45a604cdb815558ab355d3de21df5004a4bfa000
angie
  Wed Sep 9 10:41:32 2015 -0700
Hooked up hgIntegrator to hgIntegratorHelp.html in menuBar's Help menu (thanks Donna for noticing it was missing!).

diff --git src/hg/lib/web.c src/hg/lib/web.c
index 975a2ad..f8c8594 100644
--- src/hg/lib/web.c
+++ src/hg/lib/web.c
@@ -1,1480 +1,1485 @@
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include <regex.h>
 #include "hCommon.h"
 #include "obscure.h"
 #include "dnautil.h"
 #include "errAbort.h"
 #include "htmshell.h"
 #include "web.h"
 #include "hPrint.h"
 #include "hdb.h"
 #include "hui.h"
 #include "hgConfig.h"
 #include "cheapcgi.h"
 #include "dbDb.h"
 #include "hgColors.h"
 #include "hubConnect.h"
 #include "search.h"
 #include "geoMirror.h"
 #include "trackHub.h"
 #include "versionInfo.h"
 
 #ifndef GBROWSE
 #include "axtInfo.h"
 #include "wikiLink.h"
 #include "googleAnalytics.h"
 #include "jsHelper.h"
 #endif /* GBROWSE */
 
 
 /* flag that tell if the CGI header has already been outputed */
 boolean webHeadAlreadyOutputed = FALSE;
 /* flag that tell if text CGI header hsa been outputed */
 boolean webInTextMode = FALSE;
 
 struct hash *includedResourceFiles = NULL;
 
 static char *dbCgiName = "db";
 static char *orgCgiName = "org";
 static char *cladeCgiName = "clade";
 static char *extraStyle = NULL;
 
 /* globals: a cart and db for use in error handlers. */
 static struct cart *errCart = NULL;
 static char *errDb = NULL;
 
 void textVaWarn(char *format, va_list args)
 {
 vprintf(format, args);
 puts("\n");
 }
 
 void softAbort()
 {
 exit(0);
 }
 
 void webPushErrHandlers(void)
 /* Push warn and abort handler for errAbort(). */
 {
 if (webInTextMode)
     pushWarnHandler(textVaWarn);
 else
     pushWarnHandler(webVaWarn);
 pushAbortHandler(softAbort);
 hDumpStackPushAbortHandler();
 }
 
 void webPushErrHandlersCartDb(struct cart *cart, char *db)
 /* Push warn and abort handler for errAbort(); save cart and db for use in handlers. */
 {
 errCart = cart;
 errDb = db;
 webPushErrHandlers();
 }
 
 void webPopErrHandlers(void)
 /* Pop warn and abort handler for errAbort(). */
 {
 popWarnHandler();
 hDumpStackPopAbortHandler();
 popAbortHandler();
 }
 
 void webSetStyle(char *style)
 /* set a style to add to the header */
 {
 extraStyle = style;
 }
 
 void webPragmasEtc()
 /* Print out stuff that tells people not to cache us, and that we use the
  * usual character set and scripting langauge. (Normally done by webStartWrap) */
 {
 printf("<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n"
      "<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n"
      "<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n"
      "<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n"
      );
 }
 
 void webStartText()
 /* output the head for a text page */
 {
 /*printf("Content-Type: text/plain\n\n");*/
 
 webHeadAlreadyOutputed = TRUE;
 webInTextMode = TRUE;
 webPushErrHandlers();
 }
 
 static void webStartWrapperDetailedInternal(struct cart *theCart,
 	char *db, char *headerText, char *textOutBuf,
 	boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
 	boolean withHtmlHeader)
 /* output a CGI and HTML header with the given title in printf format */
 {
 char uiState[256];
 char *scriptName = cgiScriptName();
 boolean isEncode = FALSE;
 if (theCart)
     {
     char *theGenome = NULL;
     char *genomeEnc = NULL;
 
     getDbAndGenome(theCart, &db, &theGenome, NULL);
     genomeEnc = cgiEncode(theGenome);
 
     safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%s",
 	     orgCgiName, genomeEnc,
 	     dbCgiName, db,
 	     cartSessionVarName(), cartSessionId(theCart));
     }
 else
     {
     uiState[0] = 0;
     uiState[1] = 0;
     }
 if (db == NULL)
     db = hDefaultDb();
 boolean dbIsFound = hDbExists(db);
 boolean haveBlat = FALSE;
 if (dbIsFound)
     haveBlat = hIsBlatIndexedDatabase(db);
 
 if (scriptName == NULL)
     scriptName = cloneString("");
 /* don't output two headers */
 if(webHeadAlreadyOutputed)
     return;
 
 if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
     rStringIn("EncodeDataVersions", scriptName))
         isEncode = TRUE;
 
 /* Preamble. */
 dnaUtilOpen();
 
 if (withHttpHeader)
     puts("Content-type:text/html\n");
 
 if (withHtmlHeader)
     {
     char *newString, *ptr1, *ptr2;
 
     char *browserVersion;
     if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
         puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
     else
         puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
              "\"http://www.w3.org/TR/html4/loose.dtd\">");
     // Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
     puts(
 	"<HTML>" "\n"
 	"<HEAD>" "\n"
 	);
     printf("\t%s\n", headerText);
     webPragmasEtc();
 
     printf("\t<TITLE>");
 
     /* we need to take any HTML formatting out of the titlebar string */
     newString = cloneString(textOutBuf);
 
     for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
 	{
 	if (*ptr2 == '<')
 	    {
 	    for(; *ptr2 && (*ptr2 != '>'); ptr2++)
 		;
 	    }
 	else
 	    *ptr1++ = *ptr2;
 	}
     *ptr1 = 0;
     htmlTextOut(newString);
     printf("	</TITLE>\n    ");
     webIncludeResourceFile("HGStyle.css");
     if (extraStyle != NULL)
         puts(extraStyle);
     printf("</HEAD>\n");
     printBodyTag(stdout);
     htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
     puts(commonCssStyles());
     }
 webStartSectionTables();
 
 if (withLogo)
     {
     puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
     if (isEncode)
 	{
 	puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
 	     "<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
 	     "</A>");
 	puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
 	}
     else
 	{
 	puts("<IMG SRC=\"../images/title.jpg\">");
 	}
     puts("</TH></TR>" "\n"
          "" "\n" );
     }
 
 /* Put up the hot links bar. */
 
 char *menuStr = menuBar(theCart, db);
 if(menuStr)
     {
     puts(menuStr);
     }
 
 if(!skipSectionHeader)
 /* this HTML must be in calling code if skipSectionHeader is TRUE */
     {
     webFirstSection(textOutBuf);
     };
 webPushErrHandlers();
 /* set the flag */
 webHeadAlreadyOutputed = TRUE;
 errAbortSetDoContentType(FALSE);
 }	/*	static void webStartWrapperDetailedInternal()	*/
 
 void webStartWrapperDetailedArgs(struct cart *theCart, char *db,
 	char *headerText, char *format, va_list args, boolean withHttpHeader,
 	boolean withLogo, boolean skipSectionHeader, boolean withHtmlHeader)
 /* output a CGI and HTML header with the given title in printf format */
 {
 char textOutBuf[1024];
 va_list argscp;
 
 va_copy(argscp,args);
 vasafef(textOutBuf, sizeof(textOutBuf), format, argscp);
 va_end(argscp);
 
 webStartWrapperDetailedInternal(theCart, db, headerText, textOutBuf,
 	withHttpHeader, withLogo, skipSectionHeader, withHtmlHeader);
 }
 
 void webStartWrapperDetailedNoArgs(struct cart *theCart, char *db,
 	char *headerText, char *format, boolean withHttpHeader,
 	boolean withLogo, boolean skipSectionHeader, boolean withHtmlHeader)
 /* output a CGI and HTML header with the given title in printf format */
 {
 char textOutBuf[512];
 
 safecpy(textOutBuf, sizeof(textOutBuf), format);
 webStartWrapperDetailedInternal(theCart, db, headerText, textOutBuf,
 	withHttpHeader, withLogo, skipSectionHeader, withHtmlHeader);
 }
 
 void webStartWrapperGatewayHeader(struct cart *theCart, char *db,
 	char *headerText, char *format, va_list args, boolean withHttpHeader,
 	boolean withLogo, boolean skipSectionHeader)
 {
 webStartWrapperDetailedArgs(theCart, db, headerText, format, args, withHttpHeader,
 	withLogo, skipSectionHeader, TRUE);
 }
 
 void webStartWrapperGateway(struct cart *theCart, char *db, char *format, va_list args, boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader)
 /* output a CGI and HTML header with the given title in printf format */
 {
 webStartWrapperGatewayHeader(theCart, db, "", format, args, withHttpHeader,
 			     withLogo, skipSectionHeader);
 }
 
 void webStartWrapper(struct cart *theCart, char *db, char *format, va_list args, boolean withHttpHeader, boolean withLogo)
     /* allows backward compatibility with old webStartWrapper that doesn't contain the "skipHeader" arg */
 	/* output a CGI and HTML header with the given title in printf format */
 {
 webStartWrapperGatewayHeader(theCart, db, "", format, args, withHttpHeader,
                              withLogo, FALSE);
 }
 
 void webStart(struct cart *theCart, char *db, char *format, ...)
 /* Print out pretty wrapper around things when not
  * from cart. */
 {
 va_list args;
 va_start(args, format);
 webStartWrapper(theCart, db, format, args, TRUE, TRUE);
 va_end(args);
 }
 
 void webStartHeader(struct cart *theCart, char *db, char *headerText, char *format, ...)
 /* Print out pretty wrapper around things when not from cart.
  * Include headerText in the html header. */
 {
 va_list args;
 va_start(args, format);
 webStartWrapperGatewayHeader(theCart, db, headerText, format, args, TRUE, TRUE,
 			     FALSE);
 va_end(args);
 }
 
 
 void webEndSection()
 /* Close down a section */
 {
 puts(
     "" "\n"
     "	</TD><TD WIDTH=15></TD></TR></TABLE>" "\n"
 //    "<BR>"
     "	</TD></TR></TABLE>" "\n"
     "	</TD></TR></TABLE>" "\n"
     "	" );
 puts("</div>");
 }
 
 void webStartSectionTables()
 /* Put up start of nepharious table layout stuff. (Normally done by webStartWrap). */
 {
 puts(
     "<A NAME=\"TOP\"></A>" "\n"
     "<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=\"100%\">" "\n");
 }
 
 void webFirstSection(char *title)
 /* Put up the first section (normally done by webStartWrap). */
 {
 puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere)
      "<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->" "\n"
      "<TR><TD COLSPAN=3>\n"
      "<div id=firstSection>"
      "      <!--outer table is for border purposes-->\n"
      "      <TABLE WIDTH='100%' BGCOLOR='#" HG_COL_BORDER "' BORDER='0' CELLSPACING='0' "
 		 "CELLPADDING='1'><TR><TD>\n"
      "    <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%'  BORDER='0' CELLSPACING='0' "
 		 "CELLPADDING='0'><TR><TD>\n"
      "     <div class='subheadingBar'><div class='windowSize' id='sectTtl'>"
      );
 htmlTextOut(title);
 
 puts("     </div></div>\n"
      "     <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>"
 	  "<TR><TH HEIGHT=10></TH></TR>\n"
      "     <TR><TD WIDTH=10>&nbsp;</TD><TD>\n\n"
      );
 }
 
 void webNewSectionHeaderStart(boolean hasTitle)
 /* Start the header for a new section on the web page.
  * May be used to maintain table layout without a proper section header */
 {
 webEndSection();
 puts("<div>");
 puts("<!-- +++++++++++++++++++++ START NEW SECTION +++++++++++++++++++ -->");
 puts(  // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere)
     "<BR>\n\n"
     "   <!--outer table is for border purposes-->\n"
     "   <TABLE WIDTH='100%' BGCOLOR='#" HG_COL_BORDER
         "' BORDER='0' CELLSPACING='0' CELLPADDING='1'><TR><TD>\n"
     "    <TABLE BGCOLOR='#" HG_COL_INSIDE
          "' WIDTH='100%'  BORDER='0' CELLSPACING='0' CELLPADDING='0'><TR><TD>\n");
 if (hasTitle)
     puts("<div class='subheadingBar' class='windowSize'>");
 else
     puts("<div>");
 }
 
 void webNewSectionHeaderEnd()
 /* Properly close header of collapsible section on web page */
 {
 puts("     </div>\n"
      "     <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>"
           "<TR><TH HEIGHT=10></TH></TR>\n"
      "     <TR><TD WIDTH=10>&nbsp;</TD><TD>\n\n");
 }
 
 void webNewSection(char* format, ...)
 /* create a new section on the web page */
 {
 va_list args;
 va_start(args, format);
 webNewSectionHeaderStart(TRUE);
 vprintf(format, args);
 webNewSectionHeaderEnd();
 va_end(args);
 }
 
 void webNewEmptySection()
 /* create a new section on the web page to maintain table layout */
 {
 webNewSectionHeaderStart(FALSE);
 webNewSectionHeaderEnd();
 }
 
 void webEndSectionTables()
 /* Finish with section tables (but don't do /BODY /HTML like
  * webEnd does. */
 {
 webEndSection();
 puts("</TD></TR></TABLE>\n");
 }
 
 void webEnd()
 /* output the footer of the HTML page */
 {
 if(!webInTextMode)
     {
     webEndSectionTables();
 #ifndef GBROWSE
     googleAnalytics();
 #endif /* GBROWSE */
     puts( "</BODY></HTML>");
     webPopErrHandlers();
     }
 }
 
 static boolean gotWarnings = FALSE;
 
 void webVaWarn(char *format, va_list args)
 /* Warning handler that closes out page and stuff in
  * the fancy form. */
 {
 gotWarnings = TRUE;
 boolean needStart = !webHeadAlreadyOutputed;
 if (needStart)
     {
     // All callers of this (via webPushErrHandlersCartDb) have skipped Content-type
     // because they want to output text unless we hit this condition:
     puts("Content-type:text/html\n");
     cartWebStart(errCart, errDb, "Error");
     }
 htmlVaWarn(format, args);
 printf("\n<!-- HGERROR -->\n\n\n");
 }
 
 
 boolean webGotWarnings()
 /* Return TRUE if webVaWarn has been called. */
 {
 return gotWarnings;
 }
 
 void webAbort(char* title, char* format, ...)
 /* an abort function that outputs a error page */
 {
 va_list args;
 va_start(args, format);
 
 /* output the header */
 if(!webHeadAlreadyOutputed)
     webStart(errCart, NULL, title);
 
 /* in text mode, have a different error */
 if(webInTextMode)
 	printf("\n\n\n          %s\n\n", title);
 
 vprintf(format, args);
 printf("<!-- HGERROR -->\n");
 printf("\n\n");
 
 webEnd();
 
 va_end(args);
 exit(0);
 }
 
 void printCladeListHtml(char *genome, char *onChangeText)
 /* Make an HTML select input listing the clades. */
 {
 char **row = NULL;
 char *clades[128];
 char *labels[128];
 char *defaultClade = hClade(genome);
 char *defaultLabel = NULL;
 int numClades = 0;
 
 struct sqlConnection *conn = hConnectCentral();  // after hClade since it access hgcentral too
 // get only the clades that have actual active genomes
 char query[4096];
 safef(query, sizeof query, "NOSQLINJ SELECT DISTINCT(c.name), c.label FROM %s c, %s g, %s d WHERE c.name=g.clade AND d.organism=g.genome AND d.active=1 ORDER BY c.priority", cladeTable(),genomeCladeTable(), dbDbTable());
 struct sqlResult *sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     clades[numClades] = cloneString(row[0]);
     labels[numClades] = cloneString(row[1]);
     if (sameWord(defaultClade, clades[numClades]))
 	defaultLabel = clades[numClades];
     numClades++;
     if (numClades >= ArraySize(clades))
         internalErr();
     }
 sqlFreeResult(&sr);
 hDisconnectCentral(&conn);
 
 struct slPair *names = trackHubGetCladeLabels();
 
 for(; names; names = names->next)
     {
     clades[numClades] = names->name;
     labels[numClades] = names->val;
     if (sameWord(defaultClade, clades[numClades]))
 	defaultLabel = clades[numClades];
     numClades++;
     if (numClades >= ArraySize(clades))
         internalErr();
     }
 
 cgiMakeDropListFull(cladeCgiName, labels, clades, numClades,
                     defaultLabel, onChangeText);
 }
 
 static void printSomeGenomeListHtmlNamedMaybeCheck(char *customOrgCgiName,
 	 char *db, struct dbDb *dbList, char *onChangeText, boolean doCheck)
 /* Prints to stdout the HTML to render a dropdown list
  * containing a list of the possible genomes to choose from.
  * param db - a database whose genome will be the default genome.
  *                       If NULL, no default selection.
  * param onChangeText - Optional (can be NULL) text to pass in
  *                              any onChange javascript. */
 {
 char *orgList[1024];
 int numGenomes = 0;
 struct dbDb *cur = NULL;
 struct hash *hash = hashNew(10); // 2^^10 entries = 1024
 char *selGenome = hGenome(db);
 char *values [1024];
 char *cgiName;
 
 for (cur = dbList; cur != NULL; cur = cur->next)
     {
     if (!hashFindVal(hash, cur->genome) &&
 	(!doCheck || hDbExists(cur->name)))
         {
         hashAdd(hash, cur->genome, cur);
         orgList[numGenomes] = trackHubSkipHubName(cur->genome);
         values[numGenomes] = cur->genome;
         numGenomes++;
 	if (numGenomes >= ArraySize(orgList))
 	    internalErr();
         }
     }
 
 cgiName = (customOrgCgiName != NULL) ? customOrgCgiName : orgCgiName;
 cgiMakeDropListFull(cgiName, orgList, values, numGenomes,
                     selGenome, onChangeText);
 hashFree(&hash);
 }
 
 void printSomeGenomeListHtmlNamed(char *customOrgCgiName, char *db, struct dbDb *dbList, char *onChangeText)
 /* Prints to stdout the HTML to render a dropdown list
  * containing a list of the possible genomes to choose from.
  * param db - a database whose genome will be the default genome.
  *                       If NULL, no default selection.
  * param onChangeText - Optional (can be NULL) text to pass in
  *                              any onChange javascript. */
 {
 return printSomeGenomeListHtmlNamedMaybeCheck(customOrgCgiName, db, dbList,
 					      onChangeText, TRUE);
 }
 
 void printLiftOverGenomeList(char *customOrgCgiName, char *db,
 			     struct dbDb *dbList, char *onChangeText)
 /* Prints to stdout the HTML to render a dropdown list
  * containing a list of the possible genomes to choose from.
  * Databases in dbList do not have to exist.
  * param db - a database whose genome will be the default genome.
  *                       If NULL, no default selection.
  * param onChangeText - Optional (can be NULL) text to pass in
  *                              any onChange javascript. */
 {
 return printSomeGenomeListHtmlNamedMaybeCheck(customOrgCgiName, db, dbList,
 					      onChangeText, FALSE);
 }
 
 void printSomeGenomeListHtml(char *db, struct dbDb *dbList, char *onChangeText)
 /* Prints the dropdown list using the orgCgiName */
 {
 printSomeGenomeListHtmlNamed(NULL, db, dbList, onChangeText);
 }
 
 void printGenomeListHtml(char *db, char *onChangeText)
 /* Prints to stdout the HTML to render a dropdown list
  * containing a list of the possible genomes to choose from.
  * param db - a database whose genome will be the default genome.
  *                       If NULL, no default selection.
  * param onChangeText - Optional (can be NULL) text to pass in
  *                              any onChange javascript. */
 {
 printSomeGenomeListHtml(db, hGetIndexedDatabases(), onChangeText);
 }
 
 void printBlatGenomeListHtml(char *db, char *onChangeText)
 /* Prints to stdout the HTML to render a dropdown list
  * containing a list of the possible genomes to choose from.
  * param db - a database whose genome will be the default genome.
  *                       If NULL, no default selection.
  * param onChangeText - Optional (can be NULL) text to pass in
  *                              any onChange javascript. */
 {
 printSomeGenomeListHtml(db, hGetBlatIndexedDatabases(), onChangeText);
 }
 
 
 void printGenomeListForCladeHtml(char *db, char *onChangeText)
 /* Prints to stdout the HTML to render a dropdown list containing
  * a list of the possible genomes from selOrganism's clade to choose from.
  * selOrganism is the default for the select.
  */
 {
 printSomeGenomeListHtml(db, hGetIndexedDatabasesForClade(db), onChangeText);
 }
 
 void printAllAssemblyListHtmlParm(char *db, struct dbDb *dbList,
                             char *dbCgi, bool allowInactive, char *javascript)
 /* Prints to stdout the HTML to render a dropdown list containing the list
  * of assemblies for the current genome to choose from.  By default,
  * this includes only active assemblies with a database (with the
  * exception of the default assembly, which will be included even
  * if it isn't active).
  *  param db - The default assembly (the database name) to choose as selected.
  *             If NULL, no default selection.
  *  param allowInactive - if set, print all assemblies for this genome,
  *                        even if they're inactive or have no database
  */
 {
 
 char *assemblyList[128];
 char *values[128];
 int numAssemblies = 0;
 struct dbDb *cur = NULL;
 char *genome = hGenome(db);
 char *selAssembly = NULL;
 
 if (genome == NULL)
 #ifdef LOWELAB
     genome = "Pyrococcus furiosus";
 #else
     genome = "Human";
 #endif
 for (cur = dbList; cur != NULL; cur = cur->next)
     {
     /* Only for this genome */
     if (!sameWord(genome, cur->genome))
         continue;
 
     /* Save a pointer to the current assembly */
     if (sameWord(db, cur->name))
         selAssembly = cur->name;
 
     if (allowInactive ||
         ((cur->active || sameWord(cur->name, db))
                 && (trackHubDatabase(db) || sqlDatabaseExists(cur->name))))
         {
         assemblyList[numAssemblies] = cur->description;
         values[numAssemblies] = cur->name;
         numAssemblies++;
 	if (numAssemblies >= ArraySize(assemblyList))
 	    internalErr();
         }
 
     }
 cgiMakeDropListFull(dbCgi, assemblyList, values, numAssemblies,
                                 selAssembly, javascript);
 }
 
 void printSomeAssemblyListHtmlParm(char *db, struct dbDb *dbList,
                                         char *dbCgi, char *javascript)
 /* Find all the assemblies from the list that are active.
  * Prints to stdout the HTML to render a dropdown list containing the list
  * of the possible assemblies to choose from.
  * param db - The default assembly (the database name) to choose as selected.
  *    If NULL, no default selection.  */
 {
 
     printAllAssemblyListHtmlParm(db, dbList, dbCgi, TRUE, javascript);
 }
 
 void printSomeAssemblyListHtml(char *db, struct dbDb *dbList, char *javascript)
 /* Find all assemblies from the list that are active, and print
  * HTML to render dropdown list
  * param db - default assembly.  If NULL, no default selection */
 {
 printSomeAssemblyListHtmlParm(db, dbList, dbCgiName, javascript);
 }
 
 void printAssemblyListHtml(char *db, char *javascript)
 /* Find all the assemblies that pertain to the selected genome
  * Prints to stdout the HTML to render a dropdown list containing
  * a list of the possible assemblies to choose from.
  * Param db - The assembly (the database name) to choose as selected.
  * If NULL, no default selection.  */
 {
 struct dbDb *dbList = hGetIndexedDatabases();
 printSomeAssemblyListHtml(db, dbList, javascript);
 }
 
 void printAssemblyListHtmlExtra(char *db, char *javascript)
 {
 /* Find all the assemblies that pertain to the selected genome
 Prints to stdout the HTML to render a dropdown list containing a list of the possible
 assemblies to choose from.
 
 param curDb - The assembly (the database name) to choose as selected.
 If NULL, no default selection.
  */
 struct dbDb *dbList = hGetIndexedDatabases();
 printSomeAssemblyListHtmlParm(db, dbList, dbCgiName, javascript);
 }
 
 void printBlatAssemblyListHtml(char *db)
 {
 /* Find all the assemblies that pertain to the selected genome
 Prints to stdout the HTML to render a dropdown list containing a list of the possible
 assemblies to choose from.
 
 param curDb - The assembly (the database name) to choose as selected.
 If NULL, no default selection.
  */
 struct dbDb *dbList = hGetBlatIndexedDatabases();
 printSomeAssemblyListHtml(db, dbList, NULL);
 }
 
 static char *getDbForGenome(char *genome, struct cart *cart)
 /*
   Function to find the default database for the given Genome.
 It looks in the cart first and then, if that database's Genome matches the
 passed-in Genome, returns it. If the Genome does not match, it returns the default
 database that does match that Genome.
 
 param Genome - The Genome for which to find a database
 param cart - The cart to use to first search for a suitable database name
 return - The database matching this Genome type
 */
 {
 
 char *retDb = cartUsualString(cart, dbCgiName, NULL);
 
 if ((retDb == NULL) || !hDbExists(retDb))
     {
     retDb = hDefaultDb();
     }
 
 /* If genomes don't match, then get the default db for that genome */
 if (differentWord(genome, hGenome(retDb)))
     {
     retDb = hDefaultDbForGenome(genome);
     }
 
 return retDb;
 }
 
 void getDbGenomeClade(struct cart *cart, char **retDb, char **retGenome,
 		      char **retClade, struct hash *oldVars)
 /* Examine CGI and cart variables to determine which db, genome, or clade
  *  has been selected, and then adjust as necessary so that all three are
  * consistent.  Detect changes and reset db-specific cart variables.
  * Save db, genome and clade in the cart so it will be consistent hereafter.
  * The order of preference here is as follows:
  * If we got a request that explicitly names the db, that takes
  * highest priority, and we synch the organism to that db.
  * If we get a cgi request for a specific organism then we use that
  * organism to choose the DB.  If just clade, go from there.
 
  * In the cart only, we use the same order of preference.
  * If someone requests an Genome we try to give them the same db as
  * was in their cart, unless the Genome doesn't match.
  */
 {
 boolean gotClade = hGotClade();
 *retDb = cgiOptionalString(dbCgiName);
 *retGenome = cgiOptionalString(orgCgiName);
 *retClade = cgiOptionalString(cladeCgiName);
 
 /* Was the database passed in as a cgi param?
  * If so, it takes precedence and determines the genome. */
 if (*retDb && hDbExists(*retDb))
     {
     *retGenome = hGenome(*retDb);
     }
 /* If no db was passed in as a cgi param then was the organism (a.k.a. genome)
  * passed in as a cgi param?
  * If so, the we use the proper database for that genome. */
 else if (*retGenome && !sameWord(*retGenome, "0"))
     {
     *retDb = getDbForGenome(*retGenome, cart);
     *retGenome = hGenome(*retDb);
     }
 else if (*retClade && gotClade)
     {
     *retGenome = hDefaultGenomeForClade(*retClade);
     *retDb = getDbForGenome(*retGenome, cart);
     }
 /* If no cgi params passed in then we need to inspect the session */
 else
     {
     *retDb = cartOptionalString(cart, dbCgiName);
     *retGenome = cartOptionalString(cart, orgCgiName);
     *retClade = cartOptionalString(cart, cladeCgiName);
     /* If there was a db found in the session that determines everything. */
     if (*retDb && hDbExists(*retDb))
         {
         *retGenome = hGenome(*retDb);
         }
     else if (*retGenome && !sameWord(*retGenome, "0"))
 	{
 	*retDb = hDefaultDbForGenome(*retGenome);
 	}
     else if (*retClade && gotClade)
 	{
         *retGenome = hDefaultGenomeForClade(*retClade);
 	*retDb = getDbForGenome(*retGenome, cart);
 	}
     /* If no organism in the session then get the default db and organism. */
     else
 	{
 	*retDb = hDefaultDb();
 	*retGenome = hGenome(*retDb);
         }
     }
 *retDb = cloneString(*retDb);
 *retGenome = cloneString(*retGenome);
 *retClade = hClade(*retGenome);
 
 if ( (*retClade != NULL) && sameString(*retClade, "none"))
     cartRemove(cart, "position");
 /* Detect change of database and reset db-specific cart variables: */
 if (oldVars)
     {
     char *oldDb = hashFindVal(oldVars, "db");
     char *oldOrg = hashFindVal(oldVars, "org");
     char *oldClade = hashFindVal(oldVars, "clade");
     if ((!IS_CART_VAR_EMPTY(oldDb)    && differentWord(oldDb, *retDb)) ||
         (!IS_CART_VAR_EMPTY(oldOrg)   && differentWord(oldOrg, *retGenome)) ||
         (!IS_CART_VAR_EMPTY(oldClade) && differentWord(oldClade, *retClade)))
 	{
 	/* Change position to default -- unless it was passed in via CGI: */
 	if (cgiOptionalString("position") == NULL)
 	    cartSetString(cart, "position", hDefaultPos(*retDb));
 	/* hgNear search term -- unless it was passed in via CGI: */
 	if (cgiOptionalString("near_search") == NULL)
 	    cartRemove(cart, "near_search");
 	/* hgBlat results (hgUserPsl track): */
 	cartRemove(cart, "ss");
 	/* hgTables correlate: */
 	cartRemove(cart, "hgta_correlateTrack");
 	cartRemove(cart, "hgta_correlateTable");
 	cartRemove(cart, "hgta_correlateGroup");
 	cartRemove(cart, "hgta_correlateOp");
 	cartRemove(cart, "hgta_nextCorrelateTrack");
 	cartRemove(cart, "hgta_nextCorrelateTable");
 	cartRemove(cart, "hgta_nextCorrelateGroup");
 	cartRemove(cart, "hgta_nextCorrelateOp");
 	cartRemove(cart, "hgta_corrWinSize");
 	cartRemove(cart, "hgta_corrMaxLimitCount");
 	}
     }
 
 /* Save db, genome (as org) and clade in cart. */
 cartSetString(cart, "db", *retDb);
 cartSetString(cart, "org", *retGenome);
 if (gotClade)
     cartSetString(cart, "clade", *retClade);
 }
 
 void getDbAndGenome(struct cart *cart, char **retDb, char **retGenome,
 		    struct hash *oldVars)
 /* Get just the db and genome. */
 {
 char *garbage = NULL;
 getDbGenomeClade(cart, retDb, retGenome, &garbage, oldVars);
 freeMem(garbage);
 }
 
 void webIncludeFile(char *file)
 /* Include an HTML file in a CGI.
  *   The file path may begin with hDocumentRoot(); if it doesn't, it is
  *   assumed to be relative and hDocumentRoot() will be prepended. */
 {
 char *str = hFileContentsOrWarning(file);
 puts(str);
 freeMem(str);
 }
 
 void webIncludeHelpFile(char *fileRoot, boolean addHorizLine)
 /* Given a help file root name (e.g. "hgPcrResult" or "cutters"),
  * print out the contents of the file.  If addHorizLine, print out an
  * <HR> first. */
 {
 if (addHorizLine)
     htmlHorizontalLine();
 webIncludeFile(hHelpFile(fileRoot));
 }
 
 void webPrintLinkTableStart()
 /* Print link table start in our colors. */
 {
 printf("<TABLE><TR><TD BGCOLOR='#" HG_COL_BORDER "'>\n");
 printf("<TABLE CELLSPACING=1 CELLPADDING=3><TR>\n");
 }
 
 void webPrintLinkTableEnd()
 /* Print link table end in our colors. */
 {
 printf("</TR></TABLE>\n");
 printf("</TD></TR></TABLE>\n");
 }
 
 void webPrintLinkOutCellStart()
 /* Print link cell that goes out of our site. End with
  * webPrintLinkTableEnd. */
 {
 printf("<TD BGCOLOR='#" HG_COL_LOCAL_TABLE "'>");
 }
 
 void webPrintWideCellStart(int colSpan, char *bgColorRgb)
 /* Print link multi-column cell start in our colors. */
 {
 printf("<TD BGCOLOR='#%s'", bgColorRgb);
 if (colSpan > 1)
     printf(" COLSPAN=%d", colSpan);
 printf(">");
 }
 
 void webPrintLinkCellStart()
 /* Print link cell start in our colors. */
 {
 webPrintWideCellStart(1, HG_COL_TABLE);
 }
 
 void webPrintLinkCellRightStart()
 /* Print right-justified cell start in our colors. */
 {
 printf("<TD BGCOLOR='#"HG_COL_TABLE"' ALIGN='right'>");
 }
 
 void webPrintLinkCellEnd()
 /* Print link cell end in our colors. */
 {
 printf("</TD>");
 }
 
 void webPrintLinkCell(char *link)
 /* Print link cell in our colors, if links is null, print empty cell */
 {
 webPrintLinkCellStart();
 if (link != NULL)
     puts(link);
 webPrintLinkCellEnd();
 }
 
 void webPrintIntCell(int val)
 /* Print right-justified int cell in our colors. */
 {
 webPrintLinkCellRightStart();
 printf("%d", val);
 webPrintLinkCellEnd();
 }
 
 void webPrintDoubleCell(double val)
 /* Print right-justified cell in our colors with two digits to right of decimal. */
 {
 webPrintLinkCellRightStart();
 printf("%4.2f", val);
 webPrintLinkCellEnd();
 }
 
 void webPrintWideLabelCellStart(int colSpan)
 /* Print start of wrapper around a label in a table. */
 {
 printf("<TD BGCOLOR='#"HG_COL_TABLE_LABEL"'");
 if (colSpan > 1)
     printf(" COLSPAN=%d", colSpan);
 printf("><span style='color:#FFFFFF;'><B>");
 }
 
 void webPrintLabelCellStart()
 /* Print start of wrapper around a label in a table. */
 {
 webPrintWideLabelCellStart(1);
 }
 
 void webPrintLabelCellEnd()
 /* Print end of wrapper around a label in a table. */
 {
 printf("</B></span></TD>");
 }
 
 void webPrintWideLabelCell(char *label, int colSpan)
 /* Print label cell over multiple columns in our colors. */
 {
 webPrintWideLabelCellStart(colSpan);
 printf("%s", label);
 webPrintLabelCellEnd();
 }
 
 void webPrintWideCenteredLabelCell(char *label, int colSpan)
 /* Print label cell over multiple columns in our colors and centered. */
 {
 printf("<TD BGCOLOR='#" HG_COL_TABLE_LABEL "'");
 if (colSpan > 1)
     printf(" COLSPAN=%d", colSpan);
 printf("><CENTER><span style='color:#FFFFFF;'><B>%s</B></span></CENTER></TD>", label);
 }
 
 void webPrintLabelCell(char *label)
 /* Print label cell in our colors. */
 {
 webPrintWideLabelCell(label, 1);
 }
 
 void webPrintLinkTableNewRow()
 /* start a new row */
 {
 printf("</TR>\n<TR>");
 }
 
 void finishPartialTable(int rowIx, int itemPos, int maxPerRow,
 	void (*cellStart)())
 /* Fill out partially empty last row. */
 {
 if (rowIx != 0 && itemPos < maxPerRow)
     {
     int i;
     for (i=itemPos; i<maxPerRow; ++i)
         {
 	cellStart();
 	webPrintLinkCellEnd();
 	}
     }
 }
 
 void webFinishPartialLinkOutTable(int rowIx, int itemPos, int maxPerRow)
 /* Fill out partially empty last row. */
 {
 finishPartialTable(rowIx, itemPos, maxPerRow, webPrintLinkOutCellStart);
 }
 
 void webFinishPartialLinkTable(int rowIx, int itemPos, int maxPerRow)
 /* Fill out partially empty last row. */
 {
 finishPartialTable(rowIx, itemPos, maxPerRow, webPrintLinkCellStart);
 }
 
 char *webTimeStampedLinkToResource(char *fileName, boolean wrapInHtml)
 // If wrapInHtml
 //   returns versioned link embedded in style or script html (free after use).
 // else
 //   returns full path of a versioned path to the requested resource file (js, or css).
 // NOTE: png, jpg and gif should also be supported but are untested.
 //
 // In production sites we use a versioned softlink that includes the CGI version. This has the following benefits:
 // a) flushes user's web browser cache when the user visits a GB site whose version has changed since their last visit;
 // b) enforces the requirement that static files are the same version as the CGIs (something that often fails to happen in mirrors).
 // (see notes in redmine #3170).
 //
 // In dev trees we use mtime to create a pseudo-version; this forces web browsers to reload css/js file when it changes,
 // so we don't get odd behavior that can be caused by caching of mis-matched javascript and style files in dev trees.
 //
 // In either case, the actual file has to have been previously created by running make in the appropriate directory (kent/src/hg/js
 // or kent/src/hg/htdocs/style).
 {
 char baseName[PATH_LEN];
 char extension[FILEEXT_LEN];
 splitPath(fileName, NULL, baseName, extension);
 boolean js = sameString(".js",extension);
 boolean style = !js && sameString(".css",extension);
 boolean image = !js
              && !style
              && (  sameString(".png",extension)
                 || sameString(".jpg",extension)
                 || sameString(".gif",extension));
 if (!js && !style) // && !image) NOTE: This code has not been tested on images but should work.
     errAbort("webTimeStampedLinkToResource: unknown resource type for %s.\n", fileName);
 
 // Build and verify directory
 char *dirName = "";
 if (js)
     dirName = cfgOptionDefault("browser.javaScriptDir", "js");
 else if (style)
     dirName = cfgOptionDefault("browser.styleDir","style");
 else if (image)
     dirName = cfgOptionDefault("browser.styleImagesDir","style/images");
 struct dyString *fullDirName = NULL;
 char *docRoot = hDocumentRoot();
 if (docRoot != NULL)
     fullDirName = dyStringCreate("%s/%s", docRoot, dirName);
 else
     // tolerate missing docRoot (i.e. when running from command line)
     fullDirName = dyStringCreate("%s", dirName);
 if (!fileExists(dyStringContents(fullDirName)))
     errAbort("webTimeStampedLinkToResource: dir: %s doesn't exist.\n",
              dyStringContents(fullDirName));
 
 // build and verify real path to file
 struct dyString *realFileName = dyStringCreate("%s/%s", dyStringContents(fullDirName), fileName);
 if (!fileExists(dyStringContents(realFileName)))
     errAbort("webTimeStampedLinkToResource: file: %s doesn't exist.\n",
              dyStringContents(realFileName));
 
 // build and verify link path including timestamp in the form of dir/baseName + timeStamp or CGI Version + ext
 long mtime = fileModTime(dyStringContents(realFileName));
 struct dyString *linkWithTimestamp;
 
 char *scriptName = cgiScriptName();
 if (scriptName == NULL)
     scriptName = cloneString("");
 boolean nonVersionedLinks = FALSE;
 if (endsWith(scriptName, "qaPushQ"))
     nonVersionedLinks = TRUE;
 if (nonVersionedLinks)
     linkWithTimestamp = dyStringCreate("%s/%s%s", dyStringContents(fullDirName), baseName, extension);
 else if ((cfgOption("versionStamped") == NULL) &&  (hIsPreviewHost() || hIsPrivateHost()))
     linkWithTimestamp = dyStringCreate("%s/%s-%ld%s", dyStringContents(fullDirName), baseName, mtime, extension);
 else
     linkWithTimestamp = dyStringCreate("%s/%s-v%s%s", dyStringContents(fullDirName), baseName, CGI_VERSION, extension);
 
 if (hIsBrowserbox() && !fileExists(dyStringContents(linkWithTimestamp)))
     // on the browserbox, both alpha and beta binaries can run 
     {
     linkWithTimestamp = dyStringCreate("%s/%s-%ld%s", dyStringContents(fullDirName), 
         baseName, mtime, extension);
     }
 
 if (!fileExists(dyStringContents(linkWithTimestamp)))
         errAbort("Cannot find correct version of file '%s'; this is due to an installation "
         "error\n\nError details: %s does not exist", fileName, dyStringContents(linkWithTimestamp));
 
 // Free up all that extra memory
 dyStringFree(&realFileName);
 dyStringFree(&fullDirName);
 char *linkFull = dyStringCannibalize(&linkWithTimestamp);
 char *link = linkFull;
 if (docRoot != NULL)
     {
     link = cloneString(linkFull + strlen(docRoot) + 1);
     freeMem(linkFull);
     }
 
 if (wrapInHtml) // wrapped for christmas
     {
     struct dyString *wrapped = dyStringNew(0);
     if (js)
         dyStringPrintf(wrapped,"<script type='text/javascript' SRC='../%s'></script>\n", link);
     else if (style)
         dyStringPrintf(wrapped,"<LINK rel='STYLESHEET' href='../%s' TYPE='text/css' />\n", link);
     else // Will be image, since these are the only three choices allowed
         dyStringPrintf(wrapped,"<IMG src='../%s' />\n", link);
     freeMem(link);
     link = dyStringCannibalize(&wrapped);
     }
 
 return link;
 }
 
 char *webTimeStampedLinkToResourceOnFirstCall(char *fileName, boolean wrapInHtml)
 // If this is the first call, will return full path of timestamped link to the requested
 //   resource file (js, or css).  Free after use.
 // else returns NULL.  Useful to ensure multiple references to the same resource file are not made
 // NOTE: png, jpg and gif should also be supported but are untested.
 {
 if (!includedResourceFiles)
     includedResourceFiles = newHash(0);
 
 if (hashLookup(includedResourceFiles, fileName))
     return NULL;
 
 char * link = webTimeStampedLinkToResource(fileName,wrapInHtml);
 if (link)
     hashAdd(includedResourceFiles, fileName, NULL);  // Don't hash link, because
 return link;                                         // memory will be freed by caller!!!
 }
 
 boolean webIncludeResourcePrintToFile(FILE * toFile, char *fileName)
 // Converts fileName to web Resource link and prints the html reference
 // This only prints and returns TRUE on first call for this resource.
 // Passing in NULL as the file pointer results in hPrintf call
 // The reference will be to a link with timestamp.
 {
 char *link = webTimeStampedLinkToResourceOnFirstCall(fileName,TRUE);
 if (link)
     {
     if (toFile == NULL)
         hPrintf("%s",link);
     else
         fprintf(toFile,"%s",link);
     freeMem(link);
     return TRUE;
     }
 return FALSE;
 }
 
 // overrides for default context specific help link.
 char *contextSpecificHelpLink = NULL;
 char *contextSpecificHelpLabel = NULL;
 
 void setContextSpecificHelp(char *link, char *label)
 // Override default behavior for the context specific help link
 {
 if(link)
     contextSpecificHelpLink = cloneString(link);
 if(label)
     contextSpecificHelpLabel = cloneString(label);
 }
 
 char *menuBarAddUiVars(char *oldString, char *cgiPrefix, char *uiVars)
 /* Look for CGI program calls in oldString, and add session vars hgsid to them */
 {
 int len = strlen(oldString);
 char buf[4096];
 
 /* Create a regular expression and compile it */
 regex_t re;
 regmatch_t match[2];
 safef(buf, sizeof(buf), "%s[A-Za-z]+(%c%c?)", cgiPrefix, '\\', '?');
 int err = regcomp(&re, buf, REG_EXTENDED);
 if(err)
     errAbort("regcomp failed; err: %d", err);
 
 /* Search through oldString with regex, and build up new string in dy */
 struct dyString *dy = newDyString(0);
 int offset;
 for(offset = 0; offset < len && !regexec(&re, oldString + offset, ArraySize(match), match, 0); 
     offset += match[0].rm_eo)
     {
     dyStringAppendN(dy, oldString + offset, match[0].rm_eo);
     if(match[1].rm_so == match[1].rm_eo)
 	dyStringAppend(dy, "?");
     dyStringAppend(dy, uiVars);
     if(match[1].rm_so != match[1].rm_eo)
 	dyStringAppend(dy, "&");
     }
 if(offset < len)
     dyStringAppend(dy, oldString + offset);
 return dyStringCannibalize(&dy);
 }
 
 char *menuBar(struct cart *cart, char *db)
 // Return HTML for the menu bar (read from a configuration file);
 // we fixup internal CGI's to add hgsid's and include the appropriate js and css files.
 //
 // Note this function is also called by hgTracks which extends the menu bar
 //  with a View menu defined in hgTracks/menu.c
 {
 char *docRoot = hDocumentRoot();
 char *menuStr, buf[4096], uiVars[128];
 FILE *fd;
 char *navBarFile = "inc/globalNavBar.inc";
 struct stat statBuf;
 char *scriptName = cgiScriptName();
 if (cart)
     safef(uiVars, sizeof(uiVars), "%s=%s", cartSessionVarName(), cartSessionId(cart));
 else
     uiVars[0] = 0;
 
 if(docRoot == NULL)
     // tolerate missing docRoot (i.e. don't bother with menu when running from command line)
     return NULL;
 
 jsIncludeFile("jquery.js", NULL);
 jsIncludeFile("jquery.plugins.js", NULL);
 webIncludeResourceFile("nice_menu.css");
 
 // Read in menu bar html
 safef(buf, sizeof(buf), "%s/%s", docRoot, navBarFile);
 fd = mustOpen(buf, "r");
 fstat(fileno(fd), &statBuf);
 int len = statBuf.st_size;
 menuStr = needMem(len + 1);
 mustRead(fd, menuStr, statBuf.st_size);
 menuStr[len] = 0;
 carefulClose(&fd);
 
 if (cart)
     {
     char *newMenuStr = menuBarAddUiVars(menuStr, "/cgi-bin/hg", uiVars);
     freez(&menuStr);
     menuStr = newMenuStr;
     }
 
 if(scriptName)
     {
     // Provide hgTables options for some CGIs.
     char hgTablesOptions[1024] = "";
     char *track = (cart == NULL ? NULL :
                    (endsWith(scriptName, "hgGene") ?
                     cartOptionalString(cart, "hgg_type") :
                     cartOptionalString(cart, "g")));
     if (track && cart && db &&
         (endsWith(scriptName, "hgc") || endsWith(scriptName, "hgTrackUi") ||
          endsWith(scriptName, "hgGene")))
         {
         struct trackDb *tdb = hTrackDbForTrack(db, track);
         if (tdb)
 	    {
 	    struct trackDb *topLevel = trackDbTopLevelSelfOrParent(tdb); 
 	    safef(hgTablesOptions, sizeof  hgTablesOptions, 
 		    "../cgi-bin/hgTables?hgta_doMainPage=1&hgta_group=%s&hgta_track=%s&hgta_table=%s&", 
 		    topLevel->grp, topLevel->track, tdb->table);
 	    menuStr = replaceChars(menuStr, "../cgi-bin/hgTables?", hgTablesOptions);
 	    trackDbFree(&tdb);
 	    }
         }
     }
 
 if(!loginSystemEnabled())
     stripRegEx(menuStr, "<\\!-- LOGIN_START -->.*<\\!-- LOGIN_END -->", REG_ICASE);
 
 if(scriptName)
     {  // Provide optional official mirror servers menu items
     char *geoMenu = geoMirrorMenu();
     char *pattern = "<!-- OPTIONAL_MIRROR_MENU -->";
     char *newMenuStr = replaceChars(menuStr, pattern, geoMenu);
     freez(&menuStr);
     menuStr = newMenuStr;
     }
 
 
 if(scriptName)
     {
     // Provide view menu for some CGIs.
     struct dyString *viewItems = dyStringCreate("");
     boolean hasViewMenu = TRUE;
     if (endsWith(scriptName, "hgGenome"))
         {
 	safef(buf, sizeof(buf), "../cgi-bin/hgGenome?%s&hgGenome_doPsOutput=1", uiVars);
     	dyStringPrintf(viewItems, "<li><a href='%s' id='%s'>%s</a></li>\n", buf, "pdfLink", "PDF/PS");
         }
     else
 	{
 	hasViewMenu = FALSE;
 	}
     if (hasViewMenu)
 	{
 	struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n");
 	dyStringAppend(viewMenu, viewItems->string);
 	dyStringAppend(viewMenu, "</ul>\n</li>\n");
     	menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", viewMenu->string);
 	dyStringFree(&viewMenu);
 	}
     else if (!endsWith(scriptName, "hgTracks"))
 	{
     	replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", "");
 	}
     dyStringFree(&viewItems);
     }
 
 
 if(scriptName)
     {
     // Provide context sensitive help links for some CGIs.
     char *link = NULL;
     char *label = NULL;
     if (endsWith(scriptName, "hgBlat"))
         {
         link = "../goldenPath/help/hgTracksHelp.html#BLATAlign";
         label = "Help on Blat";
         }
     else if (endsWith(scriptName, "hgHubConnect"))
         {
         link = "../goldenPath/help/hgTrackHubHelp.html";
         label = "Help on Track Hubs";
         }
     else if (endsWith(scriptName, "hgNear"))
         {
         link = "../goldenPath/help/hgNearHelp.html";
         label = "Help on Gene Sorter";
         }
     else if (endsWith(scriptName, "hgTables"))
         {
         link = "../goldenPath/help/hgTablesHelp.html";
         label = "Help on Table Browser";
         }
+    else if (endsWith(scriptName, "hgIntegrator"))
+        {
+        link = "../goldenPath/help/hgIntegratorHelp.html";
+        label = "Help on Data Integrator";
+        }
     else if (endsWith(scriptName, "hgGenome"))
         {
         link = "../goldenPath/help/hgGenomeHelp.html";
         label = "Help on Genome Graphs";
         }
     else if (endsWith(scriptName, "hgSession"))
         {
         link = "../goldenPath/help/hgSessionHelp.html";
         label = "Help on Sessions";
         }
     else if (endsWith(scriptName, "hgVisiGene"))
         {
         link = "../goldenPath/help/hgTracksHelp.html#VisiGeneHelp";
         label = "Help on VisiGene";
         }
     else if (endsWith(scriptName, "hgCustom"))
         {
         link = "../goldenPath/help/customTrack.html";
         label = "Help on Custom Tracks";
         }
     // Don't overwrite any previously set defaults
     if(!contextSpecificHelpLink && link)
         contextSpecificHelpLink = link;
     if(!contextSpecificHelpLabel && label)
         contextSpecificHelpLabel = label;
     }
 if(contextSpecificHelpLink)
     {
     char buf[1024];
     safef(buf, sizeof(buf), "<li><a href='%s'>%s</a></li>", contextSpecificHelpLink, contextSpecificHelpLabel);
     menuStr = replaceChars(menuStr, "<!-- CONTEXT_SPECIFIC_HELP -->", buf);
     }
 return menuStr;
 }
 
 void checkForGeoMirrorRedirect(struct cart *cart)
 // Implement Geo/IP based redirection.
 {
 char *thisNodeStr = geoMirrorNode();
 if (thisNodeStr)   // if geo-mirroring is enabled
     {
     char *redirectCookie = findCookieData("redirect");
     char *redirect = cgiOptionalString("redirect");
 
     // if we're not already redirected
     if (redirect == NULL && redirectCookie == NULL) 
         {
         int thisNode = sqlUnsigned(thisNodeStr);
         struct sqlConnection *centralConn = hConnectCentral();
         char *ipStr = cgiRemoteAddr();
         int node = defaultNode(centralConn, ipStr);
 
         // if our node is not the node that's closest.
         if (thisNode != node)
             {
 	    char *geoSuffix = cfgOptionDefault("browser.geoSuffix","");
             char query[1056];
             sqlSafef(query, sizeof query, "select domain from gbNode%s where node = %d", geoSuffix, node);
             char *newDomain = sqlQuickString(centralConn, query);
             char *oldDomain = cgiServerName();
             char *port = cgiServerPort();
             char *uri = cgiRequestUri();
             char *sep = strchr(uri, '?') ? "&" : "?";
             int newUriSize = strlen(uri) + 1024;
             char *newUri = needMem(newUriSize);
             char *oldUri = needMem(newUriSize);
             safef(oldUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s", 
 		cgiServerHttpsIsOn() ? "s" : "", oldDomain, port, uri, sep, oldDomain);
             safef(newUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s", 
 		cgiServerHttpsIsOn() ? "s" : "", newDomain, port, uri, sep, oldDomain);
 
 	    printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">"
 	    "<div style=\"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;\">"
 	    "<h3 style=\"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;\">"
 	    "&nbsp;You might want to navigate to your nearest mirror - %s"
 	    "</h3> "
 	    "<ul style=\"margin:5px;\">",
 	    newDomain);
 	    
 	    printf("<li>User settings (sessions and custom tracks) <B>will differ</B> between sites."
 		"<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html#sessions\">Read more.</a></idiv>");
 	    printf("<li>Take me to  <a href=\"%s\">%s</a> </li>",
 		newUri, newDomain);
 	    printf("<li>Let me stay here   <a href=\"%s\">%s</a>",
 		oldUri, oldDomain );
 	    printf("</div></TD></TR>\n");
             exit(0);
             }
         hDisconnectCentral(&centralConn);
         }
     }
 }