cfed2e78dcef652dc85360454f81d7558aa1b678 kate Thu Oct 27 18:05:04 2016 -0700 Implement config panel cart vars. Moved from .html mockup to C code. refs #17369 diff --git src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c index bc47caa..6d4e87b 100644 --- src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c +++ src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c @@ -1,173 +1,397 @@ /* hgGtexTrackSettings: Configure GTEx track * * Copyright (C) 2016 The Regents of the University of California */ #include "common.h" +#include "trackDb.h" #include "cart.h" +#include "portable.h" +#include "gtexUi.h" + +/* TODO: prune */ #include "cartJson.h" #include "cheapcgi.h" #include "errCatch.h" #include "googleAnalytics.h" #include "hCommon.h" #include "hgConfig.h" #include "hdb.h" #include "htmshell.h" #include "hubConnect.h" #include "hui.h" #include "jsHelper.h" #include "jsonParse.h" #include "obscure.h" // for readInGulp -#include "regexHelper.h" -#include "suggest.h" -#include "trackHub.h" -#include "trix.h" #include "web.h" #include "gtexInfo.h" #include "gtexTissue.h" /* Global Variables */ struct cart *cart = NULL; /* CGI and other variables */ struct hash *oldVars = NULL; /* Old contents of cart before it was updated by CGI */ char *db = NULL; +char *version; /* GTEx release */ +struct trackDb *tdb = NULL; static void doCartJson() /* Perform UI commands to update the cart and/or retrieve cart vars & metadata. */ { struct cartJson *cj = cartJsonNew(cart); //e.g. cartJsonRegisterHandler(cj, "setTaxId", setTaxId); cartJsonExecute(cj); } static void doJsIncludes() /* Include JS libraries. From hgGateway (think about libifying) */ { //puts("<script src=\"../js/es5-shim.4.0.3.min.js\"></script>"); //puts("<script src=\"../js/es5-sham.4.0.3.min.js\"></script>"); //puts("<script src=\"../js/lodash.3.10.0.compat.min.js\"></script>"); puts("<script src=\"../js/cart.js\"></script>"); webIncludeResourceFile("jquery-ui.css"); jsIncludeFile("jquery-ui.js", NULL); jsIncludeFile("jquery.watermarkinput.js", NULL); jsIncludeFile("utils.js",NULL); } -static void printTrackDescription() +static void printTrackHeader() +/* Print top banner with track labels */ { -puts("<a name='TRACK_HTML'></a>"); -puts("<div class='row gbSectionBanner gbSimpleBanner'>"); -puts("<div class='col-md-11'>Track Description</div>"); -puts("<div class='col-md-1'>" - "<a href='#TRACK_TOP' title='Jump to top of page'>" - "<i class='gbBannerIcon gbGoIcon fa fa-lg fa-arrow-circle-up'></i>" - //"<i class='gbBannerIcon gbGoIcon fa fa-lg fa-level-up'></i>" - "</a></div>"); -puts("</div>"); -struct sqlConnection *conn = sqlConnect(db); -if (conn == NULL) - errAbort("Can't connect to database %s\n", db); -char query[256]; -sqlSafef(query, sizeof(query), "select html from trackDb where tableName='gtexGene'"); -char *html = sqlQuickString(conn, query); -if (html != NULL) - { - puts("<div class='trackDescriptionPanel'>"); - puts("<div class='trackDescription'>"); -puts(html); - } -sqlDisconnect(&conn); -puts("</div></div>"); -puts("</div>"); +char *assembly = stringBetween("(", ")", hFreezeFromDb(db)); + +puts( +"<a name='TRACK_TOP'></a>\n" +" <div class='row gbTrackTitle'>\n" +" <div class='col-md-10'>\n" +); + +printf( +" <span class='gbTrackName'>\n" +" %s Track\n" +" <span class='gbAssembly'>%s</span>\n" +" </span>\n" +" %s \n" +, tdb->shortLabel, assembly, tdb->longLabel); + +puts( +" <a href='#TRACK_HTML' title='Jump to the track description'><span class='gbFaStack fa-stack'><i class='gbGoIcon fa fa-circle fa-stack-2x'></i><i class='gbIconText fa fa-info fa-stack-1x'></i></span>" +" </a>" +" </div>" +" <div class='col-md-2 text-right'>" +" <div class='goButtonContainer' title='Go to the Genome Browser'>" +" <div class='gbGoButton'>GO</div>" +" <i class='gbGoIcon fa fa-play fa-2x'></i>" +" </div>" +" </div>" +" </div>" +); } -static void printTissueTable(char *version) +static void printTissueTable() /* Output HTML with tissue labels and colors, in 2 columns, to fit next to body map */ { struct gtexTissue *tis, *tissues = gtexGetTissues(version); struct gtexTissue **tisTable = NULL; int count = slCount(tissues); AllocArray(tisTable, count); int i=0, col=0; int cols = 2; int last = count/2 + 1; +puts( + " <!-- Tissue list -->" + "<div class='row gbSectionBanner'>" + " <div class='col-md-1'>Tissues</div>" + " <div class='col-md-7 gbSectionInfo'>" + " Click label below or in Body Map to set or clear a tissue" + " </div>" + " <div class='col-md-4 gbButtonContainer'>" + " <div id='setAll' class='goButtonContainer gtButton gbWhiteButton'>set all</div>" + " <div id='clearAll' class='goButtonContainer gtButton gbWhiteButton'>clear all</div>" + " </div>" + "</div>" + ); + puts("<table class='tissueTable'>"); puts("<tr>"); for (tis = tissues; tis != NULL; tis = tis->next) { if (tis->id < last) i = tis->id * 2; else i = (tis->id - last) * 2 + 1; tisTable[i] = tis; } for (i=0; i<count; i++) { tis = tisTable[i]; printf("<td class='tissueColor' bgcolor=%06X></td>" "<td class='tissueLabel' id='%s'>%s</td>", tis->color, tis->name, tis->description); col++; if (col > cols-1) { puts("</tr>\n<tr>"); col = 0; } } puts("</tr>\n"); puts("</table>"); } -static void doMainPage() -/* Send HTML with javascript to bootstrap the user interface. */ +static void printBodyMap() { -// Start web page with new banner -char *genome = NULL, *clade = NULL; -//getDbGenomeClade(cart, &db, &genome, &clade, oldVars); +puts( +" <!-- Body Map panel -->" +" <object id='bodyMapSvg' type='image/svg+xml' class='gbImage gtexBodyMap' data='/images/bodyMap.svg'>" +" Body Map illustration not found" +" </object>" +); +} -/* hardcode for now -- later, check for hg19 or hg38 */ +static void printVisSelect() +{ +enum trackVisibility vis = tdb->visibility; +vis = hTvFromString(cartUsualString(cart, tdb->track, hStringFromTv(vis))); +boolean canPack = TRUE; +hTvDropDownClassVisOnlyAndExtra(tdb->track, vis, canPack, "gbSelect normalText visDD", + trackDbSetting(tdb, "onlyVisibility"), NULL); +} -db = "hg19"; -genome = "human"; -clade = "mammal"; +static void printConfigPanel() +/* Controls for track configuration (except for tissues) */ +{ +char cartVar[1024]; +char buf[512]; -// char *chromosome = cartUsualString(cart, "c", hDefaultChrom(database)); -//char *track = cartString(cart, "g"); +char *track = tdb->track; + +puts( +" <!-- Configuration panel -->\n" + +/* Blue section header and track vis dropdown */ +" <div class='row gbSectionBanner'>\n" +" <div class='col-md-10'>Configuration</div>\n" +" <div class='col-md-2 text-right'>\n" +); +printVisSelect(); +puts( +" </div>\n" +); +puts( +" </div>\n" +); + +/* First row of config controls */ +puts( +" <!-- row 1 -->\n" +" <div class='row'>\n" + +/* Gene labels */ +" <div class='configurator col-md-5'>\n" +"<b>Label</b>: " +); +char *geneLabel = cartUsualStringClosestToHome(cart, tdb, isNameAtParentLevel(tdb, track), + GTEX_LABEL, GTEX_LABEL_DEFAULT); +safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LABEL); +cgiMakeRadioButton(cartVar, GTEX_LABEL_SYMBOL , sameString(GTEX_LABEL_SYMBOL, geneLabel)); +printf("%s ", "gene symbol"); +cgiMakeRadioButton(cartVar, GTEX_LABEL_ACCESSION, sameString(GTEX_LABEL_ACCESSION, geneLabel)); +printf("%s ", "accession"); +cgiMakeRadioButton(cartVar, GTEX_LABEL_BOTH, sameString(GTEX_LABEL_BOTH, geneLabel)); +printf("%s ", "both"); +puts( +" </div>\n" + +/* Show exons in gene model */ +" <div class='configurator col-md-7'>\n" +); +puts("<b>Show GTEx gene model</b>\n"); +safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_SHOW_EXONS); +boolean showExons = cartCgiUsualBoolean(cart, cartVar, GTEX_SHOW_EXONS_DEFAULT); +cgiMakeCheckBox(cartVar, showExons); +puts( +" </div>\n" +); +puts( +" </div>\n" +); + +/* Row 2 */ +puts( +" <!-- row 2 -->\n" +" <div class='row'>\n" +); + +/* Log transform. When selected, the next control (view limits max) is disabled */ +puts( +" <div class='configurator col-md-5'>\n" +); +puts("<b>Log10 transform:</b>\n"); +safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LOG_TRANSFORM); +boolean isLogTransform = cartCgiUsualBoolean(cart, cartVar, GTEX_LOG_TRANSFORM_DEFAULT); +safef(buf, sizeof buf, "onchange='gtexTransformChanged(\"%s\")'", track); +cgiMakeCheckBoxJS(cartVar, isLogTransform, buf); +puts( +" </div>\n" +); +/* Viewing limits max. This control is disabled if log transform is selected */ +// construct class so JS can toggle +puts( +" <div class='configurator col-md-7'>\n" +); +safef(buf, sizeof buf, "%sViewLimitsMaxLabel %s", track, isLogTransform ? "disabled" : ""); +printf("<span class='%s'><b>View limits maximum:</b></span>\n", buf); +safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_MAX_LIMIT); +int viewMax = cartCgiUsualInt(cart, cartVar, GTEX_MAX_LIMIT_DEFAULT); +cgiMakeIntVarWithExtra(cartVar, viewMax, 4, isLogTransform ? "disabled" : ""); +char *version = gtexVersion(tdb->table); +printf("<span class='%s'> RPKM (range 0-%d)</span>\n", buf, round(gtexMaxMedianScore(version))); +puts( +" </div>\n" +); +puts( +" </div>\n" +); + +/* Row 3 */ +puts( +" <!-- row 3 -->\n" +" <div class='row'>\n" +); +/* Filter on coding genes */ +puts( +" <div class='configurator col-md-5'>\n" +); +puts("<b>Limit to protein coding genes:</b>\n"); +safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_CODING_GENE_FILTER); +boolean isCodingOnly = cartCgiUsualBoolean(cart, cartVar, GTEX_CODING_GENE_FILTER_DEFAULT); +cgiMakeCheckBox(cartVar, isCodingOnly); +puts( +" </div>\n" +); + +/* Filter on score */ +puts( +" <div class='configurator col-md-7'>\n" +); +puts("<b>Limit to genes scored at or above:</b>\n"); +puts( +" <input id='scoreInput' value='' size='8'>\n" +" (range 0-1000)\n" +); +puts( +" </div>\n" +); +puts( +" </div>\n" +); +puts( +" <!-- end configure panel -->\n" +); +} + +static void printTrackConfig() +/* Print track configuration panels, including Body Map. +The layout is 2-column. Left column is body map SVG. +Right column has a top panel for configuration settings (non-tissue), +and a lower panel with a tissue selection list. +*/ +{ +puts( +" <div class='row'>\n" +); + +// TODO: remove bodyMap id here +puts( +" <div id='bodyMap' class='col-md-6'>\n" +); +printBodyMap(); +puts( +" </div>\n" +); +puts( +" <div class='col-md-6'>\n" +); +printConfigPanel(); +printTissueTable(); +puts( +" </div>\n" +); +puts( +" </div>\n" +); +} + +static void printTrackDescription() +{ +puts("<a name='TRACK_HTML'></a>"); +puts("<div class='row gbSectionBanner gbSimpleBanner'>"); +puts("<div class='col-md-11'>Track Description</div>"); +puts("<div class='col-md-1'>" + "<a href='#TRACK_TOP' title='Jump to top of page'>" + "<i class='gbBannerIcon gbGoIcon fa fa-lg fa-arrow-circle-up'></i>" + //"<i class='gbBannerIcon gbGoIcon fa fa-lg fa-level-up'></i>" + "</a></div>"); +puts("</div>"); +if (tdb->html != NULL) + { + puts("<div class='trackDescriptionPanel'>"); + puts("<div class='trackDescription'>"); +puts(tdb->html); + } +puts("</div></div>"); +puts("</div>"); +} + +static void doMainPage() +/* Send HTML with javascript to bootstrap the user interface. */ +{ +// Start web page with new banner webStartJWestNoBanner(cart, db, "Genome Browser GTEx Track Settings"); puts("<link rel=\"stylesheet\" href=\"../style/bootstrap.min.css\">"); puts("<link rel=\"stylesheet\" href=\"../style/hgGtexTrackSettings.css\">"); -// The initial visible page elements are hgGtexTrackSettings.html, -// which is transformed into a quoted .h -// file containing a string constant that we #include and print here (see makefile). -puts( -#include "hgGtexTrackSettings.html.h" -); +char *genome = NULL, *clade = NULL; +// char *chromosome = cartUsualString(cart, "c", hDefaultChrom(database)); +//char *track = cartString(cart, "g"); +getDbGenomeClade(cart, &db, &genome, &clade, oldVars); -//struct tdb *tdbList = NULL; -//struct trackDb *tdb = tdbForTrack(db, track, &tdbList); -//printTissueTable(gtexGetVersion(tdb->table)); +// Check if this is an assembly with GTEx track +struct sqlConnection *conn = sqlConnect(db); +if (conn == NULL) + errAbort("Can't connect to database %s\n", db); char *table = "gtexGene"; +version = gtexVersion(table); -printTissueTable(gtexVersion(table)); -puts("</div></div></div></div>"); +// TODO: use hdb, hTrackDbList to get table names of trackDb, +tdb = trackDbLoadWhere(conn, "trackDb", "tableName = 'gtexGene'"); +sqlDisconnect(&conn); +if (!tdb) + errAbort("No GTEx track found in database %s\n", db); +puts( +"<div class='container-fluid'>\n" +); +printTrackHeader(); +printTrackConfig(); printTrackDescription(); puts("</div>"); // end panel, section and body layout container // Track description // JS libraries doJsIncludes(); // Main JS puts("<script src='../js/hgGtexTrackSettings.js'></script>"); webIncludeFile("inc/jWestFooter.html"); @@ -178,23 +402,27 @@ void doMiddle(struct cart *theCart) /* Display the main page or execute a command and update the page */ { cart = theCart; if (cgiOptionalString(CARTJSON_COMMAND)) doCartJson(); else doMainPage(); } int main(int argc, char *argv[]) /* Process CGI / command line. */ { /* Null terminated list of CGI Variables we don't want to save * permanently. */ -char *excludeVars[] = {CARTJSON_COMMAND, NULL}; +/* TODO: check these */ +char *excludeVars[] = { "submit", "Submit", "g", NULL, "ajax", NULL,}; +//char *excludeVars[] = {CARTJSON_COMMAND, NULL}; +long enteredMainTime = clock1000(); cgiSpoof(&argc, argv); oldVars = hashNew(10); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); +cgiExitTime("hgGtexTrackSettings", enteredMainTime); return 0; }