char *wikiLinkChangePasswordUrl(char *hgsid)
/* Return the URL for the user change password page. */
{
char buf[2048];
char *retEnc = encodedHgSessionReturnUrl(hgsid);
if (loginSystemEnabled())
{
if (! wikiLinkEnabled())
errAbort("wikiLinkChangePasswordUrl called when login system is not enabled "
"(specified in hg.conf).");
safef(buf, sizeof(buf),
"http%s://%s/cgi-bin/hgLogin?hgLogin.do.changePasswordPage=1&returnto=%s",
cgiAppendSForHttps(), wikiLinkHost(), retEnc);
}
else
{
if (! wikiLinkEnabled())
errAbort("wikiLinkUserLogoutUrl called when wiki is not enable (specified "
"in hg.conf).");
safef(buf, sizeof(buf),
"http://%s/index.php?title=Special:UserlogoutUCSC&returnto=%s",
wikiLinkHost(), retEnc);
}
freez(&retEnc);
return(cloneString(buf));
}
char *wikiLinkUserLoginUrlReturning(char *hgsid, char *returnUrl)
/* Return the URL for the wiki user login page. */
{
char buf[2048];
if (loginSystemEnabled())
{
if (! wikiLinkEnabled())
errAbort("wikiLinkUserLoginUrl called when login system is not enabled "
"(specified in hg.conf).");
safef(buf, sizeof(buf),
"http%s://%s/cgi-bin/hgLogin?hgLogin.do.displayLoginPage=1&returnto=%s",
cgiAppendSForHttps(), wikiLinkHost(), returnUrl);
}
else
{
if (! wikiLinkEnabled())
errAbort("wikiLinkUserLoginUrl called when wiki is not enabled (specified "
"in hg.conf).");
safef(buf, sizeof(buf),
"http://%s/index.php?title=Special:UserloginUCSC&returnto=%s",
wikiLinkHost(), returnUrl);
}
return(cloneString(buf));
}
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 *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;
}