bf229bca8bf92e11feb9aa64a52a90974fc2f375
braney
  Wed Sep 27 12:09:42 2017 -0700
clean up C code, add support for supertracks in Available Tracks

diff --git src/hg/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c
index 2b230cb..d0f48b3 100644
--- src/hg/hgCollection/hgCollection.c
+++ src/hg/hgCollection/hgCollection.c
@@ -9,88 +9,55 @@
 #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 cart *cart;		/* CGI and other variables */
 struct hash *oldVars = NULL;	/* The cart before new cgi stuff added. */
-char *genome = NULL;		/* Name of genome - mouse, human, etc. */
-char *database = NULL;		/* Current genome database - hg17, mm5, etc. */
-char *regionType = NULL;	/* genome, ENCODE pilot regions, or specific position range. */
-struct grp *fullGroupList = NULL;	/* List of all groups. */
-struct trackDb *fullTrackList = NULL;	/* List of all tracks in database. */
- struct pipeline *compressPipeline = (struct pipeline *)NULL;
-
-
 // Null terminated list of CGI Variables we don't want to save permanently:
 char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", "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;
 };
 
 struct trackDbRef 
 {
 struct trackDbRef *next;
 struct trackDb *tdb;
 int order;
 };
 
-char *getString(char **input)
-// grab a quoted string out of text blob
-{
-char *ptr = *input;
-
-if (*ptr != '"')
-    errAbort("string must start with \"");
-ptr++;
-char *ret = ptr;
-for(; *ptr != '"'; ptr++)
-    ;
-*ptr = 0;
-ptr++;
-
-if (*ptr == ',')
-    ptr++;
-
-if (startsWith("coll_", ret))
-    ret = ret + 5;
-
-*input = ptr;
-return ret;
-}
-
-char *makeUnique(struct hash *nameHash, char *name)
+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);
@@ -163,31 +130,31 @@
 jsInlineF("</li>");
 }
 
 static void outHubHeader(FILE *f, char *db, char *hubName)
 // 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(char *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, hubName);
     fclose(f);
@@ -203,176 +170,178 @@
 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;
 }
 
-bool isSubtrackVisible(struct trackDb *tdb)
+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;
 }
 
 
-bool isParentVisible( struct trackDb *tdb)
+static bool isParentVisible(struct cart *cart, struct trackDb *tdb)
 // Are this track's parents visible?
 {
 if (tdb->parent == NULL)
     return TRUE;
 
-if (!isParentVisible(tdb->parent))
+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;
 }
 
 
-void checkForVisible(struct trackDbRef **list, struct trackDb *tdb)
+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(list, subTdb);
+        checkForVisible(cart, list, subTdb);
     }
 else
     {
-    if (isParentVisible(tdb) &&  isSubtrackVisible(tdb))
+    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);
         }
     }
 }
 
-int tdbRefCompare (const void *va, const void *vb)
+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);
 }       
 
-void addVisibleTracks()
+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 = fullTrackList; tdb; tdb = tdb->next)
+for(tdb = trackList; tdb; tdb = tdb->next)
     {
-    checkForVisible(&tdbRefList, tdb);
+    checkForVisible(cart, &tdbRefList, tdb);
     }
 
 slSort(&tdbRefList, tdbRefCompare);
 
 jsInlineF("<ul>");
 jsInlineF("<li data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop' 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>");
 }
 
-void doTable()
+static void doTable(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList)
 // output the tree table
 {
-char *hubName = hubNameFromUrl(getHubName(database));
+char *hubName = hubNameFromUrl(getHubName(cart, db));
 struct grp *curGroup;
-for(curGroup = fullGroupList; curGroup;  curGroup = curGroup->next)
+for(curGroup = groupList; curGroup;  curGroup = curGroup->next)
     {
     if ((hubName != NULL) && sameString(curGroup->name, hubName))
         break;
     }
 if (curGroup != NULL)
     {
     // print out all the tracks in this group
     struct trackDb *tdb;
     jsInlineF("$('#currentCollection').append(\"");
-    for(tdb = fullTrackList; tdb;  tdb = tdb->next)
+    for(tdb = trackList; tdb;  tdb = tdb->next)
         {
         if (sameString(tdb->grp, hubName))
             {
             jsInlineF("<div id='%s' shortLabel='%s'>", trackHubSkipHubName(tdb->track), tdb->shortLabel);
             jsInlineF("<ul>");
             printGroup("collections", tdb, TRUE, TRUE);
             jsInlineF("</ul>");
             jsInlineF("</div>");
+            printf("ignoring %s\n", tdb->track);
+            continue;
             }
         }
     jsInlineF("\");\n");
     
     // print out all the tracks in this group
     jsInlineF("$('#collectionList').append(\"");
-    for(tdb = fullTrackList; tdb;  tdb = tdb->next)
+    for(tdb = trackList; tdb;  tdb = tdb->next)
         {
         if (sameString(tdb->grp, hubName))
             {
             jsInlineF("<li data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop' id='%s'  name='%s'>%s</li>", trackHubSkipHubName(tdb->track),trackHubSkipHubName(tdb->track), tdb->shortLabel);
             //printGroup("collections", tdb, TRUE, TRUE);
             }
         }
     jsInlineF("\");\n");
     }
 jsInlineF("$('#tracks').append(\"");
-addVisibleTracks();
-for(curGroup = fullGroupList; curGroup;  curGroup = curGroup->next)
+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' name='%s'>%s", curGroup->name, curGroup->label );
     struct trackDb *tdb;
     jsInlineF("<ul>");
-    for(tdb = fullTrackList; tdb;  tdb = tdb->next)
+    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");
 }
 
@@ -405,82 +374,65 @@
 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");
 }
 
-void doMainPage()
+static void doMainPage(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList)
 /* Print out initial HTML of control page. */
 {
-webStartGbNoBanner(cart, database, "Collections");
+webStartGbNoBanner(cart, db, "Collections");
 webIncludeResourceFile("gb.css");
 webIncludeResourceFile("spectrum.min.css");
 webIncludeResourceFile("hgGtexTrackSettings.css");
 
 webIncludeFile("inc/hgCollection.html");
 
 printHelp();
-doTable();
+doTable(cart, db, groupList, trackList);
 
 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/jquery-1.12.1.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);
 }
 
-char *getUrl(struct sqlConnection *conn, char *db,  struct track *track, struct hash *nameHash)
-// get the bigDataUrl for a track
-{
-struct trackDb *tdb = hashMustFindVal(nameHash, track->name);
-
-if (tdb == NULL)
-    errAbort("cannot find trackDb for %s\n", track->name);
-
-char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
-if (bigDataUrl == NULL)
-    {
-    if (startsWith("bigWig", tdb->type))
-        bigDataUrl = getSqlBigWig(conn, db, tdb);
-    }
-return bigDataUrl;
-}
-
-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)
+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");
 char *tabs = "\t";
 if (numTabs == 2)
     tabs = "\t\t";
 
 if (bigDataUrl == NULL)
     {
     if (startsWith("bigWig", tdb->type))
         dataUrl = getSqlBigWig(conn, db, tdb);
     }
 struct hashCookie cookie = hashFirst(tdb->settingsHash);
 struct hashEl *hel;
@@ -511,35 +463,30 @@
 char *shortLabel = collection->shortLabel;
 char *longLabel = collection->longLabel;
 fprintf(f,"track %s\n\
 shortLabel %s\n\
 compositeTrack on\n\
 autoScale on\n\
 longLabel %s\n\
 %s on\n\
 color %ld,%ld,%ld \n\
 type wig \n\
 visibility full\n\n", parent, shortLabel, longLabel, CUSTOM_COMPOSITE_SETTING,
  0xff& (collection->color >> 16),0xff& (collection->color >> 8),0xff& (collection->color));
 
 }
 
-int snakePalette2[] =
-{
-0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5
-};
-
 static char *skipColl(char *str)
 {
 if (startsWith("coll_", str))
     return &str[5];
 return str;
 }
 
 static int outView(FILE *f, struct sqlConnection *conn, char *db, struct track *view, char *parent, struct hash *nameHash, struct hash *collectionNameHash, int priority)
 // output a view to a trackhub
 {
 fprintf(f,"\ttrack %s\n\
 \tshortLabel %s\n\
 \tlongLabel %s\n\
 \tview %s \n\
 \tcontainer mathWig\n\
@@ -553,34 +500,34 @@
 fprintf(f, "\n");
 
 //int useColor = 0;
 struct track *track = view->trackList;
 for(; track; track = track->next)
     {
     struct trackDb *tdb = hashMustFindVal(nameHash, skipColl(track->name));
 
     outTdb(conn, db, f, skipColl(track->name),tdb, view->name, track->visibility, track->color, track,  nameHash, collectionNameHash, 2, priority++);
     //useColor++;
     }
 
 return priority;
 }
 
-void updateHub(char *db, struct track *collectionList, struct hash *nameHash)
+static void updateHub(struct cart *cart, char *db, struct track *collectionList, struct hash *nameHash)
 // save our state to the track hub
 {
-char *hubName = getHubName(db);
+char *hubName = getHubName(cart, db);
 
 chmod(hubName, 0666);
 FILE *f = mustOpen(hubName, "w");
 struct hash *collectionNameHash = newHash(6);
 
 outHubHeader(f, db, hubName);
 //int useColor = 0;
 struct track *collection;
 struct sqlConnection *conn = hAllocConn(db);
 for(collection = collectionList; collection; collection = collection->next)
     {
     outComposite(f, collection);
     struct trackDb *tdb;
     struct track *track;
     int priority = 1;
@@ -595,49 +542,49 @@
             tdb = hashMustFindVal(nameHash, track->name);
 
             outTdb(conn, db, f, track->name,tdb, collection->name, track->visibility, track->color, track,  nameHash, collectionNameHash, 1, priority++);
             /*
             useColor++;
             if (useColor == (sizeof snakePalette2 / sizeof(int)))
                 useColor = 0;
                 */
             }
         }
     }
 fclose(f);
 hFreeConn(&conn);
 }
 
-unsigned long hexStringToLong(char *str)
+static unsigned long hexStringToLong(char *str)
 {
 /*
 char buffer[1024];
 
 strcpy(buffer, "0x");
 strcat(buffer, &str[1]);
 */
 
 return strtol(&str[1], NULL, 16);
 }
 
 struct jsonParseData
 {
 struct track **collectionList;
 struct hash *trackHash;
 };
 
-void jsonObjStart(struct jsonElement *ele, char *name,
+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);
@@ -674,38 +621,38 @@
     }
 }
 
 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;
 }
 
-void doAjax(char *db, char *jsonText, struct hash *nameHash)
+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(db, collectionList, nameHash);
+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);
     }
 }
 
@@ -748,63 +695,97 @@
 
 *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;
 }
 
-void doMiddle(struct cart *theCart)
+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 doMiddle(struct cart *cart)
 /* Set up globals and make web page */
 {
-cart = theCart;
-getDbAndGenome(cart, &database, &genome, oldVars);
+char *db;
+char *genome;
+getDbAndGenome(cart, &db, &genome, oldVars);
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
-cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE);
-pruneTrackList(&fullTrackList, &fullGroupList);
+
+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, fullTrackList);
+buildNameHash(nameHash, superList);
 
 char *jsonIn = cgiUsualString("jsonp", NULL);
 fprintf(stderr, "BRANEY %s\n", jsonIn);
 if (jsonIn != NULL)
     {
-    doAjax(database, jsonIn, nameHash);
+    doAjax(cart, db, jsonIn, nameHash);
     apiOut("{\"serverSays\": \"Collections saved successfully.\"}", NULL);
     }
 else
     {
-    doMainPage();
+    doMainPage(cart, db, groupList, superList);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 long enteredMainTime = clock1000();
-
-initGenbankTableNames(database);
-
 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;
 }