2755debd56fbb1a69333d485b22079c1a8a7495a
kate
  Wed Jan 27 11:49:42 2016 -0800
Special handling of popup configuration for GTEx track (see RM #15873 for why). refs #155645

diff --git src/hg/lib/gtexUi.c src/hg/lib/gtexUi.c
index 34d7d52..611e290 100644
--- src/hg/lib/gtexUi.c
+++ src/hg/lib/gtexUi.c
@@ -1,346 +1,372 @@
 /* GTEx (Genotype Tissue Expression) track controls */
 
 /* Copyright (C) 2015 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "cheapcgi.h"
 #include "cart.h"
 #include "hui.h"
 #include "trackDb.h"
 #include "jsHelper.h"
 #include "gtexTissue.h"
 #include "gtexUi.h"
 
 #define SYSTEM_BRAIN            "Brain"
 #define SYSTEM_REPRODUCTIVE     "Reproductive"
 #define SYSTEM_GASTRO           "Digestive"
 
 #define SYSTEM_ENDOCRINE        "Endocrine"
 #define SYSTEM_CARDIO           "Cardiovascular"
 #define SYSTEM_OTHER            "Other"
 
 
-static void initTissueTableStyle()
-{
-puts("<style>\n"
-        "#tissueTable th, #tissueTable td {\n"
-            "font-size: 75%;\n"
-        "}\n"
-    "</style>\n");
-}
+/* Restrict features on right-click (popup) version */
+static boolean isPopup = FALSE;
+
+/* Convenience functions for tissue filter controls */
 
 static char *makeTissueColorPatch(struct gtexTissue *tis)
+/* Display a box colored by defined tissue color */
 {
 char buf[256];
 safef(buf, sizeof(buf), "<td style='width:10px;' bgcolor=%X></td>", tis->color);
 return(cloneString(buf));
 }
 
 static char *makeTissueLabel(struct gtexTissue *tis)
 {
+/* Display tissue color and label */
 char buf[256];
 safef(buf, sizeof(buf), "<td style='width:10px;' bgcolor=%X></td>"
                         "<td>&nbsp;%s</td>", 
                                 tis->color, tis->description);
 return(cloneString(buf));
 }
 
 static char *getSystem(struct gtexTissue *tis)
+/* Rough categorization of tissues for filter presentation */
 {
 if (startsWith("brain", tis->name))
     return(SYSTEM_BRAIN);
 else if (sameString(tis->name, "uterus") || sameString(tis->name, "testis") ||
         sameString(tis->name, "vagina") || sameString(tis->name, "prostate") ||
         sameString(tis->name, "ovary") ||
         sameString(tis->name, "breastMamTissue") || sameString(tis->name, "ectocervix") ||
         sameString(tis->name, "endocervix") || sameString(tis->name, "fallopianTube"))
     return(SYSTEM_REPRODUCTIVE);
 else if (startsWith("esophagus", tis->name) || startsWith("colon", tis->name) ||
         sameString(tis->name, "stomach") || sameString("smallIntestine", tis->name) ||
         sameString("pancreas", tis->name) || sameString("liver", tis->name))
     return(SYSTEM_GASTRO);
 else if (sameString("adrenalGland", tis->name) || sameString("pituitary", tis->name) ||
         sameString("thyroid", tis->name))
     return(SYSTEM_ENDOCRINE);
 else if (startsWith("heart", tis->name) || startsWith("artery", tis->name))
     return(SYSTEM_CARDIO);
 else
     return(SYSTEM_OTHER);
 }
 
 struct tissueSelect
     {
     struct tissueSelect *next;
     char *name;
     char *label;
     boolean checked;
     };
 
 static void makeGroupCheckboxes(char *name, char *title, struct tissueSelect *tisSelects)
 {
 if (title != NULL)
     printf("<tr><td colspan=10><i><b>%s</b></i></td></tr><tr>\n", title);
 int count = slCount(tisSelects);
 struct tissueSelect **tisArray;
 AllocArray(tisArray, count);
 int i=0;
 struct tissueSelect *tsel;
 for (i=0, tsel = tisSelects; tsel != NULL; tsel = tsel->next, i++)
     tisArray[i] = tsel;
 int col=0;
 int row=0;
 int tableColumns=3;
 for (i=0; i<count; i++)
     {
     int j = row + col*(count/tableColumns+1);
     if (j>=count)
         {
         printf("</tr><tr>");
         row++;
         col = 0;
         }
     j = row + col*(count/tableColumns+1);
+    if (!isPopup)
+        {
         printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s></td>" "<td>%s</td>\n",
                name, tisArray[j]->name, tisArray[j]->checked ? "checked" : "", tisArray[j]->label);
+        }
     col++;
     }
 if ((i % tableColumns) != 0)
     while ((i++ % tableColumns) != 0)
         printf("<td></td>");
 printf("</tr><tr><td></td></tr>\n");
 }
 
-static void makeAllTissueCheckboxes(char *name, struct gtexTissue *tissues, struct slName *checked)
-{
-struct hash *checkHash = hashNew(0);
-struct slName *sel;
-for (sel = checked; sel != NULL; sel = sel->next)
-    hashAdd(checkHash, sel->name, sel->name);
-puts("<table borderwidth=0><tr>");
-struct tissueSelect *tsel;
-struct gtexTissue *tis;
-struct tissueSelect *allTissues = NULL;
-for (tis = tissues; tis != NULL; tis = tis->next)
+static void initTissueTableStyle()
+/* Reduce font in tissue table so more rows are visible.
+ * Specify some colors.*/
 {
-    AllocVar(tsel);
-    tsel->name = tis->name;
-    tsel->label = makeTissueLabel(tis);
-    if (hashNumEntries(checkHash) == 0)
-        tsel->checked = TRUE;
-    else
-        tsel->checked = (hashLookup(checkHash, tis->name) != NULL);
-    slAddHead(&allTissues, tsel);
-    }
-slReverse(&allTissues);
-makeGroupCheckboxes(name, NULL, allTissues);
-puts("</tr></table>");
-char buf[512];
-safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
-cgiMakeHiddenVar(buf, "0");
+puts("<style>\n"
+        "#tissueTable th, #tissueTable td {font-size: 75%;}\n"
+        ".notSortable {font-color: black;}\n"
+    "</style>\n");
 }
 
 static void makeTableTissueCheckboxes(char *name, struct gtexTissue *tissues, 
-                                        struct slName *checked, struct cart *cart)
+                                        struct slName *checked, struct cart *cart, char *track)
 {
 initTissueTableStyle();
 char *onClick = "";
 // Sortable table can't be displayed when UI is activated from right-click (popup mode)
-if (!cartVarExists(cart, "ajax"))
+if (!isPopup)
     {
     jsIncludeFile("hui.js", NULL);
     onClick = "'tableSortAtButtonPress(this);";
     }
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 //puts("<table borderwidth=0><tr>");
 puts("\n<table id='tissueTable' cellspacing='2' cellpadding='0' border='0' class='sortable'>");
 
 /* table header */
 char orderVar[256];
 safef(orderVar, sizeof(orderVar), "%s.sortOrder", name);
 char *sortOrder = cartCgiUsualString(cart, orderVar, "tissue=+ samples=+ organ=+ system=+");
 puts("\n<thead class='sortable'>");
 puts("\n<tr class='sortable'>");
+char *sortableClass = isPopup ? "notSortable" : "sortable";
+if (isPopup)
+    {
+    printf("<th>&nbsp;&nbsp;<a style='color: blue; cursor: pointer; text-decoration: none' href='%s?g=%s' "
+         "title='Sorry you cannot select tissues from the list below. To do so, click the ?.'>?</a>",
+                "../cgi-bin/hgTrackUi", track); // Better to use hgTrackUiName(), but there's an issue
+                                                        //with header includes, so punting for now
+    }
+else
+    {
     printf("\n<th>&nbsp;<input type=hidden name='%s' class='sortOrder' value='%s'></th>\n",
         orderVar, sortOrder);
+    }
 puts("<th>&nbsp;&nbsp;&nbsp;&nbsp;</th>");
-
-printf("<th id='tissue' class='sortable sort1' %s "
-        "align='left' title='Sort on tissue'>&nbsp;Tissue</th>", onClick);
-
-printf("<th id='samples' abbr='use' class='sortable sort2' %s "
-        "align='left' title='Sort on sample count'>&nbsp;Samples</th>", onClick);
-
-printf("<th id='organ' class='sortable sort3' %s "
-        "align='left' title='Sort on organ'>&nbsp;Organ</th>", onClick);
-
-printf("<th id='system' class='sortable sort4' %s "
-        "align='left' title='Sort on system'>&nbsp;System</th>", onClick);
+printf("<th id='tissue' class='%s sort1' %s align='left'>&nbsp;Tissue</th>", 
+               sortableClass, onClick);
+printf("<th id='samples' abbr='use' class='%s sort2' %s align='left'>&nbsp;Samples</th>", 
+               sortableClass, onClick);
+printf("<th id='organ' class='%s sort3' %s align='left'>&nbsp;Organ</th>", 
+               sortableClass, onClick);
+printf("<th id='system' class='%s sort4' %s align='left'>&nbsp;System</th>", 
+               sortableClass, onClick);
 puts("\n</tr>");
 puts("</thead>");
 
 /* table body */
 printf("<tbody class='sortable noAltColors initBySortOrder'>");
 struct hash *tscHash = gtexGetTissueSampleCount();
 struct gtexTissue *tis;
 boolean isChecked = FALSE;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     puts("\n<tr valign='top'>");
 
     // checkbox
     if (hashNumEntries(checkHash) == 0)
         isChecked = TRUE;
     else
         isChecked = (hashLookup(checkHash, tis->name) != NULL);
-    printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s></td>",
-               name, tis->name, isChecked ? "checked" : "");
+    printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s %s></td>",
+           name, tis->name, isChecked ? "checked" : "", isPopup ? "disabled" : "");
     // color patch
     printf("\n%s", makeTissueColorPatch(tis));
     // tissue name
     printf("\n<td>&nbsp;%s</td>", tis->description);
     // sample count
     int samples = hashIntValDefault(tscHash, tis->name, 0);
     printf("\n<td abbr='%05d' style='text-align: right; padding-right: 10px'>&nbsp;%d</td>", samples, samples);
     // organ
     printf("\n<td style='padding-right: 10px'>&nbsp;%s</td>", tis->organ);
     // system
     printf("\n<td>&nbsp;%s</td>", getSystem(tis));
 
     puts("\n</tr>");
     }
 puts("</tbody>");
 puts("</table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
 static void makeGroupedTissueCheckboxes(char *name, struct gtexTissue *tissues, struct slName *checked)
 {
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 puts("<table borderwidth=0><tr>");
 struct tissueSelect *brainTissues = NULL;
 struct tissueSelect *digestiveTissues = NULL;
 struct tissueSelect *reproductiveTissues = NULL;
 struct tissueSelect *otherTissues = NULL;
 struct tissueSelect *tsel;
 struct gtexTissue *tis;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     AllocVar(tsel);
     tsel->name = tis->name;
     tsel->label = makeTissueLabel(tis);
     if (hashNumEntries(checkHash) == 0)
         tsel->checked = TRUE;
     else
         tsel->checked = (hashLookup(checkHash, tis->name) != NULL);
     char *system = getSystem(tis);
     if (sameString(SYSTEM_BRAIN, system))
         slAddHead(&brainTissues, tsel);
     else if (sameString(SYSTEM_REPRODUCTIVE, system))
         slAddHead(&reproductiveTissues, tsel);
     else if (sameString(SYSTEM_GASTRO, system))
         slAddHead(&digestiveTissues, tsel);
     else
         slAddHead(&otherTissues, tsel);
     }
 slReverse(&brainTissues);
 slReverse(&digestiveTissues);
 slReverse(&reproductiveTissues);
 slReverse(&otherTissues);
 makeGroupCheckboxes(name, "Brain", brainTissues);
 makeGroupCheckboxes(name, "Gastrointestinal", digestiveTissues);
 makeGroupCheckboxes(name, "Reproductive", reproductiveTissues);
 makeGroupCheckboxes(name, "Other", otherTissues);
 puts("</tr></table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
+static void makeAllTissueCheckboxes(char *name, struct gtexTissue *tissues, 
+                                        struct slName *checked)
+{
+struct hash *checkHash = hashNew(0);
+struct slName *sel;
+for (sel = checked; sel != NULL; sel = sel->next)
+    hashAdd(checkHash, sel->name, sel->name);
+puts("<table borderwidth=0><tr>");
+struct tissueSelect *tsel;
+struct gtexTissue *tis;
+struct tissueSelect *allTissues = NULL;
+for (tis = tissues; tis != NULL; tis = tis->next)
+    {
+    AllocVar(tsel);
+    tsel->name = tis->name;
+    tsel->label = makeTissueLabel(tis);
+    if (hashNumEntries(checkHash) == 0)
+        tsel->checked = TRUE;
+    else
+        tsel->checked = (hashLookup(checkHash, tis->name) != NULL);
+    slAddHead(&allTissues, tsel);
+    }
+slReverse(&allTissues);
+makeGroupCheckboxes(name, NULL, allTissues);
+puts("</tr></table>");
+char buf[512];
+safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
+cgiMakeHiddenVar(buf, "0");
+}
+
 void gtexGeneUi(struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed)
 /* GTEx (Genotype Tissue Expression) per gene data */
 {
+if (cartVarExists(cart, "ajax"))
+    isPopup = TRUE;
 boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
 printf("<table%s><tr><td>", boxed ?" width='100%'":"");
 
 char cartVar[1024];
 char *selected = NULL;
 
 /* Sample selection */
 printf("<b>Samples:</b>&nbsp;");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_SAMPLES);
 selected = cartCgiUsualString(cart, cartVar, GTEX_SAMPLES_DEFAULT); 
 boolean isAllSamples = sameString(selected, GTEX_SAMPLES_ALL);
 cgiMakeRadioButton(cartVar, GTEX_SAMPLES_ALL, isAllSamples);
 printf("All\n");
 cgiMakeRadioButton(cartVar, GTEX_SAMPLES_COMPARE_SEX, !isAllSamples);
 printf("Compare by gender\n");
 printf("</p>");
 
 /* Comparison type */
 printf("<p><b>Comparison display:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_COMPARISON_DISPLAY);
 selected = cartCgiUsualString(cart, cartVar, GTEX_COMPARISON_DEFAULT); 
 boolean isMirror = sameString(selected, GTEX_COMPARISON_MIRROR);
 cgiMakeRadioButton(cartVar, GTEX_COMPARISON_DIFF, !isMirror);
 printf("Difference graph\n");
 cgiMakeRadioButton(cartVar, GTEX_COMPARISON_MIRROR, isMirror);
 printf("Two graphs\n");
 printf("</p>");
 
 /* Data transform */
 printf("<p><b>Log10 transform:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LOG_TRANSFORM);
 boolean isLogTransform = cartCgiUsualBoolean(cart, cartVar, GTEX_LOG_TRANSFORM_DEFAULT);
 cgiMakeCheckBox(cartVar, isLogTransform);
 
 /* Viewing limits max */
 printf("&nbsp;&nbsp;<b>View limits maximum:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_MAX_LIMIT);
 // TODO: set max and initial limits from gtexInfo table
 int viewMax = cartCgiUsualInt(cart, cartVar, GTEX_MAX_LIMIT_DEFAULT);
 cgiMakeIntVar(cartVar, viewMax, 4);
 printf(" RPKM (range 10-180000)<br>\n");
 printf("</p>");
 
 /* Color scheme */
-// Not sure if we still want this option
+// We don't need the rainbow color scheme, but may want another (e.g. different
+// colors for brain tissues), so leaving code in for now.
 #ifdef COLOR_SCHEME
 printf("<p><b>Tissue colors:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_COLORS);
 selected = cartCgiUsualString(cart, cartVar, GTEX_COLORS_DEFAULT); 
 boolean isGtexColors = sameString(selected, GTEX_COLORS_GTEX);
 cgiMakeRadioButton(cartVar, GTEX_COLORS_GTEX, isGtexColors);
 printf("GTEx\n");
 cgiMakeRadioButton(cartVar, GTEX_COLORS_RAINBOW, !isGtexColors);
 printf("Rainbow\n");
 printf("</p>");
 #endif
 
 /* Tissue filter */
-printf("<p><b>Tissue selection:</b>\n");
+if (!isPopup)
+    {
+    printf("<p><b>Tissue filter:</b>\n");
     safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_TISSUE_SELECT);
     jsMakeCheckboxGroupSetClearButton(cartVar, TRUE);
     puts("&nbsp;");
     jsMakeCheckboxGroupSetClearButton(cartVar, FALSE);
+    }
 struct gtexTissue *tissues = gtexGetTissues();
 struct slName *selectedValues = NULL;
 if (cartListVarExistsAnyLevel(cart, tdb, FALSE, GTEX_TISSUE_SELECT))
     selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, GTEX_TISSUE_SELECT);
 char *selectType = cgiUsualString("tis", "table");
 if (sameString(selectType, "group"))
     makeGroupedTissueCheckboxes(cartVar, tissues, selectedValues);
 else if (sameString(selectType, "table"))
-    makeTableTissueCheckboxes(cartVar, tissues, selectedValues, cart);
+    makeTableTissueCheckboxes(cartVar, tissues, selectedValues, cart, track);
 else
     makeAllTissueCheckboxes(cartVar, tissues, selectedValues);
 
 cfgEndBox(boxed);
 }