057c793acb74d78c0fe969db0c3fb21df00927c6
max
  Wed Sep 2 02:33:06 2015 -0700
Removing the 'send to' menu and replacing it with a javascript-based
dialog that closes itself. Also fixing a small bug with the / key on
firefox for the shortcuts. refs #15113

diff --git src/hg/hgTracks/menu.c src/hg/hgTracks/menu.c
index 426abfd..2a0c7f2 100644
--- src/hg/hgTracks/menu.c
+++ src/hg/hgTracks/menu.c
@@ -1,468 +1,419 @@
 // Code to create hgTracks menu bar
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "dystring.h"
 #include "ensFace.h"
 #include "agpFrag.h"
 #include "ctgPos.h"
 #include "hCommon.h"
 #include "htmshell.h"
 #include "hash.h"
 #include "liftOver.h"
 #include "wikiLink.h"
 #include "web.h"
 #include "geoMirror.h"
 #include "hgTracks.h"
 #include "trackHub.h"
 #include "extTools.h"
 #include "trackVersion.h"
 
 /* list of links to display in a menu */
 struct hotLink
     {
     struct hotLink *next;
     char *name;
     char *url;
     char *id;
     char *mouseOver;
+    char *onClick;
     boolean inactive; /* greyed out */
     boolean external;
     };
 
 static void appendLink(struct hotLink **links, char *url, char *name, char *id, boolean external)
 {
 // append to list of links for later printing and/or communication with javascript client
 struct hotLink *link;
 AllocVar(link);
 link->name = cloneString(name);
 link->url = cloneString(url);
 link->id = cloneString(id);
 link->external = external;
 link->inactive = FALSE;
 slAddTail(links, link);
 }
 
 static void appendLinkMaybeInactive(struct hotLink **links, char *url, char *name, char *id, 
     char *mouseOver, boolean external, boolean inactive)
 {
 appendLink(links, url, name, id, external);
 struct hotLink *le = slLastEl(links);
 le->inactive=inactive;
 le->mouseOver=mouseOver;
 }
 
+static void appendLinkWithOnclick(struct hotLink **links, char *url, char *name, char *id, 
+    char *mouseOver, char *onClick, boolean external, boolean inactive)
+{
+appendLinkMaybeInactive(links, url, name, id, mouseOver, external, inactive);
+struct hotLink *le = slLastEl(links);
+le->onClick=onClick;
+}
+
 static void printEnsemblAnchor(char *database, char* archive,
                                char *chrName, int start, int end, struct hotLink **links)
 /* Print anchor to Ensembl display on same window. */
 {
 char *scientificName = hScientificName(database);
 char *dir = ensOrgNameFromScientificName(scientificName);
 struct dyString *ensUrl;
 char *name;
 int localStart, localEnd;
 
 name = chrName;
 
 if (sameWord(scientificName, "Takifugu rubripes"))
     {
     /* for Fugu, must give scaffold, not chr coordinates */
     /* Also, must give "chrom" as "scaffold_N", name below. */
     if (differentWord(chromName,"chrM") &&
     !hScaffoldPos(database, chromName, winStart, winEnd,
                         &name, &localStart, &localEnd))
         /* position doesn't appear on Ensembl browser.
          * Ensembl doesn't show scaffolds < 2K */
         return;
     }
 else if (sameWord(scientificName, "Gasterosteus aculeatus"))
     {
     if (differentWord("chrM", chrName))
     {
     char *fixupName = replaceChars(chrName, "chr", "group");
     name = fixupName;
     }
     }
 else if (sameWord(scientificName, "Ciona intestinalis"))
     {
     if (stringIn("chr0", chrName))
 	{
 	char *fixupName = replaceChars(chrName, "chr0", "chr");
 	name = fixupName;
 	}
     }
 else if (sameWord(scientificName, "Saccharomyces cerevisiae"))
     {
     if (stringIn("2micron", chrName))
 	{
 	char *fixupName = replaceChars(chrName, "2micron", "2-micron");
 	name = fixupName;
 	}
     }
 
 if (sameWord(chrName, "chrM"))
     name = "chrMt";
 ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, start+1, end, archive);
 appendLink(links, ensUrl->string, "Ensembl", "ensemblLink", TRUE);
 /* NOTE: you can not freeMem(dir) because sometimes it is a literal
  * constant */
 freeMem(scientificName);
 dyStringFree(&ensUrl);
 }
 
 static void fr2ScaffoldEnsemblLink(char *archive, struct hotLink **links)
 /* print out Ensembl link to appropriate scaffold there */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr = NULL;
 char **row = NULL;
 char query[256];
 sqlSafef(query, sizeof(query),
 "select * from chrUn_gold where chrom = '%s' and chromStart<%u and chromEnd>%u",
 chromName, winEnd, winStart);
 sr = sqlGetResult(conn, query);
 
 int itemCount = 0;
 struct agpFrag *agpItem = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     agpFragFree(&agpItem);  // if there is a second one
     agpItem = agpFragLoad(row+1);
     ++itemCount;
     if (itemCount > 1)
 	break;
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 if (1 == itemCount)
     {   // verify *entirely* within single contig
     if ((winEnd <= agpItem->chromEnd) &&
 	(winStart >= agpItem->chromStart))
 	{
 	int agpStart = winStart - agpItem->chromStart;
 	int agpEnd = agpStart + winEnd - winStart;
 	printEnsemblAnchor(database, archive, agpItem->frag,
                            agpStart, agpEnd, links);
 	}
     }
 agpFragFree(&agpItem);  // the one we maybe used
 }
 
 void freeLinksAndConvert(struct hotLink *links, struct dyString *menuHtml)
 /* convert the links to html strings and append to the dyString "menu", destroying the links */
 {
 int len = slCount(links);
 int i = 0;
 struct hotLink *link = NULL;
 for(i = 0, link = links; link != NULL; i++, link = link->next)
     {
     char class[100];
     if(i == 0)
         safef(class, sizeof(class), "first");
     else if (i + 1 == len)
         safef(class, sizeof(class), "last");
     else
         class[0] = 0;
     dyStringAppend(menuHtml, "<li");
     char *encodedName = htmlEncode(link->name);
     if(*class)
         dyStringPrintf(menuHtml, " class='%s'", class);
     dyStringPrintf(menuHtml, "><a href='%s' ", link->url);
     if (link->mouseOver)
         dyStringPrintf(menuHtml, "title='%s' ", link->mouseOver); 
+    if (link->onClick)
+        dyStringPrintf(menuHtml, "onclick=\"%s\" ", link->onClick); 
     dyStringPrintf(menuHtml, "id='%s'%s>%s</a></li>\n", link->id, 
         link->external ? " TARGET='_blank'" : "", encodedName);
     freez(&encodedName);
 
     freez(&link->name);
     freez(&link->url);
     freez(&link->id);
     }
 slFreeList(links);
 }
 
-static void addSendToMenuItems(struct dyString *viewMenu, char* uiVars)
-/* add the "send to" menu to the "viewMenu" dyString */
-{
-struct hotLink *viewLinks = NULL;
-
-char url[4096];
-char label[4096];
-
-struct extTool *extTools = readExtToolRa("extTools.ra");
-struct extTool *et;
-for(et = extTools; et != NULL; et = et->next)
-    {
-
-    if (et->dbs!=NULL)
-        {
-        if (!slNameInList(et->dbs, database))
-            continue;
-        }
-    if (et->notDbs!=NULL)
-        {
-        if (slNameInList(et->notDbs, database))
-            continue;
-        }
-
-
-    safef(url, sizeof(url), "hgTracks?%s&hgt.redirectTool=%s", uiVars, et->tool);
-
-    boolean inactive = FALSE;
-    if (et->maxSize!=0)
-        {
-        inactive = TRUE;
-        if (et->maxSize>1000)
-            safef(label, sizeof(label), "%s (< %d kbp)", et->shortLabel, et->maxSize/1000);
-        else
-            safef(label, sizeof(label), "%s (< %d bp)", et->shortLabel, et->maxSize);
-        }
-    else
-        safef(label, sizeof(label), "%s", et->shortLabel);
-        
-    appendLinkMaybeInactive(&viewLinks, url, label, "extTool", et->longLabel, TRUE, inactive);
-    }
-
-freeLinksAndConvert(viewLinks, viewMenu);
-
-}
-
 void printMenuBar()
 /* Put up the special menu bar for hgTracks. */
 {
 struct hotLink *links = NULL;
 struct sqlConnection *conn = NULL;
 if (!trackHubDatabase(database))
     conn = hAllocConn(database);
 char *menuStr, buf[4096], uiVars[1024];
 safef(uiVars, sizeof(uiVars), "%s=%s", cartSessionVarName(), cartSessionId(cart));
 
 menuStr = menuBar(cart, database);
 
 // Create top items in view menu
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.psOutput=on", uiVars);
 appendLink(&links, buf, "PDF/PS", "pdfLink", FALSE);
 safef(buf, sizeof(buf), "%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s",
       hgcNameAndSettings(), winStart, chromName, winStart, winEnd, database, uiVars);
 appendLink(&links, buf, "DNA", "dnaLink", FALSE);
 safef(buf, sizeof(buf), "../cgi-bin/hgConvert?hgsid=%s&db=%s", cartSessionId(cart), database);
 appendLink(&links, buf, "In Other Genomes (Convert)", "convertMenuLink", FALSE);
 
 // Add link-outs to other dbs as appropriate for this assembly
 if (differentWord(database,"susScr2"))
     {
     /* Print Ensembl anchor for latest assembly of organisms we have
      * supported by Ensembl == if versionString from trackVersion exists */
     struct trackVersion *trackVersion = getTrackVersion(database, "ensGene");
 
     if ((conn != NULL) && sqlTableExists(conn, UCSC_TO_ENSEMBL))
         printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
     else if (sameWord(database,"hg19"))
         {
         printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
         }
     else if (sameWord(database,"hg18"))
         {
         printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd, &links);
         }
     else if (sameWord(database,"oryCun2") || sameWord(database,"anoCar2") || sameWord(database,"calJac3"))
         {
         printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links);
         }
     else if ((trackVersion != NULL) && !isEmpty(trackVersion->version))
         {
         char *archive = NULL;
         if (!isEmpty(trackVersion->dateReference) && differentWord("current", trackVersion->dateReference))
             archive = cloneString(trackVersion->dateReference);
         /*  Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */
         if (isUnknownChrom(database, chromName))
             {
             //	which table to check
             char *ctgPos = "ctgPos";
 
             if (sameWord(database,"fr2"))
                 fr2ScaffoldEnsemblLink(archive, &links);
             else if (hTableExists(database, UCSC_TO_ENSEMBL))
                 printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links);
             else if (hTableExists(database, ctgPos))
                 /* see if we are entirely within a single contig */
                 {
                 struct sqlResult *sr = NULL;
                 char **row = NULL;
                 char query[256];
                 sqlSafef(query, sizeof(query),
                       "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u",
                       ctgPos, chromName, winEnd, winStart);
                 sr = sqlGetResult(conn, query);
 
                 int itemCount = 0;
                 struct ctgPos *ctgItem = NULL;
                 while ((row = sqlNextRow(sr)) != NULL)
                     {
                     ctgPosFree(&ctgItem);   // if there is a second one
                     ctgItem = ctgPosLoad(row);
                     ++itemCount;
                     if (itemCount > 1)
                         break;
                     }
                 sqlFreeResult(&sr);
                 if (1 == itemCount)
                     {   // verify *entirely* within single contig
                     if ((winEnd <= ctgItem->chromEnd) &&
                         (winStart >= ctgItem->chromStart))
                         {
                         int ctgStart = winStart - ctgItem->chromStart;
                         int ctgEnd = ctgStart + winEnd - winStart;
                         printEnsemblAnchor(database, archive, ctgItem->contig,
                                            ctgStart, ctgEnd, &links);
                         }
                     }
                 ctgPosFree(&ctgItem);   // the one we maybe used
                 }
             }
         else
             {
             printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links);
             }
         }
     }
 hFreeConn(&conn);
 
 if (sameString(database, "hg38"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "hg19"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&build=previous&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "mm8"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "danRer2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7955&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "galGal3"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "canFam2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9615&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "rheMac2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9544&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "panTro2"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9598&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "anoGam1"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7165&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (sameString(database, "bosTau6"))
     {
     safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9913&CHR=%s&BEG=%d&END=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "NCBI", "ncbiLink", TRUE);
     }
 else if (startsWith("oryLat", database))
     {
     safef(buf, sizeof(buf), "http://medaka.utgenome.org/browser_ens_jump.php?revision=version1.0&chr=chromosome%s&start=%d&end=%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "UTGB", "medakaLink", TRUE);
     }
 else if (sameString(database, "cb3"))
     {
     safef(buf, sizeof(buf), "http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "cb4"))
     {
     safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_briggsae?name=%s:%d-%d",
           chromName, winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "ce10"))
     {
     safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "ce4"))
     {
     safef(buf, sizeof(buf), "http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 else if (sameString(database, "ce2"))
     {
     safef(buf, sizeof(buf), "http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d",
           skipChr(chromName), winStart+1, winEnd);
     appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE);
     }
 
 // finish View menu
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgTracksConfigPage=configure", uiVars);
 appendLink(&links, buf, "Configure Browser", "configureMenuLink", FALSE);
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.reset=on", uiVars);
 appendLink(&links, buf, "Default Tracks", "defaultTracksMenuLink", FALSE);
 safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.defaultImgOrder=on", uiVars);
 appendLink(&links, buf, "Default Track Order", "defaultTrackOrderMenuLink", FALSE);
 appendLink(&links, "../cgi-bin/cartReset", "Reset All User Settings", "cartResetMenuLink", FALSE);
 
 // add the sendTo menu
 if (fileExists("extTools.ra"))
     {
     appendLinkWithOnclick(&links, "#", "In external tool", "Show current region on a third-party website", "extToolLink", "showExtToolDialog()", FALSE, FALSE);
     }
 
 struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul>\n");
 freeLinksAndConvert(links, viewMenu);
-if (fileExists("extTools.ra"))
-    {
-    dyStringAppend(viewMenu, "<li class=\"menuparent\" id=\"sendTo\"><span>In external tool</span><ul>");
-    addSendToMenuItems(viewMenu, uiVars);
-    dyStringAppend(viewMenu, "</ul>\n</li>\n");
-    }
 dyStringAppend(viewMenu, "</ul>\n</li>\n");
 
-// add the sendTo menu
-if (fileExists("extTools.ra"))
-    {
-    dyStringAppend(viewMenu, "<li class=\"menuparent\" id=\"sendTo\"><span>Send To</span><ul>");
-    addSendToMenuItems(viewMenu, uiVars);
-    dyStringAppend(viewMenu, "</ul>\n</li>\n");
-    }
-
 menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", dyStringCannibalize(&viewMenu));
 menuStr = replaceChars(menuStr, "id=\"main-menu-whole\"", "id=\"hgTracks-main-menu-whole\"");
 menuStr = replaceChars(menuStr, "id=\"home-link\"", "id=\"hgTracks-home-link\"");
 hPuts(menuStr);
 freez(&menuStr);
 }