0f20260166f55679e7abbc702d955e42e71773eb
larrym
  Tue Dec 27 14:49:59 2011 -0800
cleanup and comments
diff --git src/hg/hgGateway/hgGateway.c src/hg/hgGateway/hgGateway.c
index ad69ec5..12296f7 100644
--- src/hg/hgGateway/hgGateway.c
+++ src/hg/hgGateway/hgGateway.c
@@ -1,406 +1,408 @@
 /* hgGateway - Human Genome Browser Gateway. */
 #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 "hCommon.h"
 #include "hui.h"
 #include "customTrack.h"
 #include "hubConnect.h"
 #include "hgConfig.h"
 #include "jsHelper.h"
 #include "hPrint.h"
 #include "suggest.h"
 #include "search.h"
 #include "internet.h"
 
 struct cart *cart = NULL;
 struct hash *oldVars = NULL;
 char *clade = NULL;
 char *organism = NULL;
 char *db = NULL;
 
 void hgGateway()
 /* hgGateway - Human Genome Browser Gateway. */
 {
 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 = assemblySupportsGeneSuggest(db);
 
 /* 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.
 */
 
 if (sameString(position, "genome") || sameString(position, "hgBatch"))
     position = defaultPosition;
 
 jsIncludeFile("jquery.js", NULL);
 #ifdef NEW_JQUERY
 webIncludeResourceFile("jquery-ui.css");
 jsIncludeFile("jquery-ui.js", NULL);
 printf("<script type='text/javascript'>var newJQuery=true;</script>\n");
 #else///ifndef NEW_JQUERY
 webIncludeResourceFile("autocomplete.css");
 jsIncludeFile("jquery.autocomplete.js", NULL);
 printf("<script type='text/javascript'>var newJQuery=false;</script>\n");
 #endif///ndef NEW_JQUERY
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("autocomplete.js", NULL);
 jsIncludeFile("hgGateway.js", NULL);
 jsIncludeFile("utils.js", NULL);
 
 puts(
 "<CENTER style='font-size:small;'>"
 "The UCSC Genome Browser was created by the \n"
 "<A HREF=\"../staff.html\">Genome Bioinformatics Group of UC Santa Cruz</A>.\n"
 "<BR>"
 "Software Copyright (c) The Regents of the University of California.\n"
 "All rights reserved.\n"
 "</CENTER>\n"
 );
 
 puts(
 "<FORM ACTION='../cgi-bin/hgTracks' NAME='mainForm' METHOD='GET' style='display:inline;'>\n"
 "<CENTER>"
 "<table style='background-color:#FFFEF3; border: 1px solid #CCCC99;'>\n"
 "<tr><td>\n");
 cgiMakeHiddenVar(hgHubConnectCgiDestUrl, "../cgi-bin/hgTracks");
 
 puts("<table><tr>");
 if (gotClade)
     puts("<td align=center valign=baseline>clade</td>");
 puts(
 "<td align=center valign=baseline>genome</td>\n"
 "<td align=center valign=baseline>assembly</td>\n"
 "<td align=center valign=baseline>position or search term</td>\n");
 if(supportsSuggest)
     puts("<td align=center valign=baseline><a title='click for help on gene search box' target='_blank' href='../goldenPath/help/geneSearchBox.html'>gene</a></td>\n");
 puts(
 "<td align=center valign=baseline> &nbsp; </td>\n"
 "</tr>\n<tr>"
 );
 
 if (gotClade)
     {
     puts("<td align=center>\n");
     printCladeListHtml(organism, onChangeClade);
     puts("</td>\n");
     }
 
 puts("<td align=center>\n");
 if (gotClade)
     printGenomeListForCladeHtml(db, onChangeOrg);
 else
     printGenomeListHtml(db, onChangeOrg);
 puts("</td>\n");
 
 puts("<td align=center>\n");
 printAssemblyListHtml(db, onChangeDB);
 puts("</td>\n");
 
 puts("<td align=center>\n");
 cgiMakeTextVar("position", addCommasToPos(db, position), 30);
 printf("</td>\n");
 
 if(supportsSuggest)
     {
     puts("<td align=center>\n");
     hPrintf("<input name='hgt.suggest' type='text' size='5' id='suggest' />\n"
             "<input type='hidden' name='hgt.suggestTrack' id='suggestTrack' value='%s'>\n", assemblyGeneSuggestTrack(db)
             );
     printf("</td>\n");
     }
 
 cartSetString(cart, "position", position);
 cartSetString(cart, "db", db);
 cartSetString(cart, "org", organism);
 if (gotClade)
     cartSetString(cart, "clade", clade);
 
 freez(&defaultPosition);
 position = NULL;
 
 puts("<td align=center>");
 if(supportsSuggest)
     hButtonWithOnClick("Submit", "submit", NULL, "submitButtonOnClick()");
 else
     cgiMakeButton("Submit", "submit");
 /* This is a clear submit button that browsers will use by default when enter is pressed in position box. FIXME: This should be done with js onchange event! */
 printf("<input TYPE=\"IMAGE\" BORDER=\"0\" NAME=\"hgt.dummyEnterButton\" src=\"../images/DOT.gif\" WIDTH=1 HEIGHT=1 ALT=dot>");
 cartSaveSession(cart);  /* Put up hgsid= as hidden variable. */
 puts(
 "</td>\n"
 "</tr></table>\n"
 "</td></tr>\n");
 
 puts(
 "<tr><td><CENTER><BR>\n"
 "<a HREF=\"../cgi-bin/cartReset\">Click here to reset</a> the browser user interface settings to their defaults.");
 
 #define SURVEY 1
 #ifdef SURVEY
 if (survey && differentWord(survey, "off"))
     printf("&nbsp;&nbsp;&nbsp;<span style='background-color:yellow;'><A HREF=\"%s\" TARGET=_BLANK><EM><B>%s</EM></B></A></span>", survey, surveyLabel ? surveyLabel : "Take survey");
 #endif
 
 puts(
 "<BR>\n"
 "</CENTER>\n"
 "</td></tr><tr><td><CENTER>\n"
 );
 
 puts("<TABLE BORDER=\"0\">");
 puts("<TR>");
 
 if(isSearchTracksSupported(db,cart))
     {
     puts("<TD VALIGN=\"TOP\">");
     cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT);
     puts("</TD>");
     }
 
 // custom track button. disable hgCustom button on GSID server, until
 // necessary additional work is authorized.
 puts("<TD VALIGN=\"TOP\">");
 
 /* disable CT for CGB servers for the time being */
 if (!hIsGsidServer() && !hIsCgbServer())
     {
     boolean hasCustomTracks = customTracksExist(cart, NULL);
     printf("<input TYPE=SUBMIT onclick=\"document.mainForm.action='%s';\" VALUE='%s' title='%s'>\n",
         hgCustomName(),hasCustomTracks ? CT_MANAGE_BUTTON_LABEL:CT_ADD_BUTTON_LABEL,
         hasCustomTracks ? "Manage your custom tracks" : "Add your own custom tracks"  );
     }
 puts("</TD>");
 
 if (hubConnectTableExists())
     {
     puts("<TD VALIGN=\"TOP\">");
     printf("<input TYPE=SUBMIT onclick=\"document.mainForm.action='%s';\" VALUE='%s' title='%s'>\n",
         "../cgi-bin/hgHubConnect", "track hubs", "Import tracks");
     puts("</TD>");
     }
 
 // configure button
 puts("<TD VALIGN=\"TOP\">");
 cgiMakeButtonWithMsg("hgTracksConfigPage", "configure tracks and display","Configure track selections and browser display");
 puts("</TD>");
 
 // clear possition button
 puts("<TD VALIGN=\"TOP\">");
 if(supportsSuggest)
     cgiMakeOnClickButton("document.mainForm.position.value=''; document.getElementById('suggest').value='';", "clear position");
 else
     cgiMakeOnClickButton("document.mainForm.position.value=''", "clear position");
 puts("</TD>");
 
 puts("</TR></TABLE>");
 
 puts("</CENTER>\n"
 "</td></tr></table>\n"
 );
 puts("</CENTER>");
 #ifdef NEW_JQUERY
 hPrintf("<input type='hidden' id='hgt.newJQuery' name='hgt.newJQuery' value='1'>\n");
 #endif
 
 
 if(!cartVarExists(cart, "pix"))
     // put a hidden input for pix on page so default value can be filled in on the client side
     hPrintf("<input type='hidden' name='pix' value=''>\n");
 
 puts("</FORM>");
 if (hIsPreviewHost())
     {
 puts("<P>"
 "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 "
 "      <A HREF=\"http://genome.ucsc.edu\">http://genome.ucsc.edu</A>."
 "</P><BR>");
     }
 else if (hIsPrivateHost())
     {
 puts("<P>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 "
 	 "<A HREF=\"http://genome.ucsc.edu\">genome.ucsc.edu</A> instead.");
     }
 
 if (hIsGsidServer())
     {
     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");
     }
 
 hgPositionsHelpHtml(organism, db);
 
 puts("<FORM ACTION=\"../cgi-bin/hgGateway\" METHOD=\"GET\" NAME=\"orgForm\">");
 cartSaveSession(cart);	/* Put up hgsid= as hidden variable. */
 if (gotClade)
     printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", clade);
 else
     printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", "mammal");
 
 printf("<input type=\"hidden\" name=\"org\" value=\"%s\">\n", organism);
 printf("<input type=\"hidden\" name=\"db\" value=\"%s\">\n", db);
 puts("</FORM><BR>");
 }
 
 void doMiddle(struct cart *theCart)
 /* Set up pretty web display and save cart in global. */
 {
 char *scientificName = NULL;
 cart = theCart;
 
 getDbGenomeClade(cart, &db, &organism, &clade, oldVars);
 if (! hDbIsActive(db))
     {
     db = hDefaultDb();
     organism = hGenome(db);
     clade = hClade(organism);
     }
 scientificName = hScientificName(db);
 if (hIsGsidServer())
     cartWebStart(theCart, db, "GSID %s Sequence View (UCSC Genome Browser) Gateway \n", organism);
 else
     {
     char buffer[128];
 
     /* tell html routines *not* to escape htmlOut strings*/
     htmlNoEscape();
     buffer[0] = 0;
     if (*scientificName != 0)
 	{
 	if (sameString(clade,"ancestor"))
 	    safef(buffer, sizeof(buffer), "(<I>%s</I> Ancestor) ", scientificName);
 	else
 	    safef(buffer, sizeof(buffer), "(<I>%s</I>) ", scientificName);
 	}
     cartWebStart(theCart, db, "%s %s%s Gateway\n", organism, buffer, hBrowserName());
     htmlDoEscape();
     }
 hgGateway();
 cartWebEnd();
 }
 
 char *excludeVars[] = {NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 oldVars = hashNew(10);
 cgiSpoof(&argc, argv);
 
 #ifdef SUPPORT_EURONODE
 boolean onWeb = cgiIsOnWeb();
 if (onWeb)
     {
     // check IP for redirection
     char *thisNodeStr = cfgOption("browser.node");
     if (thisNodeStr)
 	{
 	char *redirect = cgiOptionalString("redirect");
 	char *source = cgiOptionalString("source");
 	// check for the cookie called redirect (which suppress redirection)
 	char *redirectCookie = findCookieData("redirect");
 
 	fprintf(stderr, "GALT redirectCookie=%s redirect=%s source=%s\n", 
 		redirectCookie, redirect, source); fflush(stderr); // DEBUG REMOVE
 
-	if (!(redirectCookie || (redirect && !source)))
+	if (!(
+              (redirect && !source) ||   // we are on main site after user has actively choose to leave mirror and come back to the main site
+              redirectCookie             // main site after above has happened (XXXX I think)
+              ))
 	    {
-	    int thisNode = atoi(thisNodeStr);
+	    int thisNode = sqlUnsigned(thisNodeStr);
 	    struct sqlConnection *centralConn = hConnectCentral();
 	    char query[1024];
 	    char *ipStr = cgiRemoteAddr();
 	    bits32 ip = 0;
 	    internetDottedQuadToIp(ipStr, &ip);
             // we assume no overlaps in geoIpNode table, so we can use limit 1 to make query very efficient.
 	    safef(query, sizeof query, "select ipStart, ipEnd, node from geoIpNode where %u >= ipStart order by ipStart desc limit 1", ip);
 	    char **row;
-	    struct sqlResult *sr = NULL;
-	    sr = sqlGetResult(centralConn, query);
+	    struct sqlResult *sr = sqlGetResult(centralConn, query);
 	    int defaultNode = 1;
 	    if ((row = sqlNextRow(sr)) != NULL)
 		{
 		uint ipStart = sqlUnsigned(row[0]);
 		uint ipEnd = sqlUnsigned(row[1]);
 		if (ipStart <= ip && ipEnd >= ip)
 		    {
 		    defaultNode = sqlSigned(row[2]);
 		    }
 		}
 	    sqlFreeResult(&sr);
 
 	    fprintf(stderr, "GALT thisNodeStr=%s thisNode=%d ipStr=%s ip=%u defaultNode (for user) %d\n", 
 		thisNodeStr, thisNode,
 		ipStr, ip, defaultNode); fflush(stderr); // DEBUG REMOVE
 
 	    // get location of redirect node
 	    if (thisNode != defaultNode)
 		{
 		safef(query, sizeof query, "select domain from gbNode where node = %d", defaultNode);
 		char *newDomain = sqlQuickString(centralConn, query);
 		fprintf(stderr, "GALT newDomain=%s\n", newDomain); fflush(stderr); // DEBUG REMOVE
 		char *oldDomain = cgiServerName();
 		char *port = cgiServerPort();
 		char *uri = cgiRequestUri();
 		    //   /cgi-bin/test.cgi?x=15&y=youdog
 		char *sep = "?";
 		if (strchr(uri,'?') != 0)
 		    sep = "&";
 
 		int newUriSize = strlen(uri)+1024;
 		char *newUri = needMem(newUriSize);
 		// TODO what about https?
 		safef(newUri, newUriSize, "http://%s:%s%s%sredirect=mirror&source=%s", newDomain, port, uri, sep, oldDomain);
 
 		 //   "set-cookie: redirect=; path=/; expires=Mon, 18-Apr-2011 21:45:28 GMT"  
                  //     the time of the set-cookie expire was immediately now()
 		struct dyString *dy = dyStringNew(256);		
 		dyStringPrintf(dy,
 		    "HTTP/1.1 302 found: \n"
 		    "Content-Type: text/html; charset=iso-8859-1\n"
 		    "Connection: close\n"
 		    "Location: %s\n"
 		    "\n"
 		    "<html><head><title>Redirecting to closer site</title></head>\n"
 		    "<body><a href=\"%s\">%s</a></body>\n"
 		    , newUri , newUri, newUri);
 		fprintf(stderr, "GALT redirect response:\n%s", dy->string); fflush(stderr); // DEBUG REMOVE
 		puts(dyStringContents(dy));
 		exit(0);
 		}
 	    hDisconnectCentral(&centralConn);
 	    }
 	}
     }
 #endif
 
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }