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
@@ -1,200 +1,428 @@
 /* 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"
+"           &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; %s &nbsp;&nbsp;&nbsp;\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>:&nbsp;&nbsp;"
+);
+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");
 
 webEndJWest();
 }
 
 
 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;
 }