2776159fd4f68c3c5a1a114f238dc2f568a5bd64 hiram Fri Sep 27 11:07:16 2024 -0700 allow use of new genark table with more columns refs #32596 diff --git src/hg/hgGateway/hgGateway.c src/hg/hgGateway/hgGateway.c index 00f18be..f262d8e 100644 --- src/hg/hgGateway/hgGateway.c +++ src/hg/hgGateway/hgGateway.c @@ -1,1068 +1,1079 @@ /* hgGateway: make it easy to select a species and assembly * * Copyright (C) 2016 The Regents of the University of California * * This CGI has three modes of operation: * - HTML output for main page (default); most HTML is in hgGateway.html * - cart-based JSON responses to ajax requests from javascript (using hg/lib/cartJson.c) * (if CGI param CARTJSON_COMMAND exists) * - no cart; fast JSON responses to species-search autocomplete requests * (if CGI param SEARCH_TERM exists) */ #include "common.h" #include "cart.h" #include "cartJson.h" #include "cheapcgi.h" #include "errCatch.h" #include "googleAnalytics.h" #include "hCommon.h" #include "hgConfig.h" #include "hdb.h" #include "htmshell.h" #include "hubConnect.h" #include "hui.h" #include "jsHelper.h" #include "jsonParse.h" #include "obscure.h" // for readInGulp #include "regexHelper.h" #include "suggest.h" #include "trackHub.h" #include "web.h" #include "botDelay.h" #include "genark.h" +#include "assemblyList.h" /* Global Variables */ struct cart *cart = NULL; /* CGI and other variables */ struct hash *oldVars = NULL; /* Old contents of cart before it was updated by CGI */ static boolean issueBotWarning = FALSE; static int measureTiming = 0; static long enteredMainTime = 0; #define SEARCH_TERM "hggw_term" static char *maybeGetDescriptionText(char *db) /* Slurp the description.html file for db into a string (if possible, don't die if * we can't read it) and return it. */ { struct errCatch *errCatch = errCatchNew(); char *descText = NULL; if (errCatchStart(errCatch)) { char *htmlPath = hHtmlPath(db); if (isNotEmpty(htmlPath)) descText = udcFileReadAll(htmlPath, NULL, 0, NULL); } errCatchEnd(errCatch); // Just ignore errors for now. return descText; } static int trackHubCountAssemblies(struct trackHub *hub) /* Return the number of hub's genomes that are hub assemblies, i.e. that have a twoBitPath. */ { int count = 0; struct trackHubGenome *genome; for (genome = hub->genomeList; genome != NULL; genome = genome->next) { if (isNotEmpty(genome->twoBitPath)) count++; } return count; } static char *trackHubDefaultAssembly(struct trackHub *hub) /* If hub->defaultDb is an assembly genome, return it; otherwise return the first assembly. * Don't free result. */ { char *defaultDb = hub->defaultDb; char *firstAssemblyDb = NULL; struct trackHubGenome *genome; for (genome = hub->genomeList; genome != NULL; genome = genome->next) { if (isNotEmpty(genome->twoBitPath)) { if (sameString(defaultDb, genome->name)) return defaultDb; else if (firstAssemblyDb == NULL) firstAssemblyDb = genome->name; } } return firstAssemblyDb; } static void listAssemblyHubs(struct jsonWrite *jw) /* Write out JSON describing assembly hubs (not track-only hubs) connected in the cart. */ { jsonWriteListStart(jw, "hubs"); struct hubConnectStatus *status, *statusList = hubConnectStatusListFromCart(cart); for (status = statusList; status != NULL; status = status->next) { struct trackHub *hub = status->trackHub; if (hub == NULL) continue; int assemblyCount = trackHubCountAssemblies(hub); if (assemblyCount > 0) { jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "name", hub->name); jsonWriteString(jw, "shortLabel", hub->shortLabel); jsonWriteString(jw, "longLabel", hub->longLabel); jsonWriteString(jw, "defaultDb", trackHubDefaultAssembly(hub)); jsonWriteString(jw, "hubUrl", status->hubUrl); jsonWriteNumber(jw, "assemblyCount", assemblyCount); jsonWriteString(jw, "errorMessage", status->errorMessage); // We might be able to do better than this for taxId, for example if defaultDb is local // or if hub genomes ever specify taxId... jsonWriteNumber(jw, "taxId", 0); jsonWriteObjectEnd(jw); } } jsonWriteListEnd(jw); } static void writeFindPositionInfo(struct jsonWrite *jw, char *db, int taxId, char *hubUrl, char *position) /* Write JSON for the info needed to populate the 'Find Position' section. */ { char *genome = hGenome(db); if (isEmpty(genome)) { jsonWriteStringf(jw, "error", "No genome for db '%s'", db); } else { jsonWriteString(jw, "db", db); jsonWriteNumber(jw, "taxId", taxId); jsonWriteString(jw, "genome", genome); struct slPair *dbOptions = NULL; char genomeLabel[PATH_LEN*4]; if (isNotEmpty(hubUrl) && !startsWith("/gbdb", hubUrl)) { struct trackHub *hub = hubConnectGetHub(hubUrl); if (hub == NULL) { jsonWriteStringf(jw, "error", "Can't connect to hub at '%s'", hubUrl); return; } struct dbDb *dbDbList = trackHubGetDbDbs(hub->name); dbOptions = trackHubDbDbToValueLabel(dbDbList); safecpy(genomeLabel, sizeof(genomeLabel), hub->shortLabel); jsonWriteString(jw, "hubUrl", hubUrl); } else { dbOptions = hGetDbOptionsForGenome(trackHubSkipHubName(genome)); safecpy(genomeLabel, sizeof(genomeLabel), genome); } jsonWriteValueLabelList(jw, "dbOptions", dbOptions); jsonWriteString(jw, "genomeLabel", genomeLabel); jsonWriteString(jw, "position", position); char *suggestTrack = NULL; if (! trackHubDatabase(db) && (sqlMayConnect(db) != NULL)) suggestTrack = assemblyGeneSuggestTrack(db); jsonWriteString(jw, "suggestTrack", suggestTrack); char *description = maybeGetDescriptionText(db); jsonWriteString(jw, "description", description); listAssemblyHubs(jw); } } static void setTaxId(struct cartJson *cj, struct hash *paramHash) /* Set db and genome according to taxId (and/or db) and return the info we'll need * to fill in the findPosition section. */ { char *taxIdStr = cartJsonRequiredParam(paramHash, "taxId", cj->jw, "setTaxId"); char *db = cartJsonOptionalParam(paramHash, "db"); char *organism = cartJsonOptionalParam(paramHash, "org"); int taxId = atoi(taxIdStr); if (isEmpty(db)) db = hDbForTaxon(taxId); if (isEmpty(db)) jsonWriteStringf(cj->jw, "error", "No db for taxId '%s'", taxIdStr); else { writeFindPositionInfo(cj->jw, db, taxId, NULL, hDefaultPos(db)); cartSetString(cart, "db", db); if (!isEmpty(organism)) cartSetString(cart, "org", organism); cartSetString(cart, "position", hDefaultPos(db)); } } static void setHubDb(struct cartJson *cj, struct hash *paramHash) /* Set db and genome according to hubUrl (and/or db and hub) and return the info we'll need * to fill in the findPosition section. */ { char *hubUrl = cartJsonRequiredParam(paramHash, "hubUrl", cj->jw, "setHubDb"); char *taxIdStr = cartJsonOptionalParam(paramHash, "taxId"); int taxId = taxIdStr ? atoi(taxIdStr) : -1; // cart's db was already set by magic handling of hub CGI variables sent along // with this command. char *db = cartString(cart, "db"); if (isEmpty(db)) jsonWriteStringf(cj->jw, "error", "No db for hubUrl '%s'", hubUrl); else writeFindPositionInfo(cj->jw, db, taxId, hubUrl, hDefaultPos(db)); } static void setDb(struct cartJson *cj, struct hash *paramHash) /* Set taxId and genome according to db and return the info we'll need to fill in * the findPosition section. */ { char *db = cartJsonRequiredParam(paramHash, "db", cj->jw, "setDb"); char *hubUrl = cartJsonOptionalParam(paramHash, "hubUrl"); // we want to go back to the most recent position on this db // so push "lastDbPos" into the cart so cartGetPosition() can find it char *maybePosition = cartJsonOptionalParam(paramHash, "position"); if (maybePosition) cartSetString(cart, "position", maybePosition); int taxId = hTaxId(db); // look up the old position the user was browsing (if they came here from // a hub connection for instance) and start them there, otherwise use // the assembly default position char *maybeLastPos = cartGetPosition(cart, db, NULL); char *pos = maybeLastPos != NULL ? maybeLastPos : hDefaultPos(db); writeFindPositionInfo(cj->jw, db, taxId, hubUrl, pos); cartSetString(cart, "db", db); cartSetString(cart, "position", pos); } static void getUiState(struct cartJson *cj, struct hash *paramHash) /* Write out JSON for hgGateway.js's uiState object using current cart settings. */ { char *db = cartUsualString(cj->cart, "db", hDefaultDb()); char *position = cartUsualString(cart, "position", hDefaultPos(db)); char *hubUrl = NULL; if (trackHubDatabase(db)) { struct trackHub *hub = hubConnectGetHubForDb(db); hubUrl = hub->url; } writeFindPositionInfo(cj->jw, db, hTaxId(db), hubUrl, position); // If cart already has a pix setting, pass that along; otherwise the JS will // set pix according to web browser window width. int pix = cartUsualInt(cj->cart, "pix", 0); if (pix) jsonWriteNumber(cj->jw, "pix", pix); } static void doCartJson() /* Perform UI commands to update the cart and/or retrieve cart vars & metadata. */ { struct cartJson *cj = cartJsonNew(cart); cartJsonRegisterHandler(cj, "setTaxId", setTaxId); cartJsonRegisterHandler(cj, "setDb", setDb); cartJsonRegisterHandler(cj, "setHubDb", setHubDb); cartJsonRegisterHandler(cj, "getUiState", getUiState); cartJsonExecute(cj); } static void printActiveGenomes(struct dyString *dy) /* Print out JSON for an object mapping each genome that has at least one db with active=1 * to its taxId. */ { struct jsonWrite *jw = jsonWriteNew(); jsonWriteObjectStart(jw, NULL); struct sqlConnection *conn = hConnectCentral(); // Join with defaultDb because in rare cases, different taxIds (species vs. subspecies) // may be used for different assemblies of the same species. Using defaultDb means that // we send a taxId consistent with the taxId of the assembly that we'll change to when // the species is selected from the tree. struct dyString *query = sqlDyStringCreate( "select dbDb.genome, taxId, dbDb.name from dbDb, defaultDb " "where defaultDb.name = dbDb.name and active = 1 " "and taxId > 1;"); // filter out experimental hgwdev-only stuff with invalid taxIds struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query)); char **row; while ((row = sqlNextRow(sr)) != NULL) { char *genome = row[0], *db = row[2]; int taxId = atoi(row[1]); if (hDbExists(db)) jsonWriteNumber(jw, genome, taxId); } hDisconnectCentral(&conn); jsonWriteObjectEnd(jw); dyStringAppend(dy, jw->dy->string); jsonWriteFree(&jw); dyStringFree(&query); } static void doMainPage() /* Send HTML with javascript to bootstrap the user interface. */ { // Start web page with new banner char *db = NULL, *genome = NULL, *clade = NULL; getDbGenomeClade(cart, &db, &genome, &clade, oldVars); // If CGI has &lastDbPos=..., handle that here and save position to cart so it's in place for // future cartJson calls. char *position = cartGetPosition(cart, db, NULL); cartSetString(cart, "position", position); webStartJWest(cart, db, "Genome Browser Gateway"); if (cgiIsOnWeb()) checkForGeoMirrorRedirect(cart); #define HOG_WARNING_BOX_START "
" \ "
" #define HOG_WARNING_BOX_END "
" if (issueBotWarning) { char *hogHost = getenv("REMOTE_ADDR"); char *delayMsg = botDelayWarningMsg(hogHost, botDelayMillis); printf("%s%s%s\n", HOG_WARNING_BOX_START, delayMsg, HOG_WARNING_BOX_END); } #define WARNING_BOX_START "
" \ "
" #define UNDER_DEV "Data and tools on this site are under development, have not been reviewed " \ "for quality, and are subject to change at any time. " #define MAIN_SITE "The high-quality, reviewed public site of the UCSC Genome Browser is " \ "available for use at http://genome.ucsc.edu/." #define WARNING_BOX_END "
" if (hIsPreviewHost()) { puts(WARNING_BOX_START "WARNING: This is the UCSC Genome Browser preview site. " "This website is a weekly mirror of our internal development server for public access. " UNDER_DEV "We provide this site for early access, with the warning that it is less available " "and stable than our public site. " MAIN_SITE WARNING_BOX_END); } if (hIsPrivateHost() && !hHostHasPrefix("hgwdev-demo6")) { puts(WARNING_BOX_START "WARNING: This is the UCSC Genome Browser development site. " "This website is used for testing purposes only and is not intended for general public " "use. " UNDER_DEV MAIN_SITE WARNING_BOX_END); } // The visible page elements are all in ./hgGateway.html, which is transformed into a quoted .h // file containing a string constant that we #include and print here (see makefile). puts( #include "hgGateway.html.h" ); // Set global JS variables hgsid, activeGenomes, and survey* at page load time // We can't just use "var hgsid = " or the other scripts won't see it -- it has to be // "window.hgsid = ". struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, "window.%s = '%s';\n", cartSessionVarName(), cartSessionId(cart)); dyStringPrintf(dy, "window.activeGenomes =\n"); printActiveGenomes(dy); dyStringPrintf(dy, "\n;\n"); char *surveyLink = cfgOption("survey"); if (isNotEmpty(surveyLink) && !sameWord(surveyLink, "off")) { dyStringPrintf(dy, "window.surveyLink=\"%s\";\n", jsonStringEscape(surveyLink)); char *surveyLabel = cfgOptionDefault("surveyLabel", "Please take our survey"); dyStringPrintf(dy, "window.surveyLabel=\"%s\";\n", jsonStringEscape(surveyLabel)); char *surveyLabelImage = cfgOption("surveyLabelImage"); if (isNotEmpty(surveyLabelImage)) dyStringPrintf(dy, "window.surveyLabelImage=\"%s\";\n", jsonStringEscape(surveyLabelImage)); else dyStringPrintf(dy, "window.surveyLabelImage=null;\n"); } else { dyStringPrintf(dy, "window.surveyLink=null;\n"); dyStringPrintf(dy, "window.surveyLabel=null;\n"); dyStringPrintf(dy, "window.surveyLabelImage=null;\n"); } dyStringPrintf(dy, "hgGateway.init();\n"); jsInline(dy->string); dyStringFree(&dy); jsIncludeFile("es5-shim.4.0.3.min.js", NULL); jsIncludeFile("es5-sham.4.0.3.min.js", NULL); jsIncludeFile("lodash.3.10.0.compat.min.js", NULL); jsIncludeFile("cart.js", NULL); webIncludeResourceFile("jquery-ui.css"); jsIncludeFile("jquery-ui.js", NULL); jsIncludeFile("jquery.watermarkinput.js", NULL); jsIncludeFile("autocompleteCat.js",NULL); jsIncludeFile("utils.js",NULL); // Phylogenetic tree .js file, produced by dbDbTaxonomy.pl: char *defaultDbDbTree = webTimeStampedLinkToResource("dbDbTaxonomy.js", FALSE); char *dbDbTree = cfgOptionDefault("hgGateway.dbDbTaxonomy", defaultDbDbTree); if (isNotEmpty(dbDbTree)) printf("\n", dbDbTree); // Main JS for hgGateway: jsIncludeFile("hgGateway.js", NULL); #define TIMING_WARNING_BOX_START "
" \ "
" #define TIMING_WARNING_BOX_END "
" if (measureTiming) { printf("%selapsed time %ld ms (%d ms bottleneck)%s\n", TIMING_WARNING_BOX_START, clock1000() - enteredMainTime, botDelayMillis, TIMING_WARNING_BOX_END); } webIncludeFile("inc/jWestFooter.html"); cartFlushHubWarnings(); webEndJWest(); } void doMiddle(struct cart *theCart) /* Depending on invocation, either perform a query and print out results * or display the main page. */ { cart = theCart; if (cgiOptionalString(CARTJSON_COMMAND)) doCartJson(); else doMainPage(); } // We find matches from various fields of dbDb, and prefer them in this order: enum dbDbMatchType { ddmtDescription=0, ddmtGenome=1, ddmtDb=2, ddmtSciName=3 }; struct dbDbMatch // Info about a match of a search term to some field of dbDb, including info that // helps prioritize matches. { struct dbDbMatch *next; struct dbDb *dbDb; // the row of dbDb in which a match was found enum dbDbMatchType type; // which field the match was found in int offset; // offset of the search term in the dbDb value boolean isWord; // TRUE if the the search term matches the word at offset boolean isComplete; // TRUE if the search term matches the entire target string }; static struct dbDbMatch *dbDbMatchNew(struct dbDb *dbDb, enum dbDbMatchType type, int offset, boolean isWord, boolean isComplete) /* Allocate and return a new dbDbMatch. Do not free dbDb until done with this. */ { struct dbDbMatch *ddm; AllocVar(ddm); ddm->dbDb = dbDb; ddm->type = type; ddm->offset = offset; ddm->isWord = isWord; ddm->isComplete = isComplete; return ddm; } static int dbDbMatchCmp(const void *va, const void *vb) /* Compare two matches by type, orderKey, offset and genome. */ { const struct dbDbMatch *a = *((struct dbDbMatch **)va); const struct dbDbMatch *b = *((struct dbDbMatch **)vb); int diff = b->isComplete - a->isComplete; if (diff == 0) diff = b->isWord - a->isWord; if (diff == 0 && a->isWord && b->isWord) diff = a->offset - b->offset; // Use int values of type: if (diff == 0) diff = (int)(a->type) - (int)(b->type); if (diff == 0) diff = a->dbDb->orderKey - b->dbDb->orderKey; if (diff == 0) diff = a->offset - b->offset; if (diff == 0) diff = strcmp(a->dbDb->genome, b->dbDb->genome); return diff; } INLINE void safeAddN(char **pDest, int *pSize, char *src, int len) /* Copy len bytes of src into dest. Subtract len from *pSize and add len to *pDest, * for building up a string bit by bit. */ { safencpy(*pDest, *pSize, src, len); *pSize -= len; *pDest += len; } INLINE void safeAdd(char **pDest, int *pSize, char *src) /* Copy src into dest. Subtract len from *pSize and add len to *pDest, * for building up a string bit by bit. */ { safeAddN(pDest, pSize, src, strlen(src)); } static char *boldTerm(char *target, char *term, int offset, enum dbDbMatchType type) /* Return a string with term swapped in for term at offset. * If offset is negative and type is ddmtSciName, treat term as an abbreviated species * name (term = "G. species" vs. target = "Genus species"): bold the first letter of the * genus and the matching portion of the species. */ { int termLen = strlen(term); int targetLen = strlen(target); if (type == ddmtDescription) { // Search of dbDb->description skips the date that precedes the actual description which is // in parentheses. Adjust offset accordingly. char *leftP = strchr(target, '('); if (leftP) offset += (leftP+1 - target); } if (offset + termLen > targetLen) errAbort("boldTerm: invalid offset (%d) for term '%s' (length %d) in target '%s' (length %d)", offset, term, termLen, target, targetLen); else if (offset < 0 && type != ddmtSciName) errAbort("boldTerm: negative offset (%d) given for type %d", offset, type); // Allocate enough to have two bolded chunks: int resultSize = targetLen + 2*strlen("") + 1; char result[resultSize]; char *p = result; int size = sizeof(result); if (offset >= 0) { // The part of target before the term: safeAddN(&p, &size, target, offset); // The bolded term: safeAdd(&p, &size, ""); safeAddN(&p, &size, target+offset, termLen); safeAdd(&p, &size, ""); // The rest of the target after the term: safeAdd(&p, &size, target+offset+termLen); // Accounting tweak -- we allocate enough for two bolded chunks, but use only one here: size -= strlen(""); } else { // Term is abbreviated scientific name -- bold the first letter of the genus: safeAdd(&p, &size, ""); safeAddN(&p, &size, target, 1); safeAdd(&p, &size, ""); // add the rest of the genus: char *targetSpecies = skipLeadingSpaces(skipToSpaces(target)); int targetOffset = targetSpecies - target; safeAddN(&p, &size, target+1, targetOffset-1); // bold the matching portion of the species: char *termSpecies = skipLeadingSpaces(skipToSpaces(term)); termLen = strlen(termSpecies); safeAdd(&p, &size, ""); safeAddN(&p, &size, targetSpecies, termLen); safeAdd(&p, &size, ""); // add the rest of the species: safeAdd(&p, &size, targetSpecies+termLen); } if (*p != '\0' || size != 1) errAbort("boldTerm: bad arithmetic (size is %d, *p is '%c')", size, *p); return cloneStringZ(result, resultSize); } static void writeDbDbMatch(struct jsonWrite *jw, struct dbDbMatch *match, char *term, char *category) /* Write out the JSON encoding of a match in dbDb. */ { struct dbDb *dbDb = match->dbDb; jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "genome", dbDb->genome); // label includes tag to highlight the match for term. char label[PATH_LEN*4]; // value is placed in the input box when user selects the item. char value[PATH_LEN*4]; if (match->type == ddmtSciName) { safef(value, sizeof(value), "%s (%s)", dbDb->scientificName, dbDb->genome); char *bolded = boldTerm(dbDb->scientificName, term, match->offset, match->type); safef(label, sizeof(label), "%s (%s)", bolded, dbDb->genome); freeMem(bolded); } else if (match->type == ddmtGenome) { safecpy(value, sizeof(value), dbDb->genome); char *bolded = boldTerm(dbDb->genome, term, match->offset, match->type); safecpy(label, sizeof(label), bolded); freeMem(bolded); } else if (match->type == ddmtDb) { safecpy(value, sizeof(value), dbDb->name); char *bolded = boldTerm(dbDb->name, term, match->offset, match->type); safef(label, sizeof(label), "%s (%s %s)", bolded, dbDb->genome, dbDb->description); freeMem(bolded); jsonWriteString(jw, "db", dbDb->name); } else if (match->type == ddmtDescription) { safef(value, sizeof(value), "%s (%s %s)", dbDb->name, dbDb->genome, dbDb->description); char *bolded = boldTerm(dbDb->description, term, match->offset, match->type); safef(label, sizeof(label), "%s (%s %s)", dbDb->name, dbDb->genome, bolded); freeMem(bolded); jsonWriteString(jw, "db", dbDb->name); } else errAbort("writeDbDbMatch: unrecognized dbDbMatchType value %d (db %s, term %s)", match->type, dbDb->name, term); jsonWriteString(jw, "label", label); jsonWriteString(jw, "value", value); jsonWriteString(jw, "org", dbDb->organism); jsonWriteNumber(jw, "taxId", dbDb->taxId); if (isNotEmpty(category)) jsonWriteString(jw, "category", category); jsonWriteObjectEnd(jw); } int wordMatchOffset(char *term, char *target) /* If some word of target starts with term (case insensitive), return the offset of * that word in target; otherwise return -1. */ { if (startsWith(term, target)) return 0; int targetLen = strlen(target); char targetClone[targetLen+1]; safecpy(targetClone, sizeof(targetClone), target); char *p = targetClone; while (nextWord(&p) && p != NULL) { // skip punctuation like parentheses while (*p != '\0' && ! isalnum(*p)) p++; if (startsWith(term, p)) return p - targetClone; } return -1; } static void addIfFirstMatch(struct dbDb *dbDb, enum dbDbMatchType type, int offset, char *target, char *term, struct hash *matchHash, struct dbDbMatch **pMatchList) /* If target doesn't already have a match in matchHash, compute matchLength and isWord, * and then add the new match to pMatchList and add target to matchHash. */ { if (dbDb->active && ! hashLookup(matchHash, target)) { char *termInTarget = (offset >= 0) ? target+offset : target; int matchLength = countSame(term, termInTarget); // is the match complete up to a word boundary in termInTarget? boolean isWord = (matchLength == strlen(term) && (termInTarget[matchLength] == '\0' || isspace(termInTarget[matchLength]))); boolean isComplete = sameString(term, target); struct dbDbMatch *match = dbDbMatchNew(dbDb, type, offset, isWord, isComplete); slAddHead(pMatchList, match); hashStore(matchHash, target); } } static void checkTerm(char *term, char *target, enum dbDbMatchType type, struct dbDb *dbDb, struct hash *matchHash, struct dbDbMatch **pMatchList) /* If target starts with term (case-insensitive), and target is not already in matchHash, * add target to matchHash and add a new match to pMatchList. */ { // Make uppercase version of target for case-insensitive matching. int targetLen = strlen(target); char targetUpcase[targetLen + 1]; safencpy(targetUpcase, sizeof(targetUpcase), target, targetLen); touppers(targetUpcase); int offset = wordMatchOffset(term, targetUpcase); if (offset >= 0) { addIfFirstMatch(dbDb, type, offset, targetUpcase, term, matchHash, pMatchList); } else if (offset < 0 && type == ddmtSciName && term[0] == targetUpcase[0]) { // For scientific names ("Genus species"), see if the user entered the term as 'G. species' // e.g. term 'P. trog' for target 'Pan troglodytes' regmatch_t substrArr[3]; if (regexMatchSubstrNoCase(term, "^[a-z](\\.| ) *([a-z]+)", substrArr, ArraySize(substrArr))) { char *termSpecies = term + substrArr[2].rm_so; char *targetSpecies = skipLeadingSpaces(skipToSpaces(targetUpcase)); if (targetSpecies && startsWithNoCase(termSpecies, targetSpecies)) { // Keep the negative offset since we can't just bold one chunk of target... addIfFirstMatch(dbDb, type, offset, targetUpcase, term, matchHash, pMatchList); } } } } static struct dbDbMatch *searchDbDb(struct dbDb *dbDbList, char *term) /* Search various fields of dbDb for matches to term and sort by relevance. */ { struct dbDbMatch *matchList = NULL; struct hash *matchHash = hashNew(0); struct dbDb *dbDb; for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next) { checkTerm(term, dbDb->name, ddmtDb, dbDb, matchHash, &matchList); // Skip experimental stuff on hgwdev with bogus taxId unless the db name matches term. if (dbDb->taxId >= 2) { checkTerm(term, dbDb->genome, ddmtGenome, dbDb, matchHash, &matchList); checkTerm(term, dbDb->scientificName, ddmtSciName, dbDb, matchHash, &matchList); } // dbDb.description has dozens of matches for some institutions like Broad, so suppress // it for search terms that would get too many probably unwanted matches. if (! (startsWith(term, "BRO") || startsWith(term, "WU") || startsWith(term, "BAY") || startsWith(term, "AGE"))) { // dbDb.description also starts with dates followed by actual description in parentheses, // so search only the part in parentheses to avoid month prefix matches. char *leftP = strchr(dbDb->description, '('); char *toSearch = leftP ? leftP+1 : dbDb->description; checkTerm(term, toSearch, ddmtDescription, dbDb, matchHash, &matchList); } } slSort(&matchList, dbDbMatchCmp); return matchList; } // Assembly hub match: struct aHubMatch // description of an assembly hub db { struct aHubMatch *next; char *shortLabel; // hub shortLabel char *hubUrl; // hub url char *aDb; // assembly db hosted by hub char *label; // label for this db }; static struct aHubMatch *aHubMatchNew(char *shortLabel, char *hubUrl, char *aDb, char *label) /* Allocate and return a description of an assembly hub db. */ { struct aHubMatch *match; AllocVar(match); match->shortLabel = cloneString(shortLabel); match->hubUrl = cloneString(hubUrl); match->aDb = cloneString(aDb); match->label = cloneString(label); return match; } // Genark hub match: struct gHubMatch // description of an genark hub db { struct gHubMatch *next; char *gcAccession; char *hubUrl; char *asmName; char *scientificName; char *commonName; int priority; // reserver for later ranking, currently unused }; static struct gHubMatch *gHubMatchNew(char *acc, char *hubUrl, char *asmName, char *scientificName, char *commonName, int priority) /* Allocate and return a description of an assembly hub db. */ { struct gHubMatch *match; AllocVar(match); match->gcAccession = cloneString(acc); match->hubUrl = cloneString(hubUrl); match->asmName = cloneString(asmName); match->scientificName = cloneString(scientificName); match->commonName = cloneString(commonName); match->priority = priority; return match; } static struct hash *unpackHubDbUrlList(struct slName *hubDbUrlList, struct hash **labelHash) /* hubDbUrlList contains strings like "db\tlabel\thubUrl" -- split on tab and return a hash of * hubUrl to one or more dbs. */ { struct hash *hubToDb = hashNew(0); struct hash *dbToLabel = hashNew(0); struct slName *hubDbUrl; for (hubDbUrl = hubDbUrlList; hubDbUrl != NULL; hubDbUrl = hubDbUrl->next) { char *tab = strchr(hubDbUrl->name, '\t'); if (tab) { char *db = hubDbUrl->name; *tab = '\0'; char *label = tab+1; char *url = strchr(label, '\t'); if (url) { *url = '\0'; char *hubUrl = url+1; struct hashEl *hel = hashLookup(hubToDb, hubUrl); struct slName *dbList = hel ? hel->val : NULL; slAddHead(&dbList, slNameNew(db)); if (hel == NULL) hashAdd(hubToDb, hubUrl, dbList); else hel->val = dbList; } hashAdd(dbToLabel, db, label); } } *labelHash = dbToLabel; return hubToDb; } static struct aHubMatch *filterHubSearchTextMatches(struct dbDb *dbDbList, struct slName *hubDbUrlList) /* Collect the assembly hub matches (not track hub matches) from a search in hubSearchText. */ { if (hubDbUrlList == NULL) return NULL; struct aHubMatch *aHubMatchList = NULL; // Make a hash of local dbs so we can tell which hub dbs must be assembly hubs // not track hubs. struct hash *localDbs = hashNew(0); struct dbDb *dbDb; for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next) if (!sameString(dbDb->nibPath, "genark")) hashStore(localDbs, dbDb->name); struct hash *dbLabel = NULL; struct hash *hubToDb = unpackHubDbUrlList(hubDbUrlList, &dbLabel); // Build up a query to find shortLabel and dbList for each hubUrl. struct dyString *query = sqlDyStringCreate("select shortLabel,hubUrl,dbList from %s " "where hubUrl in (", hubPublicTableName()); struct hashEl *hel; struct hashCookie cookie = hashFirst(hubToDb); boolean isFirst = TRUE; while ((hel = hashNext(&cookie)) != NULL) { if (isFirst) isFirst = FALSE; else sqlDyStringPrintf(query, ", "); sqlDyStringPrintf(query, "'%s'", hel->name); } sqlDyStringPrintf(query, ")"); struct sqlConnection *conn = hConnectCentral(); struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query)); char **row; while ((row = sqlNextRow(sr)) != NULL) { char *shortLabel = row[0]; char *hubUrl = row[1]; struct slName *dbName, *matchDbList = hashFindVal(hubToDb, hubUrl); struct slName *hubDbList = slNameListFromComma(row[2]); if (slCount(matchDbList) == 1 && isEmpty(matchDbList->name)) { // top-level hub match, no specific db match; add all of hub's assembly dbs for (dbName = hubDbList; dbName != NULL; dbName = dbName->next) if (! hashLookup(localDbs, dbName->name)) slAddHead(&aHubMatchList, aHubMatchNew(shortLabel, hubUrl, dbName->name, NULL)); } else { // Add matching assembly dbs that are found in hubDbList for (dbName = matchDbList; dbName != NULL; dbName = dbName->next) if (! hashLookup(localDbs, dbName->name) && slNameInList(hubDbList, dbName->name)) { char *label = hashFindVal(dbLabel, dbName->name); if (label) slAddHead(&aHubMatchList, aHubMatchNew(shortLabel, hubUrl, dbName->name, label)); else slAddHead(&aHubMatchList, aHubMatchNew(shortLabel, hubUrl, dbName->name, NULL)); } } } slReverse(&aHubMatchList); hDisconnectCentral(&conn); dyStringFree(&query); return aHubMatchList; } static void writeAssemblyHubMatches(struct jsonWrite *jw, struct aHubMatch *aHubMatchList) /* Write out JSON for each assembly in each assembly hub that matched the search term. */ { struct aHubMatch *aHubMatch; for (aHubMatch = aHubMatchList; aHubMatch != NULL; aHubMatch = aHubMatch->next) { jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "genome", aHubMatch->shortLabel); jsonWriteString(jw, "db", aHubMatch->aDb); jsonWriteString(jw, "hubUrl", aHubMatch->hubUrl); jsonWriteString(jw, "hubName", hubNameFromUrl(aHubMatch->hubUrl)); // Add a category label for customized autocomplete-with-categories. char category[PATH_LEN*4]; safef(category, sizeof(category), "Assembly Hub: %s", aHubMatch->shortLabel); jsonWriteString(jw, "category", category); jsonWriteString(jw, "value", aHubMatch->aDb); // Use just the db as label, since shortLabel is included in the category label. jsonWriteString(jw, "label", aHubMatch->label); jsonWriteObjectEnd(jw); } } static struct aHubMatch *searchPublicHubs(struct dbDb *dbDbList, char *term) /* Search for term in public hubs -- return a list of matches to assembly hubs * (i.e. hubs that host an assembly with 2bit etc as opposed to only providing tracks.) */ { struct aHubMatch *aHubMatchList = NULL; char *hubSearchTableName = cfgOptionDefault("hubSearchTextTable", "hubSearchText"); struct sqlConnection *conn = hConnectCentral(); if (sqlTableExists(conn, hubSearchTableName)) { char query[1024]; sqlSafef(query, sizeof(query), "select distinct(concat(db, concat(concat('\t', label), concat('\t', hubUrl)))) from %s " "where track = '' and " "(db like '%s%%' or label like '%%%s%%' or text like '%s%%')", hubSearchTableName, term, term, term); struct slName *hubDbUrlList = sqlQuickList(conn, query); aHubMatchList = filterHubSearchTextMatches(dbDbList, hubDbUrlList); if (aHubMatchList == NULL) { // Try a looser query sqlSafef(query, sizeof(query), "select distinct(concat(db, concat(concat('\t', label), concat('\t', hubUrl)))) from %s " "where track = '' and text like '%% %s%%'", hubSearchTableName, term); hubDbUrlList = sqlQuickList(conn, query); aHubMatchList = filterHubSearchTextMatches(dbDbList, hubDbUrlList); } } hDisconnectCentral(&conn); return aHubMatchList; } static void writeGenarkMatches(struct jsonWrite *jw, struct gHubMatch *gHubMatchList) /* Write out JSON for each genark hub that matched the users term */ { struct gHubMatch *gHubMatch; for (gHubMatch = gHubMatchList; gHubMatch != NULL; gHubMatch = gHubMatch->next) { jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "genome", gHubMatch->gcAccession); jsonWriteString(jw, "db", gHubMatch->asmName); jsonWriteString(jw, "hubUrl", gHubMatch->hubUrl); jsonWriteString(jw, "scientificName", gHubMatch->scientificName); // Add a category label for customized autocomplete-with-categories. jsonWriteString(jw, "category", "UCSC GenArk - bulk-annotated assemblies from NCBI Genbank/RefSeq"); jsonWriteString(jw, "value", gHubMatch->asmName); // Use just the db as label, since shortLabel is included in the category label. jsonWriteStringf(jw, "label", "%s - %s", gHubMatch->commonName, gHubMatch->scientificName); jsonWriteObjectEnd(jw); } } static struct gHubMatch *filterGenarkMatches(char *genarkHubUrl, struct genark *matchList) /* Turn the sql results into a struct gHubMatch list */ { struct genark *match; struct gHubMatch *ret = NULL; for (match = matchList; match != NULL; match = match->next) { // the match contains tab-sep accession, hubUrl, asmName, scientificName, commonName char hubUrl[PATH_LEN+1]; safef(hubUrl, sizeof(hubUrl), "%s/%s", genarkHubUrl, match->hubUrl); slAddHead(&ret, gHubMatchNew(match->gcAccession, hubUrl, match->asmName, match->scientificName, match->commonName, -1)); } if (ret) slReverse(&ret); return ret; } static struct gHubMatch *searchGenark(char *term) /* Search through the genark table for hubs matches term */ { char *genarkPrefix = cfgOption("genarkHubPrefix"); if (genarkPrefix == NULL) return NULL; struct gHubMatch *gHubMatchList = NULL; char *genarkTbl = genarkTableName(); +int colCount = genArkColumnCount(); struct sqlConnection *conn = hConnectCentral(); if (sqlTableExists(conn, genarkTbl)) { char query[1024]; + if (colCount > 6) + { + sqlSafef(query, sizeof(query), "select * from %s where " + "(gcAccession like '%%%s%%' or scientificName like '%%%s%%' or commonName like '%%%s%%' or asmName like '%%%s%%') order by priority", + genarkTbl, term, term, term, term); + } + else + { sqlSafef(query, sizeof(query), "select * from %s where " "(gcAccession like '%%%s%%' or scientificName like '%%%s%%' or commonName like '%%%s%%' or asmName like '%%%s%%') order by taxId ASC, commonName DESC", genarkTbl, term, term, term, term); + } struct genark *matchList = genarkLoadByQuery(conn, query); gHubMatchList = filterGenarkMatches(genarkPrefix, matchList); } hDisconnectCentral(&conn); return gHubMatchList; } static char *getSearchTermUpperCase() /* If we don't have the SEARCH_TERM cgi param, exit with an HTTP Bad Request response. * If we do, convert it to upper case for case-insensitive matching and return it. */ { pushWarnHandler(htmlVaBadRequestAbort); pushAbortHandler(htmlVaBadRequestAbort); char *cgiTerm = cgiOptionalString(SEARCH_TERM); char *term = skipLeadingSpaces(cgiTerm); eraseTrailingSpaces(term); touppers(term); if (isEmpty(term)) errAbort("Missing required CGI parameter %s", SEARCH_TERM); popWarnHandler(); popAbortHandler(); return term; } static void lookupTerm() /* Look for matches to term in hgcentral and print as JSON for autocomplete if found. */ { char *term = getSearchTermUpperCase(); // Write JSON response with list of matches puts("Content-Type:text/javascript\n"); // Before accessing hubs, intialize udc cache location from hg.conf: setUdcCacheDir(); struct dbDb *dbDbList = hDbDbList(); struct dbDbMatch *matchList = searchDbDb(dbDbList, term); struct gHubMatch *gHubMatchList = searchGenark(term); struct aHubMatch *aHubMatchList = searchPublicHubs(dbDbList, term); struct jsonWrite *jw = jsonWriteNew(); jsonWriteListStart(jw, NULL); // Write out JSON for dbDb matches, if any; add category if we found assembly hub matches too. char *category = aHubMatchList ? "UCSC Genome Browser assemblies - annotation tracks curated by UCSC" : NULL; struct dbDbMatch *match; for (match = matchList; match != NULL; match = match->next) writeDbDbMatch(jw, match, term, category); // Write out genark matches, if any writeGenarkMatches(jw, gHubMatchList); // Write out assembly hub matches, if any. writeAssemblyHubMatches(jw, aHubMatchList); jsonWriteListEnd(jw); puts(jw->dy->string); jsonWriteFree(&jw); } int main(int argc, char *argv[]) /* Process CGI / command line. */ { /* Null terminated list of CGI Variables we don't want to save * permanently. */ char *excludeVars[] = {SEARCH_TERM, CARTJSON_COMMAND, NULL,}; cgiSpoof(&argc, argv); measureTiming = cgiOptionalInt("measureTiming", 0); enteredMainTime = clock1000(); if (cgiOptionalString(SEARCH_TERM)) { /* less bottleneck penalty for this operation, same as hgTracks */ #define delayFraction 0.25 issueBotWarning = earlyBotCheck(enteredMainTime, "hgGateway", delayFraction, 0, 0, "json"); // Skip the cart for speedy searches lookupTerm(); } else { /* standard default bottleneck penalty for this operation */ issueBotWarning = earlyBotCheck(enteredMainTime, "hgGateway", 0.0, 0, 0, "html"); oldVars = hashNew(10); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); cgiExitTime("hgGateway", enteredMainTime); } return 0; }