67ce69b2d6be585fcad3cb0dd5fc927e95c327ff chmalee Mon Oct 14 13:48:54 2019 -0700 Rework of hgHubConnect hub searching to not use trackDb or udc so searches can be sped up. The hubSearchText table now has an extra column for the parent track names (if any) of a search result to a track. hgHubConnect has been changed to use this field of the table instead of using trackDb. hubCrawl has been changed to generate this additional column, refs #23812 diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c index 6e87bfb..d5dd50f 100644 --- src/hg/hgHubConnect/hgHubConnect.c +++ src/hg/hgHubConnect/hgHubConnect.c @@ -1,1792 +1,1877 @@ /* 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>"); } void doValidateNewHub(char *hubUrl) /* Run hubCheck on a hub. */ { struct dyString *cmd = dyStringNew(0); udcSetCacheTimeout(1); dyStringPrintf(cmd, "loader/hubCheck -htmlOut -noTracks %s", hubUrl); printf("</table>"); printf("<div id=\"validateHubResult\" class=\"hubTdbTree\" style=\"overflow: auto\"></div>"); FILE *f = popen(cmd->string, "r"); if (f == NULL) errAbort("popen: error running command: \"%s\"", cmd->string); char buf[1024]; while (fgets(buf, sizeof(buf), f)) { jsInlineF("%s", buf); } if (pclose(f) == -1) errAbort("pclose: error for command \"%s\"", cmd->string); // the 'false' below prevents a few hub-search specific jstree configuration options jsInline("hubSearchTree.init(false);"); dyStringFree(&cmd); } 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 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); + + if (isNotEmpty(hst->parents)) + { + // hst->parents is a comma-sep list like "track1","track1Label","track2","track2Label" + int i; + int parentCount; + char *parentTrack = NULL; + char *parentLabel = NULL; + char *parentTrackLabels[16]; // 2 slots per parent, can tracks nest more than 8 deep? + struct tdbOutputStructure *parentTdbOut = NULL; + struct tdbOutputStructure *savedParent = NULL; + + parentCount = chopByCharRespectDoubleQuotes(cloneString(hst->parents), ',', parentTrackLabels, sizeof(parentTrackLabels)); + if (parentCount == 0 || parentCount % 2 != 0) + { + errAbort("error parsing hubSearchText->parents for %s.%s in hub: '%s'", + genomeOut->genomeName, hst->track, hub->url); + } + dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s", + hub->url, genomeOut->genomeName, parentTrackLabels[0], cartSessionId(cart), + genomeOut->positionString); + + boolean foundParent = FALSE; + boolean doAddSaveParent = FALSE; + for (i = 0; i < parentCount; i += 2) + { + parentTrack = stripEnclosingDoubleQuotes(cloneString(parentTrackLabels[i])); + parentLabel = stripEnclosingDoubleQuotes(cloneString(parentTrackLabels[i+1])); + parentTdbOut = hashFindVal(genomeOut->tdbOutHash, parentTrack); + if (parentTdbOut != NULL) + { + 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; + } + else + { + AllocVar(parentTdbOut); + parentTdbOut->shortLabel = dyStringNew(0); + parentTdbOut->metaTags = dyStringNew(0); + parentTdbOut->descriptionMatch = dyStringNew(0); + parentTdbOut->configUrl = dyStringNew(0); + dyStringPrintf(tdbOut->configUrl, + "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s", + hub->url, genomeOut->genomeName, 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); + } + } + if (!foundParent) + { + slAddHead(&(genomeOut->tracks), parentTdbOut); + } + } + else + { + dyStringPrintf(tdbOut->configUrl, "../cgi-bin/hgTrackUi?hubUrl=%s&db=%s&g=%s&hgsid=%s&%s", + hub->url, genomeOut->genomeName, 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 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); + 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*/ { 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 */ { 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); // The structure here is: // trackData[genome] = [{track 1 obj}, {track2 obj}, {track3 obj}, ... ] // trackData[track1] = [{search hit text}, {subtrack1 search hit}, {subtrack2 search hit}, ... ] // // 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 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); dyStringClear(idString); } void printHubOutputStructure(struct hubOutputStructure *hubOut, struct hubEntry *hubInfo) /* Convert a hubOutputStructure to a jstree-readable string */ { 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. */ { if (hubSearchResult != NULL) printf("<table class='hubList'><tbody>\n"); outputPublicTableRow(hubInfo, count); if (hubSearchResult != NULL) { printf("</tbody></table>\n"); 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"); 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 printHubOutputStructure(hubOut, hubInfo); } } 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) */ { int count = 0; int udcTimeoutVal = udcCacheTimeout(); char *udcOldDir = cloneString(udcDefaultDir()); char *searchUdcDir = cfgOptionDefault("hgHubConnect.cacheDir", udcOldDir); udcSetDefaultDir(searchUdcDir); udcSetCacheTimeout(1<<30); struct hubEntry *hubList = NULL; struct hubEntry *hubInfo; long slTime; long printOutputForHubTime; boolean measureTiming = cartUsualBoolean(cart, "measureTiming", FALSE); 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) { 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); 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"); 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"); } 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; if ((ta == NULL) || (tb == NULL)) return 0; return strcasecmp(tb->shortLabel, ta->shortLabel); } void doMiddle(struct cart *theCart) /* Write header and body of html page. */ { cart = theCart; if(cgiIsOnWeb()) checkForGeoMirrorRedirect(cart); if (cartVarExists(cart, hgHubDoClear)) { doClearHub(cart); cartWebEnd(); return; } if (cartVarExists(cart, hgHubCheckUrl)) { doResetHub(cart); } if (cartVarExists(cart, hgHubDoRedirect)) { if (doRedirect(cart)) { cartWebEnd(); return; } } cartWebStart(cart, NULL, "%s", pageTitle); printf( "<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); 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"); // 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 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"); cartWebEnd(); } char *excludeVars[] = {"Submit", "submit", "hc_one_url", "validateHubUrl", 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; }