44a572559459e6a2b88776be91859b98565b5a70 galt Thu Oct 4 17:40:42 2012 -0700 hopefully this is a bit more efficient diff --git src/hg/lib/web.c src/hg/lib/web.c index 75c5ca5..95cb434 100644 --- src/hg/lib/web.c +++ src/hg/lib/web.c @@ -1,1453 +1,1459 @@ #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 "hPrint.h" #include "hdb.h" #include "hui.h" #include "hgConfig.h" #include "cheapcgi.h" #include "dbDb.h" #include "hgColors.h" #include "hubConnect.h" #include "search.h" #ifndef GBROWSE #include "axtInfo.h" #include "wikiLink.h" #include "googleAnalytics.h" #include "jsHelper.h" #endif /* GBROWSE */ #include "errabort.h" // FIXME tmp hack to try to find source of popWarnHandler underflows in browse /* phoneHome business */ #include <utime.h> #include <htmlPage.h> #include <signal.h> #include "geoMirror.h" #include <regex.h> /* phoneHome business */ /* flag that tell if the CGI header has already been outputed */ boolean webHeadAlreadyOutputed = FALSE; /* flag that tell if text CGI header hsa been outputed */ boolean webInTextMode = FALSE; static char *dbCgiName = "db"; static char *orgCgiName = "org"; static char *cladeCgiName = "clade"; static char *extraStyle = NULL; /* global: a cart for use in error handlers. */ static struct cart *errCart = NULL; void textVaWarn(char *format, va_list args) { vprintf(format, args); puts("\n"); } void softAbort() { exit(0); } void webPushErrHandlers(void) /* Push warn and abort handler for errAbort(). */ { if (webInTextMode) pushWarnHandler(textVaWarn); else pushWarnHandler(webVaWarn); pushAbortHandler(softAbort); hDumpStackPushAbortHandler(); } void webPushErrHandlersCart(struct cart *cart) /* Push warn and abort handler for errAbort(); save cart for use in handlers. */ { errCart = cart; 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 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=%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 "); if (endsWith(scriptName, "qaPushQ")) // Tired of failed stylesheet versioning that messes up RR releaseLog.html (regular and ENCODE) printf(" <LINK rel='STYLESHEET' href='../style/HGStyle.css' TYPE='text/css' />\n"); else 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) { jsIncludeFile("jquery.js", NULL); 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); // TODO what about https? safef(newUri, newUriSize, "http://%s:%s/cgi-bin/hgGateway?redirect=manual&source=%s", source, port, domain); //empty TD disappears /* printf("<TR><TD COLSPAN=3 id='redirectTd' onclick=\"javascript:document.getElementById('redirectTd').innerHTML='';\">" "<center>" "You've been redirected to your nearest mirror - %s<br>" "<a href=\"%s\">Take me back to %s</a>" "</center>" "</TD></TR>\n" , domain, newUri, source ); "<h3 style=\"background-color: #2636d1; text-align: center; color:#E0F0F0; margin-top:0px;\">" */ 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;\">" "<img style=\"float:left; margin-top:4px; margin-left:3px; margin-right:4px;\" src=\"http://uswest.ensembl.org/i/info_blue_13.png\">" "You've been redirected to your nearest mirror - %s" "<img title=\"Hide hint panel\" alt=\"Hide hint panel\" style=\"float:right; margin-top:3px; margin-right:3px\" src=\"http://uswest.ensembl.org/i/close.gif\">" "</h3> " "<ul style=\"margin:5px;\">" "<li>Take me back to <a href=\"%s\">%s</a>" "</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 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 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, TRUE); 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); } static 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 webNewSection(char* format, ...) /* create a new section on the web page */ { va_list args; va_start(args, format); 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" " <div class='subheadingBar' class='windowSize'>"); vprintf(format, args); 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"); va_end(args); } 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 */ puts( "</BODY></HTML>"); webPopErrHandlers(); } } 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) webStart(errCart, NULL, "Error"); htmlVaWarn(format, args); printf("\n<!-- HGERROR -->\n"); printf("\n\n"); if (needStart) webEnd(); } boolean webGotWarnings() /* Return TRUE if webVaWarn has been called. */ { return gotWarnings; } void webAbort(char* title, char* format, ...) /* an abort function that outputs a error page */ { va_list args; va_start(args, format); /* output the header */ if(!webHeadAlreadyOutputed) webStart(errCart, NULL, 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(); va_end(args); exit(0); } void printCladeListHtml(char *genome, char *onChangeText) /* 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; struct sqlConnection *conn = hConnectCentral(); // after hClade since it access hgcentral too // get only the clades that have actual active genomes struct sqlResult *sr = sqlGetResult(conn, "SELECT DISTINCT(c.name), c.label FROM clade c, genomeClade g, dbDb d WHERE c.name=g.clade AND d.organism=g.genome AND d.active=1 ORDER BY c.priority"); 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); cgiMakeDropListFull(cladeCgiName, labels, clades, numClades, defaultLabel, onChangeText); } static void printSomeGenomeListHtmlNamedMaybeCheck(char *customOrgCgiName, char *db, struct dbDb *dbList, char *onChangeText, 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 = hGenomeOrArchive(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] = cur->genome; values[numGenomes] = cur->genome; numGenomes++; if (numGenomes >= ArraySize(orgList)) internalErr(); } } cgiName = (customOrgCgiName != NULL) ? customOrgCgiName : orgCgiName; cgiMakeDropListFull(cgiName, orgList, values, numGenomes, selGenome, onChangeText); hashFree(&hash); } void printSomeGenomeListHtmlNamed(char *customOrgCgiName, char *db, struct dbDb *dbList, char *onChangeText) /* 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. */ { return printSomeGenomeListHtmlNamedMaybeCheck(customOrgCgiName, db, dbList, onChangeText, TRUE); } void printLiftOverGenomeList(char *customOrgCgiName, char *db, struct dbDb *dbList, char *onChangeText) /* 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 onChangeText - Optional (can be NULL) text to pass in * any onChange javascript. */ { return printSomeGenomeListHtmlNamedMaybeCheck(customOrgCgiName, db, dbList, onChangeText, FALSE); } void printSomeGenomeListHtml(char *db, struct dbDb *dbList, char *onChangeText) /* Prints the dropdown list using the orgCgiName */ { printSomeGenomeListHtmlNamed(NULL, db, dbList, onChangeText); } void printGenomeListHtml(char *db, char *onChangeText) /* 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. */ { printSomeGenomeListHtml(db, hGetIndexedDatabases(), onChangeText); } void printBlatGenomeListHtml(char *db, char *onChangeText) /* 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. */ { printSomeGenomeListHtml(db, hGetBlatIndexedDatabases(), onChangeText); } void printGenomeListForCladeHtml(char *db, char *onChangeText) /* 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), onChangeText); } void printAllAssemblyListHtmlParm(char *db, struct dbDb *dbList, char *dbCgi, bool allowInactive, 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 = hGenomeOrArchive(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)) && sqlDatabaseExists(cur->name))) { assemblyList[numAssemblies] = cur->description; values[numAssemblies] = cur->name; numAssemblies++; if (numAssemblies >= ArraySize(assemblyList)) internalErr(); } } cgiMakeDropListFull(dbCgi, assemblyList, values, numAssemblies, selAssembly, javascript); } void printSomeAssemblyListHtmlParm(char *db, struct dbDb *dbList, char *dbCgi, 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, javascript); } void printSomeAssemblyListHtml(char *db, struct dbDb *dbList, 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, javascript); } void printAssemblyListHtml(char *db, 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, javascript); } void printAssemblyListHtmlExtra(char *db, 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, 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); } void printOrgAssemblyListAxtInfo(char *dbCgi, char *javascript) /* Find all the organisms/assemblies that are referenced in axtInfo, * and print the dropdown list. */ { struct dbDb *dbList = hGetAxtInfoDbs(dbCgi); char *assemblyList[128]; char *values[128]; int numAssemblies = 0; struct dbDb *cur = NULL; char *assembly = cgiOptionalString(dbCgi); char orgAssembly[256]; for (cur = dbList; ((cur != NULL) && (numAssemblies < 128)); cur = cur->next) { safef(orgAssembly, sizeof(orgAssembly), "%s %s", cur->organism, cur->description); assemblyList[numAssemblies] = cloneString(orgAssembly); values[numAssemblies] = cur->name; numAssemblies++; } #ifdef OLD // Have to use the "menu" name, not the value, to mark selected: if (assembly != NULL) { char *selOrg = hOrganism(assembly); char *selFreeze = hFreezeFromDb(assembly); safef(orgAssembly, sizeof(orgAssembly), "%s %s", selOrg, selFreeze); assembly = cloneString(orgAssembly); } #endif /* OLD */ cgiMakeDropListFull(dbCgi, assemblyList, values, numAssemblies, assembly, javascript); } 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; } static unsigned long expireSeconds = 0; static boolean lazarus = FALSE; void lazarusLives(unsigned long newExpireSeconds) /* Long running process requests more time */ { lazarus = TRUE; expireSeconds = newExpireSeconds; } /* phoneHome business */ static void cgiApoptosis(int status) /* signal handler for SIGALRM for phoneHome function and CGI expiration */ { if (lazarus) { (void) alarm(expireSeconds); /* CGI timeout */ lazarus = FALSE; return; } if (expireSeconds > 0) { /* want to see this error message in the apache error_log also */ fprintf(stderr, "cgiApoptosis: %lu seconds\n", expireSeconds); /* most of our CGIs post a polite non-fatal message with this errAbort */ errAbort("procedures have exceeded timeout: %lu seconds, function has ended.\n", expireSeconds); } exit(0); } 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() */ /* phoneHome business */ 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 = cgiOptionalString(dbCgiName); *retGenome = cgiOptionalString(orgCgiName); *retClade = cgiOptionalString(cladeCgiName); /* phoneHome business */ phoneHome(); /* Was the database passed in as a cgi param? * If so, it takes precedence and determines the genome. */ 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); *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); /* 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)); /* 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); } 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. */ { char *str = hFileContentsOrWarning(file); puts(str); freeMem(str); } 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. */ { if (addHorizLine) htmlHorizontalLine(); webIncludeFile(hHelpFile(fileRoot)); } void webPrintLinkTableStart() /* Print link table start in our colors. */ { printf("<TABLE><TR><TD BGCOLOR='#888888'>\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 webPrintWideLabelCell(char *label, int colSpan) /* Print label cell over multiple columns in our colors. */ { printf("<TD BGCOLOR='#"HG_COL_TABLE_LABEL"'"); if (colSpan > 1) printf(" COLSPAN=%d", colSpan); printf("><span style='color:#FFFFFF;'><B>%s</B></spanT></TD>", label); } 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); // 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; if(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 *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. { static struct hash *includedResourceFiles = NULL; 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 *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(); safef(uiVars, sizeof(uiVars), "%s=%u", cartSessionVarName(), cartSessionId(cart)); 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); // 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 view menu for some CGIs. - struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n"); + struct dyString *viewItems = dyStringCreate(""); boolean hasViewMenu = TRUE; if (endsWith(scriptName, "hgGenome")) { safef(buf, sizeof(buf), "../cgi-bin/hgGenome?%s&hgGenome_doPsOutput=1", uiVars); - dyStringPrintf(viewMenu, "<li><a href='%s' id='%s'>%s</a></li>\n", buf, "pdfLink", "PDF/PS"); + dyStringPrintf(viewItems, "<li><a href='%s' id='%s'>%s</a></li>\n", buf, "pdfLink", "PDF/PS"); } else { hasViewMenu = FALSE; } - dyStringAppend(viewMenu, "</ul>\n</li>\n"); if (hasViewMenu) - menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", dyStringCannibalize(&viewMenu)); + { + 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; }