示例#1
0
static void doBigFilterPage(struct sqlConnection *conn, char *db, char *table)
/* Put up filter page on given db.table. */
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];

if (strchr(table, '.'))
    htmlOpen("Filter on Fields from %s", table);
else
    htmlOpen("Filter on Fields from %s.%s", db, table);

jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
commonCssStyles();

hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
	cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);

filterControlsForTable(db, table);
dtList = extraTableList(filterLinkedTablePrefix);
showLinkedFilters(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, filterLinkedTablePrefix,
	hgtaDoFilterMore, "allow filtering using fields in checked tables");

hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
}
示例#2
0
void doMiddle(struct cart *cart)
/* Write body of web page. */
{
struct trackDb *tdbList = NULL;
char *organism = NULL;
char *db = NULL;
getDbAndGenome(cart, &db, &organism, NULL);
char *chrom = cartUsualString(cart, "c", hDefaultChrom(db));
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));

// QUESTION: Do We need track list ???  trackHash ??? Can't we just get one track and no children
trackHash = trackHashMakeWithComposites(db,chrom,&tdbList,FALSE);

cartWebStart(cart, db, "Search for " FILE_SEARCH_WHAT " in the %s %s Assembly", 
             organism, hFreezeFromDb(db));

webIncludeResourceFile("HGStyle.css");
webIncludeResourceFile("jquery-ui.css");
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("ui.dropdownchecklist.js",NULL);
jsIncludeFile("utils.js",NULL);

// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
printf("<script type='text/javascript'>$(document).ready(function() "
       "{ findTracks.updateMdbHelp(0); });</script>\n");

doFileSearch(db,organism,cart,tdbList);


printf("<BR>\n");
webEnd();
}
示例#3
0
char *jsCheckAllOnClickHandler(char *idPrefix, boolean state)
/* Returns javascript for use as an onclick attribute value to check all/uncheck all
 * all checkboxes with given idPrefix.
 * state parameter determines whether to "check all" or "uncheck all" (TRUE means "check all"). */
{
static char buf[512];
jsIncludeFile("utils.js", NULL);
safef(buf, sizeof(buf), "setCheckBoxesWithPrefix(this, '%s', %s); return false", idPrefix, state ? "true" : "false");
return buf;
}
示例#4
0
void jsInit()
/* If this is the first call, set window.onload to the operations
 * performed upon loading a page and print supporting javascript.
 * Currently this just sets the page vertical position if specified on
 * CGI, and includes jsHelper.js.
 * Subsequent calls do nothing, so this can be called many times. */
{
if (! jsInited)
    {
    // jsh_pageVertPos trick taken from
    // http://www.softcomplex.com/docs/get_window_size_and_scrollbar_position.html
    puts("<INPUT TYPE=HIDDEN NAME=\"jsh_pageVertPos\" VALUE=0>");
    int pos = cgiOptionalInt("jsh_pageVertPos", 0);
    if (pos > 0)
	{
	jsInlineF("window.onload = function () { window.scrollTo(0, %d); }\n", pos);
	}
    jsInited = TRUE;
    jsIncludeFile("jsHelper.js", NULL);
    }
}
示例#5
0
static void doMainPage()
/* Send HTML with javascript to bootstrap the user interface. */
{
// Start web page with new banner
char *db = NULL, *genome = NULL, *clade = NULL;
getDbGenomeClade(cart, &db, &genome, &clade, oldVars);
// If CGI has &lastDbPos=..., handle that here and save position to cart so it's in place for
// future cartJson calls.
char *position = cartGetPosition(cart, db, NULL);
cartSetString(cart, "position", position);
webStartJWest(cart, db, "Genome Browser Gateway");

if (cgiIsOnWeb())
    checkForGeoMirrorRedirect(cart);

#define WARNING_BOX_START "<div id=\"previewWarningRow\" class=\"jwRow\">" \
         "<div id=\"previewWarningBox\" class=\"jwWarningBox\">"

#define UNDER_DEV "Data and tools on this site are under development, have not been reviewed " \
         "for quality, and are subject to change at any time. "

#define MAIN_SITE "The high-quality, reviewed public site of the UCSC Genome Browser is " \
         "available for use at <a href=\"http://genome.ucsc.edu/\">http://genome.ucsc.edu/</a>."

#define WARNING_BOX_END "</div></div>"

if (hIsPreviewHost())
    {
    puts(WARNING_BOX_START
         "WARNING: This is the UCSC Genome Browser preview site. "
         "This website is a weekly mirror of our internal development server for public access. "
         UNDER_DEV
         "We provide this site for early access, with the warning that it is less available "
         "and stable than our public site. "
         MAIN_SITE
         WARNING_BOX_END);
    }

if (hIsPrivateHost() && !hHostHasPrefix("hgwdev-demo6"))
    {
    puts(WARNING_BOX_START
         "WARNING: This is the UCSC Genome Browser development site. "
         "This website is used for testing purposes only and is not intended for general public "
         "use. "
         UNDER_DEV
         MAIN_SITE
         WARNING_BOX_END);
    }

// The visible page elements are all in ./hgGateway.html, which is transformed into a quoted .h
// file containing a string constant that we #include and print here (see makefile).
puts(
#include "hgGateway.html.h"
);

// Set global JS variables hgsid, activeGenomes, and survey* at page load time
// We can't just use "var hgsid = " or the other scripts won't see it -- it has to be
// "window.hgsid = ".
puts("<script>");
printf("window.%s = '%s';\n", cartSessionVarName(), cartSessionId(cart));
puts("window.activeGenomes =");
printActiveGenomes();
puts(";");
char *surveyLink = cfgOption("survey");
if (isNotEmpty(surveyLink) && !sameWord(surveyLink, "off"))
    {
    printf("window.surveyLink=\"%s\";\n", jsonStringEscape(surveyLink));
    char *surveyLabel = cfgOptionDefault("surveyLabel", "Please take our survey");
    printf("window.surveyLabel=\"%s\";\n", jsonStringEscape(surveyLabel));
    char *surveyLabelImage = cfgOption("surveyLabelImage");
    if (isNotEmpty(surveyLabelImage))
        printf("window.surveyLabelImage=\"%s\";\n", jsonStringEscape(surveyLabelImage));
    else
        puts("window.surveyLabelImage=null;");
    }
else
    {
    puts("window.surveyLink=null;");
    puts("window.surveyLabel=null;");
    puts("window.surveyLabelImage=null;");
    }
puts("</script>");

puts("<script src=\"../js/es5-shim.4.0.3.min.js\"></script>");
puts("<script src=\"../js/es5-sham.4.0.3.min.js\"></script>");
puts("<script src=\"../js/lodash.3.10.0.compat.min.js\"></script>");
puts("<script src=\"../js/cart.js\"></script>");

webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("jquery.watermarkinput.js", NULL);
jsIncludeFile("utils.js",NULL);

// Phylogenetic tree .js file, produced by dbDbTaxonomy.pl:
char *dbDbTree = cfgOptionDefault("hgGateway.dbDbTaxonomy", "../js/dbDbTaxonomy.js");
if (isNotEmpty(dbDbTree))
    printf("<script src=\"%s\"></script>\n", dbDbTree);

// Main JS for hgGateway:
puts("<script src=\"../js/hgGateway.js\"></script>");

webIncludeFile("inc/jWestFooter.html");

cartFlushHubWarnings();

webEndJWest();
}
示例#6
0
void jsIncludeReactLibs()
/* Prints out <script src="..."> tags for external libraries including ReactJS & ImmutableJS
 * and our own model libs, React mixins and components. */
{
// We need a module system... webpack?
jsIncludeFile("es5-shim.4.0.3.min.js", NULL);
jsIncludeFile("es5-sham.4.0.3.min.js", NULL);
jsIncludeFile("lodash.3.10.0.compat.min.js", NULL);
puts("<script src=\"//code.jquery.com/jquery-1.9.1.min.js\"></script>");
puts("<script src=\"//code.jquery.com/ui/1.10.3/jquery-ui.min.js\"></script>");
jsIncludeFile("react-with-addons-0.12.2.min.js", NULL);
jsIncludeFile("immutable.3.7.4.min.js", NULL);
jsIncludeFile("jquery.bifrost.1.0.1.min.js", NULL);
jsIncludeFile("BackboneExtend.js", NULL);
jsIncludeFile("cart.js", NULL);
jsIncludeFile("ImModel.js", NULL);
jsIncludeFile("CladeOrgDbMixin.js", NULL);
jsIncludeFile("PositionSearchMixin.js", NULL);
jsIncludeFile("UserRegionsMixin.js", NULL);
jsIncludeFile("PathUpdate.js", NULL);
jsIncludeFile("PathUpdateOptional.js", NULL);
jsIncludeFile("ImmutableUpdate.js", NULL);
jsIncludeFile("reactLibBundle.js", NULL);
}
示例#7
0
文件: web.c 项目: elmargb/kentUtils
char *menuBar(struct cart *cart)
// Return HTML for the menu bar (read from a configuration file);
// we fixup internal CGI's to add hgsid's and include the appropriate js and css files.
{
char *docRoot = hDocumentRoot();
char *menuStr, buf[4096], uiVars[128];
FILE *fd;
int len, offset, err;
char *navBarFile = "inc/globalNavBar.inc";
struct stat statBuf;
regex_t re;
regmatch_t match[2];
char *scriptName = cgiScriptName();
if (cart)
    safef(uiVars, sizeof(uiVars), "%s=%u", cartSessionVarName(), cartSessionId(cart));
else
    uiVars[0] = 0;

if(docRoot == NULL)
    // tolerate missing docRoot (i.e. don't bother with menu when running from command line)
    return NULL;

jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery.plugins.js", NULL);
webIncludeResourceFile("nice_menu.css");

// Read in menu bar html
safef(buf, sizeof(buf), "%s/%s", docRoot, navBarFile);
fd = mustOpen(buf, "r");
fstat(fileno(fd), &statBuf);
len = statBuf.st_size;
menuStr = needMem(len + 1);
mustRead(fd, menuStr, statBuf.st_size);
menuStr[len] = 0;
carefulClose(&fd);

if (cart)
    {
    // fixup internal CGIs to have hgsid
    safef(buf, sizeof(buf), "/cgi-bin/hg[A-Za-z]+(%c%c?)", '\\', '?');
    err = regcomp(&re, buf, REG_EXTENDED);
    if(err)
	errAbort("regcomp failed; err: %d", err);
    struct dyString *dy = newDyString(0);
    for(offset = 0; offset < len && !regexec(&re, menuStr + offset, ArraySize(match), match, 0); offset += match[0].rm_eo)
	{
	dyStringAppendN(dy, menuStr + offset, match[0].rm_eo);
	if(match[1].rm_so == match[1].rm_eo)
	    dyStringAppend(dy, "?");
	dyStringAppend(dy, uiVars);
	if(match[1].rm_so != match[1].rm_eo)
	    dyStringAppend(dy, "&");
	}
    if(offset < len)
	dyStringAppend(dy, menuStr + offset);
    freez(&menuStr);
    menuStr = dyStringCannibalize(&dy);
    }
if(!loginSystemEnabled())
    stripRegEx(menuStr, "<\\!-- LOGIN_START -->.*<\\!-- LOGIN_END -->", REG_ICASE);

if(scriptName)
    {  // Provide optional official mirror servers menu items
    char *geoMenu = geoMirrorMenu();
    char *pattern = "<!-- OPTIONAL_MIRROR_MENU -->";
    char *newMenuStr = replaceChars(menuStr, pattern, geoMenu);
    freez(&menuStr);
    menuStr = newMenuStr;
    }


if(scriptName)
    {
    // Provide view menu for some CGIs.
    struct dyString *viewItems = dyStringCreate("");
    boolean hasViewMenu = TRUE;
    if (endsWith(scriptName, "hgGenome"))
        {
	safef(buf, sizeof(buf), "../cgi-bin/hgGenome?%s&hgGenome_doPsOutput=1", uiVars);
    	dyStringPrintf(viewItems, "<li><a href='%s' id='%s'>%s</a></li>\n", buf, "pdfLink", "PDF/PS");
        }
    else
	{
	hasViewMenu = FALSE;
	}
    if (hasViewMenu)
	{
	struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n");
	dyStringAppend(viewMenu, viewItems->string);
	dyStringAppend(viewMenu, "</ul>\n</li>\n");
    	menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", viewMenu->string);
	dyStringFree(&viewMenu);
	}
    dyStringFree(&viewItems);
    }


if(scriptName)
    {
    // Provide context sensitive help links for some CGIs.
    char *link = NULL;
    char *label = NULL;
    if (endsWith(scriptName, "hgBlat"))
        {
        link = "../goldenPath/help/hgTracksHelp.html#BLATAlign";
        label = "Help on Blat";
        }
    else if (endsWith(scriptName, "hgHubConnect"))
        {
        link = "../goldenPath/help/hgTrackHubHelp.html";
        label = "Help on Track Hubs";
        }
    else if (endsWith(scriptName, "hgNear"))
        {
        link = "../goldenPath/help/hgNearHelp.html";
        label = "Help on Gene Sorter";
        }
    else if (endsWith(scriptName, "hgTables"))
        {
        link = "../goldenPath/help/hgTablesHelp.html";
        label = "Help on Table Browser";
        }
    else if (endsWith(scriptName, "hgGenome"))
        {
        link = "../goldenPath/help/hgGenomeHelp.html";
        label = "Help on Genome Graphs";
        }
    else if (endsWith(scriptName, "hgSession"))
        {
        link = "../goldenPath/help/hgSessionHelp.html";
        label = "Help on Sessions";
        }
    else if (endsWith(scriptName, "hgVisiGene"))
        {
        link = "../goldenPath/help/hgTracksHelp.html#VisiGeneHelp";
        label = "Help on VisiGene";
        }
    else if (endsWith(scriptName, "hgCustom"))
        {
        link = "../goldenPath/help/customTrack.html";
        label = "Help on Custom Tracks";
        }
    // Don't overwrite any previously set defaults
    if(!contextSpecificHelpLink && link)
        contextSpecificHelpLink = link;
    if(!contextSpecificHelpLabel && label)
        contextSpecificHelpLabel = label;
    }
if(contextSpecificHelpLink)
    {
    char buf[1024];
    safef(buf, sizeof(buf), "<li><a href='%s'>%s</a></li>", contextSpecificHelpLink, contextSpecificHelpLabel);
    menuStr = replaceChars(menuStr, "<!-- CONTEXT_SPECIFIC_HELP -->", buf);
    }
return menuStr;
}
示例#8
0
static void showTableFilterControlRow(struct fieldedTable *table, struct cart *cart, 
    char *varPrefix, int maxLenField, struct hash *suggestHash)
/* Assuming we are in table already drow control row.
 * The suggestHash is keyed by field name.  If something is there we'll assume
 * it's value is slName list of suggestion values */
{
/* Include javascript and style we need  */
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery.plugins.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("jquery.watermark.js", NULL);

int i;
printf("<TR>");
for (i=0; i<table->fieldCount; ++i)
    {
    char *field = table->fields[i];
    char varName[256];
    safef(varName, sizeof(varName), "%s_f_%s", varPrefix, field);
    webPrintLinkCellStart();

#ifdef MAKES_TOO_WIDE
    /* Print out input control.  As you can see from all the commented out bits
     * this part has been a challenge.  We'd like to make the input cell fit the
     * table size, but if we do it with style it makes whole table wider. */
    char *oldVal = cartUsualString(cart, varName, "");
    printf("<input type=\"text\" name=\"%s\" style=\"display:table-cell; width=100%%\""
	   " value=\"%s\">", varName, oldVal);
#endif /* MAKES_TOO_WIDE */

    /* Approximate size of input control in characters */
    int size = fieldedTableMaxColChars(table, i);
    if (size > maxLenField)
	size = maxLenField;

#ifdef ACTUALLY_WORKS
    /* This way does work last I checked and is just a line of code.
     * Getting an id= property on the input tag though isn't possible this way. */
    cartMakeTextVar(cart, varName, "", size + 1);
#endif

    /* Print input control getting previous value from cart.  Set an id=
     * so auto-suggest can find this control. */
    char *oldVal = cartUsualString(cart, varName, "");
    printf("<INPUT TYPE=TEXT NAME=\"%s\" id=\"%s\" SIZE=%d VALUE=\"%s\">\n",
	varName, varName, size+1, oldVal);

    /* Write out javascript to initialize autosuggest on control */
    printWatermark(varName, " filter ");
    if (suggestHash != NULL)
        {
	struct slName *suggestList = hashFindVal(suggestHash, field);
	if (suggestList != NULL)
	    {
	    printSuggestScript(varName, suggestList);
	    }
	}
    webPrintLinkCellEnd();
    }


printf("</TR>");
}
示例#9
0
void doMiddle()
{
struct hash *cvHash = raReadAll((char *)cvFile(), CV_TERM);
struct hashCookie hc = hashFirst(cvHash);
struct hashEl *hEl;
struct slList *termList = NULL;
struct hash *ra;
int totalPrinted = 0;
boolean excludeDeprecated = (cgiOptionalString("deprecated") == NULL);

// Prepare an array of selected terms (if any)
int requestCount = 0;
char **requested = NULL;
char *requestVal = termOpt;
char *queryBy = CV_TERM;
if (tagOpt)
    {
    requestVal = tagOpt;
    queryBy = CV_TAG;
    }
else if (targetOpt)
    {
    requestVal = targetOpt;
    queryBy = CV_TERM;  // request target is special: lookup term, convert to target, display target
    }
else if (labelOpt)
    {
    requestVal = labelOpt;
    queryBy = CV_LABEL;
    }
if (requestVal)
    {
    (void)stripChar(requestVal,'\"');
    requestCount = chopCommas(requestVal,NULL);
    requested = needMem(requestCount * sizeof(char *));
    chopByChar(requestVal,',',requested,requestCount);
    }

char *org = NULL;
// if the org is specified in the type (eg. cell line)
// then use that for the org, otherwise use the command line option,
// otherwise use human.
char *type = findType(cvHash,requested,requestCount,&queryBy, &org, FALSE);
if (org == NULL)
    org = organismOptLower;
if (org == NULL)
    org = ORG_HUMAN;

// Special logic for requesting antibody by target
if (targetOpt && requestCount > 0 && sameWord(queryBy,CV_TERM) && sameWord(type,CV_TERM_ANTIBODY))
    {
    // Several antibodies may have same target.
    // requested target={antibody} and found antibody
    // Must now convert each of the requested terms to its target before displaying all targets
    char **targets = convertAntibodiesToTargets(cvHash,requested,requestCount);
    if (targets != NULL)
        {
        freeMem(requested);
        requested = targets;
        queryBy = CV_TARGET;
        }
    }
//warn("Query by: %s = '%s' type:%s",queryBy,requestVal?requestVal:"all",type);

// Get just the terms that match type and requested, then sort them
if (differentWord(type,CV_TOT) || typeOpt != NULL ) // If type resolves to typeOfTerm and
    {                                               // typeOfTerm was not requested,
    while ((hEl = hashNext(&hc)) != NULL)           // then just show definition
        {
        ra = (struct hash *)hEl->val;
        char *thisType = (char *)cvTermNormalized(hashMustFindVal(ra,CV_TYPE));
        if (differentWord(thisType,type) && (requested == NULL
        ||  differentWord(thisType,CV_TERM_CONTROL)))
            continue;
        // Skip all rows that do not match queryBy param if specified
        if (requested)
            {
            char *val = hashFindVal(ra, queryBy);
            if (val == NULL)
                {
                // Special case for input that has no target
                if (sameString(queryBy, CV_TARGET))
                    val = hashMustFindVal(ra, CV_TERM);
                else
                    continue;
                }
            if (-1 == stringArrayIx(val,requested,requestCount))
                continue;
            }
        else if (excludeDeprecated)
            {
            if (hashFindVal(ra, "deprecated") != NULL)
                continue;
            }
        slAddTail(&termList, ra);
        }
    }
slSort(&termList, termCmp);

boolean described = doTypeDefinition(type,FALSE,(slCount(termList) == 0));
boolean sortable = (slCount(termList) > 5);
if (sortable)
    {
    webIncludeResourceFile("HGStyle.css");
    jsIncludeFile("jquery.js",NULL);
    jsIncludeFile("utils.js",NULL);
    printf("<TABLE class='sortable' border=1 CELLSPACING=0 style='border: 2px outset #006600; "
           "background-color:%s;'>\n",COLOR_BG_DEFAULT);
    }
else
    printf("<TABLE BORDER=1 BGCOLOR=%s CELLSPACING=0 CELLPADDING=2>\n",COLOR_BG_DEFAULT);
if (slCount(termList) > 0)
    {
    doTypeHeader(type, org,sortable);

    // Print out the terms
    while ((ra = slPopHead(&termList)) != NULL)
        {
        if (doTypeRow( ra, org ))
            totalPrinted++;
        }
    }
puts("</TBODY></TABLE><BR>");
if (sortable)
    jsInline("{$(document).ready(function() "
         "{sortTable.initialize($('table.sortable')[0],true,true);});}\n");
if (totalPrinted == 0)
    {
    if (!described)
        warn("Error: Unrecognised type (%s)\n", type);
    }
else if (totalPrinted > 1)
    printf("Total = %d\n", totalPrinted);
}
示例#10
0
char *menuBar(struct cart *cart, char *db)
// Return HTML for the menu bar (read from a configuration file);
// we fixup internal CGI's to add hgsid's and include the appropriate js and css files.
//
// Note this function is also called by hgTracks which extends the menu bar
//  with a View menu defined in hgTracks/menu.c
{
char *docRoot = hDocumentRoot();
char *menuStr, buf[4096], uiVars[128];
FILE *fd;
char *navBarFile = "inc/globalNavBar.inc";
struct stat statBuf;
char *scriptName = cgiScriptName();
if (cart)
    safef(uiVars, sizeof(uiVars), "%s=%s", cartSessionVarName(), cartSessionId(cart));
else
    uiVars[0] = 0;

if(docRoot == NULL)
    // tolerate missing docRoot (i.e. don't bother with menu when running from command line)
    return NULL;

jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery.plugins.js", NULL);
webIncludeResourceFile("nice_menu.css");

// Read in menu bar html
safef(buf, sizeof(buf), "%s/%s", docRoot, navBarFile);
fd = mustOpen(buf, "r");
fstat(fileno(fd), &statBuf);
int len = statBuf.st_size;
menuStr = needMem(len + 1);
mustRead(fd, menuStr, statBuf.st_size);
menuStr[len] = 0;
carefulClose(&fd);

if (cart)
    {
    char *newMenuStr = menuBarAddUiVars(menuStr, "/cgi-bin/hg", uiVars);
    freez(&menuStr);
    menuStr = newMenuStr;
    }

if(scriptName)
    {
    // Provide hgTables options for some CGIs.
    char hgTablesOptions[1024] = "";
    char *track = (cart == NULL ? NULL :
                   (endsWith(scriptName, "hgGene") ?
                    cartOptionalString(cart, "hgg_type") :
                    cartOptionalString(cart, "g")));
    if (track && cart && db &&
        (endsWith(scriptName, "hgc") || endsWith(scriptName, "hgTrackUi") ||
         endsWith(scriptName, "hgGene")))
        {
        struct trackDb *tdb = hTrackDbForTrack(db, track);
        if (tdb)
	    {
	    struct trackDb *topLevel = trackDbTopLevelSelfOrParent(tdb); 
	    safef(hgTablesOptions, sizeof  hgTablesOptions, 
		    "../cgi-bin/hgTables?hgta_doMainPage=1&hgta_group=%s&hgta_track=%s&hgta_table=%s&", 
		    topLevel->grp, topLevel->track, tdb->table);
	    menuStr = replaceChars(menuStr, "../cgi-bin/hgTables?", hgTablesOptions);
	    trackDbFree(&tdb);
	    }
        }
    }

if(!loginSystemEnabled())
    stripRegEx(menuStr, "<\\!-- LOGIN_START -->.*<\\!-- LOGIN_END -->", REG_ICASE);

if(scriptName)
    {  // Provide optional official mirror servers menu items
    char *geoMenu = geoMirrorMenu();
    char *pattern = "<!-- OPTIONAL_MIRROR_MENU -->";
    char *newMenuStr = replaceChars(menuStr, pattern, geoMenu);
    freez(&menuStr);
    menuStr = newMenuStr;
    }


if(scriptName)
    {
    // Provide view menu for some CGIs.
    struct dyString *viewItems = dyStringCreate("");
    boolean hasViewMenu = TRUE;
    if (endsWith(scriptName, "hgGenome"))
        {
	safef(buf, sizeof(buf), "../cgi-bin/hgGenome?%s&hgGenome_doPsOutput=1", uiVars);
    	dyStringPrintf(viewItems, "<li><a href='%s' id='%s'>%s</a></li>\n", buf, "pdfLink", "PDF/PS");
        }
    else
	{
	hasViewMenu = FALSE;
	}
    if (hasViewMenu)
	{
	struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n");
	dyStringAppend(viewMenu, viewItems->string);
	dyStringAppend(viewMenu, "</ul>\n</li>\n");
    	menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", viewMenu->string);
	dyStringFree(&viewMenu);
	}
    else if (!endsWith(scriptName, "hgTracks"))
	{
    	replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", "");
	}
    dyStringFree(&viewItems);
    }


if(scriptName)
    {
    // Provide context sensitive help links for some CGIs.
    char *link = NULL;
    char *label = NULL;
    if (endsWith(scriptName, "hgBlat"))
        {
        link = "../goldenPath/help/hgTracksHelp.html#BLATAlign";
        label = "Help on Blat";
        }
    else if (endsWith(scriptName, "hgHubConnect"))
        {
        link = "../goldenPath/help/hgTrackHubHelp.html";
        label = "Help on Track Hubs";
        }
    else if (endsWith(scriptName, "hgNear"))
        {
        link = "../goldenPath/help/hgNearHelp.html";
        label = "Help on Gene Sorter";
        }
    else if (endsWith(scriptName, "hgTables"))
        {
        link = "../goldenPath/help/hgTablesHelp.html";
        label = "Help on Table Browser";
        }
    else if (endsWith(scriptName, "hgGenome"))
        {
        link = "../goldenPath/help/hgGenomeHelp.html";
        label = "Help on Genome Graphs";
        }
    else if (endsWith(scriptName, "hgSession"))
        {
        link = "../goldenPath/help/hgSessionHelp.html";
        label = "Help on Sessions";
        }
    else if (endsWith(scriptName, "hgVisiGene"))
        {
        link = "../goldenPath/help/hgTracksHelp.html#VisiGeneHelp";
        label = "Help on VisiGene";
        }
    else if (endsWith(scriptName, "hgCustom"))
        {
        link = "../goldenPath/help/customTrack.html";
        label = "Help on Custom Tracks";
        }
    // Don't overwrite any previously set defaults
    if(!contextSpecificHelpLink && link)
        contextSpecificHelpLink = link;
    if(!contextSpecificHelpLabel && label)
        contextSpecificHelpLabel = label;
    }
if(contextSpecificHelpLink)
    {
    char buf[1024];
    safef(buf, sizeof(buf), "<li><a href='%s'>%s</a></li>", contextSpecificHelpLink, contextSpecificHelpLabel);
    menuStr = replaceChars(menuStr, "<!-- CONTEXT_SPECIFIC_HELP -->", buf);
    }
return menuStr;
}
示例#11
0
void doMiddle(struct cart *theCart)
/* Write header and body of html page. */
{
boolean gotDisconnect = FALSE;

cart = theCart;

if (cartVarExists(cart, hgHubDoClear))
    {
    doClearHub(cart);
    cartWebEnd();
    return;
    }

if (cartVarExists(cart, hgHubDoDisconnect))
    {
    gotDisconnect = TRUE;
    doDisconnectHub(cart);

    // now rebuild the cart variable ("trackHubs") that has which lists which
    // hubs are on.
    hubConnectHubsInCart(cart);
    }

if (cartVarExists(cart, hgHubDoReset))
    {
    doResetHub(cart);
    }

cartWebStart(cart, NULL, "%s", pageTitle);
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);

webIncludeResourceFile("jquery-ui.css");

jsIncludeFile("ajax.js", NULL);
jsIncludeFile("hgHubConnect.js", NULL);
jsIncludeFile("jquery.cookie.js", NULL);

printf("<div id=\"hgHubConnectUI\"> <div id=\"description\"> \n");
printf(
   "<P>Track data hubs are collections of tracks from outside of UCSC that "
   "can be imported into the Genome Browser.  To import a public hub check "
   "the box in the list below. "
   "After import the hub will show up as a group of tracks with its own blue "
   "bar and label underneath the main browser graphic, and in the "
   "configure page. For more information, see the "
   "<A HREF=\"../goldenPath/help/hgTrackHubHelp.html\" TARGET=_blank>"
   "User's Guide</A>.</P>\n"
   "<P><B>NOTE: Because Track Hubs are created and maintained by external sources,"
   " UCSC is not responsible for their content.</B></P>"
   );
printf("</div>\n");

getDbAndGenome(cart, &database, &organism, oldVars);

char *survey = cfgOptionEnv("HGDB_HUB_SURVEY", "hubSurvey");
char *surveyLabel = cfgOptionEnv("HGDB_HUB_SURVEY_LABEL", "hubSurveyLabel");

if (survey && differentWord(survey, "off"))
    hPrintf("<span style='background-color:yellow;'><A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\n", survey, surveyLabel ? surveyLabel : "Take survey");
hPutc('\n');

// check to see if we have any new hubs
hubCheckForNew(cart);

// grab all the hubs that are listed in the cart
struct hubConnectStatus *hubList =  hubConnectStatusListFromCartAll(cart);

checkTrackDbs(hubList);

// here's a little form for the add new hub button
printf("<FORM ACTION=\"%s\" NAME=\"addHubForm\">\n",  "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");

// this the form for the disconnect hub button
printf("<FORM ACTION=\"%s\" NAME=\"disconnectHubForm\">\n",  "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubId", "");
cgiMakeHiddenVar(hgHubDoDisconnect, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");

// this the form for the reset hub button
printf("<FORM ACTION=\"%s\" NAME=\"resetHubForm\">\n",  "../cgi-bin/hgHubConnect");
cgiMakeHiddenVar("hubUrl", "");
cgiMakeHiddenVar(hgHubDoReset, "on");
cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
puts("</FORM>");


// ... and now the main form
if (cartVarExists(cart, hgHubConnectCgiDestUrl))
    destUrl = cartOptionalString(cart, hgHubConnectCgiDestUrl);
printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
cartSaveSession(cart);

// we have two tabs for the public and unlisted hubs
printf("<div id=\"tabs\">"
       "<ul> <li><a href=\"#publicHubs\">Public Hubs</a></li>"
       "<li><a href=\"#unlistedHubs\">My Hubs</a></li> "
       "</ul> ");

struct hash *publicHash = hgHubConnectPublic();
hgHubConnectUnlisted(hubList, publicHash);
printf("</div>");

printf("<div class=\"tabFooter\">");
cgiMakeButton("Submit", "Use Selected Hubs");

char *emailAddress = cfgOptionDefault("hub.emailAddress","*****@*****.**");
printf("<span class=\"small\">"
    "Contact <A HREF=\"mailto:%s\">%s</A> to add a public hub."
    "</span>\n", emailAddress,emailAddress);
printf("</div>");

cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");

printf("</div>\n");
puts("</FORM>");
cartWebEnd();
}
示例#12
0
void doSearchTracks(struct group *groupList)
{
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("ui.dropdownchecklist.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);

struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *nameSearch  = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
char *typeSearch  = cartUsualString(   cart, TRACK_SEARCH_ON_TYPE,ANYLABEL);
char *simpleEntry = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
char *descSearch  = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
char *groupSearch = cartUsualString(  cart, TRACK_SEARCH_ON_GROUP,ANYLABEL);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search")
                   || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int tracksFound = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];

char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
enum searchTab selectedTab = (sameString(currentTab, "advancedTab") ? advancedTab : simpleTab);

// NOTE: could support quotes in simple tab by detecting quotes and choosing
//       to use doesNameMatch() || doesDescriptionMatch()
if (selectedTab == simpleTab && !isEmpty(simpleEntry))
    stripChar(simpleEntry, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);

// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists,
// AND superTrack reshaping.

// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);

slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
    {
    groupTrackListAddSuper(cart, group);
    if (group->trackList != NULL)
        {
        groups[numGroups] = cloneString(group->name);
        labels[numGroups] = cloneString(group->label);
        numGroups++;
        if (numGroups >= ArraySize(groups))
            internalErr();
        }
    }

safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly",
      organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);

hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n",
        hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart);  // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf);  // timestamps page to avoid browser cache


hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n",
        TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);

hPrintf("<div id='tabs' style='display:none; %s'>\n<ul>\n<li><a href='#simpleTab'>"
        "<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B>"
        "</a></li>\n<li><a href='#advancedTab'>"
        "<B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B>"
        "</a></li>\n</ul>\n<div id='simpleTab' style='max-width:inherit;'>\n",
        cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");

hPrintf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' "
        "style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n",
        TRACK_SEARCH_SIMPLE,simpleEntry == NULL ? "" : simpleEntry);
if (selectedTab==simpleTab && simpleEntry)
    searchTermsExist = TRUE;

hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
        "style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' "
        "style='font-size:.8em;' onclick='findTracks.clear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
        "style='font-size:.8em;'>\n");
hPrintf("</div>\n");

// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
        "<table id='advancedTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;

// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track&nbsp;Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' "
        "onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
        TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");

// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' "
        "onkeyup='findTracks.searchButtonsEnable(true);' "
        "style='max-width:536px; width:536px; font-size:.9em;'>",
        TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(descSearch))
    searchTermsExist = TRUE;

hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch,
                    "class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(groupSearch) && !sameString(groupSearch,ANYLABEL))
    searchTermsExist = TRUE;

// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch,
                    "class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (selectedTab==advancedTab && !isEmpty(typeSearch) && !sameString(typeSearch,ANYLABEL))
    searchTermsExist = TRUE;

// mdb selects
struct slPair *mdbSelects = NULL;
if (metaDbExists)
    {
    struct slPair *mdbVars = mdbVarsSearchable(conn,TRUE,FALSE); // Tables but not file only objects
    mdbSelects = mdbSelectPairs(cart, mdbVars);
    char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,FALSE);  // not a fileSearch
    if (output)
        {
        puts(output);
        freeMem(output);
        }
    slPairFreeList(&mdbVars);
    }

hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' "
        "style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' "
        "style='font-size:.8em;' onclick='findTracks.clear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' "
        "style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n");

hPrintf("</div>\n");

hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
cgiDown(0.8);

if (measureTiming)
    measureTime("Rendered tabs");

if (doSearch)
    {
    // Now search
    struct slRef *tracks = NULL;
    if (selectedTab==simpleTab && !isEmpty(simpleEntry))
        tracks = simpleSearchForTracksstruct(simpleEntry);
    else if (selectedTab==advancedTab)
        tracks = advancedSearchForTracks(conn,groupList,nameSearch,typeSearch,descSearch,
                                         groupSearch,mdbSelects);

    if (measureTiming)
        measureTime("Searched for tracks");

    // Sort and Print results
    if (selectedTab!=filesTab)
        {
        enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
        tracksFound = slCount(tracks);
        if (tracksFound > 1)
            findTracksSort(&tracks,sortBy);

        displayFoundTracks(cart,tracks,tracksFound,sortBy);

        if (measureTiming)
            measureTime("Displayed found tracks");
        }
    slPairFreeList(&mdbSelects);
    }
hFreeConn(&conn);

webNewSection("About Track Search");
if (metaDbExists)
    hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
            "metadata.  If multiple terms are entered, only tracks with all terms "
            "will be part of the results.");
else
    hPrintf("<p>Search for terms in track descriptions, groups, and names. "
            "If multiple terms are entered, only tracks with all terms "
            "will be part of the results.");

hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}