beee82d43659b3f682f57301c4a64feec96314ff
braney
  Thu Feb 1 14:25:25 2018 -0800
add support for math on bedGraph (including custom tracks)

diff --git src/hg/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c
index b47e192..4e5a192 100644
--- src/hg/hgCollection/hgCollection.c
+++ src/hg/hgCollection/hgCollection.c
@@ -1,975 +1,977 @@
 /* hgCollection - hub builder */
 
 /* Copyright (C) 2017 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "cartTrackDb.h"
 #include "trackHub.h"
 #include "trashDir.h"
 #include "hubConnect.h"
 #include "hui.h"
 #include "grp.h"
 #include "cheapcgi.h"
 #include "jsHelper.h"
 #include "web.h"
 #include "knetUdc.h"
 #include "api.h"
 #include "genbank.h"
 #include "htmshell.h"
 #include "jsonParse.h"
 #include "customComposite.h"
 #include "stdlib.h"
 
 /* Global Variables */
 struct hash *oldVars = NULL;	/* The cart before new cgi stuff added. */
 // Null terminated list of CGI Variables we don't want to save permanently:
 char *excludeVars[] = {"Submit", "submit", "cmd", "track", "collection", "jsonp", NULL,};
 
 struct track
 {
 struct track *next;
 struct track *trackList;
 struct trackDb *tdb;
 char *name;
 char *shortLabel;
 char *longLabel;
 char *visibility;
 unsigned long color;
 char *viewFunc;        // The method by which calculated tracks should be calculated
 char *missingMethod;   // How should missing data be treated in calculated tracks
 };
 
 struct trackDbRef 
 {
 struct trackDbRef *next;
 struct trackDb *tdb;
 int order;
 };
 
 static char *makeUnique(struct hash *nameHash, char *name)
 // Make the name of this track unique.
 {
 char *skipHub = trackHubSkipHubName(name);
 if (hashLookup(nameHash, skipHub) == NULL)
     {
     hashStore(nameHash, name);
     return skipHub;
     }
 
 unsigned count = 0;
 char buffer[4096];
 
 for(;; count++)
     {
     safef(buffer, sizeof buffer, "%s%d", skipHub, count);
     if (hashLookup(nameHash, buffer) == NULL)
         {
         hashStore(nameHash, buffer);
         return cloneString(buffer);
         }
     }
 
 return NULL;
 }
 
 static boolean trackCanBeAdded(struct trackDb *tdb)
 // are we allowing this track into a custom composite
 {
 return  (tdb->subtracks == NULL) && !startsWith("wigMaf",tdb->type) &&  (startsWith("wig",tdb->type) || startsWith("bigWig",tdb->type) || startsWith("bedGraph",tdb->type)) ;
 }
 
 static void printGroup(char *parent, struct trackDb *tdb, boolean folder, boolean user)
 // output list elements for a group
 {
 char *userString = "";
 char *prefix = "";
 char *viewFunc = NULL;
 char *missingMethod = NULL;
 
 if (user)
     {
     if (tdb->parent && tdb->subtracks) 
         {
         viewFunc = trackDbSetting(tdb, "viewFunc");
         missingMethod = trackDbSetting(tdb, "missingMethod");
         userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' viewType='view' class='folder'";
         }
     else if (tdb->subtracks)
         {
         viewFunc = trackDbSetting(tdb, "viewFunc");
         missingMethod = trackDbSetting(tdb, "missingMethod");
         userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' viewType='collection' class='folder'";
         }
     else
         userString = "data-jstree='{\\\"icon\\\":\\\"fa fa-minus-square\\\"}' class='track' viewType='track'";
     }
 else
     {
     if (tdb->parent && tdb->subtracks) 
         userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop' viewType='view'";
     else if (tdb->subtracks)
         userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='collection' viewType='track'";
     else
         userString = "data-jstree='{\\\"icon\\\":\\\"fa fa-plus\\\"}' class='nodrop' viewType='track'";
     }
     
     
 #define IMAKECOLOR_32(r,g,b) ( ((unsigned int)b<<0) | ((unsigned int)g << 8) | ((unsigned int)r << 16))
 
 char buffer[1024];
 char *viewFuncString = "";
 if (viewFunc != NULL)
     {
     safef(buffer, sizeof buffer, "viewFunc='%s' ", viewFunc);
     viewFuncString = cloneString(buffer);
     }
 
 char *missingString = "";
 if (missingMethod != NULL)
     {
     safef(buffer, sizeof buffer, "missingMethod='%s' ", missingMethod);
     missingString = cloneString(buffer);
     }
 
 jsInlineF("<li shortLabel='%s' longLabel='%s' color='#%06x' %s %s visibility='%s'  name='%s%s' %s>%s",  tdb->shortLabel, tdb->longLabel,IMAKECOLOR_32(tdb->colorR,tdb->colorG,tdb->colorB), viewFuncString, missingString, hStringFromTv(tdb->visibility), prefix,  trackHubSkipHubName(tdb->track),   userString,  tdb->shortLabel );
 jsInlineF(" (%s)", tdb->longLabel);
 
 
 if (tdb->subtracks)
     {
     struct trackDb *subTdb;
 
     jsInlineF("<ul>");
     for(subTdb = tdb->subtracks; subTdb; subTdb = subTdb->next)
         printGroup(trackHubSkipHubName(tdb->track), subTdb, user && (subTdb->subtracks != NULL), user);
     jsInlineF("</ul>");
     }
 jsInlineF("</li>");
 }
 
 static void outHubHeader(FILE *f, char *db)
 // output a track hub header
 {
 fprintf(f,"hub hub1\n\
 shortLabel User Composite\n\
 longLabel User Composite\n\
 useOneFile on\n\
 email genome-www@soe.ucsc.edu\n\n");
 fprintf(f,"genome %s\n\n", db);  
 }
 
 
 static char *getHubName(struct cart *cart, char *db)
 // get the name of the hub to use for user collections
 {
 struct tempName hubTn;
 char buffer[4096];
 safef(buffer, sizeof buffer, "%s-%s", customCompositeCartName, db);
 char *hubName = cartOptionalString(cart, buffer);
 
 if (hubName == NULL)
     {
     trashDirDateFile(&hubTn, "hgComposite", "hub", ".txt");
     hubName = cloneString(hubTn.forCgi);
     cartSetString(cart, buffer, hubName);
     FILE *f = mustOpen(hubName, "a");
     outHubHeader(f, db);
     fclose(f);
     cartSetString(cart, "hubUrl", hubName);
     cartSetString(cart, hgHubConnectRemakeTrackHub, hubName);
     }
 return hubName;
 }
 
 static bool subtrackEnabledInTdb(struct trackDb *subTdb)
 /* Return TRUE unless the subtrack was declared with "subTrack ... off". */
 {
 bool enabled = TRUE;
 char *words[2];
 char *setting;
 if ((setting = trackDbLocalSetting(subTdb, "parent")) != NULL)
     {
     if (chopLine(cloneString(setting), words) >= 2)
         if (sameString(words[1], "off"))
             enabled = FALSE;
     }
 else
     return subTdb->visibility != tvHide;
 
 return enabled;
 }
 
 static bool isSubtrackVisible(struct cart *cart, struct trackDb *tdb)
 /* Has this subtrack not been deselected in hgTrackUi or declared with
  *  * "subTrack ... off"?  -- assumes composite track is visible. */
 {
 boolean overrideComposite = (NULL != cartOptionalString(cart, tdb->track));
 bool enabledInTdb = subtrackEnabledInTdb(tdb);
 char option[1024];
 safef(option, sizeof(option), "%s_sel", tdb->track);
 boolean enabled = cartUsualBoolean(cart, option, enabledInTdb);
 if (overrideComposite)
     enabled = TRUE;
 return enabled;
 }
 
 
 static bool isParentVisible(struct cart *cart, struct trackDb *tdb)
 // Are this track's parents visible?
 {
 if (tdb->parent == NULL)
     return TRUE;
 
 if (!isParentVisible(cart, tdb->parent))
     return FALSE;
 
 char *cartVis = cartOptionalString(cart, tdb->parent->track);
 boolean vis;
 if (cartVis != NULL) 
     vis =  differentString(cartVis, "hide");
 else if (tdbIsSuperTrack(tdb->parent))
     vis = tdb->parent->isShow;
 else
     vis = tdb->parent->visibility != tvHide;
 
 return vis;
 }
 
 
 static void checkForVisible(struct cart *cart, struct trackDbRef **list, struct trackDb *tdb)
 /* Walk the trackDb hierarchy looking for visible leaf tracks. */
 {
 struct trackDb *subTdb;
 char buffer[4096];
 
 if (tdb->subtracks)
     {
     for(subTdb = tdb->subtracks; subTdb; subTdb = subTdb->next)
         checkForVisible(cart, list, subTdb);
     }
 else
     {
     if (isParentVisible(cart, tdb) &&  isSubtrackVisible(cart, tdb))
         {
         struct trackDbRef *tdbRef;
         AllocVar(tdbRef);
         tdbRef->tdb = tdb;
         slAddHead(list, tdbRef);
         safef(buffer, sizeof buffer, "%s_imgOrd", tdb->track);
 
         tdbRef->order = cartUsualInt(cart, buffer, 0);
         }
     }
 }
 
 static int tdbRefCompare (const void *va, const void *vb)
 // Compare to sort on imgTrack->order.
 {
 const struct trackDbRef *a = *((struct trackDbRef **)va);
 const struct trackDbRef *b = *((struct trackDbRef **)vb);
 return (a->order - b->order);
 }       
 
 static void addVisibleTracks(struct cart *cart, struct trackDb *trackList)
 // add the visible tracks table rows.
 {
 struct trackDb *tdb;
 struct trackDbRef *tdbRefList = NULL, *tdbRef;
 //checkForVisible(fullTrackList);
 for(tdb = trackList; tdb; tdb = tdb->next)
     {
     checkForVisible(cart, &tdbRefList, tdb);
     }
 
 slSort(&tdbRefList, tdbRefCompare);
 
 jsInlineF("<ul>");
 jsInlineF("<li data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop folder' name='%s'>%s", "visibile", "Visible Tracks");
 jsInlineF("<ul>");
 for(tdbRef = tdbRefList; tdbRef; tdbRef = tdbRef->next)
     printGroup("visible", tdbRef->tdb, FALSE, FALSE);
 
 jsInlineF("</ul>");
 jsInlineF("</li>");
 jsInlineF("</ul>");
 }
 
 static void doTable(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList)
 // output the tree table
 {
 char *hubName = hubNameFromUrl(getHubName(cart, db));
 struct grp *curGroup;
 for(curGroup = groupList; curGroup;  curGroup = curGroup->next)
     {
     if ((hubName != NULL) && sameString(curGroup->name, hubName))
         break;
     }
 
 jsInlineF("$('#currentCollection').append(\"");
 jsInlineF("<div id='root'>");
 if (curGroup != NULL)
     {
     // print out all the tracks in all the collections
     struct trackDb *tdb;
     for(tdb = trackList; tdb;  tdb = tdb->next)
         {
         if (sameString(tdb->grp, hubName))
             {
             jsInlineF("<ul>");
             printGroup("collections", tdb, TRUE, TRUE);
             jsInlineF("</ul>");
             }
         }
     }
 jsInlineF("</div>");
 jsInlineF("\");\n");
 
 jsInlineF("$('#tracks').append(\"");
 addVisibleTracks(cart, trackList);
 for(curGroup = groupList; curGroup;  curGroup = curGroup->next)
     {
     if ((hubName != NULL) && sameString(curGroup->name, hubName))
         continue;
     jsInlineF("<ul>");
     jsInlineF("<li data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop folder' name='%s'>%s", curGroup->name, curGroup->label );
     struct trackDb *tdb;
     jsInlineF("<ul>");
     for(tdb = trackList; tdb;  tdb = tdb->next)
         {
         if ( sameString(tdb->grp, curGroup->name))
             {
             printGroup(curGroup->name, tdb, FALSE, FALSE);
             }
         }
     jsInlineF("</ul>");
     jsInlineF("</li>");
     jsInlineF("</ul>");
 
     }
 jsInlineF("\");\n");
 jsInlineF("hgCollection.init();\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 printHelp()
 // print out the help page
 {
 puts(
 "<a name='INFO_SECTION'></a>\n"
 "    <div class='row mygbSectionBanner'>\n"
 "        <div class='col-md-11'>Help</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'>");
 puts("</div>");
 webIncludeHelpFileSubst("hgCollectionHelp", NULL, FALSE);
 
 puts("<div class='dataInfo'>");
 puts("</div>");
 
 puts(
 "     </div>\n"
 "   </div>\n");
 }
 
 static void doMainPage(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList)
 /* Print out initial HTML of control page. */
 {
 webStartGbNoBanner(cart, db, "Collections");
 webIncludeResourceFile("gb.css");
 webIncludeResourceFile("spectrum.min.css");
 webIncludeResourceFile("hgGtexTrackSettings.css");
 
 jsReloadOnBackButton(cart);
 
 webIncludeFile("inc/hgCollection.html");
 char *assembly = stringBetween("(", ")", hFreezeFromDb(db));
 jsInlineF("$('#assembly').text('%s');\n",assembly);
 
 printHelp();
 doTable(cart, db, groupList, trackList);
 
 puts("<link rel='stylesheet' href='https://code.jquery.com/ui/1.10.3/themes/smoothness/jquery-ui.css'>");
 puts("<link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/themes/default/style.min.css' />");
 puts("<script src='https://cdnjs.cloudflare.com/ajax/libs/jquery/1.12.1/jquery.min.js'></script>");
 puts("<script src=\"//code.jquery.com/ui/1.10.3/jquery-ui.min.js\"></script>");
 puts("<script src=\"https://cdnjs.cloudflare.com/ajax/libs/jstree/3.3.4/jstree.min.js\"></script>\n");
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("spectrum.min.js", NULL);
 jsIncludeFile("hgCollection.js", NULL);
 webEndGb();
 }
 
 static char *getSqlBigWig(struct sqlConnection *conn, char *db, struct trackDb *tdb)
 // figure out the bigWig for native tables
 {
 char buffer[4096];
 
 safef(buffer, sizeof buffer, "NOSQLINJ select fileName from %s", tdb->table);
 return sqlQuickString(conn, buffer);
 }
 
 void dumpTdbAndParents(struct dyString *dy, struct trackDb *tdb, struct hash *existHash, struct hash *wantHash)
 /* Put a trackDb entry into a dyString, stepping up the tree for some variables. */
 {
 struct hashCookie cookie = hashFirst(tdb->settingsHash);
 struct hashEl *hel;
 while ((hel = hashNext(&cookie)) != NULL)
     {
     if (!hashLookup(existHash, hel->name) && ((wantHash == NULL) || hashLookup(wantHash, hel->name)))
         {
         dyStringPrintf(dy, "%s %s\n", hel->name, (char *)hel->val);
         hashStore(existHash, hel->name);
         }
     }
 
 struct hash *newWantHash = newHash(4);
 hashStore(newWantHash, "type"); // right now we only want type from parents
 if (tdb->parent)
     dumpTdbAndParents(dy, tdb->parent, existHash, newWantHash);
 }
 
 struct dyString *trackDbString(struct trackDb *tdb)
 /* Convert a trackDb entry into a dyString. */
 {
 struct dyString *dy;
 struct hash *existHash = newHash(5);
 struct hashEl *hel;
 
 hel = hashLookup(tdb->settingsHash, "track");
 if (hel == NULL)
     errAbort("can't find track variable in tdb");
 
 dy = newDyString(200);
 dyStringPrintf(dy, "track %s\n", (char *)hel->val);
 hashStore(existHash, "track");
 
 dumpTdbAndParents(dy, tdb, existHash, NULL);
 
 return dy;
 }
 
 
 static void outTdb(struct sqlConnection *conn, char *db, FILE *f, char *name,  struct trackDb *tdb, char *parent, char *visibility, unsigned int color, struct track *track, struct hash *nameHash, struct hash *collectionNameHash, int numTabs, int priority)
 // out the trackDb for one track
 {
 char *dataUrl = NULL;
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 
 if (bigDataUrl == NULL)
     {
     if (startsWith("bigWig", tdb->type))
         {
         dataUrl = getSqlBigWig(conn, db, tdb);
         hashReplace(tdb->settingsHash, "bigDataUrl", dataUrl);
         }
     }
 
 char *tdbType = trackDbSetting(tdb, "tdbType");
 if (tdbType != NULL)
     hashReplace(tdb->settingsHash, "type", tdbType);
 
 hashReplace(tdb->settingsHash, "parent", parent);
+hashReplace(tdb->settingsHash, "shortLabel", track->shortLabel);
+hashReplace(tdb->settingsHash, "longLabel", track->longLabel);
 hashReplace(tdb->settingsHash, "track", makeUnique(collectionNameHash, name));
 char priBuf[128];
 safef(priBuf, sizeof priBuf, "%d", priority);
 hashReplace(tdb->settingsHash, "priority", cloneString(priBuf));
 char colorString[64];
 safef(colorString, sizeof colorString, "%d,%d,%d", (color >> 16) & 0xff,(color >> 8) & 0xff,color & 0xff);
 hashReplace(tdb->settingsHash, "color", colorString);
 
 struct dyString *dy = trackDbString(tdb);
 
 fprintf(f, "%s",  dy->string);
 fprintf(f, "\n");
 }
 
 static void outComposite(FILE *f, struct track *collection, int priority)
 // output a composite header for user composite
 {
 char *parent = collection->name;
 char *shortLabel = collection->shortLabel;
 char *longLabel = collection->longLabel;
 fprintf(f,"track %s\n\
 shortLabel %s\n\
 compositeTrack on\n\
 autoScale on\n\
 maxHeightPixels 100:30:11 \n\
 showSubtrackColorOnUi on\n\
 aggregate  none\n\
 longLabel %s\n\
 %s on\n\
 color %ld,%ld,%ld \n\
 type mathWig\n\
 priority %d\n\
 visibility full\n\n", parent, shortLabel, longLabel, CUSTOM_COMPOSITE_SETTING,
  0xff& (collection->color >> 16),0xff& (collection->color >> 8),0xff& (collection->color),  priority);
 
 }
 
 static void modifyName(struct trackDb *tdb, char *hubName, struct hash  *collectionNameHash)
 /* If this is a new track in the collection we want to make sure
  * it gets a different name than the track in trackDb.
  * If it's a native track, we want to squirrel away the original track name. */
 {
 if ((tdb->grp == NULL) || (hubName == NULL) || differentString(tdb->grp, hubName))
     {
     if (collectionNameHash)
         hashStore(collectionNameHash,  tdb->track);
 
     char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
     if (bigDataUrl == NULL)
         {
         char *table = trackDbSetting(tdb, "table");
         if (table == NULL)
             hashAdd(tdb->settingsHash, "table", tdb->track);
         }
     }
 }
 
 static int outView(FILE *f, struct sqlConnection *conn, char *db, struct track *view, char *parent, struct hash *nameHash, struct hash *collectionNameHash, int priority, char *hubName)
 // output a view to a trackhub
 {
 fprintf(f,"\ttrack %s\n\
 \tshortLabel %s\n\
 \tlongLabel %s\n\
 \tview %s \n\
 \tcontainer mathWig\n\
 \tautoScale on  \n\
 \tparent %s \n\
 \tcolor %ld,%ld,%ld \n\
 \tpriority %d\n\
 \tviewFunc %s \n\
 \tmissingMethod %s \n\
 \tvisibility %s\n", view->name, view->shortLabel, view->longLabel, view->name, parent, 0xff& (view->color >> 16),0xff& (view->color >> 8),0xff& (view->color), priority++, view->viewFunc, view->missingMethod, view->visibility);
 fprintf(f, "\n");
 
 struct track *track = view->trackList;
 for(; track; track = track->next)
     {
     struct trackDb *tdb = hashMustFindVal(nameHash, track->name);
     modifyName(tdb, hubName, collectionNameHash);
 
     outTdb(conn, db, f, track->name,tdb, view->name, track->visibility, track->color, track,  nameHash, collectionNameHash, 2, priority++);
     }
 
 return priority;
 }
 
 static void updateHub(struct cart *cart, char *db, struct track *collectionList, struct hash *nameHash)
 // save our state to the track hub
 {
 char *filename = getHubName(cart, db);
 char *hubName = hubNameFromUrl(filename);
 
 FILE *f = mustOpen(filename, "w");
 chmod(filename, 0666);
 
 struct hash *collectionNameHash = newHash(6);
 
 outHubHeader(f, db);
 struct track *collection;
 struct sqlConnection *conn = hAllocConn(db);
 int priority = 1;
 for(collection = collectionList; collection; collection = collection->next)
     {
     if (collection->trackList == NULL)  // don't output composites without children
         continue;
     outComposite(f, collection, priority++);
     struct trackDb *tdb;
     struct track *track;
     for (track = collection->trackList; track; track = track->next)
         {
         if (track->viewFunc != NULL)
             {
             priority = outView(f, conn, db, track, collection->name,  nameHash, collectionNameHash, priority, hubName);
             }
         else
             {
             tdb = hashMustFindVal(nameHash, track->name);
             modifyName(tdb, hubName, collectionNameHash);
 
             outTdb(conn, db, f, track->name,tdb, collection->name, track->visibility, track->color, track,  nameHash, collectionNameHash, 1, priority++);
             }
         }
     }
 fclose(f);
 hFreeConn(&conn);
 }
 
 static unsigned long hexStringToLong(char *str)
 {
 return strtol(&str[1], NULL, 16);
 }
 
 struct jsonParseData
 {
 struct track **collectionList;
 struct hash *trackHash;
 };
 
 static void jsonObjStart(struct jsonElement *ele, char *name,
     boolean isLast, void *context)
 {
 struct jsonParseData *jpd = (struct jsonParseData *)context;
 struct track **collectionList = jpd->collectionList;
 struct hash *trackHash = jpd->trackHash;
 struct track *track;
 
 if ((name == NULL) && (ele->type == jsonObject))
     {
     struct hash *objHash = jsonObjectVal(ele, "name");
 
     struct jsonElement *parentEle = hashFindVal(objHash, "id");
     char *parentId = jsonStringEscape(parentEle->val.jeString);
     parentEle = hashFindVal(objHash, "parent");
     char *parentName = jsonStringEscape(parentEle->val.jeString);
 
     AllocVar(track);
     struct jsonElement *attEle = hashFindVal(objHash, "li_attr");
     if (attEle)
         {
         struct hash *attrHash = jsonObjectVal(attEle, "name");
         struct jsonElement *strEle = (struct jsonElement *)hashFindVal(attrHash, "name");
         if (strEle == NULL)
             return;
         track->name = jsonStringEscape(strEle->val.jeString);
         hashAdd(trackHash, parentId, track);
 
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "shortlabel");
         track->shortLabel = jsonStringEscape(strEle->val.jeString);
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "longlabel");
         track->longLabel = jsonStringEscape(strEle->val.jeString);
         track->visibility = "pack";
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "color");
         track->color = hexStringToLong(jsonStringEscape(strEle->val.jeString));
         /*
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "visibility");
         track->visibility = jsonStringEscape(strEle->val.jeString);
         strEle = (struct jsonElement *)hashMustFindVal(attrHash, "color");
         track->color = hexStringToLong(jsonStringEscape(strEle->val.jeString));
         strEle = (struct jsonElement *)hashFindVal(attrHash, "viewfunc");
         if (strEle)
             track->viewFunc = jsonStringEscape(strEle->val.jeString);
         strEle = (struct jsonElement *)hashFindVal(attrHash, "missingmethod");
         if (strEle)
             track->missingMethod = jsonStringEscape(strEle->val.jeString);
             */
         }
 
     if (sameString(parentName, "#"))
         slAddHead(collectionList, track);
     else
         {
         struct track *parent = hashMustFindVal(trackHash, parentName);
         slAddTail(&parent->trackList, track);
         }
 
     }
 }
 
 static struct track *parseJsonElements( struct jsonElement *collectionElements)
 // parse the JSON returned from the ap
 {
 struct track *collectionList = NULL;
 struct hash *trackHash = hashNew(5);
 struct jsonParseData jpd = {&collectionList, trackHash};
 jsonElementRecurse(collectionElements, NULL, FALSE, jsonObjStart, NULL, &jpd);
 
 slReverse(&collectionList);
 return collectionList;
 }
 
 static void doAjax(struct cart *cart, char *db, char *jsonText, struct hash *nameHash)
 // Save our state
 {
 cgiDecodeFull(jsonText, jsonText, strlen(jsonText));
 struct jsonElement *collectionElements = jsonParse(jsonText);
 struct track *collectionList = parseJsonElements(collectionElements);
 
 updateHub(cart, db, collectionList, nameHash);
 }
 
 static void buildNameHash(struct hash *nameHash, struct trackDb *list)
 {
 if (list == NULL)
     return;
 
 struct trackDb *tdb = list;
 for(tdb = list; tdb;  tdb = tdb->next)
     {
     hashAdd(nameHash, trackHubSkipHubName(tdb->track), tdb);
     buildNameHash(nameHash, tdb->subtracks);
     }
 }
 
 static struct trackDb *traverseTree(struct trackDb *oldList, struct hash *groupHash)
 // add acceptable tracks to our tree
 {
 struct trackDb *newList = NULL, *tdb, *tdbNext;
 
 for(tdb = oldList;  tdb ; tdb = tdbNext)
     {
     tdbNext = tdb->next;
     if (tdb->subtracks)
         {
         tdb->subtracks = traverseTree(tdb->subtracks, groupHash);
 
         if (tdb->subtracks)
             {
             hashStore(groupHash, tdb->grp);
             slAddHead(&newList, tdb);
             }
         }
     else
         {
         if (trackCanBeAdded(tdb))
             {
             hashStore(groupHash, tdb->grp);
             slAddHead(&newList, tdb);
             }
         }
     }
 slReverse(&newList);
 
 return newList;
 }
 
 static void pruneTrackList(struct trackDb **fullTrackList, struct grp **fullGroupList)
 // drop track types we don't grok yet
 {
 struct hash *groupHash = newHash(5);
 
 *fullTrackList = traverseTree(*fullTrackList, groupHash);
 struct grp *newGroupList = NULL, *grp, *nextGrp;
 
 for (grp = *fullGroupList; grp; grp = nextGrp)
     {
     nextGrp = grp->next;
 
     if (hashLookup(groupHash, grp->name))
         slAddHead(&newGroupList, grp);
     }
 slReverse(&newGroupList);
 *fullGroupList = newGroupList;
 }
 
 static struct trackDb *addSupers(struct trackDb *trackList)
 /* Insert supertracks into the hierarchy. */
 {
 struct trackDb *newList = NULL;
 struct trackDb *tdb, *nextTdb;
 struct hash *superHash = newHash(5);
 
 for(tdb = trackList; tdb;  tdb = nextTdb)
     {
     nextTdb = tdb->next;
 
     if (tdb->parent)
         {
         // part of a super track
         if (hashLookup(superHash, tdb->parent->track) == NULL)
             {
             hashStore(superHash, tdb->parent->track);
 
             slAddHead(&newList, tdb->parent);
             }
         slAddHead(&tdb->parent->subtracks, tdb);
         }
     else
         slAddHead(&newList, tdb);
     }
 
 slReverse(&newList);
 
 return newList;
 }
 
 static void outOneTdb(char *db, struct sqlConnection *conn, FILE *f, struct trackDb *tdb, int numTabs)
 /* Put out a single trackDb entry to our collections hub. */
 {
 char *tabs = "";
 if (numTabs == 1)
     tabs = "\t";
 else if (numTabs == 2)
     tabs = "\t\t";
 else if (numTabs == 3)
     tabs = "\t\t\t";
 
 struct hashEl *hel = hashLookup(tdb->settingsHash, "track");
 fprintf(f, "%s%s %s\n", tabs,hel->name, trackHubSkipHubName((char *)hel->val));
 
 char *dataUrl = NULL;
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 if (bigDataUrl == NULL)
     {
     if (startsWith("bigWig", tdb->type))
         dataUrl = getSqlBigWig(conn, db, tdb);
     }
 
 struct hashCookie cookie = hashFirst(tdb->settingsHash);
 while ((hel = hashNext(&cookie)) != NULL)
     {
     if (sameString("parent", hel->name))
         fprintf(f, "%s%s %s\n", tabs,hel->name, trackHubSkipHubName((char *)hel->val));
     else if (!(sameString("track", hel->name) || sameString("polished", hel->name) || sameString("group", hel->name)))
         fprintf(f, "%s%s %s\n", tabs,hel->name, (char *)hel->val);
     }
 
 if (bigDataUrl == NULL)
     {
     if (dataUrl != NULL)
         fprintf(f, "%sbigDataUrl %s\n", tabs,dataUrl);
     }
 
 fprintf(f, "\n");
 }
 
 static void outTrackDbList(char *db, struct sqlConnection *conn, FILE *f, char *hubName, struct trackDb *list, char *collectionName, struct trackDb *newTdb,  int numTabs)
 /* Put a list of trackDb entries into a collection, adding a new track to the collection. */
 {
 if (list == NULL)
     return;
 
 struct trackDb *tdb;
 for(tdb = list; tdb; tdb = tdb->next)
     {
     if (tdb->grp != NULL)
         if ((hubName == NULL) || differentString(hubName, tdb->grp))
                 continue;
 
     outOneTdb(db, conn, f, tdb, numTabs);
 
     struct hashEl *hel = hashLookup(tdb->settingsHash, "track");
     if ((hel != NULL) && (hel->val != NULL) &&  sameString((char *)hel->val, collectionName))
         outOneTdb(db, conn, f, newTdb, numTabs + 1);
 
     outTrackDbList(db, conn, f, hubName,  tdb->subtracks, collectionName, newTdb, numTabs + 1);
     }
 }
 
 static void doAddTrack(struct cart *cart, char *db, struct trackDb *trackList,  char *trackName, char *collectionName, struct hash *nameHash)
 /* Add a track to a collection in a hub. */
 {
 char *fileName = getHubName(cart, db);
 char *hubName = hubNameFromUrl(fileName);
 FILE *f = fopen(fileName, "w");
 struct trackDb *newTdb = hashMustFindVal(nameHash, trackHubSkipHubName(trackName));
 hashReplace(newTdb->settingsHash, "track", makeUnique(nameHash, trackName));
 hashReplace(newTdb->settingsHash, "parent", trackHubSkipHubName(collectionName));
 
 outHubHeader(f, db);
 struct sqlConnection *conn = hAllocConn(db);
 modifyName(newTdb, hubName, NULL);
 outTrackDbList(db, conn, f, hubName, trackList, collectionName, newTdb,  0);
 
 hFreeConn(&conn);
 fclose(f);
 }
 
 static void doMiddle(struct cart *cart)
 /* Set up globals and make web page */
 {
 char *db;
 char *genome;
 getDbAndGenome(cart, &db, &genome, oldVars);
 initGenbankTableNames(db);
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 struct trackDb *trackList;
 struct grp *groupList;
 cartTrackDbInit(cart, &trackList, &groupList, TRUE);
 pruneTrackList(&trackList, &groupList);
 
 struct trackDb *superList = addSupers(trackList);
 struct hash *nameHash = newHash(5);
 buildNameHash(nameHash, superList);
 
 char *cmd = cartOptionalString(cart, "cmd");
 if (cmd == NULL)
     {
     doMainPage(cart, db, groupList, superList);
     }
 else if (sameString("addTrack", cmd))
     {
     char *trackName = cgiString("track");
     char *collectionName = cgiString("collection");
     doAddTrack(cart, db, superList, trackName, collectionName, nameHash);
     apiOut("{\"serverSays\": \"added %s to collection\"}", NULL);
     }
 else if (sameString("newCollection", cmd))
     {
     char *trackName = cgiString("track");
     char *collectionName = makeUnique(nameHash, "coll");
     char *shortLabel = "New Collection";
     char *longLabel = "Description of New Collection";
     struct trackDb *tdb;
 
     AllocVar(tdb);
     slAddHead(&superList, tdb);
     tdb->settingsHash = newHash(5);
     tdb->type = cloneString("wig");
 
     hashAdd(tdb->settingsHash, "track", collectionName);
     hashAdd(tdb->settingsHash, "shortLabel", shortLabel);
     hashAdd(tdb->settingsHash, "longLabel", longLabel);
     hashAdd(tdb->settingsHash, "autoScale", "on");
     hashAdd(tdb->settingsHash, "compositeTrack", "on");
     hashAdd(tdb->settingsHash, "aggregate", "none");
     hashAdd(tdb->settingsHash, "type", "wig");
     hashAdd(tdb->settingsHash, "visibility", "full");
     hashAdd(tdb->settingsHash, "color", "0,0,0");
     hashAdd(tdb->settingsHash, CUSTOM_COMPOSITE_SETTING, "on");
 
     doAddTrack(cart, db, superList, trackName, collectionName, nameHash);
     apiOut("{\"serverSays\": \"new %s to collection\"}", NULL);
     }
 else if (sameString("saveCollection", cmd))
     {
     char *jsonIn = cgiUsualString("jsonp", NULL);
     doAjax(cart, db, jsonIn, nameHash);
     apiOut("{\"serverSays\": \"Collections gaved successfully.\"}", NULL);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 long enteredMainTime = clock1000();
 cgiSpoof(&argc, argv);
 
 boolean isCommandLine = (cgiOptionalString("cgiSpoof") != NULL);
 if (!isCommandLine)
     htmlPushEarlyHandlers(); /* Make errors legible during initialization. */
 oldVars = hashNew(10);
 
 cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars);
 
 if (! isCommandLine)
     cgiExitTime("hgCollection", enteredMainTime);
 return 0;
 }