981ef07d25e4560559dae28d3e316913569944d7 tdreszer Fri Jul 6 17:51:06 2012 -0700 Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way. diff --git src/hg/lib/web.c src/hg/lib/web.c index 53187d4..80b8818 100644 --- src/hg/lib/web.c +++ src/hg/lib/web.c @@ -1,1454 +1,1485 @@ #include "common.h" #include #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 #include #include #include "geoMirror.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(); } // NEW_MENUS is used to experiment with using jabico derived menus (see redmine #5245) // curently only used in larrym's tree // #define NEW_MENUS 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; #ifndef NEW_MENUS boolean isGsid = hIsGsidServer(); boolean isGisaid = hIsGisaidServer(); #endif 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(""); else - puts(""); + puts(""); // Strict would be nice since it fixes atleast one IE problem (use of :hover CSS pseudoclass) - //puts(""); puts( "" "\n" "" "\n" ); printf("\t%s\n", headerText); printf("\t" "\n" "\t" "\n" "\t" "\n" "\t" "\n" "\t" ); /* 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(" \n "); if (endsWith(scriptName, "qaPushQ")) // Tired of failed stylesheet versioning that messes up RR releaseLog.html (regular and ENCODE) printf(" \n"); else webIncludeResourceFile("HGStyle.css"); if (extraStyle != NULL) puts(extraStyle); printf("" "\n" "", hgColOutside()); htmlWarnBoxSetup(stdout);// Sets up a warning box which can be filled with errors as they occur puts(commonCssStyles()); } puts( "" "\n" "" "\n" "" "\n"); if (withLogo) { puts("" "\n" "" "\n" ); } /* Put up the hot links bar. */ #ifdef NEW_MENUS char *docRoot = hDocumentRoot(); jsIncludeFile("jquery.js", NULL); if(docRoot != NULL) { struct dyString *file = dyStringCreate("%s/%s", docRoot, "NavBar.html"); FILE *fd = fopen(dyStringContents(file), "r"); if(fd == NULL) // fail some other way (e.g. HTTP 500)? errAbort("Couldn't open header file '%s' for reading", dyStringContents(file)); else { char buf[4096]; while(TRUE) { size_t n = fread(buf, 1, sizeof(buf), fd); if(n) fwrite(buf, 1, n, stdout); else break; } fclose(fd); printf("\n"); } } else { // tolerate missing docRoot (i.e. when running from command line) // XXXX ???? } #else if (isGisaid) { - printf("
"); if (isEncode) { puts("" "\"ENCODE" ""); puts("\"ENCODE"); } else { puts(""); } puts("
\n"); - printf("\n"); // Home + printf("
Home
\n"); + printf("\n"); if (haveBlat) - printf("\n"); // Blat - printf("\n"); // Subject View - printf("\n",uiState); // Sequence View - printf("\n"); // Table View - printf("
HomeBlatSample ViewSequence ViewTable View 
\n"); // last column squeezes other columns left + printf("Blat\n"); + printf("Sample View\n"); + printf("Sequence View\n",uiState); + printf("Table View\n"); + printf(" \n"); + // last column squeezes other columns left } else if (isGsid) { printf("\n"); - printf("\n"); // Home + printf("\n"); if (haveBlat) - printf("\n"); // Blat - printf("\n"); // Subject View - printf("\n",uiState); // Sequence View - printf("\n"); // Table View + printf("\n"); + printf("\n"); + printf("\n",uiState); + printf("\n"); if (endsWith(scriptName, "hgBlat")) - printf("\n"); // Help + printf("\n"); else - printf("\n"); // Help - printf("
HomeHomeBlatSubject ViewSequence ViewTable ViewBlatSubject ViewSequence ViewTable ViewHelpHelpHelp 
\n"); // last column squeezes other columns left + printf("Help\n"); + printf(" \n"); + // last column squeezes other columns left } else if (dbIsFound) { - puts("\n"); + puts("\n" + ""); puts(""); if (isEncode) printf("\n"); else { printf("\n", uiState); if (isGsid) - printf("\n",uiState); + printf("\n", + uiState); else - printf("\n",uiState); + printf("\n", + uiState); if (endsWith(scriptName, "hgTracks") || endsWith(scriptName, "hgGene") || endsWith(scriptName, "hgTables") || endsWith(scriptName, "hgTrackUi") || endsWith(scriptName, "hgSession") || endsWith(scriptName, "hgCustom") || endsWith(scriptName, "hgHubConnect") || endsWith(scriptName, "hgc") || endsWith(scriptName, "hgPal")) - printf("\n",uiState,TRACK_SEARCH); + printf("\n",uiState,TRACK_SEARCH); if (haveBlat && !endsWith(scriptName, "hgBlat")) - printf("\n",theCart ? "&" : "", uiState+1 ); + printf("\n",theCart ? "&" : "", uiState+1 ); } if (!isGsid && !hIsCgbServer()) // disable TB for both GSID and CGB servers { 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("\n"); } - if (!endsWith(scriptName, "hgNear") && db != NULL && hgNearOk(db)) // possible to make this conditional: if (db != NULL && hgNearOk(db)) + if (!endsWith(scriptName, "hgNear") && db != NULL && hgNearOk(db)) { if (isGsid) - printf("\n",uiState); + printf("\n", + uiState); else - printf("\n",uiState); + printf("\n", + uiState); } if ((!endsWith(scriptName, "hgPcr")) && (db == NULL || hgPcrOk(db))) printf("\n",uiState); if (endsWith(scriptName, "hgGenome")) - printf("\n",uiState); + printf("\n",uiState); if (endsWith(scriptName, "hgHeatmap")) - printf("\n",uiState); + printf("\n",uiState); #ifndef GBROWSE if (wikiLinkEnabled() && !endsWith(scriptName, "hgSession")) - printf("\n",uiState, theCart ? "&" : "?" ); + printf("\n",uiState, theCart ? "&" : "?" ); #endif /* GBROWSE */ if (!isGsid) printf(""); if (!isGsid) { if (endsWith(scriptName, "hgBlat")) printf("\n"); } } - printf("
HomeHomeSubject ViewSubject ViewGenomesGenomesGenome BrowserGenome BrowserBlatBlat", + printf("", uiState, tdb->grp, tdb->track, tdb->table); else - printf("", uiState); + printf("", + uiState); trackDbFree(&tdb); } else printf("", uiState, theCart ? "&" : "?" ); printf("TablesTable ViewTable ViewGene SorterGene SorterPCRPDF/PS" + "PDF/PSPDF/PS" + "PDF/PSSession" + "SessionFAQHelp 
\n"); // last column squeezes other columns left + printf(" \n"); + // last column squeezes other columns left puts("\n"); #endif 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("" "
" "You've been redirected to your nearest mirror - %s
" "Take me back to %s" "
" "\n" , domain, newUri, source ); "

" */ printf("" "
" "

" "" "You've been redirected to your nearest mirror - %s" "\"Hide" "

" "
    " "
  • Take me back to %s" "
    • " "
" "
" "\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) "" "\n" "\n" "
" " \n" - "
\n" - "
\n" + "
\n" + "
\n" "
" ); htmlTextOut(textOutBuf); puts( "
\n" - " \n" + "
" + "\n" "
 \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" "
" "\n" // "
" "
" "\n" "
" "\n" " " ); puts(""); } void webNewSection(char* format, ...) /* create a new section on the web page */ { va_list args; va_start(args, format); webEndSection(); puts("
"); puts(""); puts( // TODO: Replace nested tables with CSS (difficulty is that tables are closed elsewhere) "
\n\n" " \n" - "
\n" - "
\n" + "
\n" + " "); } 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("", label); } void webPrintWideCenteredLabelCell(char *label, int colSpan) /* Print label cell over multiple columns in our colors and centered. */ { printf("", label); } void webPrintLabelCell(char *label) /* Print label cell in our colors. */ { webPrintWideLabelCell(label, 1); } void webPrintLinkTableNewRow() /* start a new row */ { printf("\n"); } 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\n", link); else if (style) dyStringPrintf(wrapped,"\n", link); else // Will be image, since these are the only three choices allowed dyStringPrintf(wrapped,"\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. +// 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; + 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; }
\n" "
" ); vprintf(format, args); puts( "
\n" - " \n" + "
" + "\n" "
 \n\n" ); va_end(args); } void webEndSectionTables() /* Finish with section tables (but don't do /BODY /HTML lik * webEnd does. */ { webEndSection(); puts("
\n"); } void webEnd() /* output the footer of the HTML page */ { if(!webInTextMode) { webEndSectionTables(); #ifndef GBROWSE googleAnalytics(); #endif /* GBROWSE */ puts( ""); 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\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("\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; } 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 *
first. */ { if (addHorizLine) htmlHorizontalLine(); webIncludeFile(hHelpFile(fileRoot)); } void webPrintLinkTableStart() /* Print link table start in our colors. */ { printf("
\n"); printf("\n"); } void webPrintLinkTableEnd() /* Print link table end in our colors. */ { printf("
\n"); printf("
\n"); } void webPrintLinkOutCellStart() /* Print link cell that goes out of our site. End with * webPrintLinkTableEnd. */ { printf("		"); } void webPrintWideCellStart(int colSpan, char *bgColorRgb) /* Print link multi-column cell start in our colors. */ { printf(" 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(""); } void webPrintLinkCellEnd() /* Print link cell end in our colors. */ { printf(" 1) printf(" COLSPAN=%d", colSpan); printf(">%s 1) printf(" COLSPAN=%d", colSpan); printf(">
%s