108d1fce0f31f8d58cfc0940a5fdb5a1deb7c14e braney Sat Jan 21 15:25:47 2023 -0800 be smarter about how we deal with curated hubs. Fixes #30510 diff --git src/hg/lib/web.c src/hg/lib/web.c index 06b3446..9b9e119 100644 --- src/hg/lib/web.c +++ src/hg/lib/web.c @@ -1,1645 +1,1645 @@ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include <regex.h> #include "hCommon.h" #include "obscure.h" #include "dnautil.h" #include "errAbort.h" #include "htmshell.h" #include "web.h" #include "dupTrack.h" #include "hPrint.h" #include "hdb.h" #include "hui.h" #include "hgConfig.h" #include "hVarSubst.h" #include "cheapcgi.h" #include "dbDb.h" #include "hgColors.h" #include "hubConnect.h" #include "search.h" #include "geoMirror.h" #include "trackHub.h" #include "versionInfo.h" #include "asmAlias.h" #ifndef GBROWSE #include "axtInfo.h" #include "wikiLink.h" #include "googleAnalytics.h" #include "jsHelper.h" #endif /* GBROWSE */ /* flag that tell if the CGI header has already been outputed */ boolean webHeadAlreadyOutputed = FALSE; /* flag that tell if text CGI header has been outputed */ boolean webInTextMode = FALSE; struct hash *includedResourceFiles = NULL; static char *dbCgiName = "db"; static char *orgCgiName = "org"; static char *cladeCgiName = "clade"; static char *extraStyle = NULL; /* globals: a cart and db for use in error handlers. */ static struct cart *errCart = NULL; static char *errDb = NULL; void textVaWarn(char *format, va_list args) { vprintf(format, args); puts("\n"); } void softAbort() { if (!webInTextMode) webEnd(); exit(0); } void webPushErrHandlers(void) /* Push warn and abort handler for errAbort(). */ { if (webInTextMode) pushWarnHandler(textVaWarn); else pushWarnHandler(webVaWarn); pushAbortHandler(softAbort); hDumpStackPushAbortHandler(); } void webPushErrHandlersCartDb(struct cart *cart, char *db) /* Push warn and abort handler for errAbort(); save cart and db for use in handlers. */ { errCart = cart; errDb = db; webPushErrHandlers(); } void webPopErrHandlers(void) /* Pop warn and abort handler for errAbort(). */ { popWarnHandler(); hDumpStackPopAbortHandler(); popAbortHandler(); } void webSetStyle(char *style) /* set a style to add to the header */ { extraStyle = style; } void webPragmasEtc() /* Print out stuff that tells people not to cache us, and that we use the * usual character set and scripting langauge. (Normally done by webStartWrap) */ { printf("<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n" "<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n" "<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n" "<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n" ); } void webCirmPragmasEtc() /* Print out stuff similar to webPragmasEtc (don't cache us, character set, etc.), but * use values appropriate for a more modern website (like CIRM). */ { printf("\t\t<meta charset=\"windows-1252\">\n" // Be nice to be utf-8, but that's a bigger issue to tackle "\t\t<meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\">\n" "\t\t<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">\n" "\t\t<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->\n"); } void webStartText() /* output the head for a text page */ { /*printf("Content-Type: text/plain\n\n");*/ webHeadAlreadyOutputed = TRUE; webInTextMode = TRUE; webPushErrHandlers(); } 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; unfortunately this feature has disappeared // if (dbIsFound) this needs to be resurrected in the new menu // haveBlat = hIsBlatIndexedDatabase(db); bar system in menuBar() 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" ); generateCspMetaHeader(stdout); 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()); } /* Put up the hot links bar. */ char *menuStr = menuBar(theCart, db); if(menuStr) { puts(menuStr); } 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" ); } 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() */ void webStartWrapperDetailedArgs(struct cart *theCart, char *db, char *headerText, char *format, va_list args, boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader, boolean withHtmlHeader) /* output a CGI and HTML header with the given title in printf format */ { char textOutBuf[1024]; va_list argscp; va_copy(argscp,args); vasafef(textOutBuf, sizeof(textOutBuf), format, argscp); va_end(argscp); webStartWrapperDetailedInternal(theCart, db, headerText, textOutBuf, withHttpHeader, withLogo, skipSectionHeader, withHtmlHeader); } void webStartWrapperDetailedNoArgs(struct cart *theCart, char *db, char *headerText, char *format, boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader, boolean withHtmlHeader) /* output a CGI and HTML header with the given title in printf format */ { char textOutBuf[512]; safecpy(textOutBuf, sizeof(textOutBuf), format); webStartWrapperDetailedInternal(theCart, db, headerText, textOutBuf, withHttpHeader, withLogo, skipSectionHeader, withHtmlHeader); } void webStartWrapperGatewayHeader(struct cart *theCart, char *db, char *headerText, char *format, va_list args, boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader) { webStartWrapperDetailedArgs(theCart, db, headerText, format, args, withHttpHeader, withLogo, skipSectionHeader, TRUE); } void webStartWrapperGateway(struct cart *theCart, char *db, char *format, va_list args, boolean withHttpHeader, boolean withLogo, boolean skipSectionHeader) /* output a CGI and HTML header with the given title in printf format */ { webStartWrapperGatewayHeader(theCart, db, "", format, args, withHttpHeader, withLogo, skipSectionHeader); } void webStartWrapper(struct cart *theCart, char *db, char *format, va_list args, boolean withHttpHeader, boolean withLogo) /* allows backward compatibility with old webStartWrapper that doesn't contain the "skipHeader" arg */ /* output a CGI and HTML header with the given title in printf format */ { webStartWrapperGatewayHeader(theCart, db, "", format, args, withHttpHeader, withLogo, FALSE); } void webStartExt(boolean withHttpHeader, struct cart *theCart, char *db, char *format, ...) /* Print out pretty wrapper around things when not * from cart. Do not output an http header.*/ { va_list args; va_start(args, format); webStartWrapper(theCart, db, format, args, withHttpHeader, TRUE); va_end(args); } void webStart(struct cart *theCart, char *db, char *format, ...) /* Print out pretty wrapper around things when not * from cart. */ { va_list args; va_start(args, format); webStartWrapper(theCart, db, format, args, TRUE, FALSE); va_end(args); } void webStartHeader(struct cart *theCart, char *db, char *headerText, char *format, ...) /* Print out pretty wrapper around things when not from cart. * Include headerText in the html header. */ { va_list args; va_start(args, format); webStartWrapperGatewayHeader(theCart, db, headerText, format, args, TRUE, TRUE, FALSE); va_end(args); } void webEndSection() /* Close down a section */ { puts( "" "\n" " </TD><TD WIDTH=15></TD></TR></TABLE>" "\n" // "<BR>" " </TD></TR></TABLE>" "\n" " </TD></TR></TABLE>" "\n" " " ); puts("</div>"); } void webStartSectionTables() /* Put up start of nepharious table layout stuff. (Normally done by webStartWrap). */ { puts( "<A NAME=\"TOP\"></A>" "\n" "<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH=\"100%\">" "\n"); } void webFirstSection(char *title) /* Put up the first section (normally done by webStartWrap). */ { 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 CLASS='hgInside' BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' BORDER='0' CELLSPACING='0' " "CELLPADDING='0'><TR><TD>\n" " <div class='subheadingBar'><div class='windowSize' id='sectTtl'>" ); // FIXME: Need a more general solution here to support styling in blue bar title. // Perhaps support escaped < and > by doubling or backslash htmlTextOut(title); puts(" </div></div>\n" " <TABLE CLASS='hgInside' BGCOLOR='#" HG_COL_INSIDE "' WIDTH='100%' CELLPADDING=0>" "<TR><TH HEIGHT=10></TH></TR>\n" " <TR><TD WIDTH=10> </TD><TD>\n\n" ); } void webNewSectionHeaderStart() /* Start the header for a new section on the web page. * May be used to maintain table layout without a proper section header */ { webEndSection(); puts("<div>"); puts("<!-- +++++++++++++++++++++ START NEW SECTION +++++++++++++++++++ -->"); puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere) "<BR>\n\n" " <!--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"); puts("<div class='subheadingBar windowSize'>"); } void webNewSectionHeaderEnd() /* Properly close header of collapsible section on web page */ { puts(" </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"); } void webNewSection(char* format, ...) /* create a new section on the web page */ { va_list args; va_start(args, format); webNewSectionHeaderStart(); vprintf(format, args); webNewSectionHeaderEnd(); va_end(args); } void webNewEmptySection() /* create a new section on the web page to maintain table layout */ { webNewSectionHeaderStart(); webNewSectionHeaderEnd(); } void webEndSectionTables() /* Finish with section tables (but don't do /BODY /HTML like * webEnd does. */ { webEndSection(); puts("</TD></TR></TABLE>\n"); } void webEnd() /* output the footer of the HTML page */ { if(!webInTextMode) { webEndSectionTables(); #ifndef GBROWSE googleAnalytics(); #endif /* GBROWSE */ jsInlineFinish(); puts( "</BODY></HTML>"); webPopErrHandlers(); } } static void webStartGbOptionalBanner(struct cart *cart, char *db, char *title, boolean doBanner, boolean hgGateway) /* Start HTML with new header and footer design by JWest. Optionally display banner above menubar. Use flag with hgGateway, till that is migrated. */ { puts("Content-type:text/html\n"); char *csp = getCspMetaHeader(); if (hgGateway) { printf( #include "jWestHeader.h" , csp, title , webTimeStampedLinkToResource("HGStyle.css", TRUE) , webTimeStampedLinkToResource("jWest.css", TRUE)); } else { printf( #include "gbHeader.h" , csp, title); } if (doBanner) { printf( #include "jWestBanner.h" , title); } freeMem(csp); webPushErrHandlersCartDb(cart, db); htmlWarnBoxSetup(stdout); // Add hotlinks bar char *navBar = menuBar(cart, db); if (navBar) { puts(navBar); // Override nice-menu.css's menu background and fonts: webIncludeResourceFile("gbAfterMenu.css"); } webHeadAlreadyOutputed = TRUE; errAbortSetDoContentType(FALSE); } void webStartGbNoBanner(struct cart *cart, char *db, char *title) /* Start HTML with new header and footer design by jWest, but no banner */ { webStartGbOptionalBanner(cart, db, title, FALSE, FALSE); } void webEndGb() /* End HTML that was started with webStartJWest. */ { googleAnalytics(); jsInlineFinish(); puts("</body></html>"); webPopErrHandlers(); } void webStartJWest(struct cart *cart, char *db, char *title) /* Start HTML with new banner and footer design by jWest (with modifications). */ { webStartGbOptionalBanner(cart, db, title, TRUE, TRUE); } void webEndJWest() /* End HTML that was started with webStartJWest. */ { webEndGb(); } static boolean gotWarnings = FALSE; void webVaWarn(char *format, va_list args) /* Warning handler that closes out page and stuff in * the fancy form. */ { gotWarnings = TRUE; boolean needStart = !webHeadAlreadyOutputed; if (needStart) { // All callers of this (via webPushErrHandlersCartDb) have skipped Content-type // because they want to output text unless we hit this condition: puts("Content-type:text/html\n"); cartWebStart(errCart, errDb, "Error"); } htmlVaWarn(format, args); printf("\n<!-- HGERROR -->\n\n\n"); } boolean webGotWarnings() /* Return TRUE if webVaWarn has been called. */ { return gotWarnings; } void webAbortExt(boolean withHttpHeader, char* title, char *format, va_list args) /* an abort function that outputs a error page */ { /* output the header */ if(!webHeadAlreadyOutputed) webStartExt(withHttpHeader, errCart, NULL, "%s", title); /* in text mode, have a different error */ if(webInTextMode) printf("\n\n\n %s\n\n", title); vprintf(format, args); printf("<!-- HGERROR -->\n"); printf("\n\n"); webEnd(); exit(0); } void webAbortNoHttpHeader(char* title, char* format, ...) /* an abort function that outputs a error page. No http header output. */ { va_list args; va_start(args, format); webAbortExt(FALSE, title, format, args); va_end(args); } void webAbort(char* title, char* format, ...) /* an abort function that outputs a error page */ { va_list args; va_start(args, format); webAbortExt(TRUE, title, format, args); va_end(args); } void printCladeListHtml(char *genome, char *event, char *javascript) /* Make an HTML select input listing the clades. */ { char **row = NULL; char *clades[128]; char *labels[128]; char *defaultClade = hClade(genome); char *defaultLabel = NULL; int numClades = 0; if (hubConnectIsCurated(trackHubSkipHubName(genome))) defaultClade = hClade(trackHubSkipHubName(genome)); else defaultClade = hClade(genome); struct sqlConnection *conn = hConnectCentral(); // after hClade since it access hgcentral too // get only the clades that have actual active genomes char query[4096]; sqlSafef(query, sizeof query, "SELECT DISTINCT(c.name), c.label " // mysql 5.7: SELECT list w/DISTINCT must include all fields in ORDER BY list (#18626) ", c.priority " "FROM %s c, %s g, %s d WHERE c.name=g.clade AND d.organism=g.genome AND d.active=1 " "ORDER BY c.priority", cladeTable(), genomeCladeTable(), dbDbTable()); struct sqlResult *sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { clades[numClades] = cloneString(row[0]); labels[numClades] = cloneString(row[1]); if (sameWord(defaultClade, clades[numClades])) defaultLabel = clades[numClades]; numClades++; if (numClades >= ArraySize(clades)) internalErr(); } sqlFreeResult(&sr); hDisconnectCentral(&conn); struct slPair *names = trackHubGetCladeLabels(); for(; names; names = names->next) { clades[numClades] = names->name; labels[numClades] = names->val; if (sameWord(defaultClade, clades[numClades])) defaultLabel = clades[numClades]; numClades++; if (numClades >= ArraySize(clades)) internalErr(); } cgiMakeDropListFull(cladeCgiName, labels, clades, numClades, defaultLabel, event, javascript); } static void printSomeGenomeListHtmlNamedMaybeCheck(char *customOrgCgiName, char *db, struct dbDb *dbList, char *event, char *javascript, boolean doCheck) /* Prints to stdout the HTML to render a dropdown list * containing a list of the possible genomes to choose from. * param db - a database whose genome will be the default genome. * If NULL, no default selection. * param onChangeText - Optional (can be NULL) text to pass in * any onChange javascript. */ { char *orgList[1024]; int numGenomes = 0; struct dbDb *cur = NULL; struct hash *hash = hashNew(10); // 2^^10 entries = 1024 char *selGenome = hGenome(db); char *values [1024]; char *cgiName; for (cur = dbList; cur != NULL; cur = cur->next) { if (!hashFindVal(hash, cur->genome) && (!doCheck || hDbExists(cur->name))) { hashAdd(hash, cur->genome, cur); orgList[numGenomes] = trackHubSkipHubName(cur->genome); values[numGenomes] = cur->genome; numGenomes++; if (numGenomes >= ArraySize(orgList)) internalErr(); } } cgiName = (customOrgCgiName != NULL) ? customOrgCgiName : orgCgiName; cgiMakeDropListFull(cgiName, orgList, values, numGenomes, selGenome, event, javascript); hashFree(&hash); } void printSomeGenomeListHtmlNamed(char *customOrgCgiName, char *db, struct dbDb *dbList, char *event, char *javascript) /* Prints to stdout the HTML to render a dropdown list * containing a list of the possible genomes to choose from. * param db - a database whose genome will be the default genome. * If NULL, no default selection. * param event e.g. "change" * javascript - Optional (can be NULL) onEvent javascript. */ { return printSomeGenomeListHtmlNamedMaybeCheck(customOrgCgiName, db, dbList, event, javascript, TRUE); } void printLiftOverGenomeList(char *customOrgCgiName, char *db, struct dbDb *dbList, char *event, char *javascript) /* Prints to stdout the HTML to render a dropdown list * containing a list of the possible genomes to choose from. * Databases in dbList do not have to exist. * param db - a database whose genome will be the default genome. * If NULL, no default selection. * param event e.g. "change" * javascript - Optional (can be NULL) onEvent javascript. */ { return printSomeGenomeListHtmlNamedMaybeCheck(customOrgCgiName, db, dbList, event, javascript, FALSE); } void printSomeGenomeListHtml(char *db, struct dbDb *dbList, char *event, char *javascript) /* Prints the dropdown list using the orgCgiName */ { printSomeGenomeListHtmlNamed(NULL, db, dbList, event, javascript); } void printGenomeListHtml(char *db, char *event, char *javascript) /* Prints to stdout the HTML to render a dropdown list * containing a list of the possible genomes to choose from. * param db - a database whose genome will be the default genome. * If NULL, no default selection. * param event e.g. "change" * javascript - Optional (can be NULL) onEvent javascript. */ { printSomeGenomeListHtml(db, hGetIndexedDatabases(), event, javascript); } void printBlatGenomeListHtml(char *db, char *event, char *javascript) /* Prints to stdout the HTML to render a dropdown list * containing a list of the possible genomes to choose from. * param db - a database whose genome will be the default genome. * If NULL, no default selection. * param event e.g. "change" * javascript - Optional (can be NULL) onEvent javascript. */ { printSomeGenomeListHtml(db, hGetBlatIndexedDatabases(), event, javascript); } void printGenomeListForCladeHtml(char *db, char *event, char *javascript) /* Prints to stdout the HTML to render a dropdown list containing * a list of the possible genomes from selOrganism's clade to choose from. * selOrganism is the default for the select. */ { printSomeGenomeListHtml(db, hGetIndexedDatabasesForClade(db), event, javascript); } void printAllAssemblyListHtmlParm(char *db, struct dbDb *dbList, char *dbCgi, bool allowInactive, char *event, char *javascript) /* Prints to stdout the HTML to render a dropdown list containing the list * of assemblies for the current genome to choose from. By default, * this includes only active assemblies with a database (with the * exception of the default assembly, which will be included even * if it isn't active). * param db - The default assembly (the database name) to choose as selected. * If NULL, no default selection. * param allowInactive - if set, print all assemblies for this genome, * even if they're inactive or have no database */ { char *assemblyList[128]; char *values[128]; int numAssemblies = 0; struct dbDb *cur = NULL; char *genome = hGenome(db); char *selAssembly = NULL; if (genome == NULL) #ifdef LOWELAB genome = "Pyrococcus furiosus"; #else genome = "Human"; #endif for (cur = dbList; cur != NULL; cur = cur->next) { /* Only for this genome */ if (!sameWord(genome, cur->genome)) continue; /* Save a pointer to the current assembly */ if (sameWord(db, cur->name)) selAssembly = cur->name; if (allowInactive || ((cur->active || sameWord(cur->name, db)) && (trackHubDatabase(db) || sqlDatabaseExists(cur->name)))) { assemblyList[numAssemblies] = cur->description; values[numAssemblies] = cur->name; numAssemblies++; if (numAssemblies >= ArraySize(assemblyList)) internalErr(); } } cgiMakeDropListFull(dbCgi, assemblyList, values, numAssemblies, selAssembly, event, javascript); } void printSomeAssemblyListHtmlParm(char *db, struct dbDb *dbList, char *dbCgi, char *event, char *javascript) /* Find all the assemblies from the list that are active. * Prints to stdout the HTML to render a dropdown list containing the list * of the possible assemblies to choose from. * param db - The default assembly (the database name) to choose as selected. * If NULL, no default selection. */ { printAllAssemblyListHtmlParm(db, dbList, dbCgi, TRUE, event, javascript); } void printSomeAssemblyListHtml(char *db, struct dbDb *dbList, char *event, char *javascript) /* Find all assemblies from the list that are active, and print * HTML to render dropdown list * param db - default assembly. If NULL, no default selection */ { printSomeAssemblyListHtmlParm(db, dbList, dbCgiName, event, javascript); } void printAssemblyListHtml(char *db, char *event, char *javascript) /* Find all the assemblies that pertain to the selected genome * Prints to stdout the HTML to render a dropdown list containing * a list of the possible assemblies to choose from. * Param db - The assembly (the database name) to choose as selected. * If NULL, no default selection. */ { struct dbDb *dbList = hGetIndexedDatabases(); printSomeAssemblyListHtml(db, dbList, event, javascript); } void printAssemblyListHtmlExtra(char *db, char *event, char *javascript) { /* Find all the assemblies that pertain to the selected genome Prints to stdout the HTML to render a dropdown list containing a list of the possible assemblies to choose from. param curDb - The assembly (the database name) to choose as selected. If NULL, no default selection. */ struct dbDb *dbList = hGetIndexedDatabases(); printSomeAssemblyListHtmlParm(db, dbList, dbCgiName, event, javascript); } void printBlatAssemblyListHtml(char *db) { /* Find all the assemblies that pertain to the selected genome Prints to stdout the HTML to render a dropdown list containing a list of the possible assemblies to choose from. param curDb - The assembly (the database name) to choose as selected. If NULL, no default selection. */ struct dbDb *dbList = hGetBlatIndexedDatabases(); printSomeAssemblyListHtml(db, dbList, NULL, NULL); } static char *getDbForGenome(char *genome, struct cart *cart) /* Function to find the default database for the given Genome. It looks in the cart first and then, if that database's Genome matches the passed-in Genome, returns it. If the Genome does not match, it returns the default database that does match that Genome. param Genome - The Genome for which to find a database param cart - The cart to use to first search for a suitable database name return - The database matching this Genome type */ { char *retDb = cartUsualString(cart, dbCgiName, NULL); if ((retDb == NULL) || !hDbExists(retDb)) { retDb = hDefaultDb(); } /* If genomes don't match, then get the default db for that genome */ if (differentWord(genome, hGenome(retDb))) { retDb = hDefaultDbForGenome(genome); } return retDb; } void getDbGenomeClade(struct cart *cart, char **retDb, char **retGenome, char **retClade, struct hash *oldVars) /* Examine CGI and cart variables to determine which db, genome, or clade * has been selected, and then adjust as necessary so that all three are * consistent. Detect changes and reset db-specific cart variables. * Save db, genome and clade in the cart so it will be consistent hereafter. * The order of preference here is as follows: * If we got a request that explicitly names the db, that takes * highest priority, and we synch the organism to that db. * If we get a cgi request for a specific organism then we use that * organism to choose the DB. If just clade, go from there. * In the cart only, we use the same order of preference. * If someone requests an Genome we try to give them the same db as * was in their cart, unless the Genome doesn't match. */ { boolean gotClade = hGotClade(); -*retDb = (dbOveride != NULL) ? dbOveride : cgiOptionalString(dbCgiName); +*retDb = cgiOptionalString(dbCgiName); if (*retDb == NULL) // if db is not in URL, but genome is, use it for db *retDb = cgiOptionalString(hgHubGenome); *retGenome = cgiOptionalString(orgCgiName); *retClade = cgiOptionalString(cladeCgiName); /* Was the database passed in as a cgi param? * If so, it takes precedence and determines the genome. */ *retDb = asmAliasFind(*retDb); if (*retDb && hDbExists(*retDb)) { *retGenome = hGenome(*retDb); } /* If no db was passed in as a cgi param then was the organism (a.k.a. genome) * passed in as a cgi param? * If so, the we use the proper database for that genome. */ else if (*retGenome && !sameWord(*retGenome, "0")) { *retDb = getDbForGenome(*retGenome, cart); *retGenome = hGenome(*retDb); } else if (*retClade && gotClade) { *retGenome = hDefaultGenomeForClade(*retClade); *retDb = getDbForGenome(*retGenome, cart); } /* If no cgi params passed in then we need to inspect the session */ else { *retDb = cartOptionalString(cart, dbCgiName); *retDb = asmAliasFind(*retDb); *retGenome = cartOptionalString(cart, orgCgiName); *retClade = cartOptionalString(cart, cladeCgiName); /* If there was a db found in the session that determines everything. */ if (*retDb && hDbExists(*retDb)) { *retGenome = hGenome(*retDb); } else if (*retGenome && !sameWord(*retGenome, "0")) { *retDb = hDefaultDbForGenome(*retGenome); } else if (*retClade && gotClade) { *retGenome = hDefaultGenomeForClade(*retClade); *retDb = getDbForGenome(*retGenome, cart); } /* If no organism in the session then get the default db and organism. */ else { *retDb = hDefaultDb(); *retGenome = hGenome(*retDb); } } *retDb = cloneString(*retDb); *retGenome = cloneString(*retGenome); *retClade = hClade(*retGenome); if ( (*retClade != NULL) && sameString(*retClade, "none")) cartRemove(cart, "position"); /* Detect change of database and reset db-specific cart variables: */ if (oldVars) { char *oldDb = hashFindVal(oldVars, "db"); char *oldOrg = hashFindVal(oldVars, "org"); char *oldClade = hashFindVal(oldVars, "clade"); if ((!IS_CART_VAR_EMPTY(oldDb) && differentWord(oldDb, *retDb)) || (!IS_CART_VAR_EMPTY(oldOrg) && differentWord(oldOrg, *retGenome)) || (!IS_CART_VAR_EMPTY(oldClade) && differentWord(oldClade, *retClade))) { /* Change position to default -- unless it was passed in via CGI: */ if (cgiOptionalString("position") == NULL) cartSetString(cart, "position", hDefaultPos(*retDb)); // remove virtual chrom cart vars related to position cartRemove(cart, "virtMode"); cartRemove(cart, "virtModeType"); cartRemove(cart, "lastVirtModeExtraState"); cartRemove(cart, "lastVirtModeType"); cartRemove(cart, "nonVirtPosition"); cartRemove(cart, "oldPosition"); /* hgNear search term -- unless it was passed in via CGI: */ if (cgiOptionalString("near_search") == NULL) cartRemove(cart, "near_search"); /* hgBlat results (hgUserPsl track): */ cartRemove(cart, "ss"); /* hgTables correlate: */ cartRemove(cart, "hgta_correlateTrack"); cartRemove(cart, "hgta_correlateTable"); cartRemove(cart, "hgta_correlateGroup"); cartRemove(cart, "hgta_correlateOp"); cartRemove(cart, "hgta_nextCorrelateTrack"); cartRemove(cart, "hgta_nextCorrelateTable"); cartRemove(cart, "hgta_nextCorrelateGroup"); cartRemove(cart, "hgta_nextCorrelateOp"); cartRemove(cart, "hgta_corrWinSize"); cartRemove(cart, "hgta_corrMaxLimitCount"); } } /* Save db, genome (as org) and clade in cart. */ cartSetString(cart, "db", *retDb); cartSetString(cart, "org", *retGenome); if (gotClade) cartSetString(cart, "clade", *retClade); } void getDbAndGenome(struct cart *cart, char **retDb, char **retGenome, struct hash *oldVars) /* Get just the db and genome. */ { char *garbage = NULL; getDbGenomeClade(cart, retDb, retGenome, &garbage, oldVars); freeMem(garbage); } static void webIncludeFileSubst(char *file, struct cart *cart) /* Include an HTML file in a CGI. If cart is non-null, invoke hVarSubstWithCart. * The file path may begin with hDocumentRoot(); if it doesn't, it is * assumed to be relative and hDocumentRoot() will be prepended. */ { char *str = hFileContentsOrWarning(file); if (cart != NULL) { char *db = cartString(cart, "db"); hVarSubstWithCart("webIncludeFileSubst", cart, NULL, db, &str); } puts(str); freeMem(str); } void webIncludeFile(char *file) /* Include an HTML file in a CGI. * The file path may begin with hDocumentRoot(); if it doesn't, it is * assumed to be relative and hDocumentRoot() will be prepended. */ { return webIncludeFileSubst(file, NULL); } void webIncludeHelpFileSubst(char *fileRoot, struct cart *cart, boolean addHorizLine) /* Given a help file root name (e.g. "hgPcrResult" or "cutters"), * print out the contents of the file. If cart is non-NULL, invoke hVarSubstWithCart * before printing. If addHorizLine, print out an <HR> first. */ { if (addHorizLine) htmlHorizontalLine(); char *file = hHelpFile(fileRoot); webIncludeFileSubst(file, cart); } void webIncludeHelpFile(char *fileRoot, boolean addHorizLine) /* Given a help file root name (e.g. "hgPcrResult" or "cutters"), * print out the contents of the file. If addHorizLine, print out an * <HR> first. */ { return webIncludeHelpFileSubst(fileRoot, NULL, addHorizLine); } void webPrintLinkTableStart() /* Print link table start in our colors. */ { printf("<TABLE><TR><TD BGCOLOR='#" HG_COL_BORDER "'>\n"); printf("<TABLE CELLSPACING=1 CELLPADDING=3><TR>\n"); } void webPrintLinkTableEnd() /* Print link table end in our colors. */ { printf("</TR></TABLE>\n"); printf("</TD></TR></TABLE>\n"); } void webPrintLinkOutCellStart() /* Print link cell that goes out of our site. End with * webPrintLinkTableEnd. */ { printf("<TD BGCOLOR='#" HG_COL_LOCAL_TABLE "'>"); } void webPrintWideCellStart(int colSpan, char *bgColorRgb) /* Print link multi-column cell start in our colors. */ { printf("<TD BGCOLOR='#%s'", bgColorRgb); if (colSpan > 1) printf(" COLSPAN=%d", colSpan); printf(">"); } void webPrintLinkCellStart() /* Print link cell start in our colors. */ { webPrintWideCellStart(1, HG_COL_TABLE); } void webPrintLinkCellRightStart() /* Print right-justified cell start in our colors. */ { printf("<TD BGCOLOR='#"HG_COL_TABLE"' ALIGN='right'>"); } void webPrintLinkCellEnd() /* Print link cell end in our colors. */ { printf("</TD>"); } void webPrintLinkCell(char *link) /* Print link cell in our colors, if links is null, print empty cell */ { webPrintLinkCellStart(); if (link != NULL) puts(link); webPrintLinkCellEnd(); } void webPrintIntCell(int val) /* Print right-justified int cell in our colors. */ { webPrintLinkCellRightStart(); printf("%d", val); webPrintLinkCellEnd(); } void webPrintDoubleCell(double val) /* Print right-justified cell in our colors with two digits to right of decimal. */ { webPrintLinkCellRightStart(); printf("%4.2f", val); webPrintLinkCellEnd(); } void webPrintWideLabelCellStart(int colSpan) /* Print start of wrapper around a label in a table. */ { printf("<TD BGCOLOR='#"HG_COL_TABLE_LABEL"'"); if (colSpan > 1) printf(" COLSPAN=%d", colSpan); printf("><span style='color:#FFFFFF;'><B>"); } void webPrintLabelCellStart() /* Print start of wrapper around a label in a table. */ { webPrintWideLabelCellStart(1); } void webPrintLabelCellEnd() /* Print end of wrapper around a label in a table. */ { printf("</B></span></TD>"); } void webPrintWideLabelCell(char *label, int colSpan) /* Print label cell over multiple columns in our colors. */ { webPrintWideLabelCellStart(colSpan); printf("%s", label); webPrintLabelCellEnd(); } void webPrintWideCenteredLabelCell(char *label, int colSpan) /* Print label cell over multiple columns in our colors and centered. */ { printf("<TD BGCOLOR='#" HG_COL_TABLE_LABEL "'"); if (colSpan > 1) printf(" COLSPAN=%d", colSpan); printf("><CENTER><span style='color:#FFFFFF;'><B>%s</B></span></CENTER></TD>", label); } void webPrintLabelCell(char *label) /* Print label cell in our colors. */ { webPrintWideLabelCell(label, 1); } void webPrintLinkTableNewRow() /* start a new row */ { printf("</TR>\n<TR>"); } void finishPartialTable(int rowIx, int itemPos, int maxPerRow, void (*cellStart)()) /* Fill out partially empty last row. */ { if (rowIx != 0 && itemPos < maxPerRow) { int i; for (i=itemPos; i<maxPerRow; ++i) { cellStart(); webPrintLinkCellEnd(); } } } void webFinishPartialLinkOutTable(int rowIx, int itemPos, int maxPerRow) /* Fill out partially empty last row. */ { finishPartialTable(rowIx, itemPos, maxPerRow, webPrintLinkOutCellStart); } void webFinishPartialLinkTable(int rowIx, int itemPos, int maxPerRow) /* Fill out partially empty last row. */ { finishPartialTable(rowIx, itemPos, maxPerRow, webPrintLinkCellStart); } 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); char *httpHost = hHttpHost(); // 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. (host: %s)\n", dyStringContents(fullDirName), httpHost); // 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; linkWithTimestamp = dyStringCreate("%s/%s%s?v=%ld", dyStringContents(fullDirName), baseName, extension, mtime); // Free up all that extra memory dyStringFree(&realFileName); dyStringFree(&fullDirName); char *linkFull = dyStringCannibalize(&linkWithTimestamp); char *link = linkFull; if (docRoot != NULL) { struct dyString *relativeLink = dyStringCreate("../%s", linkFull + strlen(docRoot) + 1); link = dyStringCannibalize(&relativeLink); 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 *webTimeStampedLinkToResourceOnFirstCall(char *fileName, boolean wrapInHtml) // If this is the first call, will return full path of timestamped link to the requested // resource file (js, or css). Free after use. // else returns NULL. Useful to ensure multiple references to the same resource file are not made // NOTE: png, jpg and gif should also be supported but are untested. { if (!includedResourceFiles) includedResourceFiles = newHash(0); if (hashLookup(includedResourceFiles, fileName)) return NULL; char * link = webTimeStampedLinkToResource(fileName,wrapInHtml); if (link) hashAdd(includedResourceFiles, fileName, NULL); // Don't hash link, because return link; // memory will be freed by caller!!! } boolean webIncludeResourcePrintToFile(FILE * toFile, char *fileName) // Converts fileName to web Resource link and prints the html reference // This only prints and returns TRUE on first call for this resource. // Passing in NULL as the file pointer results in hPrintf call // The reference will be to a link with timestamp. { char *link = webTimeStampedLinkToResourceOnFirstCall(fileName,TRUE); if (link) { if (toFile == NULL) hPrintf("%s",link); else fprintf(toFile,"%s",link); freeMem(link); return TRUE; } return FALSE; } // overrides for default context specific help link. char *contextSpecificHelpLink = NULL; char *contextSpecificHelpLabel = NULL; void setContextSpecificHelp(char *link, char *label) // Override default behavior for the context specific help link { if(link) contextSpecificHelpLink = cloneString(link); if(label) contextSpecificHelpLabel = cloneString(label); } char *menuBarAddUiVars(char *oldString, char *cgiPrefix, char *uiVars) /* Look for CGI program calls in oldString, and add session vars hgsid to them */ { int len = strlen(oldString); char buf[4096]; /* Create a regular expression and compile it */ regex_t re; regmatch_t match[2]; safef(buf, sizeof(buf), "%s[A-Za-z]+(%c%c?)", cgiPrefix, '\\', '?'); int err = regcomp(&re, buf, REG_EXTENDED); if(err) errAbort("regcomp failed; err: %d", err); /* Search through oldString with regex, and build up new string in dy */ struct dyString *dy = dyStringNew(0); int offset; for(offset = 0; offset < len && !regexec(&re, oldString + offset, ArraySize(match), match, 0); offset += match[0].rm_eo) { dyStringAppendN(dy, oldString + 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, oldString + offset); return dyStringCannibalize(&dy); } 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); jsIncludeFile("utils.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, "hgGtexTrackSettings") || endsWith(scriptName, "hgGene"))) { struct trackDb *tdb = hTrackDbForTrack(db, track); if (tdb) { struct trackDb *topLevel = trackDbTopLevelSelfOrParent(tdb); char *undupedTrack = dupTrackSkipToSourceName(topLevel->track); safef(hgTablesOptions, sizeof hgTablesOptions, "../cgi-bin/hgTables?hgta_doMainPage=1&hgta_group=%s&hgta_track=%s&hgta_table=%s&", topLevel->grp, undupedTrack, 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("%s",""); 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, "hgIntegrator")) { link = "../goldenPath/help/hgIntegratorHelp.html"; label = "Help on Data Integrator"; } 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); } // links to hgTracks need to use the web browser width and set the hgTracks image // size in pixels correctly to match the hgGateway "GO" button jsInline("$(\"#tools1 ul li a\").each( function (a) {\n" " if (this.href && this.href.indexOf(\"hgTracks\") !== -1) {\n" " var obj = this;\n" " obj.onclick = function(e) {\n" " var pix = calculateHgTracksWidth();\n" " e.currentTarget.href += \"&pix=\" + pix;\n" " }\n" " }\n" "});\n"); return menuStr; } void checkForGeoMirrorRedirect(struct cart *cart) // Implement Geo/IP based redirection. { char *thisNodeStr = geoMirrorNode(); if (thisNodeStr) // if geo-mirroring is enabled { char *redirectCookie = findCookieData("redirect"); char *redirect = cgiOptionalString("redirect"); // if we're not already redirected if (redirect == NULL && redirectCookie == NULL) { int thisNode = sqlUnsigned(thisNodeStr); struct sqlConnection *centralConn = hConnectCentral(); char *ipStr = cgiRemoteAddr(); int node = geoMirrorDefaultNode(centralConn, ipStr); // if our node is not the node that's closest. if (thisNode != node) { char *geoSuffix = cfgOptionDefault("browser.geoSuffix",""); char query[1056]; sqlSafef(query, sizeof query, "select domain from gbNode%s where node = %d", geoSuffix, node); char *newDomain = sqlQuickString(centralConn, query); char *oldDomain = cgiServerName(); char *port = cgiServerPort(); char *uri = cgiRequestUri(); char *sep = strchr(uri, '?') ? "&" : "?"; int newUriSize = strlen(uri) + 1024; char *newUri = needMem(newUriSize); char *oldUri = needMem(newUriSize); safef(oldUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s", cgiServerHttpsIsOn() ? "s" : "", oldDomain, port, uri, sep, oldDomain); safef(newUri, newUriSize, "http%s://%s:%s%s%sredirect=manual&source=%s", cgiServerHttpsIsOn() ? "s" : "", newDomain, port, uri, sep, oldDomain); printf("<TR><TD COLSPAN=3 id='redirectTd'>" "<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 might want to navigate to your nearest mirror - %s" "</h3> " "<ul style=\"margin:5px;\">", newDomain); jsOnEventById("click","redirectTd", "document.getElementById('redirectTd').innerHTML='';"); printf("<li>User settings (sessions and custom tracks) <B>will differ</B> between sites." "<idiv style=\"float:right;\"><a href=\"../goldenPath/help/genomeEuro.html#sessions\">Read more.</a></idiv>"); printf("<li>Take me to <a href=\"%s\">%s</a> </li>", newUri, newDomain); printf("<li>Let me stay here <a href=\"%s\">%s</a>", oldUri, oldDomain ); printf("</div></TD></TR>\n"); jsInlineFinish(); cartCheckout(&cart); exit(0); } hDisconnectCentral(¢ralConn); } } }