661ed410515150835be535b6a3563d784e878fe3 kate Thu Feb 9 16:42:34 2017 -0800 Add GO button to Configuration subsection (next to vis dropdown), as per request by B0b. refs #18556 diff --git src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c index 68738c3..f6d6402 100644 --- src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c +++ src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c @@ -1,372 +1,383 @@ /* hgGtexTrackSettings: Configure GTEx track, with tissues selected from Body Map or list * * Copyright (C) 2016 The Regents of the University of California */ #include "common.h" #include "trackDb.h" #include "cart.h" #include "portable.h" #include "cheapcgi.h" #include "web.h" #include "hCommon.h" #include "hui.h" #include "gtexUi.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 */ static void printTrackHeader(char *db, struct trackDb *tdb) /* Print top banner with track labels */ // TODO: Try to simplify layout { char *assembly = stringBetween("(", ")", hFreezeFromDb(db)); puts( "<a name='TRACK_TOP'></a>\n" " <div class='row gbTrackTitleBanner'>\n" " <div class='col-md-10'>\n" ); printf( " <span class='gbTrackName'>\n" " %s Track\n" " <span class='gbAssembly'> %s </span>\n" " </span>" " <span class='gbTrackTitle'> %s </span>\n" , tdb->shortLabel, assembly, tdb->longLabel); puts( "<!-- Info icon built from stacked fa icons -->\n" " <a href='#INFO_SECTION' title='Jump to the track description'>\n" " <span class='gbIconSmall fa-stack'>\n" " <i class='gbBlueDarkColor fa fa-circle fa-stack-2x'></i>\n" " <i class='gbWhiteColor fa fa-info fa-stack-1x'></i>\n" " </span></a>\n" " </div>\n" " <div class='col-md-2 text-right'>\n" " <div class='gbButtonGoContainer' title='Go to the Genome Browser'>\n" " <div class='gbButtonGo'>GO</div>\n" " <i class='gbIconGo fa fa-play fa-2x'></i>\n" " </div>\n" " </div>\n" " </div>\n"); } static void printBodyMap() { puts( " <!-- Body Map panel -->\n" " <object id='bodyMapSvg' type='image/svg+xml' data='/images/gtexBodyMap.svg'>\n" " GTEx Body Map illustration not found\n" " </object>\n"); puts("<div class='gbmCredit'>Credit: jwestdesign</div>\n"); } +static void printGoButton() +{ +puts( +" <div class='gbButtonGoContainer' title='Go to the Genome Browser'>\n" +" <div class='gbButtonGo'>GO</div>\n" +" <i class='gbIconGo fa fa-play fa-2x'></i>\n" +" </div>\n" +); +} + static void printVisSelect(struct trackDb *tdb) /* Track visibility dropdown */ { 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); } static void printScoreFilter(struct cart *cart, char *track, struct trackDb *tdb) /* Filter on overall gene expression score */ { char buf[512]; puts("<b>Limit to genes scored at or above:</b>\n"); safef(buf, sizeof(buf), "%s.%s", tdb->track, SCORE_FILTER); int score = cartUsualInt(cart, buf, 0); int minScore = 0, maxScore = 1000; cgiMakeIntVarWithLimits(buf, score, "Minimum score", 0, minScore, maxScore); printf( " (range %d-%d)\n", minScore, maxScore); } static void printConfigPanel(struct trackDb *tdb) /* Controls for track configuration (except for tissues) */ { char *track = tdb->track; puts( " <!-- Configuration panel -->\n" " <div class='row gbSectionBanner'>\n" -" <div class='col-md-10'>Configuration</div>\n" -" <div class='col-md-2 text-right'>\n"); +" <div class='col-md-8'>Configuration</div>\n" +" <div class='col-md-4 gbButtonContainer text-right'>\n"); /* Track vis dropdown */ printVisSelect(tdb); +printGoButton(); puts( " </div>\n" " </div>\n"); /* GTEx-specific track controls, layout in 3 rows */ puts( " <!-- row 1 -->\n" " <div class='row'>\n" " <div class='gbControl col-md-5'>\n"); gtexGeneUiGeneLabel(cart, track, tdb); puts( " </div>\n" " <div class='gbControl col-md-7'>\n"); gtexGeneUiGeneModel(cart, track, tdb); puts( " </div>\n" " </div>\n"); puts( " <!-- row 2 -->\n" " <div class='row'>\n" " <div class='gbControl col-md-5'>\n"); gtexGeneUiLogTransform(cart, track, tdb); puts( " </div>\n"); puts( " <div class='gbControl col-md-7'>\n"); gtexGeneUiViewLimits(cart, track, tdb); puts( " </div>\n" " </div>\n"); puts( " <!-- row 3 -->\n" " <div class='row'>\n"); puts( " <div class='gbControl col-md-5'>\n"); gtexGeneUiCodingFilter(cart, track, tdb); puts( " </div>\n"); /* Filter on score */ puts( " <div class='gbControl col-md-7'>\n"); printScoreFilter(cart, track, tdb); puts( " </div>\n" " </div>\n"); puts( " <!-- end configure panel -->\n"); } static void printTissueTable(struct trackDb *tdb) /* Output HTML with tissue labels and colors, in 2 columns, to fit next to body map */ { char *version = gtexVersion(tdb->track); struct gtexTissue *tis, *tissues = gtexGetTissues(version); char var[512]; safef(var, sizeof var, "%s.%s", tdb->track, GTEX_TISSUE_SELECT); struct hash *selectedHash = cartHashList(cart, var); 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 -->\n" "<div class='row gbSectionBanner'>\n" " <div class='col-md-1'>Tissues</div>\n" " <div class='col-md-7 gbSectionInfo'>\n" " Click label below or in Body Map to set or clear a tissue\n" " </div>\n" " <div class='col-md-4 gbButtonContainer'>\n" " <div id='setAll' class='gbButtonSetClear gbButton'>set all</div>\n" " <div id='clearAll' class='gbButtonSetClear gbButton'>clear all</div>\n" " </div>\n" "</div>\n" ); puts( "<table class='gbmTissueTable'>\n"); puts( "<tr>\n"); 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; } boolean all = (hashNumEntries(selectedHash) == 0) ? TRUE : FALSE; for (i=0; i<count; i++) { tis = tisTable[i]; boolean isChecked = all || (hashLookup(selectedHash, tis->name) != NULL); printf( "<td class='gbmTissueColorPatch %s' " "data-tissueColor=#%06X ", isChecked ? "" : "gbmTissueNotSelectedColor", tis->color); printf( "style='background-color: #%06X;" "border-color: #%06X;'></td>\n", isChecked ? tis->color : 0xFFFFFF, tis->color); printf( "<td class='gbmTissueLabel %s' id='%s'>%s", isChecked ? "gbmTissueSelected" : "", tis->name, tis->description); // Hidden checkbox stores value for cart printf( "<input type='checkbox' name='%s' value='%s' %s style='display: none;'>", var, tis->name, isChecked ? "checked" : ""); puts( "</td>"); col++; if (col > cols-1) { puts("</tr>\n<tr>"); col = 0; } } puts( "</tr>\n"); puts( "</table>"); char buf[512]; safef(buf, sizeof(buf), "%s%s.%s", cgiMultListShadowPrefix(), tdb->track, GTEX_TISSUE_SELECT); cgiMakeHiddenVar(buf, "0"); } static void printTrackConfig(struct trackDb *tdb) /* Print track configuration panels, including Body Map. The layout is 2-column. Right column is body map SVG. Left column has a top panel for configuration settings (non-tissue), and a lower panel with a tissue selection list. */ { puts( "<!-- Track Configuration Panels -->\n" " <div class='row'>\n" " <div class='col-md-6'>\n"); printConfigPanel(tdb); printTissueTable(tdb); puts( " </div>\n" " <div class='col-md-6'>\n"); printBodyMap(); puts( " </div>\n" " </div>\n"); } static void printDataInfo(char *db, struct trackDb *tdb) { puts( "<a name='INFO_SECTION'></a>\n" " <div class='row gbSectionBanner'>\n" " <div class='col-md-11'>Data Information</div>\n" " <div class='col-md-1'>\n" // TODO: move click handler to JS " <i title='Jump to top of page' onclick=\"$('html,body').scrollTop(0);\" " " class='gbIconArrow fa fa-lg fa-arrow-circle-up'></i>\n" " </div>\n" " </div>\n" ); puts( " <div class='row gbTrackDescriptionPanel'>\n" " <div class='gbTrackDescription'>\n"); puts("<div class='dataInfo'>"); printUpdateTime(db, tdb, NULL); puts("</div>"); puts("<div class='dataInfo'>"); makeSchemaLink(db, tdb, "View table schema"); puts("</div>"); puts( " </div>\n" " </div>\n"); } static void printTrackDescription(struct trackDb *tdb) { puts( "<a name='TRACK_HTML'></a>\n" " <div class='row gbSectionBanner'>\n" " <div class='col-md-11'>Track Description</div>\n" " <div class='col-md-1'>\n" " <i title='Jump to top of page' onclick=\"$('html,body').scrollTop(0);\" " " class='gbIconArrow fa fa-lg fa-arrow-circle-up'></i>\n" " </div>\n" " </div>\n" " <div class='row gbTrackDescriptionPanel'>\n" " <div class='gbTrackDescription'>\n"); puts(tdb->html); puts( " </div>\n" " </div>\n"); } static struct trackDb *getTrackDb(char *db, char *track) /* Check if this is an assembly with GTEx track and get trackDb */ { struct sqlConnection *conn = sqlConnect(db); if (conn == NULL) errAbort("Can't connect to database %s\n", db); char where[256]; safef(where, sizeof(where), "tableName='%s'", track); // TODO: use hdb, hTrackDbList to get table names of trackDb, struct trackDb *tdb = trackDbLoadWhere(conn, "trackDb", where); trackDbAddTableField(tdb); sqlDisconnect(&conn); return tdb; } static void doMiddle(struct cart *theCart) /* Send HTML with javascript to display the user interface. */ { cart = theCart; char *db = NULL, *genome = NULL, *clade = NULL; getDbGenomeClade(cart, &db, &genome, &clade, oldVars); // Start web page with new-style header webStartGbNoBanner(cart, db, "Genome Browser GTEx Track Settings"); puts("<link rel='stylesheet' href='../style/gb.css'>"); // NOTE: This will likely go to web.c puts("<link rel='stylesheet' href='../style/hgGtexTrackSettings.css'>"); char *track = cartUsualString(cart, "g", "gtexGene"); struct trackDb *tdb = getTrackDb(db, track); if (!tdb) errAbort("No GTEx track %s found in database %s\n", track, db); // Container for bootstrap grid layout puts( "<div class='container-fluid'>\n"); // Print form with configuration HTML, and track description printf( "<form action='%s' name='MAIN_FORM' method=%s>\n\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); printTrackHeader(db, tdb); printTrackConfig(tdb); puts( "</form>"); printDataInfo(db, tdb); if (tdb->html) printTrackDescription(tdb); puts( "</div>"); // Initialize illustration display and handle mouseover and clicks puts("<script type='text/javascript' src='../js/hgGtexTrackSettings.js'></script>"); webIncludeFile("inc/gbFooter.html"); webEndJWest(); } int main(int argc, char *argv[]) /* Process CGI / command line. */ { /* Null terminated list of CGI Variables we don't want to save to cart */ /* TODO: check these */ char *excludeVars[] = {"submit", "Submit", "g", NULL}; long enteredMainTime = clock1000(); cgiSpoof(&argc, argv); oldVars = hashNew(10); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); cgiExitTime("hgGtexTrackSettings", enteredMainTime); return 0; }