8715d83d38d8bb18adfdd9ce05771b4cede85407
angie
  Fri Dec 5 09:52:07 2014 -0800
Moved some hgTables code that had been copied into a couple differentplaces into a new lib module, cartTrackDb.  hgGenome/import.c has code
that is fairly similar but that also needs to filter out custom tracks
that were generated by hgGenome.

diff --git src/hg/hgTables/mainPage.c src/hg/hgTables/mainPage.c
index 25c7ec9..e4d8195 100644
--- src/hg/hgTables/mainPage.c
+++ src/hg/hgTables/mainPage.c
@@ -1,1055 +1,953 @@
 /* mainPage - stuff to put up the first table browser page. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "htmshell.h"
 #include "cheapcgi.h"
 #include "cart.h"
+#include "cartTrackDb.h"
 #include "textOut.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "web.h"
 #include "jsHelper.h"
 #include "hui.h"
 #include "hgColors.h"
 #include "trackDb.h"
 #include "grp.h"
 #include "hgTables.h"
 #include "joiner.h"
 #include "hubConnect.h"
 #include "trackHub.h"
 #include "hgConfig.h"
 
 
 int trackDbCmpShortLabel(const void *va, const void *vb)
 /* Sort track by shortLabel. */
 {
 const struct trackDb *a = *((struct trackDb **)va);
 const struct trackDb *b = *((struct trackDb **)vb);
 return strcmp(a->shortLabel, b->shortLabel);
 }
 
 static struct dyString *onChangeStart()
 /* Start up a javascript onChange command */
 {
 struct dyString *dy = jsOnChangeStart();
 jsDropDownCarryOver(dy, hgtaTrack);
 jsDropDownCarryOver(dy, hgtaGroup);
 jsTrackedVarCarryOver(dy, hgtaRegionType, "regionType");
 jsTextCarryOver(dy, hgtaRange);
 jsDropDownCarryOver(dy, hgtaOutputType);
 jsTextCarryOver(dy, hgtaOutFileName);
 return dy;
 }
 
 static char *onChangeClade()
 /* Return javascript executed when they change clade. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, hgtaTable);
 dyStringAppend(dy, " document.hiddenForm.org.value=0;");
 dyStringAppend(dy, " document.hiddenForm.db.value=0;");
 dyStringAppend(dy, " document.hiddenForm.position.value='';");
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeOrg()
 /* Return javascript executed when they change organism. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "org");
 jsDropDownCarryOver(dy, hgtaTable);
 dyStringAppend(dy, " document.hiddenForm.db.value=0;");
 dyStringAppend(dy, " document.hiddenForm.position.value='';");
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeDb()
 /* Return javascript executed when they change database. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "db");
 jsDropDownCarryOver(dy, hgtaTable);
 dyStringAppend(dy, " document.hiddenForm.position.value='';");
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeGroupOrTrack()
 /* Return javascript executed when they change group. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "db");
 jsDropDownCarryOver(dy, "org");
 dyStringPrintf(dy, " document.hiddenForm.%s.value=0;", hgtaTable);
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeTable()
 /* Return javascript executed when they change group. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "db");
 jsDropDownCarryOver(dy, "org");
 jsDropDownCarryOver(dy, hgtaTable);
 return jsOnChangeEnd(&dy);
 }
 
 void makeRegionButton(char *val, char *selVal)
 /* Make region radio button including a little Javascript
  * to save selection state. */
 {
 jsMakeTrackingRadioButton(hgtaRegionType, "regionType", val, selVal);
 }
 
 struct grp *showGroupField(char *groupVar, char *groupScript,
     struct sqlConnection *conn, boolean allTablesOk)
 /* Show group control. Returns selected group. */
 {
 struct grp *group, *groupList = fullGroupList;
 struct grp *selGroup = findSelectedGroup(groupList, groupVar);
 hPrintf("<B>group:</B>\n");
 hPrintf("<SELECT NAME=%s %s>\n", groupVar, groupScript);
 for (group = groupList; group != NULL; group = group->next)
     {
+    if (allTablesOk || differentString(group->name, "allTables"))
         hPrintf(" <OPTION VALUE=%s%s>%s\n", group->name,
                 (group == selGroup ? " SELECTED" : ""),
                 group->label);
     }
 hPrintf("</SELECT>\n");
 return selGroup;
 }
 
 static void addIfExists(struct hash *hash, struct slName **pList, char *name)
 /* Add name to tail of list if it exists in hash. */
 {
 if (hashLookup(hash, name))
     slNameAddTail(pList, name);
 }
 
 struct slName *getDbListForGenome()
 /* Get list of selectable databases. */
 {
 struct hash *hash = sqlHashOfDatabases();
 struct slName *dbList = NULL;
 addIfExists(hash, &dbList, database);
 addIfExists(hash, &dbList, "uniProt");
 addIfExists(hash, &dbList, "proteome");
 addIfExists(hash, &dbList, "go");
 addIfExists(hash, &dbList, "hgFixed");
 addIfExists(hash, &dbList, "visiGene");
 addIfExists(hash, &dbList, "ultra");
 return dbList;
 }
 
 char *findSelDb()
 /* Find user selected database (as opposed to genome database). */
 {
 struct slName *dbList = getDbListForGenome();
 char *selDb = cartUsualString(cart, hgtaTrack, NULL);
 if (!slNameInList(dbList, selDb))
     selDb = cloneString(dbList->name);
 slFreeList(&dbList);
 return selDb;
 }
 
 struct trackDb *showTrackField(struct grp *selGroup,
 	char *trackVar, char *trackScript)
 /* Show track control. Returns selected track. */
 {
 struct trackDb *track, *selTrack = NULL;
 if (trackScript == NULL)
     trackScript = "";
 if (sameString(selGroup->name, "allTables"))
     {
     char *selDb = findSelDb();
     struct slName *dbList = getDbListForGenome(), *db;
     hPrintf("<B>database:</B>\n");
     hPrintf("<SELECT NAME=%s %s>\n", trackVar, trackScript);
     for (db = dbList; db != NULL; db = db->next)
 	{
 	hPrintf(" <OPTION VALUE=%s%s>%s\n", db->name,
 		(sameString(db->name, selDb) ? " SELECTED" : ""),
 		db->name);
 	}
     hPrintf("</SELECT>\n");
     }
 else
     {
     boolean allTracks = sameString(selGroup->name, "allTracks");
     hPrintf("<B>track:</B>\n");
     hPrintf("<SELECT NAME=\"%s\" %s>\n", trackVar, trackScript);
     if (allTracks)
         {
 	selTrack = findSelectedTrack(fullTrackList, NULL, trackVar);
 	slSort(&fullTrackList, trackDbCmpShortLabel);
 	}
     else
 	{
 	selTrack = findSelectedTrack(fullTrackList, selGroup, trackVar);
 	}
     for (track = fullTrackList; track != NULL; track = track->next)
 	{
 	if (allTracks || sameString(selGroup->name, track->grp))
 	    {
 	    hPrintf(" <OPTION VALUE=\"%s\"%s>%s\n", track->track,
 		(track == selTrack ? " SELECTED" : ""),
 		track->shortLabel);
 	    }
 	}
     hPrintf("</SELECT>\n");
     }
 hPrintf("\n");
 return selTrack;
 }
 
 char *unsplitTableName(char *table)
 /* Convert chr*_name to name */
 {
 if (startsWith("chr", table))
     {
     char *s = strrchr(table, '_');
     if (s != NULL)
         {
 	table = s + 1;
 	}
     }
 return table;
 }
 
 
-static char *chopAtFirstDot(char *string)
-/* Terminate string at first '.' if found.  Return string for convenience. */
-{
-char *ptr = strchr(string, '.');
-if (ptr != NULL)
-    *ptr = '\0';
-return string;
-}
-
-static void hashAddSlName(struct hash *hash, char *key, char *val)
-/* If key is already in hash, add an slName for val to the head of the list;
- * otherwise just store key -> slName for val. */
-{
-struct slName *sln = slNameNew(val);
-struct hashEl *hel = hashLookup(hash, key);
-if (hel == NULL)
-    hashAdd(hash, key, sln);
-else
-    slAddHead(&(hel->val), sln);
-}
-
-static struct hash *accessControlInit(struct sqlConnection *conn)
-/* Return a hash associating restricted table/track names in the given db/conn
- * with virtual hosts, or NULL if there is no tableAccessControl table and no
- * forbiddenTrackList (see getFullTrackList). */
-{
-struct hash *acHash = NULL;
-if (sqlTableExists(conn, "tableAccessControl"))
-    {
-    struct sqlResult *sr = NULL;
-    char **row = NULL;
-    acHash = newHash(0);
-    sr = sqlGetResult(conn, "NOSQLINJ select name,host from tableAccessControl");
-    while ((row = sqlNextRow(sr)) != NULL)
-	hashAddSlName(acHash, row[0], chopAtFirstDot(row[1]));
-    sqlFreeResult(&sr);
-    }
-if (forbiddenTrackList != NULL)
-    {
-    if (acHash == NULL)
-	acHash = newHash(0);
-    struct trackDb *tdb;
-    for (tdb = forbiddenTrackList;  tdb != NULL;  tdb = tdb->next)
-	{
-	char *tbOff = cloneString(trackDbSetting(tdb, "tableBrowser"));
-	if (isEmpty(tbOff))
-	    errAbort("bug: tdb for %s is in forbiddenTrackList without 'tableBrowser off' setting",
-		     tdb->track);
-	hashAddSlName(acHash, tdb->table, "-");
-	// skip "off" and look for additional table names:
-	nextWord(&tbOff);
-	char *tbl;
-	while ((tbl = nextWord(&tbOff)) != NULL)
-	    hashAddSlName(acHash, tbl, "-");
-	}
-    }
-return acHash;
-}
-
-boolean accessControlDenied(char *db, char *table)
-/* Return TRUE if table access is restricted to some host(s) other than
- * the one we're running on. */
-{
-static char *currentHost = NULL;
-struct slName *enabledHosts = NULL;
-struct slName *sln = NULL;
-static struct hash *dbToAcHash = NULL;
-
-if (dbToAcHash == NULL)
-    dbToAcHash = hashNew(0);
-
-struct hash *acHash = hashFindVal(dbToAcHash, db);
-if (acHash == NULL)
-    {
-    struct sqlConnection *conn = hAllocConn(db);
-    acHash = accessControlInit(conn);
-    hFreeConn(&conn);
-    hashAdd(dbToAcHash, db, acHash);
-    }
-
-if (acHash == NULL)
-    return FALSE;
-enabledHosts = (struct slName *)hashFindVal(acHash, table);
-if (enabledHosts == NULL)
-    return FALSE;
-if (currentHost == NULL)
-    {
-    currentHost = cloneString(cgiServerName());
-    if (currentHost == NULL)
-	{
-	warn("accessControl: unable to determine current host");
-	return FALSE;
-	}
-    else
-	chopAtFirstDot(currentHost);
-    }
-for (sln = enabledHosts;  sln != NULL;  sln = sln->next)
-    {
-    if (sameString(currentHost, sln->name))
-	return FALSE;
-    }
-return TRUE;
-}
-
 
 struct slName *tablesForDb(char *db)
 /* Find tables associated with database. */
 {
 boolean isGenomeDb = sameString(db, database);
 struct sqlConnection *conn = hAllocConn(db);
 struct slName *raw, *rawList = sqlListTables(conn);
 struct slName *cooked, *cookedList = NULL;
 struct hash *uniqHash = newHash(0);
 
 hFreeConn(&conn);
 for (raw = rawList; raw != NULL; raw = raw->next)
     {
     if (isGenomeDb)
 	{
 	/* Deal with tables split across chromosomes. */
 	char *root = unsplitTableName(raw->name);
-	if (accessControlDenied(db, root) || accessControlDenied(db, raw->name))
+	if (cartTrackDbIsAccessDenied(db, root) || cartTrackDbIsAccessDenied(db, raw->name))
 	    continue;
 	if (!hashLookup(uniqHash, root))
 	    {
 	    hashAdd(uniqHash, root, NULL);
 	    cooked = slNameNew(root);
 	    slAddHead(&cookedList, cooked);
 	    }
 	}
     else
         {
 	char dbTable[256];
-	if (accessControlDenied(db, raw->name))
+	if (cartTrackDbIsAccessDenied(db, raw->name))
 	    continue;
 	safef(dbTable, sizeof(dbTable), "%s.%s", db, raw->name);
 	cooked = slNameNew(dbTable);
 	slAddHead(&cookedList, cooked);
 	}
     }
 hashFree(&uniqHash);
 slFreeList(&rawList);
 slSort(&cookedList, slNameCmp);
 return cookedList;
 }
 
 char *showTableField(struct trackDb *track, char *varName, boolean useJoiner)
 /* Show table control and label. */
 {
 struct slName *name, *nameList = NULL;
 char *selTable;
 
 if (track == NULL)
     nameList = tablesForDb(findSelDb());
 else
-    nameList = tablesForTrack(track, useJoiner);
+    nameList = cartTrackDbTablesForTrack(database, track, useJoiner);
 
 /* Get currently selected table.  If it isn't in our list
  * then revert to first in list. */
 selTable = cartUsualString(cart, varName, nameList->name);
 if (!slNameInListUseCase(nameList, selTable))
     selTable = nameList->name;
 
 /* Print out label and drop-down list. */
 hPrintf("<B>table: </B>");
 hPrintf("<SELECT NAME=\"%s\" %s>\n", varName, onChangeTable());
 struct trackDb *selTdb = NULL;
 for (name = nameList; name != NULL; name = name->next)
     {
     struct trackDb *tdb = NULL;
     if (track != NULL)
 	tdb = findTdbForTable(database,track,name->name, ctLookupName);
     hPrintf("<OPTION VALUE=\"%s\"", name->name);
     if (sameString(selTable, name->name))
         {
         hPrintf(" SELECTED");
         selTdb = tdb;
         }
     if (tdb != NULL)
 	if ((curTrack == NULL) || differentWord(tdb->shortLabel, curTrack->shortLabel))
 	    hPrintf(">%s (%s)\n", tdb->shortLabel, name->name);
 	else
 	    hPrintf(">%s\n", name->name);
     else
 	hPrintf(">%s\n", name->name);
     }
 hPrintf("</SELECT>\n");
 if (!trackHubDatabase(database))
     {
     char *restrictDate = encodeRestrictionDateDisplay(database,selTdb);
     if (restrictDate)
 	{
 	hPrintf("<A HREF=\'%s\' TARGET=BLANK>restricted until:</A>&nbsp;%s",
 		    ENCODE_DATA_RELEASE_POLICY, restrictDate);
 	freeMem(restrictDate);
 	}
     }
 return selTable;
 }
 
 
 
 struct outputType
 /* Info on an output type. */
     {
     struct outputType *next;
     char *name;		/* Symbolic name of type. */
     char *label;	/* User visible label. */
     };
 
 static void showOutDropDown(struct outputType *otList, struct outputType *otDefault)
 /* Display output drop-down. */
 {
 struct outputType *ot;
 char *outputType = cartUsualString(cart, hgtaOutputType, otList->name);
 if (otDefault != NULL && otDefault != otList)
     {
     boolean otInOtList = FALSE;
     for (ot = otList; ot != NULL; ot = ot->next)
 	if (sameString(ot->name, outputType))
 	    {
 	    otInOtList = TRUE;
 	    break;
 	    }
     if (! otInOtList)
 	outputType = otDefault->name;
     }
 hPrintf("<SELECT NAME=\"%s\">", hgtaOutputType);
 for (ot = otList; ot != NULL; ot = ot->next)
     {
     hPrintf(" <OPTION VALUE=%s", ot->name);
     if (sameString(ot->name, outputType))
 	hPrintf(" SELECTED");
     if (sameString(ot->name, outBed) || sameString(ot->name, outWigBed))
         hPrintf(" id=\"outBed\"");
     hPrintf(">%s\n", ot->label);
     }
 hPrintf("</SELECT>\n");
 hPrintf(" ");
 
 if (!cfgOptionBooleanDefault("hgta.disableSendOutput", FALSE))
     {
     hPrintf(" Send output to ");
     struct dyString *dy = dyStringNew(256);
     dyStringAppend(dy, 
 	"onclick=\"document.getElementById('checkboxGreat').checked=false;");
     if (isGenomeSpaceEnabled())
 	dyStringAppend(dy, 
 	      	  "document.getElementById('checkboxGenomeSpace').checked=false;");
     dyStringAppend(dy, 
 	      	  "return true;\"");
     cgiMakeCheckBoxIdAndJS("sendToGalaxy", doGalaxy(),
         "checkboxGalaxy", dy->string);
     hPrintf("<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A>\n");
     nbSpaces(2);
     cgiMakeCheckBoxIdAndJS("sendToGreat", doGreat(),
         "checkboxGreat",
         "onclick=\"return onSelectGreat();\"");
     hPrintf(" <A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>");
     if (isGenomeSpaceEnabled())
 	{
 	nbSpaces(2);
 	cgiMakeCheckBoxIdAndJS("sendToGenomeSpace", doGenomeSpace(),
 	    "checkboxGenomeSpace",
 	    "onclick=\"document.getElementById('checkboxGreat').checked=false;"
 		      "document.getElementById('checkboxGalaxy').checked=false; return true;\"");
 	hPrintf(" <A HREF=\"http://www.genomespace.org\" target=_BLANK>GenomeSpace</A>");
 	}
     }
 
 hPrintf("</TD></TR>\n");
 }
 
 struct outputType otAllFields = { NULL,	outPrimaryTable,"all fields from selected table", };
 struct outputType otSelected =  { NULL, outSelectedFields,
                                   "selected fields from primary and related tables",  };
 struct outputType otSequence =  { NULL, outSequence,    "sequence", };
 struct outputType otPal =       { NULL, outPalOptions,
                                   "CDS FASTA alignment from multiple alignment", };
 struct outputType otGff =         { NULL, outGff,         "GTF - gene transfer format", };
 struct outputType otBed =         { NULL, outBed,         "BED - browser extensible data", };
 struct outputType otCustomTrack = { NULL, outCustomTrack, "custom track", };
 struct outputType otHyperlinks =  { NULL, outHyperlinks,  "hyperlinks to Genome Browser", };
 struct outputType otWigData =     { NULL, outWigData,     "data points", };
 struct outputType otWigBed =      { NULL, outWigBed,      "bed format", };
 struct outputType otMaf =         { NULL, outMaf,         "MAF - multiple alignment format", };
 struct outputType otChromGraphData =      { NULL, outChromGraphData,       "data points", };
 struct outputType otMicroarrayNames =     { NULL, outMicroarrayNames,     "microarray names", };
 struct outputType otMicroarrayGroupings = { NULL, outMicroarrayGroupings, "microarray groupings", };
 
 static void showOutputTypeRow(boolean isWig, boolean isBedGr,
     boolean isPositional, boolean isMaf, boolean isChromGraphCt,
     boolean isPal, boolean isMicroarray, boolean isHalSnake)
 /* Print output line. */
 {
 struct outputType *otList = NULL, *otDefault = NULL;
 boolean bedifiedOnly = (anySubtrackMerge(database, curTable) || anyIntersection());
 
 hPrintf("<TR><TD><B>output format:</B>\n");
 
 if (isBedGr)
     {
     if (! bedifiedOnly)
 	{
 	slAddTail(&otList, &otAllFields);
 	slAddTail(&otList, &otSelected);
 	}
     slAddTail(&otList, &otWigData);
     slAddTail(&otList, &otWigBed);
     slAddTail(&otList, &otCustomTrack);
     slAddTail(&otList, &otHyperlinks);
     }
 else if (isWig)
     {
     slAddTail(&otList, &otWigData);
     slAddTail(&otList, &otWigBed);
     slAddTail(&otList, &otCustomTrack);
     // hyperlinks output works for db-wiggle but not for bigWig
     }
 else if (isHalSnake)
     {
     slAddTail(&otList, &otMaf);
     }
 else if (isMaf)
     {
     slAddTail(&otList, &otMaf);
     if (! bedifiedOnly)
 	slAddTail(&otList, &otAllFields);
     }
 else if (isChromGraphCt)
     {
     slAddTail(&otList, &otChromGraphData);
     }
 else if (isMicroarray)
     {
     slAddTail(&otList, &otMicroarrayNames);
     slAddTail(&otList, &otAllFields);
     slAddTail(&otList, &otSelected);
     slAddTail(&otList, &otHyperlinks);
     }
 else if (isPositional)
     {
     if (! bedifiedOnly)
 	{
 	slAddTail(&otList, &otAllFields);
 	slAddTail(&otList, &otSelected);
 	}
     else
 	otDefault = &otBed;
     slAddTail(&otList, &otSequence);
     slAddTail(&otList, &otGff);
     if (isPal)
 	slAddTail(&otList, &otPal);
     slAddTail(&otList, &otBed);
     slAddTail(&otList, &otCustomTrack);
     slAddTail(&otList, &otHyperlinks);
     }
 else
     {
     slAddTail(&otList, &otAllFields);
     slAddTail(&otList, &otSelected);
     }
 showOutDropDown(otList, otDefault);
 }
 
 void nbSpaces(int count)
 /* Print some non-breaking spaces. */
 {
 int i;
 for (i=0; i<count; ++i)
     hPrintf("&nbsp;");
 }
 
 void showMainControlTable(struct sqlConnection *conn)
 /* Put up table with main controls for main page. */
 {
 struct grp *selGroup;
 boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE,
         isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE;
 boolean gotClade = hGotClade();
 struct hTableInfo *hti = NULL;
 
 hPrintf("<TABLE BORDER=0>\n");
 
 /* Print clade, genome and assembly line. */
     {
     if (gotClade)
         {
         hPrintf("<TR><TD><B>clade:</B>\n");
         printCladeListHtml(hGenome(database), onChangeClade());
         nbSpaces(3);
         hPrintf("<B>genome:</B>\n");
         printGenomeListForCladeHtml(database, onChangeOrg());
         }
     else
         {
         hPrintf("<TR><TD><B>genome:</B>\n");
         printGenomeListHtml(database, onChangeOrg());
         }
     nbSpaces(3);
     hPrintf("<B>assembly:</B>\n");
     printAssemblyListHtml(database, onChangeDb());
     hPrintf("</TD></TR>\n");
     }
 
 /* Print group and track line. */
     {
     hPrintf("<TR><TD>");
-    selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, allowAllTables());
+    selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables());
     nbSpaces(3);
     curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack());
     nbSpaces(3);
     boolean hasCustomTracks = FALSE;
     struct trackDb *t;
     for (t = fullTrackList;  t != NULL;  t = t->next)
         {
         if (isCustomTrack(t->table))
             {
             hasCustomTracks = TRUE;
             break;
             }
         }
     hOnClickButton("document.customTrackForm.submit();return false;",
                    hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
 
     hPrintf(" ");
     if (hubConnectTableExists())
 	hOnClickButton("document.trackHubForm.submit();return false;", "track hubs");
 
     hPrintf("</TD></TR>\n");
     }
 
 /* Print table line. */
     {
     hPrintf("<TR><TD>");
     curTable = showTableField(curTrack, hgtaTable, TRUE);
     if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL))  /* In same database */
         {
         hti = getHti(database, curTable, conn);
         isPositional = htiIsPositional(hti);
         }
     isBam = isBamTable( curTable);
     isVcf = isVcfTable(curTable, NULL);
     isWig = isWiggle(database, curTable);
     if (isBigWigTable(curTable))
         {
         isPositional = TRUE;
         isWig = TRUE;
         }
     isHalSnake = isHalTable( curTable);
     isMaf = isMafTable(database, curTrack, curTable);
     isBedGr = isBedGraph(curTable);
     isArray = isMicroarray(curTrack, curTable);
     struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
     isPal = isPalCompatible(conn, tdb, curTable);
     nbSpaces(1);
     if (isCustomTrack(curTable))
         {
         isChromGraphCt = isChromGraph(tdb);
         }
     cgiMakeButton(hgtaDoSchema, "describe table schema");
     hPrintf("</TD></TR>\n");
     }
 
 if (curTrack == NULL)
     {
     struct trackDb *tdb = hTrackDbForTrack(database, curTable);
     struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb);
     if (cTdb)
         curTrack = cTdb;
     else
         curTrack = tdb;
     isMaf = isMafTable(database, curTrack, curTable);
     }
 
 /* Region line */
 {
 char *regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome);
 char *range = cartUsualString(cart, hgtaRange, "");
 if (isPositional)
     {
     boolean doEncode = FALSE; 
 
     if (!trackHubDatabase(database))
 	doEncode = sqlTableExists(conn, "encodeRegions");
 
     hPrintf("<TR><TD><B>region:</B>\n");
 
     /* If regionType not allowed force it to "genome". */
     if ((sameString(regionType, hgtaRegionTypeUserRegions) &&
 	 userRegionsFileName() == NULL) ||
 	(sameString(regionType, hgtaRegionTypeEncode) && !doEncode))
 	regionType = hgtaRegionTypeGenome;
     jsTrackingVar("regionType", regionType);
     makeRegionButton(hgtaRegionTypeGenome, regionType);
     hPrintf("&nbsp;genome&nbsp;");
     if (doEncode)
         {
 	makeRegionButton(hgtaRegionTypeEncode, regionType);
 	hPrintf("&nbsp;ENCODE Pilot regions&nbsp;");
 	}
     makeRegionButton(hgtaRegionTypeRange, regionType);
     hPrintf("&nbsp;position&nbsp;");
     hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
     	hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
     cgiMakeButton(hgtaDoLookupPosition, "lookup");
     hPrintf("&nbsp;");
     if (userRegionsFileName() != NULL)
 	{
 	makeRegionButton(hgtaRegionTypeUserRegions, regionType);
 	hPrintf("&nbsp;defined regions&nbsp;");
 	cgiMakeButton(hgtaDoSetUserRegions, "change");
 	hPrintf("&nbsp;");
 	cgiMakeButton(hgtaDoClearUserRegions, "clear");
 	}
     else
 	cgiMakeButton(hgtaDoSetUserRegions, "define regions");
     hPrintf("</TD></TR>\n");
     }
 else
     {
     /* Need to put at least stubs of cgi variables in for JavaScript to work. */
     jsTrackingVar("regionType", regionType);
     cgiMakeHiddenVar(hgtaRange, range);
     cgiMakeHiddenVar(hgtaRegionType, regionType);
     }
 
 /* Select identifiers line (if applicable). */
 if (!isWig && getIdField(database, curTrack, curTable, hti) != NULL)
     {
     hPrintf("<TR><TD><B>identifiers (names/accessions):</B>\n");
     cgiMakeButton(hgtaDoPasteIdentifiers, "paste list");
     hPrintf(" ");
     cgiMakeButton(hgtaDoUploadIdentifiers, "upload list");
     if (identifierFileName() != NULL)
         {
 	hPrintf("&nbsp;");
 	cgiMakeButton(hgtaDoClearIdentifiers, "clear list");
 	}
     hPrintf("</TD></TR>\n");
     }
 }
 
 /* microarray options */
 /*   button for option page here (median/log-ratio, etc)  */
 
 /* Filter line. */
 {
 hPrintf("<TR><TD><B>filter:</B>\n");
 if (anyFilter())
     {
     cgiMakeButton(hgtaDoFilterPage, "edit");
     hPrintf(" ");
     cgiMakeButton(hgtaDoClearFilter, "clear");
     if (isWig || isBedGr)
 	wigShowFilter(conn);
     }
 else
     {
     cgiMakeButton(hgtaDoFilterPage, "create");
     }
 hPrintf("</TD></TR>\n");
 }
 
 /* Composite track subtrack merge line. */
 boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf);
 if (canSubtrackMerge)
     {
     hPrintf("<TR><TD><B>subtrack merge:</B>\n");
     if (anySubtrackMerge(database, curTable))
 	{
 	cgiMakeButton(hgtaDoSubtrackMergePage, "edit");
 	hPrintf(" ");
 	cgiMakeButton(hgtaDoClearSubtrackMerge, "clear");
 	}
     else
 	{
 	cgiMakeButton(hgtaDoSubtrackMergePage, "create");
 	}
     hPrintf("</TD></TR>\n");
     }
 
 /* Intersection line. */
 if (isPositional)
     {
     if (anyIntersection())
         {
 	hPrintf("<TR><TD><B>intersection with %s:</B>\n",
 		cartString(cart, hgtaIntersectTable));
 	cgiMakeButton(hgtaDoIntersectPage, "edit");
 	hPrintf(" ");
 	cgiMakeButton(hgtaDoClearIntersect, "clear");
 	}
     else if (canIntersect(database, curTable))
         {
 	hPrintf("<TR><TD><B>intersection:</B>\n");
 	cgiMakeButton(hgtaDoIntersectPage, "create");
 	}
     hPrintf("</TD></TR>\n");
     }
 
 /* Correlation line. */
 struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
 if (correlateTrackTableOK(tdb, curTable))
     {
     char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none");
     hPrintf("<TR><TD><B>correlation:</B>\n");
     if (differentWord(table2,"none") && strlen(table2))
         {
         struct grp *groupList = fullGroupList;
         struct grp *selGroup = findSelectedGroup(groupList, hgtaCorrelateGroup);
         struct trackDb *tdb2 = findSelectedTrack(fullTrackList, selGroup,hgtaCorrelateTrack);
         if (tdbIsComposite(tdb2))
             {
 	    struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb2->subtracks);
 	    struct slRef *tdbRef;
 	    for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
                 {
 		struct trackDb *subTdb = tdbRef->val;
                 if (sameString(table2, subTdb->table))
                     {
                     tdb2 = subTdb;
                     break;
                     }
                 }
 	    slFreeList(&tdbRefList);
             }
         cgiMakeButton(hgtaDoCorrelatePage, "calculate");
         cgiMakeButton(hgtaDoClearCorrelate, "clear");
         if (tdb2 && tdb2->shortLabel)
             hPrintf("&nbsp;(with:&nbsp;&nbsp;%s)", tdb2->shortLabel);
 
 #ifdef NOT_YET
         /* debugging 	dbg	vvvvv	*/
         if (curTrack && curTrack->type)		/*	dbg	*/
             {
             hPrintf("<BR>&nbsp;(debug:&nbsp;'%s',&nbsp;'%s(%s)')",
                     curTrack->type, tdb2->type, table2);
             }
         /* debugging 	debug	^^^^^	*/
 #endif
 
         }
     else
         cgiMakeButton(hgtaDoCorrelatePage, "create");
 
     hPrintf("</TD></TR>\n");
     }
 
 /* Print output type line. */
 showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake);
 
 /* Print output destination line. */
     {
     char *compressType =
 	cartUsualString(cart, hgtaCompressType, textOutCompressNone);
     char *fileName = cartUsualString(cart, hgtaOutFileName, "");
     hPrintf("<TR><TD>\n");
     hPrintf("<B>output file:</B>&nbsp;");
     cgiMakeTextVar(hgtaOutFileName, fileName, 29);
     hPrintf("&nbsp;(leave blank to keep output in browser)</TD></TR>\n");
     hPrintf("<TR><TD>\n");
     hPrintf("<B>file type returned:&nbsp;</B>");
     cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
 	sameWord(textOutCompressNone, compressType));
     hPrintf("&nbsp;plain text&nbsp&nbsp");
     cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
 	sameWord(textOutCompressGzip, compressType));
     hPrintf("&nbsp;gzip compressed");
     hPrintf("</TD></TR>\n");
     }
 
 hPrintf("</TABLE>\n");
 
 
 /* Submit buttons. */
     {
     hPrintf("<BR>\n");
     if (isWig || isBam || isVcf)
 	{
 	char *name;
 	extern char *maxOutMenu[];
 	char *maxOutput = maxOutMenu[0];
 
 	if (isCustomTrack(curTable))
 	    name=filterFieldVarName("ct", curTable, "_", filterMaxOutputVar);
 	else
 	    name=filterFieldVarName(database,curTable, "_",filterMaxOutputVar);
 
 	maxOutput = cartUsualString(cart, name, maxOutMenu[0]);
 
 	if (isWig)
 	    hPrintf(
 		"<I>Note: to return more than %s lines, change the filter setting"
 		" (above). The entire data set may be available for download as"
 		" a very large file that contains the original data values (not"
 		" compressed into the wiggle format) -- see the Downloads page."
 		"</I><BR>", maxOutput);
 	else if (isBam || isVcf)
 	    hPrintf(
 		"<I>Note: to return more than %s lines, change the filter setting"
 		" (above). Please consider downloading the entire data from our Download pages."
 		"</I><BR>", maxOutput);
 	}
     else if (anySubtrackMerge(database, curTable) || anyIntersection())
 	{
 	hPrintf("<I>Note: The all fields and selected fields output formats "
 		"are not available when a%s has been specified.</I><BR>",
 		canSubtrackMerge ? " subtrack merge or intersection" : "n intersection");
 	}
     cgiMakeButton(hgtaDoTopSubmit, "get output");
     hPrintf(" ");
     if (isPositional || isWig)
 	{
 	cgiMakeButton(hgtaDoSummaryStats, "summary/statistics");
 	hPrintf(" ");
 	}
 
 #ifdef SOMETIMES
     hPrintf(" ");
     cgiMakeButton(hgtaDoTest, "test");
 #endif /* SOMETIMES */
     }
 hPrintf("<P>"
 	"To reset <B>all</B> user cart settings (including custom tracks), \n"
 	"<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n",
 	getScriptName());
 
 }
 
 static char *getGenomeSpaceText()
 /* fetch GenomeSpace text if enabled */
 {
 if (isGenomeSpaceEnabled())
     {
     return 
   "Send data to "
   "<A HREF=\"http://www.genomespace.org\" target=_BLANK>GenomeSpace</A> for use with diverse computational tools. ";
     }
 else
     {
     return "";
     }
 }
 
 void mainPageAfterOpen(struct sqlConnection *conn)
 /* Put up main page assuming htmlOpen()/htmlClose()
  * will happen in calling routine. */
 {
 hPrintf(
   "Use this program to retrieve the data associated with a track in text "
   "format, to calculate intersections between tracks, and to retrieve "
   "DNA sequence covered by a track. For help in using this application "
   "see <A HREF=\"#Help\">Using the Table Browser</A> for a description "
   "of the controls in this form, the "
   "<A HREF=\"../goldenPath/help/hgTablesHelp.html\">User's Guide</A> for "
   "general information and sample queries, and the OpenHelix Table Browser "
   "<A HREF=\"http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28\" "
   "TARGET=_blank>tutorial</A> for a narrated presentation of the software "
   "features and usage. "
   "For more complex queries, you may want to use "
   "<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A> or "
   "our <A HREF=\"../goldenPath/help/mysql.html\">public "
   "MySQL server</A>. "
   "To examine the biological function of your set through annotation "
   "enrichments, send the data to "
   "<A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>. "
   "%s"
   "Refer to the "
   "<A HREF=\"../goldenPath/credits.html\">Credits</A> page for the list of "
   "contributors and usage restrictions associated with these data. "
   "All tables can be downloaded in their entirety from the "
   "<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html\""
   ">Sequence and Annotation Downloads</A> page."
    , getGenomeSpaceText()
    );
 
 hPrintf("<script type=\"text/javascript\">\n");
 hPrintf("function onSelectGreat() {\n");
 hPrintf("document.getElementById('checkboxGalaxy').checked=false;\n");
 if (isGenomeSpaceEnabled())
     hPrintf("document.getElementById('checkboxGenomeSpace').checked=false;\n");
 hPrintf("document.getElementById('outBed').selected=true;\n");
 hPrintf("return true;\n");
 hPrintf("}\n");
 hPrintf("</script>\n");
 
 
 /* Main form. */
 hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n",
 	getScriptName(), cartUsualString(cart, "formMethod", "POST"));
 cartSaveSession(cart);
 jsInit();
 showMainControlTable(conn);
 hPrintf("</FORM>\n");
 
 /* Hidden form - for benefit of javascript. */
     {
     static char *saveVars[] = {
       "clade", "org", "db", hgtaGroup, hgtaTrack, hgtaTable, hgtaRegionType,
       hgtaRange, hgtaOutputType, hgtaOutFileName};
     jsCreateHiddenForm(cart, getScriptName(), saveVars, ArraySize(saveVars));
     }
 
 /* Hidden form for jumping to custom tracks CGI. */
 hPrintf("<FORM ACTION='%s' NAME='customTrackForm'>", hgCustomName());
 cartSaveSession(cart);
 hPrintf("</FORM>\n");
 
 /* Hidden form for jumping to track hub manager CGI. */
 hPrintf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName());
 cartSaveSession(cart);
 hPrintf("</FORM>\n");
 
 webNewSection("<A NAME=\"Help\"></A>Using the Table Browser\n");
 printMainHelp();
 cartFlushHubWarnings();
 }
 
 void doMainPage(struct sqlConnection *conn)
 /* Put up the first page user sees. */
 {
 htmlOpen("Table Browser");
 mainPageAfterOpen(conn);
 htmlClose();
 }