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;
}
int documentLink(struct hash *ra, char *term, char *docTerm,char *dir,
char *title,boolean genericDoc)
// Compare controlled vocab based on term value
{
boolean docsPrinted = 0;
char *s;
if (title == NULL)
title = docTerm;
//can use hg.conf to direct links back to main UCSC server if a mirror doesn't
//want all the PDFs
char *baseUrl = cfgOptionDefault("hgEncodeVocabDocBaseUrl", "");
// add links to protocol doc if it exists
char docUrl[PATH_LEN];
char docFile[PATH_LEN];
// parse setting
s = hashFindVal(ra,docTerm);
if (s != NULL)
{
if (sameWord(s,"missing"))
printf(" <em>missing</em>\n");
else
{
char *docSetting = cloneString(s);
char *settings=docSetting;
int count=0;
while ((s = nextWord(&settings)) != NULL)
{
char *docTitle = NULL;
char *fileName = NULL;
if (strchr(s,':')) // lab Specific setting
{
docTitle = strSwapChar(s,':',0);
fileName = docTitle + strlen(docTitle) + 1;
}
else
{
docTitle = title;
fileName = s;
}
if (count>0)
printf("<BR>");
count++;
docTitle = htmlEncode(strSwapChar(docTitle,'_',' '));
if (sameWord(fileName,"missing"))
printf("%s<em>missing</em>\n",docTitle);
else
{
safef(docUrl, sizeof(docUrl), "%s%s%s", baseUrl, dir, fileName);
safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl);
printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,docTitle);
docsPrinted++;
}
freeMem(docTitle);
}
freeMem(docSetting);
}
}
else if (genericDoc)
{ // generate a standard name
safef(docUrl, sizeof(docUrl), "%s%s%s_protocol.pdf", baseUrl, dir, term);
safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl);
if (fileExists(docFile))
{
printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,title);
docsPrinted++;
}
}
return docsPrinted;
}
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;
}
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;
}
