05ccc5f7743fcccebdfd8b59c11374c23ad61bc7 Merge parents a7843fa b505056 larrym Mon Jun 25 11:28:23 2012 -0700 resolve merge conflict with master diff --cc src/hg/hgGateway/hgGateway.c index aae3bf9,e4a61ac..9d5a4d3 --- src/hg/hgGateway/hgGateway.c +++ src/hg/hgGateway/hgGateway.c @@@ -1,361 -1,367 +1,358 @@@ /* 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); +jsIncludeFile("jquery.watermarkinput.js", NULL); - 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" - ); - - 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"); + 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"); + + 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" - "<td align=center valign=baseline>assembly</td>\n" - "<td align=center valign=baseline>position or search term</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); +hPrintf("<span class='positionDisplay' id='positionDisplay' title='click to copy position to input box'>%s</span>", addCommasToPos(db, position)); +hPrintf("<input type='hidden' name='position' id='position' value='%s'>\n", addCommasToPos(db, position)); +hPrintf("<input class='positionInput' type='text' name='hgt.positionInput' id='positionInput' size='60'>\n"); +if(assemblySupportsGeneSuggest(db)) + hPrintf("<input type='hidden' name='hgt.suggestTrack' id='suggestTrack' value='%s'>\n", assemblyGeneSuggestTrack(db)); 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>"); +hButton("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>"); cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ - puts( - "</td>\n" - "</tr></table>\n" - "</td></tr>\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" - "</CENTER>\n" - "</td></tr><tr><td><CENTER>\n" - ); + puts("<BR>\n" + "</CENTER>\n" + "</td></tr><tr><td><CENTER>\n"); puts("<TABLE BORDER=\"0\">"); puts("<TR>"); - if(isSearchTracksSupported(db,cart)) + 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"); + "../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"); + cgiMakeOnClickButton("document.mainForm.position.value=''; document.getElementById('positionInput').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; }