+tabix, BAM, CRAM, bigPsl, HiC, etc), not text files (BED, VCF, PSL, etc), which are stored at UCSC.</div>"); // output the measureTiming button char *timeLabel = "Show timings"; char *timeVal = "on"; char *timeDesc = "Show no timing measurements."; char *timeStatus = "OFF"; if (cartNonemptyString(cart, "measureTiming")) { timeLabel = "Hide timings"; timeVal = ""; timeDesc = "Shows loading time in milliseconds for each track, to help debug performance problems."; timeStatus = "ON"; } printf("<b style='font-size:90%%'>Show load times: %s</b> ", timeStatus); printf("<button type='submit' name='measureTiming' value='%s'>Change to: %s</button>", timeVal, timeLabel); printf("<div class='help'>Current setting: %s</div>\n", timeDesc); puts("</FORM>"); puts("</div>"); // margin-left puts("</div>"); // tabSection puts("</div>"); // #hubDeveloper jsOnEventById("click", "hubValidateButton", "makeIframe(event)"); } void printSearchAndFilterBoxes(int searchEnabled, char *hubSearchTerms, char *dbFilter) /* Create the text boxes for search and database filtering along with the required * javscript */ { printf("<FORM ACTION=\"%s\" NAME=\"searchHubForm\">\n", "../cgi-bin/hgHubConnect"); if (searchEnabled) { cgiMakeHiddenVar(hgHubDoSearch, "on"); cgiMakeHiddenVar(hgHubDbFilter, ""); cartSaveSession(cart); printf("The list below can be filtered on words in the hub description pages or by assemblies.<BR>" "Search terms: " "<input name=\"hubSearchTerms\" id=\"hubSearchTerms\" class=\"hubField\" " "placeholder='e.g. methylation' type=\"text\" size=\"50\" value=\"%s\"> \n", hubSearchTerms!=NULL?hubSearchTerms:""); printf("\n"); } printf("Assembly: " "<input name=\"%s\" id=\"hubDbFilter\" class=\"hubField\" " "type=\"text\" size=\"15\" value=\"%s\" placeholder='e.g. hg38'> \n" "<input name=\"hubSearchButton\" id='hubSearchButton' " "class=\"hubField\" type=\"submit\" value=\"Search Public Hubs\">\n", hgHubDbFilter, dbFilter!=NULL?dbFilter:""); puts("</FORM>"); } 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 above search terms</B> \n"); 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("<table id=\"publicHubsTable\" class=\"hubList\"> " "<thead><tr> " "<th>Display</th> " "<th>Hub Name</th> " "<th>Description</th> " "<th>Assemblies<span class='assemblyClickNote'>Click to connect and browse directly</span></th> " "</tr></thead><tbody>"); } void printHubListFooter() /* Write out the header for a list of hubs in its own table */ { puts("</tbody></table>"); } 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, FALSE); printf("</tr>\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; } 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 tdbOutputStructure *hstToTdbOutput(struct hubSearchText *hst, struct genomeOutputStructure *genomeOut, struct trackHub *hub) /* Convert a hubSearchText entry to a (list of) tdbOutputStructure(s) */ { struct tdbOutputStructure *tdbOut = hashFindVal(genomeOut->tdbOutHash, hst->track); if (tdbOut == NULL) { genomeOut->trackCount++; AllocVar(tdbOut); tdbOut->shortLabel = dyStringNew(0); tdbOut->metaTags = dyStringNew(0); tdbOut->descriptionMatch = dyStringNew(0); tdbOut->configUrl = dyStringNew(0); dyStringPrintf(tdbOut->shortLabel, "%s", hst->label); char *hubId = hubNameFromUrl(hub->url); if (isNotEmpty(hst->parents)) { // hst->parents is a comma-sep list like "track1","track1Label","track2","track2Label" int i; int parentCount; int parentTypesCount; char *parentTrack = NULL; char *parentLabel = NULL; char *parentTrackLabels[16]; // 2 slots per parent, can tracks nest more than 8 deep? char *parentTypes[16]; // the types of parents, "comp", "super", "view", "other" for each track in parentTrackLabels struct tdbOutputStructure *parentTdbOut = NULL; struct tdbOutputStructure *savedParent = NULL; parentCount = chopByCharRespectDoubleQuotes(cloneString(hst->parents), ',', parentTrackLabels, sizeof(parentTrackLabels)); parentTypesCount = chopCommas(cloneString(hst->parentTypes), parentTypes); if (parentCount == 0 || parentCount % 2 != 0) { errAbort("error parsing hubSearchText->parents for %s.%s in hub: '%s'", genomeOut->genomeName, hst->track, hub->url); } if (parentTypesCount != (parentCount / 2)) { errAbort("error parsing hubSearchText->parentTypes: '%s' for %s.%s in hub: '%s'", hst->parentTypes, genomeOut->genomeName, hst->track, hub->url); } boolean foundParent = FALSE; boolean doAddSaveParent = FALSE; for (i = 0; i < parentCount; i += 2) { parentTrack = stripEnclosingDoubleQuotes(cloneString(parentTrackLabels[i])); parentLabel = stripEnclosingDoubleQuotes(cloneString(parentTrackLabels[i+1])); // wait until the first valid trackui page for the track hit if (isEmpty(dyStringContents(tdbOut->configUrl)) && sameString(parentTypes[i/2], "comp")) { dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s_%s&hgsid=%s&%s", hub->url, genomeOut->genomeName, hubId, parentTrack, cartSessionId(cart), genomeOut->positionString); } else if (isEmpty(dyStringContents(tdbOut->configUrl)) && sameString(parentTypes[i/2], "super")) { dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s_%s&hgsid=%s&%s", hub->url, genomeOut->genomeName, hubId, hst->track, cartSessionId(cart), genomeOut->positionString); } parentTdbOut = hashFindVal(genomeOut->tdbOutHash, parentTrack); if (parentTdbOut == NULL) { AllocVar(parentTdbOut); parentTdbOut->shortLabel = dyStringNew(0); parentTdbOut->metaTags = dyStringNew(0); parentTdbOut->descriptionMatch = dyStringNew(0); parentTdbOut->configUrl = dyStringNew(0); // views will be in the parent list, but the &g parameter to trackUi should be the view's parent if (sameString(parentTypes[(i/2)], "view")) dyStringPrintf(parentTdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s_%s&hgsid=%s&%s", hub->url, genomeOut->genomeName, hubId, stripEnclosingDoubleQuotes(parentTrackLabels[(i/2)+2]), cartSessionId(cart), genomeOut->positionString); else // everything else has the correct &g param dyStringPrintf(parentTdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s_%s&hgsid=%s&%s", hub->url, genomeOut->genomeName, hubId, parentTrack, cartSessionId(cart), genomeOut->positionString); dyStringPrintf(parentTdbOut->shortLabel, "%s", parentLabel); parentTdbOut->childCount += 1; if (savedParent) slAddHead(&(parentTdbOut->children), savedParent); else slAddHead(&(parentTdbOut->children), tdbOut); savedParent = parentTdbOut; doAddSaveParent = TRUE; hashAdd(genomeOut->tdbOutHash, parentTrack, parentTdbOut); } else { foundParent = TRUE; // don't add this track to the genomeOut->tracks hash again if (savedParent && doAddSaveParent) { parentTdbOut->childCount += 1; slAddHead(&(parentTdbOut->children), savedParent); } else if (!savedParent) { parentTdbOut->childCount += 1; slAddHead(&(parentTdbOut->children), tdbOut); } savedParent = parentTdbOut; doAddSaveParent = FALSE; } } if (!foundParent) { slAddHead(&(genomeOut->tracks), parentTdbOut); } } else { dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s_%s&hgsid=%s&%s", hub->url, genomeOut->genomeName, hubId, hst->track, cartSessionId(cart), genomeOut->positionString); slAddHead(&(genomeOut->tracks), tdbOut); } hashAdd(genomeOut->tdbOutHash, hst->track, tdbOut); } return tdbOut; } 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 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 tdbOutputStructure *tdbOut = hstToTdbOutput(hst, genomeOut, 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 char *tdbOutputStructureLabelToId(struct tdbOutputStructure *tdbOut) /* Make an array name out of a tdbOutputStruct */ { struct dyString *id = dyStringNew(0); dyStringPrintf(id, "%s", htmlEncode(dyStringContents(tdbOut->shortLabel))); if (tdbOut->childCount > 0) { dyStringPrintf(id, " (%d subtrack%s)", tdbOut->childCount, tdbOut->childCount == 1 ? "" : "s"); } return dyStringCannibalize(&id); } static void printTdbOutputStructureToDyString(struct tdbOutputStructure *tdbOut, struct dyString *dy, char *arrayName) /* Print a tdbOutputStructure to a dyString, recursive for subtracks. */ { dyStringPrintf(dy, "trackData['%s'] = [", arrayName); if (tdbOut->childCount > 0) { struct dyString *subtrackDy = dyStringNew(0); struct tdbOutputStructure *child = tdbOut->children; while (child != NULL) { char *childId = tdbOutputStructureLabelToId(child); dyStringPrintf(dy, "\n\t{\n\tid: '%s',\n\tparent: '%s',\n\t" "li_attr: {nodetype:'track', configlink:'%s'},\n\ttext: \'%s ", childId, arrayName, dyStringContents(child->configUrl), childId); if (isNotEmpty(dyStringContents(child->metaTags))) { dyStringPrintf(dy, "<br><span class=\\'descriptionMatch\\'><em>Metadata: %s</em></span>", htmlEncode(dyStringContents(child->metaTags))); } if (isNotEmpty(dyStringContents(child->descriptionMatch))) { dyStringPrintf(dy, "<br><span class=\\'descriptionMatch\\'><em>Description: %s</em></span>", htmlEncode(dyStringContents(child->descriptionMatch))); } dyStringPrintf(dy, "\'"); if (child->childCount > 0) { dyStringPrintf(dy, ",\n\tchildren: true"); printTdbOutputStructureToDyString(child, subtrackDy, childId); } dyStringPrintf(dy, "\n\t},"); child = child->next; } dyStringPrintf(dy, "];\n"); if (isNotEmpty(dyStringContents(subtrackDy))) dyStringPrintf(dy, "%s", subtrackDy->string); } else dyStringPrintf(dy, "];\n"); } void printGenomeOutputStructureToDyString(struct genomeOutputStructure *genomeOut, struct dyString *dy, char *genomeNameId) /* Print a genomeOutputStructure to a dyString. The structure here is: * trackData[genome] = [{track 1 obj}, {track2 obj}, {track3 obj}, ... ] * trackData[track1] = [{search hit text}, {subtrack1 obj}, {subtrack2 obj}, ... ] * * if track1, track2, track3 are container tracks, then the recursive function * tdbOutputStructureToDystring creates the above trackData[track1] = [{}] for * each of the containers, otherwise a single child of the genome is sufficient */ { struct tdbOutputStructure *tdbOut = NULL; static struct dyString *tdbArrayDy = NULL; // the dyString for all of the tdb objects static struct dyString *idString = NULL; // the special id of this track if (tdbArrayDy == NULL) tdbArrayDy = dyStringNew(0); if (idString == NULL) idString = dyStringNew(0); dyStringPrintf(dy, "trackData['%s'] = [", genomeNameId); if (genomeOut->tracks != NULL) { tdbOut = genomeOut->tracks; slReverse(&tdbOut); while (tdbOut != NULL) { dyStringPrintf(idString, "%s", tdbOutputStructureLabelToId(tdbOut)); dyStringPrintf(dy, "\n\t{\n\t'id': '%s',\n\t'parent': '%s',\n\t" "'li_attr': {'nodetype':'track', configlink: '%s'},\n\t'text': \'%s ", idString->string, genomeNameId, dyStringContents(tdbOut->configUrl), idString->string); if (isNotEmpty(dyStringContents(tdbOut->metaTags))) { dyStringPrintf(dy, "<br><span class=\\'descriptionMatch\\'><em>Metadata: %s</em></span>", htmlEncode(dyStringContents(tdbOut->metaTags))); } if (isNotEmpty(dyStringContents(tdbOut->descriptionMatch))) { dyStringPrintf(dy, "<br><span class=\\'descriptionMatch\\'><em>Description: %s</em></span>", htmlEncode(dyStringContents(tdbOut->descriptionMatch))); } dyStringPrintf(dy, "\'"); // above we took care of both non-heirarchical tracks and the top-level containers, // now do container children, which also takes care of any deeper heirarchies if (tdbOut->childCount > 0) dyStringPrintf(dy, ",\n\t'children': true"); dyStringPrintf(dy, "\n\t},\n"); if (tdbOut->childCount > 0) printTdbOutputStructureToDyString(tdbOut, tdbArrayDy, idString->string); tdbOut = tdbOut->next; dyStringClear(idString); } } dyStringPrintf(dy, "];\n"); // close off genome node dyStringPrintf(dy, "%s\n", tdbArrayDy->string); dyStringClear(tdbArrayDy); } void printHubOutputStructure(struct hubOutputStructure *hubOut, struct hubEntry *hubInfo) /* Convert a hubOutputStructure to a jstree-readable string. This function forms the root * node for each hub search tree, whose children are the hub description match and each individual * genome node. A simplified structure is: * trackData['#_hubId'] = [{id:'descriptionMatch',...},{id:'assembly1',...},...] * * The id's become new "trackData[id]" entries with their own arrays later if they have * sub-trees (via printGenomeOutputStructureToDyString() and printTdbOutputStructureToDyString(). */ { struct dyString *dy = dyStringNew(0); // The leading '#' tells the javascript this is a 'root' node dyStringPrintf(dy, "trackData['#_%d'] = [", hubInfo->id); if (isNotEmpty(dyStringContents(hubOut->descriptionMatch))) { dyStringPrintf(dy, "{'id':'%d_descriptionMatchText','parent':'#_%d'," "'state':{'opened': true},'text': 'Hub Description: " "<span class=\"descriptionMatch\"><em>%s</em></span>'},", hubInfo->id, hubInfo->id, htmlEncode(dyStringContents(hubOut->descriptionMatch))); } struct genomeOutputStructure *genomeOut = hubOut->genomes; struct dyString *genomeDy = dyStringNew(0); if (genomeOut != NULL) { dyStringPrintf(dy, "{'id':'%d_assemblies', 'text':'%d Matching Assembl%s', 'parent':'#_%d', " "'children':true, 'li_attr': {'state':{'opened': 'false'}}}];\n", hubInfo->id, hubOut->genomeCount, hubOut->genomeCount == 1 ? "y" : "ies", hubInfo->id); dyStringPrintf(dy, "trackData['%d_assemblies'] = [", hubInfo->id); while (genomeOut != NULL) { char *assemblyName = htmlEncode(dyStringContents(genomeOut->shortLabel)); char genomeNameId[512]; safef(genomeNameId, sizeof(genomeNameId), "%d_%s", hubInfo->id, assemblyName); dyStringPrintf(dy, "{'id': '%s', 'parent': '%d_assemblies', 'children': true, " "'li_attr': {'assemblylink': '%s','nodetype': 'assembly'}," "'text': \"%s", genomeNameId, hubInfo->id, dyStringContents(genomeOut->assemblyLink), assemblyName); if (genomeOut->trackCount > 0) { dyStringPrintf(dy, " (%d track%s) ", genomeOut->trackCount, genomeOut->trackCount == 1 ? "" : "s"); } if (isNotEmpty(dyStringContents(genomeOut->metaTags))) { dyStringPrintf(dy, "<br><span class='descriptionMatch'><em>%s</em></span>", htmlEncode(dyStringContents(genomeOut->metaTags))); } if (isNotEmpty(dyStringContents(genomeOut->descriptionMatch))) { dyStringPrintf(dy, "<br><em>Assembly Description:</em> %s", htmlEncode(dyStringContents(genomeOut->descriptionMatch))); } dyStringPrintf(dy, "\"},"); printGenomeOutputStructureToDyString(genomeOut, genomeDy, genomeNameId); genomeOut = genomeOut->next; } } dyStringPrintf(dy, "];\n"); dyStringPrintf(dy, "%s", genomeDy->string); jsInline(dy->string); dyStringClear(dy); } 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. */ { outputPublicTableRow(hubInfo, count); if (hubSearchResult != NULL) { printf("<tr><td colspan=4 style='text-align:left;'>\n"); struct trackHub *hub = fetchTrackHub(hubInfo); if (hub != NULL) { 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("<div id='tracks%d'></div>", hubInfo->id); // div for the jstree for this hub's search result(s) printf("</div>\n"); printHubOutputStructure(hubOut, hubInfo); } printf("</td></tr>\n"); } } int hubEntryCmp(const void *va, const void *vb) /* Compare to sort based on shortLabel */ { const struct hubEntry *a = *((struct hubEntry **)va); const struct hubEntry *b = *((struct hubEntry **)vb); return strcasecmp(a->shortLabel, b->shortLabel); } 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) */ { printf("<FORM ACTION=\"%s\" id='publicHubForm' NAME=\"publicHubForm\">\n", "../cgi-bin/hgGateway"); cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on"); cartSaveSession(cart); int count = 0; struct hubEntry *hubList = NULL; struct hubEntry *hubInfo; long slTime; long printOutputForHubTime; if (hubsToPrint != NULL) { printHubListHeader(); struct slName *thisHubName = NULL; for (thisHubName = hubsToPrint; thisHubName != NULL; thisHubName = thisHubName->next) { 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; } slAddHead(&hubList, hubInfo); } slSort(&hubList, hubEntryCmp); slTime = clock1000(); for (hubInfo = hubList; hubInfo != NULL; hubInfo = hubInfo->next) { struct hubSearchText *searchResult = NULL; if (searchResultHash != NULL) { searchResult = (struct hubSearchText *) hashMustFindVal(searchResultHash, hubInfo->hubUrl); } printOutputForHub(hubInfo, searchResult, count); count++; } printOutputForHubTime = clock1000(); if (measureTiming) printf("hgHubConnect: printOutputForHubTime before js execution: %lu millis<BR>\n", printOutputForHubTime - slTime); printHubListFooter(); } 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"); for (hubInfo = hubList; hubInfo != NULL; hubInfo = hubInfo->next) { 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" ); if (searchResultHash != NULL) jsInline("hubSearchTree.init(true);\n"); puts("</FORM>"); } 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. long lastTime= clock1000(); addPublicHubsToHubStatus(cart, conn, publicTable, statusTable); if (measureTiming) printf("Time of addPublicHubsToHubStatus: %ld <br>", (clock1000()-lastTime)); // build full public hub lookup hash, taking each URL to struct hubEntry * for that hub struct hash *hubLookup = buildPublicLookupHash(conn, publicTable, statusTable, pHash); puts("<div id=\"publicHubs\" class=\"hubList\">"); puts("<div class='tabSection' style='border-bottom:none'>"); printf( "<P>" "Track data hubs are collections of external tracks that can be added to the UCSC Genome Browser. " "Click <B>Connect</B> to attach a hub and redirect to the assembly gateway page. " "Hub tracks will then show up in the hub's own blue bar track group under the browser graphic. " "For more information, including <A HREF=\"../goldenPath/help/hgTrackHubHelp#Hosting\" " "style='color:#121E9A' target=_blank>where to host your track hub</a>, see our " "<A HREF=\"../goldenPath/help/hgTrackHubHelp.html\" TARGET=_blank style='color:#121E9A'>" "User's Guide</A>. " "</P>" "<P>Track Hubs are created and maintained by external sources." " UCSC is not responsible for their content.<BR></P>\n" ); char *hubSearchTableName = hubSearchTextTableName(); 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; searchResultHash = newHash(5); getHubSearchResults(conn, hubSearchTableName, hubSearchTerms, checkDescriptions, lcDbFilter, hubLookup, &searchResultHash, &hubsToPrint, NULL); } 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); printf("</div>\n"); // .tabSection printHubList(hubsToPrint, hubLookup, searchResultHash); printf("</div>"); // #publicHubs 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(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&position=lastDbPos\">%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) { long beforeCheck = clock1000(); struct hubConnectStatus *hub = hubList; boolean foundFirstGenome = FALSE; struct hash *trackDbNameHash = newHash(5); for(; hub; hub = hub->next) { struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { - hubAddTracks(hub, database, &foundFirstGenome, trackDbNameHash); + hubAddTracks(hub, database, &foundFirstGenome, trackDbNameHash, NULL); } errCatchEnd(errCatch); if (errCatch->gotError) { hub->errorMessage = cloneString(errCatch->message->string); hubUpdateStatus( errCatch->message->string, hub); } else hubUpdateStatus(NULL, hub); } if (measureTiming) printf("hgHubConnect: checkTrackDbs time: %lu millis<BR>\n", clock1000() - beforeCheck); } 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 printIncludes() /* print the CSS and javascript include lines */ { 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); jsIncludeFile("spectrum.min.js", NULL); // there is no color picker used anywhere on this page. why include this? } void blankWarn() /* Dummy warn handler used in the iframe for returning hubCheck output */ { } void doMiddle(struct cart *theCart) /* Write header and body of html page. */ { cart = theCart; // hgHubConnect's own timing is tied to a special value of measureTiming, since now // our users use measureTiming a lot more, we need to keep a special mode for us measureTiming = sameString(cartUsualString(cart, "measureTiming", ""), "full"); 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; } } if (cartVarExists(cart, hgHubDoHubCheck)) { // we aren't calling cartWebStart so we need to push 3 error handlers: webPushErrHandlers(); pushWarnHandler(blankWarn); puts("<html>"); puts("<body>"); puts("<link rel='stylesheet' href='../style/HGStyle.css' type='text/css'>"); printIncludes(); jsInline("trackData = [];\n"); char *hubUrl = cgiOptionalString("validateHubUrl"); jsInline("document.body.style.margin = 0;\n"); // simulate the look and feel of a dialog window with a blue bar at the top puts("<div id='titlebar' style='background: #D9E4F8; border: 1px outset #000088; padding: 10px'>" "<span id='title' style='font-weight: bold; margin: .2em 0 .1em; color: #000088'>Hub Check</span>" "<a href='#' id='windowX' style='float: right' class='ui-dialog-titlebar-close ui-corner-all ui-state-hover' role='button'>" "<span class='ui-icon ui-icon-closethick'>close</span></a></div>"); puts("<div id='content' style='margin:10px; padding: 2px'>"); jsOnEventByIdF("click", "windowX", "closeIframe()"); if (isEmpty(hubUrl)) printf("Please wait, loading and checking hub. This usually takes a minute or two but can take up to 20 minutes for big hubs."); else { puts("<p><button id='reloadButton'>Check again</button>"); puts(" <button id='closeButton'>Close this window</button></p>"); jsOnEventByIdF("click", "reloadButton", "reloadIframe()"); jsOnEventByIdF("click", "closeButton", "closeIframe()"); jsInline("document.onkeydown = function(evt) { if (evt.keyCode===27) { closeIframe() } };"); int retVal = doValidateNewHub(hubUrl); if (retVal == 0) printf("<div>Finished checking %s</div>", hubUrl); puts("<hr>"); puts("<p>Our command line tool <a target=_blank href='https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads'>hubCheck</a> " "can be used to obtain the same output from a Unix command line.</p>"); puts("<p>To download the hubCheck tool for Linux, run these commands" " (replace 'linux' with 'macOSX' on a x86 Mac):<br>" "<pre>wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hubCheck\n" "chmod a+x hubCheck\n" "hubCheck https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt</pre></p>"); puts("<p>You can use the 'Esc' key to close this window.</p>"); } puts("</div>"); // margin 10px puts("</div>"); // ui-dialog-titlebar puts("</div>"); // ui-dialog cartWebEnd(); return; } cartWebStart(cart, NULL, "%s", pageTitle); printIncludes(); // 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("<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 invisible 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 invisible 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 invisible form for the disconnect hub button - it's submitted via javascript 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 invisible form for the reset hub button - it's submitted via javascript printf("<FORM ACTION=\"%s\" NAME=\"resetHubForm\">\n", "../cgi-bin/hgHubConnect"); cgiMakeHiddenVar(hgHubCheckUrl, ""); cartSaveSession(cart); puts("</FORM>"); // ... and now the main form // we have three tabs for the public and unlisted hubs and hub development printf("<div id=\"tabs\">" "<ul> <li><a class=\"defaultDesc\" href=\"#publicHubs\">Public Hubs</a></li>" "<li><a class=\"defaultDesc\" href=\"#unlistedHubs\">Connected Hubs</a></li> "); if (cfgOptionBooleanDefault("hgHubConnect.validateHub", TRUE)) printf("<li><a class=\"hubDeveloperDesc\" href=\"#hubDeveloper\">Hub Development</a></li>"); printf("</ul> "); // The public hubs table is getting big and takes a while to download. // Jquery UI's tabs() command will layout the page, but because of // jsInlining, it will only be called at the end of the page. This can lead to the page "jumping". // To make the inline code run now, let's flush JS inlines. // I'm not sure that this makes a visible difference, but it doesn't do any harm either jsInlineFinish(); jsInlineReset(); struct hash *publicHash = hgHubConnectPublic(); hgHubConnectUnlisted(hubList, publicHash); if (cfgOptionBooleanDefault("hgHubConnect.validateHub", TRUE)) hgHubConnectDeveloperMode(); printf("</div>"); // #tabs cartWebEnd(); } char *excludeVars[] = {"Submit", "submit", "hc_one_url", hgHubDoHubCheck, hgHubCheckUrl, hgHubDoClear, hgHubDoRefresh, 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; }