2d3028934575643575ea1523ee3a3c0cd9d02430 angie Fri Oct 22 14:50:49 2010 -0700 Redmine Feature #1470 (create ability to not have a blat server for anassembly): 1. In hgBlat, if db does not have a blat server, search for an alternate as hgPcr does: if there's a blat server for the same organism, use that, otherwise just default to the db with a blat server & the lowest dbDb.orderKey. If we default to some other db's blat server, notify the user. 2. In hgPcr, if we default to some other db's blat server, notify the user. 3. If db doesn't have a blat server, suppress the blat links in the hot links bar in webStartWrapperDetailedInternal. (hgTracks.c's hot links already did this). Our static html hotlinks include Blat and PCR links, so it is still necessary for hgBlat and hgPcr to handle db's that don't have blat servers. 4. Also in webStartWrapperDetailedInternal, call getDbAndGenome (part of uiState construction) *before* we test db for NULL and default the local db variable to hDefaultDb. When the defaulting happened before getDbAndGenome (as in hgVisiGene which passes in NULL db), db was hDefaultDb for a while and then the cart db, and the hot links weren't constructed correctly. diff --git src/hg/lib/web.c src/hg/lib/web.c index 8afa230..9742f01 100644 --- src/hg/lib/web.c +++ src/hg/lib/web.c @@ -1,1372 +1,1377 @@ #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 "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 (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; 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 "); 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" ); } -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("
"); if (isEncode) { puts("" "\"ENCODE" ""); puts("\"ENCODE"); } else { puts(""); } puts("
\n"); printf("\n"); /* Home */ printf(""); /* Blat */ + if (haveBlat) printf(""); /* Subject View */ printf("", "Sample View"); /* Sequence View */ printf("", uiState); /* Table View */ printf("", "Table View"); /* Help */ /* disable help for the time being */ /* if (endsWith(scriptName, "hgBlat")) { printf("", "Help"); } else { printf("", "Help"); } */ printf("
HomeBlat%sSequence View%s%s%s
"); printf("
\n"); } else if (isGsid) { printf("
\n"); printf("\n"); /* Home */ printf(""); /* Blat */ + if (haveBlat) printf(""); /* Subject View */ printf("", "Subject View"); /* Sequence View */ printf("", uiState); /* Table View */ printf("", "Table View"); /* Help */ if (endsWith(scriptName, "hgBlat")) { printf("", "Help"); } else { printf("", "Help"); } printf("
HomeBlat%sSequence View%s%s%s
"); printf("
\n"); } else if (dbIsFound) { puts( "" "\n" "" "\n" "" "\n" "
" "\n" " " "\n " " " "\n" "
 " "\n" ); if (isEncode) { printf(" " "\n"); puts(" Home"); } else { printf(" " "\n", uiState); puts(" Home    "); if (isGsid) { printf(" \n", uiState); puts(" Subject View    "); } if (!isGsid) { printf(" \n", uiState); puts(" Genomes    "); } 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")) { printf(" \n", uiState,searchTracks); puts(" Genome Browser    "); } - if (!endsWith(scriptName, "hgBlat")) + if (haveBlat && !endsWith(scriptName, "hgBlat")) { printf(" ", theCart ? "&" : "", uiState+1 ); puts(" Blat    "); } } { 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", // uiState, tdb->grp, table, table); uiState, tdb->grp, tdb->track, tdb->table); else printf(" \n", uiState); trackDbFree(&tdb); } else printf(" \n", uiState, theCart ? "&" : "?" ); } /* disable TB for both GSID and CGB servers */ if (!isGsid && !hIsCgbServer()) puts(" Tables    "); if (!endsWith(scriptName, "hgNear")) /* possible to make this conditional: if (db != NULL && hgNearOk(db)) */ if (db != NULL && hgNearOk(db)) { if (isGsid) { printf(" \n", uiState); puts(" Table View    "); } else { printf(" \n", uiState); puts(" Gene Sorter    "); } } if ((!endsWith(scriptName, "hgPcr")) && (db == NULL || hgPcrOk(db))) { printf(" \n", uiState); puts(" PCR    "); } if (endsWith(scriptName, "hgGenome")) { printf(" \n", uiState); puts(" PDF/PS    "); } if (endsWith(scriptName, "hgHeatmap")) { printf(" \n", uiState); puts(" PDF/PS    "); } #ifndef GBROWSE if (wikiLinkEnabled() && !endsWith(scriptName, "hgSession")) { printf("Session", uiState, theCart ? "&" : "?" ); puts("   "); } #endif /* GBROWSE */ if (!isGsid) puts(" " "\n" " FAQ    " "\n" ); if (!isGsid) { if (endsWith(scriptName, "hgBlat")) puts(" "); puts(" Help "); } } puts(" 
" "\n" "
" "\n" " " "\n" "" "\n" ); if(!skipSectionHeader) /* this HTML must be in calling code if skipSectionHeader is TRUE */ { puts( "" "\n" " " "\n" " " "\n" "
" "\n" "
" "\n" "
" "\n" "  " ); htmlTextOut(textOutBuf); puts( "
" "\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" " " ); } void webNewSection(char* format, ...) /* create a new section on the web page */ { va_list args; va_start(args, format); webEndSection(); puts(""); puts( "
" "\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; inext) { 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,"\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. // 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; }
" "\n" "
" "\n" "   " ); vprintf(format, args); puts( "
" "\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(); } } 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\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("\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 *
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