3a3e7f9931622d8837bf08c3de5dfb328c384203 tdreszer Fri Jun 22 15:59:56 2012 -0700 Third batch of many checkins as dictated by Jim's OCD. 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. Only affect is to my sanity and Jim's. diff --git src/hg/hgGateway/hgGateway.c src/hg/hgGateway/hgGateway.c index 1b07885..e4a61ac 100644 --- src/hg/hgGateway/hgGateway.c +++ src/hg/hgGateway/hgGateway.c @@ -1,369 +1,367 @@ /* hgGateway - Human Genome Browser Gateway. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "htmshell.h" #include "obscure.h" #include "web.h" #include "cart.h" #include "hdb.h" #include "dbDb.h" #include "hgFind.h" #include "hCommon.h" #include "hui.h" #include "customTrack.h" #include "hubConnect.h" #include "hgConfig.h" #include "jsHelper.h" #include "hPrint.h" #include "suggest.h" #include "search.h" #include "geoMirror.h" struct cart *cart = NULL; struct hash *oldVars = NULL; char *clade = NULL; char *organism = NULL; char *db = NULL; void hgGateway() /* hgGateway - Human Genome Browser Gateway. */ { char *defaultPosition = hDefaultPos(db); char *position = cloneString(cartUsualString(cart, "position", defaultPosition)); boolean gotClade = hGotClade(); char *survey = cfgOptionEnv("HGDB_SURVEY", "survey"); char *surveyLabel = cfgOptionEnv("HGDB_SURVEY_LABEL", "surveyLabel"); boolean supportsSuggest = assemblySupportsGeneSuggest(db); /* JavaScript to copy input data on the change genome button to a hidden form This was done in order to be able to flexibly arrange the UI HTML */ char *onChangeDB = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\""; char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\""; char *onChangeClade = "onchange=\"document.orgForm.clade.value = document.mainForm.clade.options[document.mainForm.clade.selectedIndex].value; document.orgForm.org.value = 0; document.orgForm.db.value = 0; document.orgForm.submit();\""; /* If we are changing databases via explicit cgi request, then remove custom track data which will be irrelevant in this new database . If databases were changed then use the new default position too. */ if (sameString(position, "genome") || sameString(position, "hgBatch")) position = defaultPosition; jsIncludeFile("jquery.js", NULL); webIncludeResourceFile("jquery-ui.css"); jsIncludeFile("jquery-ui.js", NULL); jsIncludeFile("ajax.js", NULL); jsIncludeFile("autocomplete.js", NULL); jsIncludeFile("hgGateway.js", NULL); jsIncludeFile("utils.js", NULL); -puts( -"<CENTER style='font-size:small;'>" +puts("<CENTER style='font-size:small;'>" "The UCSC Genome Browser was created by the \n" "<A HREF=\"../staff.html\">Genome Bioinformatics Group of UC Santa Cruz</A>.\n" "<BR>" "Software Copyright (c) The Regents of the University of California.\n" "All rights reserved.\n" -"</CENTER>\n" -); + "</CENTER>\n"); -puts( -"<FORM ACTION='../cgi-bin/hgTracks' NAME='mainForm' METHOD='GET' style='display:inline;'>\n" +puts("<FORM ACTION='../cgi-bin/hgTracks' NAME='mainForm' METHOD='GET' style='display:inline;'>\n" "<CENTER>" "<table style='background-color:#FFFEF3; border: 1px solid #CCCC99;'>\n" "<tr><td>\n"); cgiMakeHiddenVar(hgHubConnectCgiDestUrl, "../cgi-bin/hgTracks"); puts("<table><tr>"); if (gotClade) puts("<td align=center valign=baseline>clade</td>"); -puts( -"<td align=center valign=baseline>genome</td>\n" +puts("<td align=center valign=baseline>genome</td>\n" "<td align=center valign=baseline>assembly</td>\n" "<td align=center valign=baseline>position or search term</td>\n"); if(supportsSuggest) puts("<td align=center valign=baseline><a title='click for help on gene search box' target='_blank' href='../goldenPath/help/geneSearchBox.html'>gene</a></td>\n"); puts( "<td align=center valign=baseline> </td>\n" "</tr>\n<tr>" ); if (gotClade) { puts("<td align=center>\n"); printCladeListHtml(organism, onChangeClade); puts("</td>\n"); } puts("<td align=center>\n"); if (gotClade) printGenomeListForCladeHtml(db, onChangeOrg); else printGenomeListHtml(db, onChangeOrg); puts("</td>\n"); puts("<td align=center>\n"); printAssemblyListHtml(db, onChangeDB); puts("</td>\n"); puts("<td align=center>\n"); cgiMakeTextVar("position", addCommasToPos(db, position), 30); printf("</td>\n"); if(supportsSuggest) { puts("<td align=center>\n"); hPrintf("<input name='hgt.suggest' type='text' size='5' id='suggest' />\n" "<input type='hidden' name='hgt.suggestTrack' id='suggestTrack' value='%s'>\n", assemblyGeneSuggestTrack(db) ); printf("</td>\n"); } cartSetString(cart, "position", position); cartSetString(cart, "db", db); cartSetString(cart, "org", organism); if (gotClade) cartSetString(cart, "clade", clade); freez(&defaultPosition); position = NULL; puts("<td align=center>"); if(supportsSuggest) hButtonWithOnClick("Submit", "submit", NULL, "submitButtonOnClick()"); else cgiMakeButton("Submit", "submit"); -/* This is a clear submit button that browsers will use by default when enter is pressed in position box. FIXME: This should be done with js onchange event! */ -printf("<input TYPE=\"IMAGE\" BORDER=\"0\" NAME=\"hgt.dummyEnterButton\" src=\"../images/DOT.gif\" WIDTH=1 HEIGHT=1 ALT=dot>"); +// This is a clear submit button that browsers will use by default when enter is pressed +// in position box. FIXME: This should be done with js onchange event! +printf("<input TYPE=\"IMAGE\" BORDER=\"0\" NAME=\"hgt.dummyEnterButton\" " + "src=\"../images/DOT.gif\" WIDTH=1 HEIGHT=1 ALT=dot>"); cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ -puts( -"</td>\n" +puts("</td>\n" "</tr></table>\n" "</td></tr>\n"); -puts( -"<tr><td><CENTER><BR>\n" -"<a HREF=\"../cgi-bin/cartReset\">Click here to reset</a> the browser user interface settings to their defaults."); +puts("<tr><td><CENTER><BR>\n" + "<a HREF=\"../cgi-bin/cartReset\">Click here to reset</a> " + "the browser user interface settings to their defaults."); #define SURVEY 1 #ifdef SURVEY if (survey && differentWord(survey, "off")) - printf(" <span style='background-color:yellow;'><A HREF=\"%s\" TARGET=_BLANK><EM><B>%s</EM></B></A></span>", survey, surveyLabel ? surveyLabel : "Take survey"); + printf(" <span style='background-color:yellow;'>" + "<A HREF=\"%s\" TARGET=_BLANK><EM><B>%s</EM></B></A></span>", + survey, surveyLabel ? surveyLabel : "Take survey"); #endif -puts( -"<BR>\n" +puts("<BR>\n" "</CENTER>\n" -"</td></tr><tr><td><CENTER>\n" -); + "</td></tr><tr><td><CENTER>\n"); puts("<TABLE BORDER=\"0\">"); puts("<TR>"); if(isSearchTracksSupported(db,cart)) { puts("<TD VALIGN=\"TOP\">"); cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT); puts("</TD>"); } // custom track button. disable hgCustom button on GSID server, until // necessary additional work is authorized. puts("<TD VALIGN=\"TOP\">"); /* disable CT for CGB servers for the time being */ if (!hIsGsidServer() && !hIsCgbServer()) { boolean hasCustomTracks = customTracksExist(cart, NULL); printf("<input TYPE=SUBMIT onclick=\"document.mainForm.action='%s';\" VALUE='%s' title='%s'>\n", hgCustomName(),hasCustomTracks ? CT_MANAGE_BUTTON_LABEL:CT_ADD_BUTTON_LABEL, hasCustomTracks ? "Manage your custom tracks" : "Add your own custom tracks" ); } puts("</TD>"); if (hubConnectTableExists()) { puts("<TD VALIGN=\"TOP\">"); printf("<input TYPE=SUBMIT onclick=\"document.mainForm.action='%s';\" VALUE='%s' title='%s'>\n", "../cgi-bin/hgHubConnect", "track hubs", "Import tracks"); puts("</TD>"); } // configure button puts("<TD VALIGN=\"TOP\">"); -cgiMakeButtonWithMsg("hgTracksConfigPage", "configure tracks and display","Configure track selections and browser display"); +cgiMakeButtonWithMsg("hgTracksConfigPage", "configure tracks and display", + "Configure track selections and browser display"); puts("</TD>"); // clear possition button puts("<TD VALIGN=\"TOP\">"); if(supportsSuggest) cgiMakeOnClickButton("document.mainForm.position.value=''; document.getElementById('suggest').value='';", "clear position"); else cgiMakeOnClickButton("document.mainForm.position.value=''", "clear position"); puts("</TD>"); puts("</TR></TABLE>"); puts("</CENTER>\n" "</td></tr></table>\n" ); puts("</CENTER>"); if(!cartVarExists(cart, "pix")) // put a hidden input for pix on page so default value can be filled in on the client side hPrintf("<input type='hidden' name='pix' value=''>\n"); puts("</FORM>"); if (hIsPreviewHost()) { puts("<P>" "WARNING: This is our preview site. It is a weekly mirror of our internal development server for public access. " "Data and tools here are under construction, have not been quality reviewed, and are subject to change " "at any time. We provide this site for early access, with the warning that it is less available " "and stable than our public site. For high-quality reviewed annotations on our production server, visit " " <A HREF=\"http://genome.ucsc.edu\">http://genome.ucsc.edu</A>." "</P><BR>"); } else if (hIsPrivateHost()) { puts("<P>WARNING: This is our development and test site. It usually works, but it is filled with tracks in various " "stages of construction, and others of little interest to people outside of our local group. " "It is usually slow because we are building databases on it. The documentation is poor. " "More data than usual is flat out wrong. Maybe you want to go to " "<A HREF=\"http://genome.ucsc.edu\">genome.ucsc.edu</A> instead."); } if (hIsGsidServer()) { webNewSection("%s", "Sequence View\n"); - printf("%s", - "Sequence View is a customized version of the UCSC Genome Browser, which is specifically tailored to provide functions needed for the GSID HIV Data Browser.\n"); + printf("%s","Sequence View is a customized version of the UCSC Genome Browser, which is " + "specifically tailored to provide functions needed for the GSID HIV Data Browser.\n"); } hgPositionsHelpHtml(organism, db); puts("<FORM ACTION=\"../cgi-bin/hgGateway\" METHOD=\"GET\" NAME=\"orgForm\">"); cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ if (gotClade) printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", clade); else printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", "mammal"); printf("<input type=\"hidden\" name=\"org\" value=\"%s\">\n", organism); printf("<input type=\"hidden\" name=\"db\" value=\"%s\">\n", db); puts("</FORM><BR>"); } void doMiddle(struct cart *theCart) /* Set up pretty web display and save cart in global. */ { char *scientificName = NULL; cart = theCart; getDbGenomeClade(cart, &db, &organism, &clade, oldVars); if (! hDbIsActive(db)) { db = hDefaultDb(); organism = hGenome(db); clade = hClade(organism); } scientificName = hScientificName(db); if (hIsGsidServer()) cartWebStart(theCart, db, "GSID %s Sequence View (UCSC Genome Browser) Gateway \n", organism); else { char buffer[128]; /* tell html routines *not* to escape htmlOut strings*/ htmlNoEscape(); buffer[0] = 0; if (*scientificName != 0) { if (sameString(clade,"ancestor")) safef(buffer, sizeof(buffer), "(<I>%s</I> Ancestor) ", scientificName); else safef(buffer, sizeof(buffer), "(<I>%s</I>) ", scientificName); } cartWebStart(theCart, db, "%s %s%s Gateway\n", organism, buffer, hBrowserName()); htmlDoEscape(); } hgGateway(); cartWebEnd(); } static void checkForGeoMirrorRedirect() { // Implement Geo/IP based redirection // // NOTE that we want to redirect people as quickly as possible, so for efficiency purposes, this code is designed to be // called from main BEFORE the cart is loaded (so we only use CGI parameters and/or cookies). char *thisNodeStr = geoMirrorNode(); if (thisNodeStr) { char *redirectCookie = findCookieData("redirect"); char *redirect = cgiOptionalString("redirect"); fprintf(stderr, "GALT redirectCookie=%s redirect=%s\n", redirectCookie, redirect); fflush(stderr); // DEBUG REMOVE if (redirect == NULL && redirectCookie == NULL) { int thisNode = sqlUnsigned(thisNodeStr); struct sqlConnection *centralConn = hConnectCentral(); char *ipStr = cgiRemoteAddr(); int node = defaultNode(centralConn, ipStr); // get location of redirect node if (thisNode != node) { char query[1056]; safef(query, sizeof query, "select domain from gbNode where node = %d", node); char *newDomain = sqlQuickString(centralConn, query); fprintf(stderr, "GALT newDomain=%s\n", newDomain); fflush(stderr); // DEBUG REMOVE char *oldDomain = cgiServerName(); char *port = cgiServerPort(); char *uri = cgiRequestUri(); char *sep = strchr(uri, '?') ? "&" : "?"; int newUriSize = strlen(uri) + 1024; char *newUri = needMem(newUriSize); // TODO what about https? safef(newUri, newUriSize, "http://%s:%s%s%sredirect=auto&source=%s", newDomain, port, uri, sep, oldDomain); struct dyString *dy = dyStringNew(256); dyStringPrintf(dy, "HTTP/1.1 302 found: \n" "Content-Type: text/html; charset=iso-8859-1\n" "Connection: close\n" "Location: %s\n" "\n" "<html><head><title>Redirecting to closer site</title></head>\n" "<body><a href=\"%s\">%s</a></body>\n" , newUri , newUri, newUri); fprintf(stderr, "GALT redirect response:\n%s", dy->string); fflush(stderr); // DEBUG REMOVE puts(dyStringContents(dy)); exit(0); } hDisconnectCentral(¢ralConn); } } } char *excludeVars[] = {NULL}; int main(int argc, char *argv[]) /* Process command line. */ { oldVars = hashNew(10); cgiSpoof(&argc, argv); if(cgiIsOnWeb()) checkForGeoMirrorRedirect(); cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }