7033f67074594c3d9cc3487f079456928fdf3260
angie
Tue Apr 12 13:46:14 2016 -0700
Major change to hgGateway: the contents are replaced by a new page designed by a graphic artist.
It has icons for selecting popular species, an autocomplete input for typing in species or common names,
as well as a phylogenetic tree display that shows the relationships of the species that we host.
It has a menu for selecting the assembly of the selected species' genome and the usual assembly
description.
refs #15277
diff --git src/hg/hgGateway/hgGateway.c src/hg/hgGateway/hgGateway.c
index 330bce8..fc5a359 100644
--- src/hg/hgGateway/hgGateway.c
+++ src/hg/hgGateway/hgGateway.c
@@ -1,310 +1,741 @@
-/* hgGateway - Human Genome Browser Gateway. */
-
-/* Copyright (C) 2014 The Regents of the University of California
- * See README in this or parent directory for licensing information. */
+/* 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 "linefile.h"
-#include "hash.h"
-#include "cheapcgi.h"
-#include "htmshell.h"
-#include "obscure.h"
-#include "web.h"
#include "cart.h"
-#include "hdb.h"
-#include "dbDb.h"
-#include "hgFind.h"
+#include "cartJson.h"
+#include "cheapcgi.h"
+#include "errCatch.h"
+#include "googleAnalytics.h"
#include "hCommon.h"
-#include "hui.h"
-#include "customTrack.h"
-#include "hubConnect.h"
#include "hgConfig.h"
+#include "hdb.h"
+#include "htmshell.h"
+#include "hubConnect.h"
+#include "hui.h"
#include "jsHelper.h"
-#include "hPrint.h"
+#include "jsonParse.h"
+#include "obscure.h" // for readInGulp
+#include "regexHelper.h"
#include "suggest.h"
-#include "search.h"
-#include "geoMirror.h"
#include "trackHub.h"
+#include "trix.h"
+#include "web.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 */
+
+#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);
+ 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;
+}
-struct cart *cart = NULL;
-struct hash *oldVars = NULL;
-char *clade = NULL;
-char *organism = NULL;
-char *db = NULL;
+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 = hubConnectStatusListFromCartAll(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);
+}
-// TODO REMOVE AFTER AUTOUPGRADE COMPLETE: (added 2014-03-09)
-extern struct dyString *dyUpgradeError;
-void hgGateway()
-/* hgGateway - Human Genome Browser Gateway. */
+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))
{
-char *defaultPosition = hDefaultPos(db);
-char *position = cloneString(cartUsualString(cart, "position", defaultPosition));
-boolean gotClade = hGotClade();
-char *survey = cfgOptionEnv("HGDB_SURVEY", "survey");
-char *surveyLabel = cfgOptionEnv("HGDB_SURVEY_LABEL", "surveyLabel");
-boolean supportsSuggest = FALSE;
+ 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))
+ {
+ 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(genome);
+ safecpy(genomeLabel, sizeof(genomeLabel), genome);
+ }
+ jsonWriteValueLabelList(jw, "dbOptions", dbOptions);
+ jsonWriteString(jw, "genomeLabel", genomeLabel);
+ jsonWriteString(jw, "position", position);
+ char *suggestTrack = NULL;
if (! trackHubDatabase(db))
- supportsSuggest = assemblySupportsGeneSuggest(db);
+ suggestTrack = assemblyGeneSuggestTrack(db);
+ jsonWriteString(jw, "suggestTrack", suggestTrack);
+ char *description = maybeGetDescriptionText(db);
+ //#*** TODO: move jsonStringEscape inside jsonWriteString
+ char *encoded = jsonStringEscape(description);
+ jsonWriteString(jw, "description", encoded);
+ listAssemblyHubs(jw);
+ }
+}
-/* JavaScript to copy input data on the change genome button to a hidden form
-This was done in order to be able to flexibly arrange the UI HTML
-*/
-char *onChangeDB = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\"";
-char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\"";
-char *onChangeClade = "onchange=\"document.orgForm.clade.value = document.mainForm.clade.options[document.mainForm.clade.selectedIndex].value; document.orgForm.org.value = 0; document.orgForm.db.value = 0; document.orgForm.submit();\"";
-
-/*
- If we are changing databases via explicit cgi request,
- then remove custom track data which will
- be irrelevant in this new database .
- If databases were changed then use the new default position too.
-*/
+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");
+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);
+ 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");
+int taxId = hTaxId(db);
+writeFindPositionInfo(cj->jw, db, taxId, hubUrl, hDefaultPos(db));
+cartSetString(cart, "db", db);
+cartSetString(cart, "position", hDefaultPos(db));
+}
+
+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 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);
+webStartJWest(cart, db, "Genome Browser Gateway");
+
+// Edit the HTML in hgGateway.html (see makefile):
+puts(
+#include "hgGateway.html.h"
+);
-if (sameString(position, "genome") || sameString(position, "hgBatch"))
- position = defaultPosition;
+// Set global JS variable hgsid
+// We can't just use "var hgsid = " or the other scripts won't see it -- it has to be
+// "window.hgsid = ".
+puts("");
+
+puts("");
+puts("");
+puts("");
+puts("");
-jsIncludeFile("jquery.js", NULL);
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("jquery-ui.js", NULL);
-jsIncludeFile("ajax.js", NULL);
-jsIncludeFile("autocomplete.js", NULL);
-jsIncludeFile("hgGateway.js", NULL);
-jsIncludeFile("utils.js", NULL);
jsIncludeFile("jquery.watermarkinput.js", NULL);
+jsIncludeFile("utils.js",NULL);
-puts(""
- "The UCSC Genome Browser was created by the \n"
- "Genome Bioinformatics Group of UC Santa Cruz.\n"
- "
"
- "Software Copyright (c) The Regents of the University of California.\n"
- "All rights reserved.\n"
- "\n");
-
-puts("");
-if (hIsPreviewHost())
+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);
+if (match->type == ddmtDb)
+ jsonWriteString(jw, "db", dbDb->name);
+// 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)
{
-puts(""
-"WARNING: This is our preview site. It is a weekly mirror of our internal development server for public access. "
-"Data and tools here are under construction, have not been quality reviewed, and are subject to change "
-"at any time. We provide this site for early access, with the warning that it is less available "
-"and stable than our public site. For high-quality reviewed annotations on our production server, visit "
-" http://genome.ucsc.edu."
-"
");
+ 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 (hIsPrivateHost())
+else if (match->type == ddmtGenome)
{
-puts("WARNING: This is our development and test site. It usually works, but it is filled with tracks in various "
-"stages of construction, and others of little interest to people outside of our local group. "
-"It is usually slow because we are building databases on it. The documentation is poor. "
- "More data than usual is flat out wrong. Maybe you want to go to "
- "genome.ucsc.edu instead.");
+ 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)
+ {
+ safef(value, sizeof(value), "%s (%s %s)",
+ dbDb->name, dbDb->genome, dbDb->description);
+ char *bolded = boldTerm(dbDb->name, term, match->offset, match->type);
+ safef(label, sizeof(label), "%s (%s %s)",
+ bolded, dbDb->genome, dbDb->description);
+ freeMem(bolded);
+ }
+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);
+ }
+else
+ errAbort("writeDbDbMatch: unrecognized dbDbMatchType value %d (db %s, term %s)",
+ match->type, dbDb->name, term);
+jsonWriteString(jw, "label", label);
+jsonWriteString(jw, "value", value);
+jsonWriteNumber(jw, "taxId", dbDb->taxId);
+if (isNotEmpty(category))
+ jsonWriteString(jw, "category", category);
+jsonWriteObjectEnd(jw);
}
-if (hIsGsidServer())
+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)
{
- webNewSection("%s", "Sequence View\n");
- printf("%s","Sequence View is a customized version of the UCSC Genome Browser, which is "
- "specifically tailored to provide functions needed for the GSID HIV Data Browser.\n");
+ // skip punctuation like parentheses
+ while (*p != '\0' && ! isalnum(*p))
+ p++;
+ if (startsWith(term, p))
+ return p - targetClone;
+ }
+return -1;
}
-hgPositionsHelpHtml(organism, db);
+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 (! 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);
+ }
+}
-puts("
");
+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 is a little too much for autocomplete ("br" would match dozens
+ // of Broad assemblies), but we do need to recognize "GRC".
+ if (startsWith("GR", term))
+ checkTerm(term, dbDb->description, ddmtDescription, dbDb, matchHash, &matchList);
+ }
+slSort(&matchList, dbDbMatchCmp);
+return matchList;
}
-void doMiddle(struct cart *theCart)
-/* Set up pretty web display and save cart in global. */
+// Assembly hub match:
+
+struct aHubMatch
+ // description of an assembly hub db
{
-char *scientificName = NULL;
-cart = theCart;
+ struct aHubMatch *next;
+ char *shortLabel; // hub shortLabel
+ char *hubUrl; // hub url
+ char *aDb; // assembly db hosted by hub
+ };
+
+static struct aHubMatch *aHubMatchNew(char *shortLabel, char *hubUrl, char *aDb)
+/* 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);
+return match;
+}
-if(cgiIsOnWeb())
- checkForGeoMirrorRedirect(cart);
-getDbGenomeClade(cart, &db, &organism, &clade, oldVars);
-if (! hDbIsActive(db))
+static struct aHubMatch *filterTrixSearchMatches(struct dbDb *dbDbList,
+ struct trixSearchResult *tsrList)
+/* Collect the assembly hub matches (not track hub matches) from a search in hub trix files. */
+{
+if (tsrList == 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)
+ hashStore(localDbs, dbDb->name);
+
+// tsrList gives hub URLs which we can then look up in hubPublic.
+struct dyString *query = sqlDyStringCreate("select shortLabel,hubUrl,dbList from %s "
+ "where hubUrl in (",
+ hubPublicTableName());
+struct trixSearchResult *tsr;
+for (tsr = tsrList; tsr != NULL; tsr = tsr->next)
{
- db = hDefaultDb();
- organism = hGenome(db);
- clade = hClade(organism);
+ if (tsr != tsrList)
+ dyStringAppend(query, ", ");
+ dyStringPrintf(query, "'%s'", tsr->itemId);
}
-scientificName = hScientificName(db);
-if (hIsGsidServer())
- cartWebStart(theCart, db, "GSID %s Sequence View (UCSC Genome Browser) Gateway \n", organism);
-else
+dyStringAppendC(query, ')');
+struct sqlConnection *conn = hConnectCentral();
+struct sqlResult *sr = sqlGetResult(conn, query->string);
+char **row;
+while ((row = sqlNextRow(sr)) != NULL)
{
- char buffer[128];
-
- /* tell html routines *not* to escape htmlOut strings*/
- htmlNoEscape();
- buffer[0] = 0;
- if ((scientificName != NULL) && (*scientificName != 0))
+ char *shortLabel = row[0];
+ char *hubUrl = row[1];
+ struct slName *dbName, *dbList = slNameListFromComma(row[2]);
+ for (dbName = dbList; dbName != NULL; dbName = dbName->next)
+ if (! hashLookup(localDbs, dbName->name))
{
- if (sameString(clade,"ancestor"))
- safef(buffer, sizeof(buffer), "(%s Ancestor) ", scientificName);
- else
- safef(buffer, sizeof(buffer), "(%s) ", scientificName);
+ slAddHead(&aHubMatchList, aHubMatchNew(shortLabel, hubUrl, dbName->name));
}
- cartWebStart(theCart, db, "%s %s%s Gateway\n", trackHubSkipHubName(organism), buffer, hBrowserName());
- htmlDoEscape();
+ }
+slReverse(&aHubMatchList);
+hDisconnectCentral(&conn);
+return aHubMatchList;
}
-cartFlushHubWarnings();
-hgGateway();
+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->aDb);
+ jsonWriteObjectEnd(jw);
+ }
+}
-// TODO REMOVE AFTER AUTOUPGRADE COMPLETE: (added 2014-03-09)
-if (dyUpgradeError)
- warn("%s", dyUpgradeError->string);
+static struct aHubMatch *searchPublicHubs(struct dbDb *dbDbList, char *term)
+/* Search for term in public hub trix files -- 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 *trixFile = cfgOptionEnvDefault("HUBSEARCHTRIXFILE", "hubSearchTrixFile",
+ hReplaceGbdb("/gbdb/hubs/public.ix"));
+if (fileExists(trixFile))
+ {
+ struct trix *trix = trixOpen(trixFile);
+ char termCopy[strlen(term)+1];
+ safecpy(termCopy, sizeof(termCopy), term);
+ tolowers(termCopy);
+ char *words[512];
+ int wordCount = chopByWhite(termCopy, words, ArraySize(words));
+ struct trixSearchResult *tsrList = trixSearch(trix, wordCount, words, tsmFirstFive);
+ aHubMatchList = filterTrixSearchMatches(dbDbList, tsrList);
+ trixClose(&trix);
+ }
+return aHubMatchList;
+}
-cartWebEnd();
+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. */
+{
+pushAbortHandler(htmlVaBadRequestAbort);
+char *term = cgiOptionalString(SEARCH_TERM);
+touppers(term);
+if (isEmpty(term))
+ errAbort("Missing required CGI parameter %s", SEARCH_TERM);
+popAbortHandler();
+return term;
}
-char *excludeVars[] = {NULL};
+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");
+
+struct dbDb *dbDbList = hDbDbList();
+struct dbDbMatch *matchList = searchDbDb(dbDbList, 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 databases" : NULL;
+struct dbDbMatch *match;
+for (match = matchList; match != NULL; match = match->next)
+ writeDbDbMatch(jw, match, term, category);
+// 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 command line. */
+/* Process CGI / command line. */
{
-long enteredMainTime = clock1000();
-oldVars = hashNew(10);
+/* Null terminated list of CGI Variables we don't want to save
+ * permanently. */
+char *excludeVars[] = {SEARCH_TERM, CARTJSON_COMMAND, NULL,};
cgiSpoof(&argc, argv);
-
setUdcCacheDir();
-
-
-cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
-cgiExitTime("hgGateway", enteredMainTime);
+if (cgiOptionalString(SEARCH_TERM))
+ // Skip the cart for speedy searches
+ lookupTerm();
+else
+ cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
return 0;
}