037fad09eb0c322d3ede8e3a20fad478777d58f3
braney
  Tue Jul 9 14:28:33 2013 -0700
resolve newly introduced error in menu bar, notify users that hgVai doesn't work with assembly hubs, and resolve caching problems with assembly hubs (set udc cache timeout before opening hubs (otherwise the default is 0), don't open 2bit files until they are actually used)
diff --git src/hg/hgTracks/menu.c src/hg/hgTracks/menu.c
index ffa4d41..4d04ed1 100644
--- src/hg/hgTracks/menu.c
+++ src/hg/hgTracks/menu.c
@@ -1,366 +1,369 @@
 // Code to create hgTracks menu bar
 
 #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"
 
 /* list of links to display in a menu */
 struct hotLink
     {
     struct hotLink *next;
     char *name;
     char *url;
     char *id;
     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;
 slAddTail(links, link);
 }
 
 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 printMenuBar()
 /* Put up the menu bar. */
 {
 struct hotLink *link, *links = NULL;
 int i, len;
-struct sqlConnection *conn = hAllocConn(database);
+struct sqlConnection *conn = NULL;
+if (!trackHubDatabase(database))
+    conn = hAllocConn(database);
 char *menuStr, buf[4096], uiVars[1024];
 safef(uiVars, sizeof(uiVars), "%s=%u", cartSessionVarName(), cartSessionId(cart));
 
 menuStr = menuBar(cart);
 
 // 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=%d&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 */
     char ensVersionString[256], ensDateReference[256];
     ensGeneTrackVersion(database, ensVersionString, ensDateReference, sizeof(ensVersionString));
 
-    if (sqlTableExists(conn, UCSC_TO_ENSEMBL))
+    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 (ensVersionString[0])
         {
         char *archive = NULL;
         if (ensDateReference[0] && differentWord("current", ensDateReference))
             archive = cloneString(ensDateReference);
         /*  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, "hg18"))
     {
     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, "hg19"))
     {
     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, "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);
 
 struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n");
 len = slCount(links);
 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;
     char *encodedName = htmlEncode(link->name);
     dyStringAppend(viewMenu, "<li");
     if(*class)
         dyStringPrintf(viewMenu, " class='%s'", class);
     dyStringPrintf(viewMenu, "><a href='%s' id='%s'%s>%s</a></li>\n", link->url, link->id,
                    link->external ? " TARGET='_blank'" : "", encodedName);
     freez(&encodedName);
     }
 dyStringAppend(viewMenu, "</ul>\n</li>\n");
 
 menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", dyStringCannibalize(&viewMenu));
 hPuts(menuStr);
 freez(&menuStr);
 }