747eae7a2f3f12196fe59f6b2340f2c61eedac45 kate Tue Nov 15 14:44:59 2016 -0800 Add last updated and schema link. refs #17369 diff --git src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c index 060c1d5..cbb7ff9 100644 --- src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c +++ src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c @@ -1,339 +1,370 @@ /* 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 */ char *db = NULL; char *version; /* GTEx release */ struct trackDb *trackDb = NULL; static void printTrackHeader() /* Print top banner with track labels */ // TODO: Try to simplify layout { char *assembly = stringBetween("(", ")", hFreezeFromDb(db)); puts( "\n" "
\n" "
\n" ); printf( " \n" " %s Track\n" " %s\n" " \n" "       %s    \n" , trackDb->shortLabel, assembly, trackDb->longLabel); puts( -" \n" +" \n" "
\n" "
\n" "
\n" "
GO
\n" " \n" "
\n" "
\n" "
\n"); } static void printBodyMap() { puts( " \n" " \n" " GTEx Body Map illustration not found\n" " \n"); } static void printVisSelect() /* Track visibility dropdown */ { enum trackVisibility vis = trackDb->visibility; vis = hTvFromString(cartUsualString(cart, trackDb->track, hStringFromTv(vis))); boolean canPack = TRUE; hTvDropDownClassVisOnlyAndExtra(trackDb->track, vis, canPack, "gbSelect normalText visDD", trackDbSetting(trackDb, "onlyVisibility"), NULL); } static void printScoreFilter(struct cart *cart, char *track) /* Filter on overall gene expression score */ { char buf[512]; puts("Limit to genes scored at or above:\n"); safef(buf, sizeof(buf), "%s.%s", trackDb->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() /* Controls for track configuration (except for tissues) */ { char *track = trackDb->track; puts( " \n" "
\n" "
Configuration
\n" "
\n"); /* Track vis dropdown */ printVisSelect(); puts( "
\n" "
\n"); /* GTEx-specific track controls, layout in 3 rows */ puts( " \n" "
\n" "
\n"); gtexGeneUiGeneLabel(cart, track, trackDb); puts( "
\n" "
\n"); gtexGeneUiGeneModel(cart, track, trackDb); puts( "
\n" "
\n"); puts( " \n" "
\n" "
\n"); gtexGeneUiLogTransform(cart, track, trackDb); puts( "
\n"); puts( "
\n"); gtexGeneUiViewLimits(cart, track, trackDb); puts( "
\n" "
\n"); puts( " \n" "
\n"); puts( "
\n"); gtexGeneUiCodingFilter(cart, track, trackDb); puts( "
\n"); /* Filter on score */ puts( "
\n"); printScoreFilter(cart, track); puts( "
\n" "
\n"); puts( " \n"); } 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); char var[512]; safef(var, sizeof var, "%s.%s", trackDb->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( " \n" "
\n" "
Tissues
\n" "
\n" " Click label below or in Body Map to set or clear a tissue\n" "
\n" "
\n" "
set all
\n" "
clear all
\n" "
\n" "
\n" ); puts( "\n"); puts( "\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; iname) != NULL); printf( "\n", isChecked ? tis->color : 0xFFFFFF, tis->color); printf( ""); col++; if (col > cols-1) { puts("\n"); col = 0; } } puts( "\n"); puts( "
color); printf( "style='background-color: #%06X;" "border-style: solid; border-width: 2px;" "border-color: #%06X;'>%s", isChecked ? "tissueSelected" : "", tis->name, tis->description); printf( "", var, tis->name, isChecked ? "checked" : ""); puts( "
"); char buf[512]; safef(buf, sizeof(buf), "%s%s.%s", cgiMultListShadowPrefix(), trackDb->track, GTEX_TISSUE_SELECT); cgiMakeHiddenVar(buf, "0"); } 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( "\n" "
\n" "
\n"); printBodyMap(); puts( "
\n" "
\n"); printConfigPanel(); printTissueTable(); puts( "
\n" "
\n"); } +static void printDataInfo() +{ +puts( +"\n" +"
\n" +"
Data Information
\n" +"
\n" +" \n" +" \n" +" \n" +"
\n" +"
\n" +); +puts( +"
\n" +"
\n"); +puts("
"); +printUpdateTime(db, trackDb, NULL); +puts("
"); + +puts("
"); +makeSchemaLink(db, trackDb, "View table schema"); +puts("
"); + +puts( +"
\n" +"
\n"); +} + static void printTrackDescription() { puts( "\n" "
\n" "
Track Description
\n" "
\n" " \n" " \n" " \n" "
\n" "
\n" "
\n" "
\n"); puts(trackDb->html); puts( "
\n" "
\n"); } static struct trackDb *getTrackDb(char *database, 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; // Start web page with new-style header webStartJWestNoBanner(cart, db, "Genome Browser GTEx Track Settings"); puts(""); puts(""); char *genome = NULL, *clade = NULL; getDbGenomeClade(cart, &db, &genome, &clade, oldVars); char *track = cartString(cart, "g"); trackDb = getTrackDb(db, track); if (!trackDb) errAbort("No GTEx track %s found in database %s\n", track, db); version = gtexVersion(track); // Container for bootstrap grid layout puts( "
\n"); // Print form with configuration HTML, and track description printf( "
\n\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); printTrackHeader(); printTrackConfig(); puts( "
"); +printDataInfo(); if (trackDb->html) printTrackDescription(); puts( "
"); // Initialize illustration display and handle mouseover and clicks puts(""); webIncludeFile("inc/jWestFooter.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; }