47ea57080b515e5dad5f658c58feb8944a7e7d61
chmalee
  Thu Jan 29 15:30:26 2026 -0800
Replace clade/assembly dropdowns with a search bar on most CGIs. Add a recents list to hgGateway and to the species bar and to the 'Genomes' dropdown menu. Track recently selected species in localStorage. Add toGenome and fromGenome arguemnts to hubApi/liftOver in order to find appropriate liftover assemblies, refs #36232

diff --git src/hg/hgMenubar/hgMenubar.c src/hg/hgMenubar/hgMenubar.c
index e0e86341860..2ae5fca7093 100644
--- src/hg/hgMenubar/hgMenubar.c
+++ src/hg/hgMenubar/hgMenubar.c
@@ -1,108 +1,111 @@
 /*
  * This CGI is used by static html pages to show a menu bar.
  * On an Apache with activated SSI, a html statement like
  * <!--#include virtual="../cgi-bin/hgMenubar"-->
  * will include the menu bar into a static page.
  */
 #include "common.h"
 #include "cheapcgi.h"
 #include "dystring.h"
 #include "filePath.h"
 #include "linefile.h"
 #include "jsHelper.h"
 
 #define CGI_NAME "cgi-bin/hgMenubar"
 #define NAVBAR_INC_PATH "/inc/globalNavBar.inc"
 #define OLD_HREF "href=\"../"
 
 char* errMessage;
 
 char *incFilePath(char *cgiPath, char *filePath, char *docRoot)
 /* Replace CGI_NAME in cgiPath with docRoot/filePath.  filePath must begin with "/" eg "/inc/..." */
 {
 char *incPath = replaceChars(cgiPath, "/"CGI_NAME, filePath);
 return catTwoStrings(docRoot, incPath);
 }
 
 void printIncludes(char* baseDir)
 {
 printf ("<noscript><div class='noscript'><div class='noscript-inner'><p><b>JavaScript is disabled in your web browser</b></p><p>You must have JavaScript enabled in your web browser to use the Genome Browser</p></div></div></noscript>\n");
 printf ("<script type='text/javascript' SRC='%sjs/jquery.js'></script>\n", baseDir);
 printf ("<script type='text/javascript' SRC='%sjs/jquery.plugins.js'></script>\n", baseDir);
 printf("<script type='text/javascript' SRC='%s/js/utils.js'></script>\n", baseDir);
 printf ("<LINK rel='STYLESHEET' href='%sstyle/nice_menu.css' TYPE='text/css'>\n", baseDir);
 }
 
 void printMenuBar(char *cgiPath, char *docRoot, char *pagePath, char *filePath)
 {
 char *navBarLoc = incFilePath(cgiPath, filePath, docRoot);
 struct lineFile *menuFile = lineFileOpen(navBarLoc, TRUE);
 char* oldLine = NULL;
 int lineSize = 0;
 
 char *cgiContainerPath = replaceChars(cgiPath, CGI_NAME, "");
 char *newPath = makeRelativePath(pagePath, cgiContainerPath);
 
 char *newHref = catTwoStrings("href=\"", newPath);
 
 printf ("Content-type: text/html\r\n\r\n");
 
 if (sameString(filePath, NAVBAR_INC_PATH))
     printIncludes(newPath);
 
 while (lineFileNext(menuFile, &oldLine, &lineSize))
     {
     // Not quite as robust as perl search and replace - no variable whitespace handling
     // Also lots of memory leakage - every line is reallocated and forgotten
     char *newLine = replaceChars(oldLine, OLD_HREF, newHref);
     printf("%s\n", newLine);
     }
 
 lineFileClose(&menuFile);
 // links to hgTracks need to use the web browser width and set the hgTracks image
 // size in pixels correctly to match the hgGateway "GO" button
 jsInline("$(\"#tools1 ul li a\").each( function (a) {\n"
 "    if (this.href && this.href.indexOf(\"hgTracks\") !== -1) {\n"
 "        var obj = this;\n"
 "        obj.onclick = function(e) {\n"
 "            var pix = calculateHgTracksWidth();\n"
 "            e.currentTarget.href += \"&pix=\" + pix;\n"
 "        }\n"
 "    }\n"
 "});\n");
+// if the user has previously searched for assemblies, add them to the "Genomes" menu heading,
+// above the "other" assemblies link
+jsInline("addRecentGenomesToMenuBar();\n");
 jsInlineFinish();
 }
 
 
 void parseEnvOrDie (char **cgiPath, char** docRoot, char** pagePath)
 {
 *cgiPath = getenv("SCRIPT_NAME");
 *docRoot = getenv("DOCUMENT_ROOT");
 *pagePath = getenv("REDIRECT_URL");
 if (*pagePath == NULL)
     *pagePath = getenv("DOCUMENT_URI");
 if (*pagePath == NULL)
     {
     *pagePath = cloneString("/inc/");
     errMessage = "Error: hgMenubar was run without the REDIRECT_URL or DOCUMENT_URI variable set. Looks like it wasn't run from an SSI statement. Defaulting to the 'inc/' directory, avoids errors in the Apache error log.";
     }
 
 if ( (*cgiPath == NULL) || (*docRoot == NULL) || (*pagePath == NULL) )
     {
     fprintf (stderr, "Error: bad invocation of menubar\n");
     exit (1);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 char *cgiPath, *docRoot, *pagePath;
 parseEnvOrDie(&cgiPath, &docRoot, &pagePath);
 cgiSpoof(&argc, argv);
 char *incFile = cgiUsualString("incFile", NAVBAR_INC_PATH);
 printMenuBar(cgiPath, docRoot, pagePath, incFile);
 if (errMessage)
     puts(errMessage);
 return 0;
 }