static void getHasHubTable(struct cartJson *cj, struct hash *paramHash)
/* Tell whether central database has a hub table (i.e. server can do hubs). */
{
jsonWriteBoolean(cj->jw, "hasHubTable", hubConnectTableExists());
}
示例#2
0
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, isLongTabix = 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, hAllowAllTables());
    nbSpaces(3);
    curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE);
    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);
        }
    isLongTabix = isLongTabixTable( curTable);
    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;
    // Is "genome" is not allowed because of tdb 'tableBrowser noGenome'?
    boolean disableGenome = ((curTrack && cartTrackDbIsNoGenome(database, curTrack->table)) ||
                             (curTable && cartTrackDbIsNoGenome(database, curTable)));
    // If "genome" is selected but not allowed, force it to "range":
    if (sameString(regionType, hgtaRegionTypeGenome) && disableGenome)
        regionType = hgtaRegionTypeRange;
    jsTrackingVar("regionType", regionType);
    if (disableGenome)
        {
        makeRegionButtonExtraHtml(hgtaRegionTypeGenome, regionType, "DISABLED");
        hPrintf("&nbsp;<span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
                "&nbsp;");
        }
    else
        {
        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 && !isLongTabix);
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");
        hPrintf("</TD></TR>\n");
	}
    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) && ! isNoGenomeDisabled(database, 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 || isLongTabix)
	{
	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 || isLongTabix)
	    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());

}