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();
}
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();
}
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;
}
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);
}
}
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();
}
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);
}
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;
}
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>");
}
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);
}
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;
}
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();
}
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 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 </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 </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 </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();
}
