da1f0d67fe492b997b07bbebe6e5f4a86170331b
angie
  Wed May 4 10:07:18 2016 -0700
Same as in hgGateway (d30337d4), I forgot to initialize oldVars (thanks Hiram for noticing!) and also wasn't using getDbGenomeClade which handles position reset when db changes.  refs #17267#note-5.

diff --git src/hg/hgChooseDb/hgChooseDb.c src/hg/hgChooseDb/hgChooseDb.c
index df28237..bc19308 100644
--- src/hg/hgChooseDb/hgChooseDb.c
+++ src/hg/hgChooseDb/hgChooseDb.c
@@ -1,283 +1,285 @@
 /* hgChooseDb - bootstrapper / back end for demo app: auto-complete db/organism search
  * This CGI has three modes of operation:
  *  - HTML output for minimal main page with a <div> container to be filled in by javascript
  *    (default, in the absence of special CGI params)
  *  - 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)
  * The UI view top level is in ../js/react/hgChooseDb/hgChooseDb.jsx
  * The UI model top level is in ../js/model/hgChooseDb/hgChooseDbModel.js
  */
 #include "common.h"
 #include "cart.h"
 #include "cartJson.h"
 #include "cheapcgi.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "hui.h"
 #include "jsHelper.h"
 #include "jsonParse.h"
 #include "obscure.h"  // for readInGulp
 #include "trackHub.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 "hgcd_term"
 
 static char *getPhotoForGenome(char *genome, char *db)
 /* If the expected file for this genome's description page photo exists, return the filename. */
 {
 if (db == NULL)
     db = hDefaultDbForGenome(genome);
 char baseName[PATH_LEN];
 if (sameString("Human", genome))
     safecpy(baseName, sizeof(baseName), "human.jpg");
 else
     {
     safef(baseName, sizeof(baseName), "%s.jpg", hScientificName(db));
     subChar(baseName, ' ', '_');
     }
 char fileName[PATH_LEN];
 safef(fileName, sizeof(fileName), "%s/images/%s", hDocumentRoot(), baseName);
 if (fileExists(fileName))
     {
     // Reformat for URL:
     safef(fileName, sizeof(fileName), "../images/%s", baseName);
     return cloneString(fileName);
     }
 else
     return NULL;
 }
 
 static void writeGenomeInfo(struct jsonWrite *jw, char *genome, char *db)
 // Write menu options, selected db etc. for genome and db.  If db is NULL use default for genome.
 {
 if (db == NULL)
     db = hDefaultDbForGenome(genome);
 struct slPair *dbOptions = hGetDbOptionsForGenome(genome);
 jsonWriteValueLabelList(jw, "dbOptions", dbOptions);
 jsonWriteString(jw, "db", db);
 jsonWriteString(jw, "genome", genome);
 jsonWriteString(jw, "img", getPhotoForGenome(genome, db));
 }
 
 static void writeDbMenuData(struct jsonWrite *jw, char *genome, char *db)
 // Set dbMenuData to use genome's info.
 {
 jsonWriteObjectStart(jw, "dbMenuData");
 writeGenomeInfo(jw, genome, db);
 jsonWriteObjectEnd(jw);
 }
 
 static void getDbMenu(struct cartJson *cj, struct hash *paramHash)
 /* Write a dbMenu for the selected search term match.  */
 {
 char *genome = cartJsonRequiredParam(paramHash, "genome", cj->jw, "getDbMenu");
 char *db = cartJsonOptionalParam(paramHash, "db");
 writeDbMenuData(cj->jw, genome, db);
 }
 
 static char *popularSpecies[] =
     { "Human", "Mouse", "Rat", "D. melanogaster", "C. elegans", NULL };
 
 static void writeOnePopularSpecies(struct jsonWrite *jw, char *genome, char *db)
 // Write a nameless object with info about this species.
 {
 jsonWriteObjectStart(jw, NULL);
 writeGenomeInfo(jw, genome, db);
 jsonWriteObjectEnd(jw);
 }
 
 static void getPopularSpecies(struct cartJson *cj, struct hash *paramHash)
 /* Return a list of popular species' names, images and db menu info. */
 {
 jsonWriteListStart(cj->jw, "popularSpecies");
 char *currentDb = cartOptionalString(cart, "db");
 char *currentGenome = currentDb ? hGenome(currentDb) : NULL;
 boolean gotCurrent = FALSE;
 int i;
 for (i = 0;  popularSpecies[i] != NULL;  i++)
     {
     char *db = NULL;
     if (sameOk(popularSpecies[i], currentGenome))
         {
         gotCurrent = TRUE;
         db = currentDb;
         }
     writeOnePopularSpecies(cj->jw, popularSpecies[i], db);
     }
 if (! gotCurrent)
     writeOnePopularSpecies(cj->jw, currentGenome, currentDb);
 jsonWriteListEnd(cj->jw);
 if (currentGenome != NULL)
     writeDbMenuData(cj->jw, currentGenome, currentDb);
 }
 
 static void getDescriptionHtml(struct cartJson *cj, struct hash *paramHash)
 /* Return assembly description html for the given db. */
 {
 char *db = cartJsonRequiredParam(paramHash, "db", cj->jw, "getDescriptionHtml");
 char *htmlPath = hHtmlPath(db);
 char *htmlString = NULL;
 if (htmlPath != NULL)
     {
     if (fileExists(htmlPath))
 	readInGulp(htmlPath, &htmlString, NULL);
     else if (   startsWith("http://" , htmlPath) ||
 		startsWith("https://", htmlPath) ||
 		startsWith("ftp://"  , htmlPath))
 	{
 	struct lineFile *lf = udcWrapShortLineFile(htmlPath, NULL, 256*1024);
 	htmlString =  lineFileReadAll(lf);
 	lineFileClose(&lf);
 	}
     }
 if (isNotEmpty(htmlString))
     {
 //#*** TODO: move jsonStringEscape inside jsonWriteString
     htmlString = jsonStringEscape(htmlString);
     jsonWriteObjectStart(cj->jw, "assemblyDescription");
     jsonWriteString(cj->jw, "db", db);
     jsonWriteString(cj->jw, "description", htmlString);
     jsonWriteObjectEnd(cj->jw);
     }
 }
 
 static void doCartJson()
 /* Perform UI commands to update the cart and/or retrieve cart vars & metadata. */
 {
 struct cartJson *cj = cartJsonNew(cart);
 cartJsonRegisterHandler(cj, "getPopularSpecies", getPopularSpecies);
 cartJsonRegisterHandler(cj, "getDbMenu", getDbMenu);
 cartJsonRegisterHandler(cj, "getDescriptionHtml", getDescriptionHtml);
 cartJsonExecute(cj);
 }
 
 static void doMainPage()
 /* Send HTML with javascript to bootstrap the user interface. */
 {
 //#*** A lot of this is copied from hgIntegrator... libify!
 
-char *db = cartUsualString(cart, "db", hDefaultDb());
+char *db = NULL, *genome = NULL, *clade = NULL;
+getDbGenomeClade(cart, &db, &genome, &clade, oldVars);
 webStartWrapperDetailedNoArgs(cart, trackHubSkipHubName(db),
                               "", "UCSC Genome Browser Databases",
                               TRUE, FALSE, TRUE, TRUE);
 
 // Ideally these would go in the <HEAD>
 puts("<link rel=\"stylesheet\" href=\"//code.jquery.com/ui/1.10.3/themes/smoothness/jquery-ui.css\">");
 puts("<link rel=\"stylesheet\" href=\"//netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css\">");
 
 puts("<div id=\"appContainer\">Loading...</div>");
 
 // Set a global JS variable hgsid.
 // Plain old "var ..." doesn't work (other scripts can't see it), it has to belong to window.
 printf("<script>window.%s='%s';</script>\n", cartSessionVarName(), cartSessionId(cart));
 
 jsIncludeReactLibs();
 puts("<script src=\"../js/reactHgChooseDb.js\"></script>");
 puts("<script src=\"../js/hgChooseDbModel.js\"></script>");
 
 // Invisible form for jumping to hgTracks
 printf("\n<form action=\"%s\" method=%s id='mainForm'>\n",
        hgTracksName(), cartUsualString(cart, "formMethod", "GET"));
 cartSaveSession(cart);
 cgiMakeHiddenVar("db", db);
 puts("</form>");
 webEnd();
 }
 
 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();
 }
 
 static void fail(char *msg)
 //#*** Copied from hgSuggest... libify to cheapCgi?
 {
 puts("Status: 400\n\n");
 puts(msg);
 exit(-1);
 }
 
 INLINE void addIfStartsWithNoCase(char *term, char *target, struct dbDb *dbDb,
                                   struct hash *matchHash)
 {
 if (startsWithNoCase(term, target))
     {
     if (! hashLookup(matchHash, target))
         hashAdd(matchHash, target, dbDb);
     }
 }
 
 static void lookupTerm()
 /* Look for matches to term in hgCentral and print as JSON if found. */
 {
 char *term = cgiOptionalString(SEARCH_TERM);
 if (isEmpty(term))
     fail("Missing search term parameter");
 
 // Write JSON response with list of matches
 puts("Content-Type:text/javascript\n");
 struct jsonWrite *jw = jsonWriteNew();
 jsonWriteListStart(jw, NULL);
 
 // Search dbDb for matches
 struct hash *matchHash = hashNew(0);
 struct dbDb *dbDbList = hDbDbList(), *dbDb;
 for (dbDb = dbDbList;  dbDb != NULL; dbDb = dbDb->next)
     {
     if (startsWithNoCase(term, dbDb->name))
         {
         jsonWriteObjectStart(jw, NULL);
         char description[PATH_LEN];
         safef(description, sizeof(description), "%s (%s %s)",
               dbDb->name, dbDb->genome, dbDb->description);
         jsonWriteString(jw, "value", description);
         jsonWriteString(jw, "genome", dbDb->genome);
         jsonWriteString(jw, "db", dbDb->name);
         jsonWriteObjectEnd(jw);
         }
     addIfStartsWithNoCase(term, dbDb->genome, dbDb, matchHash);
     addIfStartsWithNoCase(term, dbDb->scientificName, dbDb, matchHash);
     addIfStartsWithNoCase(term, dbDb->sourceName, dbDb, matchHash);
     }
 
 struct hashEl *hel;
 struct hashCookie cookie = hashFirst(matchHash);
 while ((hel = hashNext(&cookie)) != NULL)
     {
     dbDb = hel->val;
     jsonWriteObjectStart(jw, NULL);
     jsonWriteString(jw, "value", hel->name);
     jsonWriteString(jw, "genome", dbDb->genome);
     jsonWriteObjectEnd(jw);
     }
 jsonWriteListEnd(jw);
 puts(jw->dy->string);
 }
 
 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,};
-struct hash *oldVars = NULL;
 cgiSpoof(&argc, argv);
 setUdcCacheDir();
+oldVars = hashNew(10);
 if (cgiOptionalString(SEARCH_TERM))
     // Skip the cart for speedy searches
     lookupTerm();
 else
     cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }