8140039c43fa2879af5555345000c5cad6a73ddb braney Fri Oct 22 09:01:18 2010 -0700 add ability to put styleDir and styleImagesDir in hg.conf diff --git src/hg/lib/web.c src/hg/lib/web.c index 0f73f91..43e2e22 100644 --- src/hg/lib/web.c +++ src/hg/lib/web.c @@ -1,1377 +1,1377 @@ #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 "searchTracks.h" #ifndef GBROWSE #include "axtInfo.h" #include "wikiLink.h" #include "googleAnalytics.h" #endif /* GBROWSE */ #include "errabort.h" // FIXME tmp hack to try to find source of popWarnHandler underflows in browse static char const rcsid[] = "$Id: web.c,v 1.173 2010/05/20 03:14:17 kent Exp $"; /* 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); hDumpStackPushAbortHandler(); pushAbortHandler(softAbort); } 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; boolean isGsid = hIsGsidServer(); boolean isGisaid = hIsGisaidServer(); if (db == NULL) db = hDefaultDb(); boolean dbIsFound = hDbExists(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; puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 3.2//EN\">"); puts( "<HTML>" "\n" "<HEAD>" "\n" ); printf("\t%s\n", headerText); printf("\t<META HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html;CHARSET=iso-8859-1\">" "\n" "\t<META http-equiv=\"Content-Script-Type\" content=\"text/javascript\">" "\n" "\t<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">" "\n" "\t<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">" "\n" "\t<TITLE>" ); /* we need to take any HTML formatting out of the titlebar string */ newString = cloneString(textOutBuf); for(ptr1=newString, ptr2=textOutBuf; *ptr2 ; ptr2++) { if (*ptr2 == '<') { for(; *ptr2 && (*ptr2 != '>'); ptr2++) ; } else *ptr1++ = *ptr2; } *ptr1 = 0; htmlTextOut(newString); printf(" </TITLE>\n "); webIncludeResourceFile("HGStyle.css"); if (extraStyle != NULL) puts(extraStyle); printf("</HEAD>" "\n" "<BODY BGCOLOR=\"#%s\" LINK=\"#0000CC\" VLINK=\"#330066\" ALINK=\"#6600FF\">", hgColOutside()); 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" ); } 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; } /* Put up the hot links bar. */ if (isGisaid) { printf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#000000\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>\n"); printf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#2636D1\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"2\"><TR>\n"); /* Home */ printf("<TD ALIGN=CENTER><A HREF=\"../index.html\" class=\"topbar\"><FONT COLOR=\"#FFFFFF\">Home</FONT></A></TD>"); /* Blat */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgBlat?command=start\" class=\"topbar\"><FONT COLOR=\"#FFFFFF\">Blat</FONT></A></TD>"); /* Subject View */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gisaidSample\" class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Sample View</FONT>"); /* Sequence View */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgTracks%s\" class=\"topbar\"><FONT COLOR=\"#FFFFFF\">Sequence View</FONT></A></TD>", uiState); /* Table View */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gisaidTable\" class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Table View</FONT>"); /* Help */ /* disable help for the time being */ /* if (endsWith(scriptName, "hgBlat")) { printf("<TD ALIGN=CENTER><A HREF=\"/goldenPath/help/gsidTutorial.html#BLAT\" TARGET=_blank class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Help</FONT>"); } else { printf("<TD ALIGN=CENTER><A HREF=\"/goldenPath/help/sequenceViewHelp.html\" TARGET=_blank class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Help</FONT>"); } */ printf("</TR></TABLE>"); printf("</TD></TR></TABLE>\n"); } else if (isGsid) { printf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#000000\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>\n"); printf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#2636D1\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"2\"><TR>\n"); /* Home */ printf("<TD ALIGN=CENTER><A HREF=\"../index.html\" class=\"topbar\"><FONT COLOR=\"#FFFFFF\">Home</FONT></A></TD>"); /* Blat */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgBlat?command=start\" class=\"topbar\"><FONT COLOR=\"#FFFFFF\">Blat</FONT></A></TD>"); /* Subject View */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gsidSubj\" class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Subject View</FONT>"); /* Sequence View */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgTracks%s\" class=\"topbar\"><FONT COLOR=\"#FFFFFF\">Sequence View</FONT></A></TD>", uiState); /* Table View */ printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gsidTable\" class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Table View</FONT>"); /* Help */ if (endsWith(scriptName, "hgBlat")) { printf("<TD ALIGN=CENTER><A HREF=\"/goldenPath/help/gsidTutorial.html#BLAT\" TARGET=_blank class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Help</FONT>"); } else { printf("<TD ALIGN=CENTER><A HREF=\"/goldenPath/help/sequenceViewHelp.html\" TARGET=_blank class=\"topbar\">%s</A></TD>", "<FONT COLOR=\"#FFFFFF\">Help</FONT>"); } printf("</TR></TABLE>"); printf("</TD></TR></TABLE>\n"); } else if (dbIsFound) { puts( "<!-- +++++++++++++++++++++ HOTLINKS BAR +++++++++++++++++++ -->" "\n" "<TR><TD COLSPAN=3 HEIGHT=40 >" "\n" "<table bgcolor=\"#000000\" cellpadding=\"1\" cellspacing=\"1\" width=\"100%%\" height=\"27\">" "\n" "<tr bgcolor=\"#"HG_COL_HOTLINKS"\"><td valign=\"middle\">" "\n" " <table BORDER=0 CELLSPACING=0 CELLPADDING=0 bgcolor=\"#"HG_COL_HOTLINKS"\" height=\"24\"><TR>" "\n " " <TD VALIGN=\"middle\"><font color=\"#89A1DE\"> " "\n" ); if (isEncode) { printf(" <A HREF=\"../encode/\" class=\"topbar\">" "\n"); puts(" Home</A>"); } else { printf(" <A HREF=\"../index.html%s\" class=\"topbar\">" "\n", uiState); puts(" Home</A> "); if (isGsid) { printf(" <A HREF=\"../cgi-bin/gsidSubj%s\" class=\"topbar\">\n", uiState); puts(" Subject View</A> "); } if (!isGsid) { printf(" <A HREF=\"../cgi-bin/hgGateway%s\" class=\"topbar\">\n", uiState); puts(" Genomes</A> "); } if (endsWith(scriptName, "hgTracks") || endsWith(scriptName, "hgGene") || endsWith(scriptName, "hgTables") || endsWith(scriptName, "hgTrackUi") || endsWith(scriptName, "hgSession") || endsWith(scriptName, "hgCustom") || endsWith(scriptName, "hgc") || endsWith(scriptName, "hgPal")) { #ifdef TRACK_SEARCH printf(" <A HREF='../cgi-bin/hgTracks%s&hgTracksConfigPage=notSet&%s=0' class='topbar'>\n", uiState,TRACK_SEARCH); #else///ifndef TRACK_SEARCH printf(" <A HREF='../cgi-bin/hgTracks%s&hgTracksConfigPage=notSet' class='topbar'>\n", uiState); #endif///ndef TRACK_SEARCH puts(" Genome Browser</A> "); } if (!endsWith(scriptName, "hgBlat")) { printf(" <A HREF=\"../cgi-bin/hgBlat?command=start%s%s\" class=\"topbar\">", theCart ? "&" : "", uiState+1 ); puts(" Blat</A> "); } } { char *table = (theCart == NULL ? NULL : (endsWith(scriptName, "hgGene") ? cartOptionalString(theCart, "hgg_type") : cartOptionalString(theCart, "g"))); if (table && theCart && (endsWith(scriptName, "hgc") || endsWith(scriptName, "hgTrackUi") || endsWith(scriptName, "hgGene"))) { struct trackDb *tdb = hTrackDbForTrack(db, table); if (tdb != NULL) printf(" <A HREF=\"../cgi-bin/hgTables%s&hgta_doMainPage=1&" "hgta_group=%s&hgta_track=%s&hgta_table=%s\" " "class=\"topbar\">\n", // uiState, tdb->grp, table, table); uiState, tdb->grp, tdb->track, tdb->table); else printf(" <A HREF=\"../cgi-bin/hgTables%s&hgta_doMainPage=1\" " "class=\"topbar\">\n", uiState); trackDbFree(&tdb); } else printf(" <A HREF=\"../cgi-bin/hgTables%s%shgta_doMainPage=1\" " "class=\"topbar\">\n", uiState, theCart ? "&" : "?" ); } /* disable TB for both GSID and CGB servers */ if (!isGsid && !hIsCgbServer()) puts(" Tables</A> "); if (!endsWith(scriptName, "hgNear")) /* possible to make this conditional: if (db != NULL && hgNearOk(db)) */ if (db != NULL && hgNearOk(db)) { if (isGsid) { printf(" <A HREF=\"../cgi-bin/gsidTable%s\" class=\"topbar\">\n", uiState); puts(" Table View</A> "); } else { printf(" <A HREF=\"../cgi-bin/hgNear%s\" class=\"topbar\">\n", uiState); puts(" Gene Sorter</A> "); } } if ((!endsWith(scriptName, "hgPcr")) && (db == NULL || hgPcrOk(db))) { printf(" <A HREF=\"../cgi-bin/hgPcr%s\" class=\"topbar\">\n", uiState); puts(" PCR</A> "); } if (endsWith(scriptName, "hgGenome")) { printf(" <A HREF=\"../cgi-bin/hgGenome%s&hgGenome_doPsOutput=on\" class=\"topbar\">\n", uiState); puts(" PDF/PS</A> "); } if (endsWith(scriptName, "hgHeatmap")) { printf(" <A HREF=\"../cgi-bin/hgHeatmap%s&hgHeatmap_doPsOutput=on\" class=\"topbar\">\n", uiState); puts(" PDF/PS</A> "); } #ifndef GBROWSE if (wikiLinkEnabled() && !endsWith(scriptName, "hgSession")) { printf("<A HREF=\"../cgi-bin/hgSession%s%shgS_doMainPage=1\" " "class=\"topbar\">Session</A>", uiState, theCart ? "&" : "?" ); puts(" "); } #endif /* GBROWSE */ if (!isGsid) puts(" <A HREF=\"../FAQ/\" class=\"topbar\">" "\n" " FAQ</A> " "\n" ); if (!isGsid) { if (endsWith(scriptName, "hgBlat")) puts(" <A HREF=\"../goldenPath/help/hgTracksHelp.html#BLATAlign\""); else if (endsWith(scriptName, "hgText")) puts(" <A HREF=\"../goldenPath/help/hgTextHelp.html\""); else if (endsWith(scriptName, "hgNear")) puts(" <A HREF=\"../goldenPath/help/hgNearHelp.html\""); else if (endsWith(scriptName, "hgTables")) puts(" <A HREF=\"../goldenPath/help/hgTablesHelp.html\""); else if (endsWith(scriptName, "hgGenome")) puts(" <A HREF=\"../goldenPath/help/hgGenomeHelp.html\""); else if (endsWith(scriptName, "hgSession")) puts(" <A HREF=\"../goldenPath/help/hgSessionHelp.html\""); else if (endsWith(scriptName, "pbGateway")) puts(" <A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\""); else if (endsWith(scriptName, "hgVisiGene")) puts(" <A HREF=\"../goldenPath/help/hgTracksHelp.html#VisiGeneHelp\""); else puts(" <A HREF=\"../goldenPath/help/hgTracksHelp.html\""); puts(" class=\"topbar\">"); puts(" Help</A> "); } } puts(" </font></TD>" "\n" " </TR></TABLE>" "\n" "</TD></TR></TABLE>" "\n" "</TD></TR> " "\n" "" "\n" ); if(!skipSectionHeader) /* this HTML must be in calling code if skipSectionHeader is TRUE */ { puts( "<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->" "\n" "<TR><TD COLSPAN=3> " "\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" " <TABLE BGCOLOR=\"#"HG_COL_HEADER"\" BACKGROUND=\"../images/hr.gif\" WIDTH=\"100%\"><TR><TD class='windowSize'>" "\n" " <FONT SIZE=\"4\" id='sectTtl'><b> " ); htmlTextOut(textOutBuf); puts( "</b></FONT></TD><TD></TD></TR></TABLE>" "\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" " " ); } void webNewSection(char* format, ...) /* create a new section on the web page */ { va_list args; va_start(args, format); webEndSection(); puts("<!-- +++++++++++++++++++++ START NEW SECTION +++++++++++++++++++ -->"); puts( "<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" " <TABLE BGCOLOR=\"#"HG_COL_HEADER"\" BACKGROUND=\"../images/hr.gif\" WIDTH=\"100%\"><TR><TD>" "\n" " <FONT SIZE=\"4\"><b> " ); vprintf(format, args); puts( " </b></FONT></TD></TR></TABLE>" "\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 lik * 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(); } } void webVaWarn(char *format, va_list args) /* Warning handler that closes out page and stuff in * the fancy form. */ { boolean needStart = !webHeadAlreadyOutputed; if (needStart) webStart(errCart, NULL, "Error"); htmlVaWarn(format, args); printf("\n<!-- HGERROR -->\n"); printf("\n\n"); if (needStart) webEnd(); } 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 struct sqlResult *sr = sqlGetResult(conn, "select name, label from clade order by 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(); } 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; } #ifdef NOT static void phoneHome() { static boolean beenHere = FALSE; if (beenHere) /* one at a time please */ return; beenHere = TRUE; char *scriptName = cgiScriptName(); char *ip = getenv("SERVER_ADDR"); if (scriptName && ip) { struct sqlConnection *conn = hConnectCentral(); if (conn) { #define REGO_DB "UCSCRegistration" if (sqlTableExists(conn, REGO_DB)) return; char query[256]; safef(query, sizeof(query), "create table %s", REGO_DB); struct sqlResult *sr = sqlGetResult(conn, query); sqlFreeResult(&sr); hDisconnectCentral(&conn); fprintf(stderr, "phoneHome: scriptName: %s, ip: %s\n", scriptName, ip); } else fprintf(stderr, "phoneHome: scriptName: %s, ip: %s can not connect\n", scriptName, ip); } else fprintf(stderr, "phoneHome: scriptName: %s or ip %s are null\n", scriptName, ip); } #endif 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); #ifdef NOT phoneHome(); #endif /* 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 ((oldDb && differentWord(oldDb, *retDb)) || (oldOrg && differentWord(oldOrg, *retGenome)) || (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("><FONT COLOR=\"#FFFFFF\"><B>%s</B></FONT></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><FONT COLOR=\"#FFFFFF\"><B>%s</B></FONT></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) // Returns full path of timestamped link to the requested resource file (js, or css). // If wrapInHtml, then returns link embedded in style or script html. Free after use. // NOTE: png, jpg and gif should also be supported but are untested. { 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 = "style"; + dirName = cfgOptionDefault("browser.styleDir","style"); else if (image) - dirName = "style/images"; + dirName = cfgOptionDefault("browser.styleImagesDir","style/images"); struct dyString *fullDirName = NULL; char *docRoot = hDocumentRoot(); if(docRoot != NULL) // tolerate missing docRoot (i.e. when running from command line) fullDirName = dyStringCreate("%s/%s", docRoot, dirName); else 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.ext long mtime = fileModTime(dyStringContents(realFileName)); // We add mtime to create a pseudo-version; this forces browsers to reload css/js file when it changes struct dyString *linkWithTimestamp = dyStringCreate("%s/%s-%ld%s", dyStringContents(fullDirName), baseName, mtime, extension); // If link does not exist, then create it !! if(!fileExists(dyStringContents(linkWithTimestamp))) { // The versioned copy should be created by the install process; however, mirrors may fail // to preserve mtime's when copying over the javascript/css files, in which case the // versioned softlinks won't match the real file; in that case, we try to create // the versioned links on the fly (which requires write access to the javascript or style directory!). // Remove older links struct dyString *pattern = dyStringCreate("%s-[0-9]+\\%s", baseName, extension); struct slName *file, *files = listDirRegEx(dyStringContents(fullDirName), dyStringContents(pattern), REG_EXTENDED); struct dyString *oldLink = dyStringNew(256); for (file = files; file != NULL; file = file->next) { dyStringClear(oldLink); dyStringPrintf(oldLink, "%s/%s", dyStringContents(fullDirName), file->name); unlink(dyStringContents(oldLink)); } dyStringFree(&oldLink); slFreeList(&files); dyStringFree(&pattern); // Create new link if(symlink(dyStringContents(realFileName), dyStringContents(linkWithTimestamp))) { int err = errno; errAbort("webTimeStampedLinkToResource: symlink failed: errno: %d (%s); the directory '%s' must be writeable by user '%s'; alternatively, the installation process must create the versioned files\n", err, strerror(err), dyStringContents(fullDirName), getUser()); } } // 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 memory will be freed by caller!!! return link; } 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; }