7b7d273fd3aeee222d5ee8540298ac6dee662605
kate
  Wed Sep 13 11:45:23 2017 -0700
Add UI setting to toggle display of tissue color patches (for single-tissue eQTL's.  It can be distracting in large regions. refs #15646

diff --git src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
index ccbe5fe..b646917 100644
--- src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
+++ src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
@@ -1,478 +1,480 @@
 /* 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 "jsHelper.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 *database = NULL;
 
 static void printGoButton()
 /* HTML for GO button and 'play' icon */
 {
 puts(
 "           <div class='gbButtonGoContainer text-right' 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 printBodyMap()
 /* Include BodyMap SVG in HTML */
 {
 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 printTrackHeader(char *db, struct trackDb *tdb)
 /* Print top banner with track labels */
 {
 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"
 );
 if (tdb->parent)
     {
     // link to supertrack
     char *encodedMapName = cgiEncode(tdb->parent->track);
     char *chromosome = cartUsualString(cart, "c", hDefaultChrom(database));
     puts("&nbsp;");
     printf(
     "       <a href='%s?%s=%s&c=%s&g=%s' title='Go to container track (%s)'>\n"
     "           <i class='gbIconLevelUp fa fa-level-up'></i>\n"
     "       </a>\n",
                 hgTrackUiName(), cartSessionVarName(), cartSessionId(cart),
                 chromosome, encodedMapName, tdb->parent->shortLabel
     );
     freeMem(encodedMapName);
     }
 puts(
 "       </div>\n"
 );
 puts(
 "       <div class='col-md-2 text-right'>\n"
 );
 printGoButton();
 puts(
 "       </div>\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 printGtexEqtlConfigPanel(struct trackDb *tdb, char *track)
 /* GTEx eQTL track specific controls */
 {
 puts(
 "        <!-- row 1 -->\n"
 "        <div class='row'>\n"
 "            <div class='gbControl col-md-12'>\n");
-gtexEqtlGene(cart, track, tdb);
+gtexEqtlUiGene(cart, track, tdb);
 puts(
 "            </div>\n"
 "        </div>\n");
 puts(
 "        <!-- row 2 -->\n"
 "        <div class='row'>\n"
 "            <div class='gbControl col-md-12'>\n");
-gtexEqtlEffectSize(cart, track, tdb);
+gtexEqtlUiEffectSize(cart, track, tdb);
 puts(
 "            </div>\n"
 "        </div>\n");
 puts(
 "        <!-- row 3 -->\n"
 "        <div class='row'>\n"
 "            <div class='gbControl col-md-12'>\n");
-gtexEqtlProbability(cart, track, tdb);
+gtexEqtlUiProbability(cart, track, tdb);
+puts("&nbsp;&nbsp;&nbsp;&nbsp;");
+gtexEqtlUiTissueColor(cart, track, tdb);
 puts(
 "            </div>\n"
 "        </div>\n");
 }
 
 static void printGtexGeneConfigPanel(struct trackDb *tdb, char *track)
 /* GTEx Gene track specific 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");
 }
 
 static void printConfigPanel(struct trackDb *tdb)
 /* Controls for track configuration (except for tissues) */
 {
 puts(
 "        <!-- Configuration panel -->\n"
 "        <div class='row gbSectionBanner'>\n"
 "            <div class='col-md-8'>Configuration</div>\n"
 "            <div class='col-md-4 text-right'>\n");
 
 /* Track vis dropdown */
 printVisSelect(tdb);
 printGoButton();
 puts(
 "            </div>\n"
 "        </div>\n");
 
 /* Track-specific config */
 char *track = tdb->track;
 if (gtexIsGeneTrack(track))
     printGtexGeneConfigPanel(tdb, track);
 else if (gtexIsEqtlTrack(track))
     printGtexEqtlConfigPanel(tdb, track);
 else
     errAbort("Unknown GTEx track: %s\n", track);
 
 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 text-right'>\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 onclickJumpToTop(char *id)
 /* CSP-safe click handler arrows that cause scroll to top */
 {
 jsOnEventById("click", id, "$('html,body').scrollTop(0);");
 }
 
 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"
 );
 #define DATA_INFO_JUMP_ARROW_ID    "hgGtexDataInfo_jumpArrow"
 printf(
 "            <i id='%s' title='Jump to top of page' \n"
 "               class='gbIconArrow fa fa-lg fa-arrow-circle-up'></i>\n",
 DATA_INFO_JUMP_ARROW_ID
 );
 onclickJumpToTop(DATA_INFO_JUMP_ARROW_ID);
 puts(
 "       </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"
 );
 #define TRACK_INFO_JUMP_ARROW_ID    "hgGtexTrackInfo_jumpArrow"
 printf(
 "            <i id='%s' title='Jump to top of page' \n"
 "               class='gbIconArrow fa fa-lg fa-arrow-circle-up'></i>\n",
 TRACK_INFO_JUMP_ARROW_ID
 );
 onclickJumpToTop(TRACK_INFO_JUMP_ARROW_ID);
 puts(
 "       </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);
 // WARNING: this will break in sandboxes unless trackDb entry is pushed to hgwdev.
 // The fix of using hTrackDbList() would slow for all users, so leaving as is.
 #define TRACKDB "trackDb"
 struct trackDb *tdb = trackDbLoadWhere(conn, TRACKDB, where);
 trackDbAddTableField(tdb);
 char *parent = trackDbLocalSetting(tdb, "parent");
 struct trackDb *parentTdb;
 if (parent)
     {
     safef(where, sizeof(where), "tableName='%s'", parent);
     parentTdb = trackDbLoadWhere(conn, TRACKDB, where);
     if (parentTdb)
         tdb->parent = parentTdb;
     }
 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);
 database = db;
 
 // 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
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("hgGtexTrackSettings.js", NULL);
 
 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 */
 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;
 }