void palOptions(struct cart *cart,
struct sqlConnection *conn, void (*addButtons)(),
char *extraVar)
/* output the options dialog (select MAF file, output options */
{
char *database = sqlGetDatabase(conn);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=POST>\n", cgiScriptName());
cartSaveSession(cart);
char *mafTable = outMafTableDrop(cart, conn);
char *numColumns = cartUsualString(cart, hgtaCGINumColumns, "");
printf("<BR><BR><B>Formatting options:</B><BR>\n");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneExons, hgtaJSGeneExons, FALSE);
printf("Separate into exons<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneNoTrans, hgtaJSGeneNoTrans, FALSE);
printf("Show nucleotides<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneOutBlank, hgtaJSGeneOutBlank, FALSE);
printf("Output lines with just dashes<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIOutTable, hgtaJSOutTable, FALSE);
printf("Format output as table ");
jsMakeTrackingCheckBox(cart, hgtaCGITruncHeader, hgtaJSTruncHeader, FALSE);
printf("Truncate headers at ");
cgiMakeTextVar(hgtaCGINumColumns, numColumns, 2);
printf("characters (enter zero for no headers)<BR>");
printf("<BR>");
struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
/* get maf parent (if any) */
maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
wigMafSpeciesTable(cart, maftdb, mafTable, database);
addButtons();
cartSaveSession(cart);
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(curVars);
assert(varCount < (sizeof saveVars / sizeof(char *)));
memcpy(saveVars, curVars, varCount * sizeof(saveVars[0]));
if (extraVar != NULL)
{
assert(varCount + 1 < (sizeof saveVars / sizeof(char *)));
saveVars[varCount] = extraVar;
varCount++;
}
jsCreateHiddenForm(cart, cgiScriptName(), saveVars, varCount);
}
}
void jsReloadOnBackButton(struct cart *cart)
/* Add some javascript to detect that the back button (or reload) has been pressed,
* and to resubmit in that case to redraw the page with the latest cart contents. */
// __detectback trick from
// http://siphon9.net/loune/2009/07/detecting-the-back-or-refresh-button-click/
// Yes, I know this along with every other inline <script> here belongs in a .js module
{
jsInlineF(
"document.write(\"<form style='display: none'><input name='__detectback' id='__detectback' "
"value=''></form>\");\n"
"function checkPageBackOrRefresh() {\n"
" if (document.getElementById('__detectback').value) {\n"
" return true;\n"
" } else {\n"
" document.getElementById('__detectback').value = 'been here';\n"
" return false;\n"
" }\n"
"}\n"
"window.onload = function() { "
" if (checkPageBackOrRefresh()) { \n"
" if (window.location.search == '?%s') { \n"
// We already have the hgsid-only URL that we want, reload it.
// (necessary for IE because IE doesn't reload on replace,
// unless window.location and/or window.search changes)
" window.location.reload(true);\n"
" } else { \n"
" window.location.replace('%s?%s');\n"
" } \n"
" } "
"};\n"
, cartSidUrlString(cart), cgiScriptName(), cartSidUrlString(cart));
}
static void doBigSelectPage(char *db, char *table)
/* Put up big field selection page. Assumes html page open already*/
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];
cartSetString(cart, hgtaFieldSelectTable, getDbTable(db, table));
if (strchr(table, '.'))
htmlOpen("Select Fields from %s", table);
else
htmlOpen("Select Fields from %s.%s", db, table);
hPrintf("<FORM NAME=\"mainForm\" ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);
showTableFields(db, table, TRUE);
dtList = extraTableList(selFieldLinkedTablePrefix());
showLinkedFields(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, selFieldLinkedTablePrefix(),
hgtaDoSelectFieldsMore, "allow selection from checked tables");
/* clean up. */
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
joinerFree(&joiner);
}
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 printGreatSubmitButtons()
/* print submit button to create data and then send query results to GREAT. */
{
cartSetString(cart, hgtaCompressType, textOutCompressNone);
cartSetString(cart, hgtaOutFileName, "");
cgiMakeHiddenVar(hgtaCompressType, textOutCompressNone);
cgiMakeHiddenVar(hgtaOutFileName, "");
cgiMakeHiddenVar(hgtaDoGreatOutput, "on");
cgiMakeHiddenVar(hgtaPrintCustomTrackHeaders, "on");
cgiMakeButton(hgtaDoGreatQuery, "Send query to GREAT");
hPrintf("</FORM>\n");
hPrintf(" ");
/* new form as action is different */
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", cgiScriptName());
cgiMakeButton(hgtaDoMainPage, "Cancel");
hPrintf("</FORM>\n");
}
void jsMakeSetClearButton(struct cart *cart,
char *form, char *buttonVar, char *buttonLabel,
char *cartVarPrefix, struct slName *cartVarSuffixList,
char *anchor, boolean currentPos, boolean isSet)
/* Make a button for setting or clearing all of a list of boolean
* cart variables (i.e. checkboxes). If this button was just pressed,
* set or clear those cart variables.
* Optional html anchor is appended to the form's action if given.
* If currentPos, anchor is ignored and jsSetVerticalPosition is used so
* that the new page gets the same vertical offset as the current page. */
{
struct slName *suffix;
char javascript[2048];
char *vertPosJs = "";
if (currentPos)
{
anchor = NULL;
jsInit();
vertPosJs = jsSetVerticalPosition(form);
}
cgiMakeHiddenVar(buttonVar, "");
safef(javascript, sizeof javascript,
"document.%s.action = '%s%s%s'; document.%s.%s.value='%s'; %s"
"document.%s.submit();",
form, cgiScriptName(),
(isNotEmpty(anchor) ? "#" : ""), (isNotEmpty(anchor) ? anchor : ""),
form, buttonVar, buttonLabel, vertPosJs, form);
cgiMakeOnClickButton(javascript, buttonLabel);
if (isNotEmpty(cgiOptionalString(buttonVar)))
{
char option[1024];
if (cartVarPrefix == NULL)
cartVarPrefix = "";
for (suffix = cartVarSuffixList; suffix != NULL; suffix = suffix->next)
{
safef(option, sizeof(option), "%s%s", cartVarPrefix, suffix->name);
cartSetBoolean(cart, option, isSet);
}
}
}
static void phoneHome()
{
static boolean beenHere = FALSE;
if (beenHere) /* one at a time please */
return;
beenHere = TRUE;
char *expireTime = cfgOptionDefault("browser.cgiExpireMinutes", "20");
unsigned expireMinutes = sqlUnsigned(expireTime);
expireSeconds = expireMinutes * 60;
char trashFile[PATH_LEN];
safef(trashFile, sizeof(trashFile), "%s/registration.txt", trashDir());
/* trashFile does not exist during command line execution */
if(fileExists(trashFile)) /* update access time for trashFile */
{
struct utimbuf ut;
struct stat mystat;
ZeroVar(&mystat);
if (stat(trashFile,&mystat)==0)
{
ut.actime = clock1();
ut.modtime = mystat.st_mtime;
}
else
{
ut.actime = ut.modtime = clock1();
}
(void) utime(trashFile, &ut);
if (expireSeconds > 0)
{
(void) signal(SIGALRM, cgiApoptosis);
(void) alarm(expireSeconds); /* CGI timeout */
}
return;
}
char *scriptName = cgiScriptName();
char *ip = getenv("SERVER_ADDR");
if (scriptName && ip) /* will not be true from command line execution */
{
FILE *f = fopen(trashFile, "w");
if (f) /* rigamarole only if we can get a trash file */
{
time_t now = time(NULL);
char *localTime;
extern char *tzname[2];
struct tm *tm = localtime(&now);
localTime = sqlUnixTimeToDate(&now,FALSE); /* FALSE == localtime */
fprintf(f, "%s, %s, %s %s, %s\n", scriptName, ip, localTime,
tm->tm_isdst ? tzname[1] : tzname[0], trashFile);
fclose(f);
chmod(trashFile, 0666);
pid_t pid0 = fork();
if (0 == pid0) /* in child */
{
close(STDOUT_FILENO); /* do not hang up Apache finish for parent */
expireSeconds = 0; /* no error message from this exit */
(void) signal(SIGALRM, cgiApoptosis);
(void) alarm(6); /* timeout here in 6 seconds */
#include "versionInfo.h"
char url[1024];
safef(url, sizeof(url), "%s%s%s%s%s%s", "http://",
"genomewiki.", "ucsc.edu/", "cgi-bin/useCount?", "version=browser.v",
CGI_VERSION);
/* 6 second alarm will exit this page fetch if it does not work */
(void) htmlPageGetWithCookies(url, NULL); /* ignore return */
exit(0);
} /* child of fork has done exit(0) normally or via alarm */
} /* trash file open OK */
if (expireSeconds > 0)
{
(void) signal(SIGALRM, cgiApoptosis);
(void) alarm(expireSeconds); /* CGI timeout */
}
} /* an actual CGI binary */
} /* phoneHome() */
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;
}
char *webTimeStampedLinkToResource(char *fileName, boolean wrapInHtml)
// If wrapInHtml
// returns versioned link embedded in style or script html (free after use).
// else
// returns full path of a versioned path to the requested resource file (js, or css).
// NOTE: png, jpg and gif should also be supported but are untested.
//
// In production sites we use a versioned softlink that includes the CGI version. This has the following benefits:
// a) flushes user's web browser cache when the user visits a GB site whose version has changed since their last visit;
// b) enforces the requirement that static files are the same version as the CGIs (something that often fails to happen in mirrors).
// (see notes in redmine #3170).
//
// In dev trees we use mtime to create a pseudo-version; this forces web browsers to reload css/js file when it changes,
// so we don't get odd behavior that can be caused by caching of mis-matched javascript and style files in dev trees.
//
// In either case, the actual file has to have been previously created by running make in the appropriate directory (kent/src/hg/js
// or kent/src/hg/htdocs/style).
{
char baseName[PATH_LEN];
char extension[FILEEXT_LEN];
splitPath(fileName, NULL, baseName, extension);
boolean js = sameString(".js",extension);
boolean style = !js && sameString(".css",extension);
boolean image = !js
&& !style
&& ( sameString(".png",extension)
|| sameString(".jpg",extension)
|| sameString(".gif",extension));
if (!js && !style) // && !image) NOTE: This code has not been tested on images but should work.
errAbort("webTimeStampedLinkToResource: unknown resource type for %s.\n", fileName);
// Build and verify directory
char *dirName = "";
if (js)
dirName = cfgOptionDefault("browser.javaScriptDir", "js");
else if (style)
dirName = cfgOptionDefault("browser.styleDir","style");
else if (image)
dirName = cfgOptionDefault("browser.styleImagesDir","style/images");
struct dyString *fullDirName = NULL;
char *docRoot = hDocumentRoot();
if (docRoot != NULL)
fullDirName = dyStringCreate("%s/%s", docRoot, dirName);
else
// tolerate missing docRoot (i.e. when running from command line)
fullDirName = dyStringCreate("%s", dirName);
if (!fileExists(dyStringContents(fullDirName)))
errAbort("webTimeStampedLinkToResource: dir: %s doesn't exist.\n",
dyStringContents(fullDirName));
// build and verify real path to file
struct dyString *realFileName = dyStringCreate("%s/%s", dyStringContents(fullDirName), fileName);
if (!fileExists(dyStringContents(realFileName)))
errAbort("webTimeStampedLinkToResource: file: %s doesn't exist.\n",
dyStringContents(realFileName));
// build and verify link path including timestamp in the form of dir/baseName + timeStamp or CGI Version + ext
long mtime = fileModTime(dyStringContents(realFileName));
struct dyString *linkWithTimestamp;
char *scriptName = cgiScriptName();
if (scriptName == NULL)
scriptName = cloneString("");
boolean nonVersionedLinks = FALSE;
if (endsWith(scriptName, "qaPushQ"))
nonVersionedLinks = TRUE;
if (nonVersionedLinks)
linkWithTimestamp = dyStringCreate("%s/%s%s", dyStringContents(fullDirName), baseName, extension);
else if ((cfgOption("versionStamped") == NULL) && (hIsPreviewHost() || hIsPrivateHost()))
linkWithTimestamp = dyStringCreate("%s/%s-%ld%s", dyStringContents(fullDirName), baseName, mtime, extension);
else
linkWithTimestamp = dyStringCreate("%s/%s-v%s%s", dyStringContents(fullDirName), baseName, CGI_VERSION, extension);
if (!fileExists(dyStringContents(linkWithTimestamp)))
errAbort("Cannot find correct version of file '%s'; this is due to an installation error\n\nError details: %s does not exist",
fileName, dyStringContents(linkWithTimestamp));
// Free up all that extra memory
dyStringFree(&realFileName);
dyStringFree(&fullDirName);
char *linkFull = dyStringCannibalize(&linkWithTimestamp);
char *link = linkFull;
if (docRoot != NULL)
{
link = cloneString(linkFull + strlen(docRoot) + 1);
freeMem(linkFull);
}
if (wrapInHtml) // wrapped for christmas
{
struct dyString *wrapped = dyStringNew(0);
if (js)
dyStringPrintf(wrapped,"<script type='text/javascript' SRC='/%s'></script>\n", link);
else if (style)
dyStringPrintf(wrapped,"<LINK rel='STYLESHEET' href='/%s' TYPE='text/css' />\n", link);
else // Will be image, since these are the only three choices allowed
dyStringPrintf(wrapped,"<IMG src='/%s' />\n", link);
freeMem(link);
link = dyStringCannibalize(&wrapped);
}
return link;
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%u",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
printf("\t<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n"
"\t<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n"
"\t<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n"
"\t<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n"
"\t<TITLE>"
);
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
puts(
"<A NAME=\"TOP\"></A>" "\n"
"" "\n"
"<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=\"100%\">" "\n");
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart);
if(menuStr)
{
puts(menuStr);
}
if (endsWith(scriptName, "hgGateway") && geoMirrorEnabled())
{
// Show an opt-out alert if user is on a host to which user has been automatically redirected (just once, right after they have been redirected)
char *source = cgiOptionalString("source");
char *redirect = cgiOptionalString("redirect");
if (source != NULL && redirect != NULL && sameString(redirect, "auto"))
{
char *domain = cgiServerName();
char *port = cgiServerPort();
// We don't bother maintaining stuff in request URI, because it may contain items like hgsid and other host specific values
int newUriSize = 2048;
char *newUri = needMem(newUriSize);
safef(newUri, newUriSize, "http%s://%s:%s/cgi-bin/hgGateway?redirect=manual&source=%s",
cgiServerHttpsIsOn() ? "s" : "", source, port, domain);
printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">"
"<div style=\"margin: 10px 25%%; border-style:solid; border-width:thin; border-color:#97D897;\">"
"<h3 style=\"background-color: #97D897; text-align: left; margin-top:0px; margin-bottom:0px;\">"
" You've been redirected to your nearest mirror - %s"
"<idiv style=\"float:right;\">[x]</idiv>"
"</h3> "
"<ul style=\"margin:5px;\">"
"<li>Take me back to <a href=\"%s\">%s</a>"
"<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html\">What is this?</a></idiv>"
"</li>"
"</ul>"
"</div>"
"</TD></TR>\n"
, domain, newUri, source );
}
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere)
"<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->" "\n"
"<TR><TD COLSPAN=3>\n"
"<div id=firstSection>"
" <!--outer table is for border purposes-->\n"
" <TABLE WIDTH='100%' BGCOLOR='#" HG_COL_BORDER "' BORDER='0' CELLSPACING='0' "
"CELLPADDING='1'><TR><TD>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' BORDER='0' CELLSPACING='0' "
"CELLPADDING='0'><TR><TD>\n"
" <div class='subheadingBar'><div class='windowSize' id='sectTtl'>"
);
htmlTextOut(textOutBuf);
puts(" </div></div>\n"
" <TABLE BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>"
"<TR><TH HEIGHT=10></TH></TR>\n"
" <TR><TD WIDTH=10> </TD><TD>\n\n"
);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
} /* static void webStartWrapperDetailedInternal() */
void gvDisclaimer ()
/* displays page with disclaimer forwarding query string that got us here */
{
struct cgiVar *cv, *cvList = cgiVarList();
cartHtmlStart("PhenCode Disclaimer");
printf("<TABLE WIDTH=\"%s\" BGCOLOR=\"#888888\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>", "100%");
printf("<TABLE BGCOLOR=\"fffee8\" WIDTH=\"%s\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"0\"><TR><TD>", "100%");
printf("<TABLE BGCOLOR=\"D9E4F8\" BACKGROUND=\"../../images/hr.gif\" WIDTH=%s><TR><TD>", "100%");
printf("<FONT SIZE=\"4\"><b> PhenCode Disclaimer </B></FONT> ");
printf("</TD></TR></TABLE>");
printf("<TABLE BGCOLOR=\"fffee8\" WIDTH=\"%s\" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR>", "100%");
printf("<TR><TD WIDTH=10> </TD><TD>");
printf("<b>Usage</b>\n");
printf("<p>\n");
printf("PhenCode is intended for research purposes only. Although the data\n");
printf("are freely available to all, users should treat the reported mutations\n");
printf("with extreme caution in clinical settings or for any diagnostic or\n");
printf("population screening purpose. This information requires expertise\n");
printf("to interpret properly; clinical diagnosis and/or treatment\n");
printf("recommendations should be made only by medical professionals.\n");
printf("<p>\n");
printf("Patients and doctors should not make treatment decisions based on the\n");
printf("information in PhenCode. In particular, <b>PhenCode should not be used\n");
printf("to assess disease risk</b>. Some of these variants are not associated\n");
printf("with disease at all, and for many others the association is slight,\n");
printf("depends on other factors, and/or may not be causative. The mere fact\n");
printf("that a variant is listed here does NOT mean that a particular patient\n");
printf("will become ill.\n");
printf("<p>");
printf("<b>Errors</b>\n");
printf("<p>\n");
printf("The PhenCode track (including, but not limited to, \"Locus Variants\"\n");
printf(") is a compilation of freely-available data\n");
printf("obtained from other sources. While reasonable effort is made to\n");
printf("promote accuracy, nevertheless there may be errors in the original\n");
printf("data and/or the compilation process. <b>By using these data, you\n");
printf("agree and acknowledge that the information is not guaranteed to be\n");
printf("accurate.</b> If you do find any errors, please report them to the\n");
printf("addresses listed on the <a href=\"http://phencode.bx.psu.edu/phencode/contact.html\">Contact us</a> page.\n");
printf("<p>");
printf("<b>Disclaimer</b>\n");
printf("<p>\n");
printf("This resource and data are provided \"as is\", \"where is\" and without\n");
printf("any express or implied warranties, including, but not limited to, any\n");
printf("implied warranties of merchantability and/or fitness for a particular\n");
printf("purpose. In no event shall\n");
printf("<a href=\"http://www.psu.edu/\">The Pennsylvania State University</a>,\n");
printf("<a href=\"http://www.ucsc.edu/\">The University of California Santa Cruz</a>,\n");
printf("or any data contributors,\n");
printf("nor their respective agents, employees or representatives be liable\n");
printf("for any direct, indirect, incidental, special, exemplary, or\n");
printf("consequential damages (including, but not limited to, procurement of\n");
printf("substitute goods or services; loss of use, data, or profits; business\n");
printf("interruption; medical or legal expenses; or pain and suffering),\n");
printf("however caused and on any theory of liability, whether in contract,\n");
printf("strict liability, or tort (including negligence or otherwise) arising\n");
printf("in any way or form out of the use of this resource or data, even if\n");
printf("advised of the possibility of such damage.\n");
printf("<p>\n");
printf("Users assume all risk and responsibility for the accuracy,\n");
printf("completeness, and usefulness, or lack thereof, of any information,\n");
printf("apparatus, product, or process disclosed, and also all risk and\n");
printf("responsibility that the use hereof would or would not infringe the\n");
printf("rights of any other party.\n");
printf("<p>\n");
printf("<br>\n");
printf("<FORM ACTION=\"%s\" METHOD=POST>\n", cgiScriptName());
for (cv = cvList; cv != NULL; cv = cv->next)
{
cgiContinueHiddenVar(cv->name);
}
cgiMakeButtonWithMsg("gvDisclaimer", "Agree", NULL);
printf(" ");
cgiMakeButtonWithMsg("gvDisclaimer", "Disagree", NULL);
printf("</FORM>\n");
printf("</td></tr></table></td></tr></table></td></tr></table>");
cartHtmlEnd();
exit(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;
}
static void webStartWrapperDetailedInternal(struct cart *theCart,
char *db, char *headerText, char *textOutBuf,
boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader,
boolean withHtmlHeader)
/* output a CGI and HTML header with the given title in printf format */
{
char uiState[256];
char *scriptName = cgiScriptName();
boolean isEncode = FALSE;
if (theCart)
{
char *theGenome = NULL;
char *genomeEnc = NULL;
getDbAndGenome(theCart, &db, &theGenome, NULL);
genomeEnc = cgiEncode(theGenome);
safef(uiState, sizeof(uiState), "?%s=%s&%s=%s&%s=%s",
orgCgiName, genomeEnc,
dbCgiName, db,
cartSessionVarName(), cartSessionId(theCart));
}
else
{
uiState[0] = 0;
uiState[1] = 0;
}
if (db == NULL)
db = hDefaultDb();
boolean dbIsFound = hDbExists(db);
boolean haveBlat = FALSE;
if (dbIsFound)
haveBlat = hIsBlatIndexedDatabase(db);
if (scriptName == NULL)
scriptName = cloneString("");
/* don't output two headers */
if(webHeadAlreadyOutputed)
return;
if (sameString(cgiUsualString("action",""),"encodeReleaseLog") ||
rStringIn("EncodeDataVersions", scriptName))
isEncode = TRUE;
/* Preamble. */
dnaUtilOpen();
if (withHttpHeader)
puts("Content-type:text/html\n");
if (withHtmlHeader)
{
char *newString, *ptr1, *ptr2;
char *browserVersion;
if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8')
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">");
else
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" "
"\"http://www.w3.org/TR/html4/loose.dtd\">");
// Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass)
puts(
"<HTML>" "\n"
"<HEAD>" "\n"
);
printf("\t%s\n", headerText);
webPragmasEtc();
printf("\t<TITLE>");
/* we need to take any HTML formatting out of the titlebar string */
newString = cloneString(textOutBuf);
for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++)
{
if (*ptr2 == '<')
{
for(; *ptr2 && (*ptr2 != '>'); ptr2++)
;
}
else
*ptr1++ = *ptr2;
}
*ptr1 = 0;
htmlTextOut(newString);
printf(" </TITLE>\n ");
webIncludeResourceFile("HGStyle.css");
if (extraStyle != NULL)
puts(extraStyle);
printf("</HEAD>\n");
printBodyTag(stdout);
htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur
puts(commonCssStyles());
}
webStartSectionTables();
if (withLogo)
{
puts("<TR><TH COLSPAN=1 ALIGN=\"left\">");
if (isEncode)
{
puts("<A HREF=\"http://www.genome.gov/10005107\" TARGET=\"_BLANK\">"
"<IMG SRC=\"../images/ENCODE_scaleup_logo.png\" height=50 ALT=\"ENCODE Project at NHGRI\">"
"</A>");
puts("<IMG SRC=\"../images/encodeDcc.jpg\" ALT=\"ENCODE Project at UCSC\">");
}
else
{
puts("<IMG SRC=\"../images/title.jpg\">");
}
puts("</TH></TR>" "\n"
"" "\n" );
}
/* Put up the hot links bar. */
char *menuStr = menuBar(theCart, db);
if(menuStr)
{
puts(menuStr);
}
if(!skipSectionHeader)
/* this HTML must be in calling code if skipSectionHeader is TRUE */
{
webFirstSection(textOutBuf);
};
webPushErrHandlers();
/* set the flag */
webHeadAlreadyOutputed = TRUE;
errAbortSetDoContentType(FALSE);
} /* static void webStartWrapperDetailedInternal() */
