ccbd240668585b6eb8eec4f244a56f5d4660288b
tdreszer
  Tue Oct 19 13:39:25 2010 -0700
Fixed number 18 on Katrina's list.  Supertrack childen were showing as visibile when their parent was hide
diff --git src/hg/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c
index 57b6e16..e812f90 100644
--- src/hg/hgTracks/searchTracks.c
+++ src/hg/hgTracks/searchTracks.c
@@ -1,874 +1,873 @@
 /* Track search code used by hgTracks CGI */
 
 #include "common.h"
 #include "searchTracks.h"
 #include "hCommon.h"
 #include "memalloc.h"
 #include "obscure.h"
 #include "dystring.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "hPrint.h"
 #include "htmshell.h"
 #include "cart.h"
 #include "hgTracks.h"
 #include "web.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "mdb.h"
 #include "trix.h"
 #include "jsHelper.h"
 #include "imageV2.h"
 
 static char const rcsid[] = "$Id: searchTracks.c,v 1.11 2010/06/11 18:21:40 larrym Exp $";
 
 #define ANYLABEL "Any"
 #define METADATA_NAME_PREFIX "hgt.metadataName"
 #define METADATA_VALUE_PREFIX "hgt.metadataValue"
 
 static int gCmpGroup(const void *va, const void *vb)
 /* Compare groups based on label. */
 {
 const struct group *a = *((struct group **)va);
 const struct group *b = *((struct group **)vb);
 return strcmp(a->label, b->label);
 }
 
 // Would like to do a radio button choice ofsorts
 #define SORT_BY_VAR           "hgt_sortFound"
 enum sortBy
     {
     sbRelevance=0,
     sbAbc      =1,
     sbHierarchy=2,
     };
 static int gCmpTrackHierarchy(const void *va, const void *vb)
 /* Compare tracks based on longLabel. */
 {
 const struct slRef *aa = *((struct slRef **)va);
 const struct slRef *bb = *((struct slRef **)vb);
 const struct track *a = ((struct track *) aa->val);
 const struct track *b = ((struct track *) bb->val);
      if ( tdbIsFolder(a->tdb) && !tdbIsFolder(b->tdb))
         return -1;
 else if (!tdbIsFolder(a->tdb) &&  tdbIsFolder(b->tdb))
         return 1;
      if ( tdbIsContainer(a->tdb) && !tdbIsContainer(b->tdb))
         return -1;
 else if (!tdbIsContainer(a->tdb) &&  tdbIsContainer(b->tdb))
         return 1;
      if (!tdbIsContainerChild(a->tdb) &&  tdbIsContainerChild(b->tdb))
         return -1;
 else if ( tdbIsContainerChild(a->tdb) && !tdbIsContainerChild(b->tdb))
         return 1;
 return strcasecmp(a->longLabel, b->longLabel);
 }
 
 static int gCmpTrack(const void *va, const void *vb)
 /* Compare tracks based on longLabel. */
 {
 const struct slRef *aa = *((struct slRef **)va);
 const struct slRef *bb = *((struct slRef **)vb);
 const struct track *a = ((struct track *) aa->val);
 const struct track *b = ((struct track *) bb->val);
 return strcasecmp(a->longLabel, b->longLabel);
 }
 
 static void findTracksSort(struct slRef **pTrack, boolean simpleSearch, enum sortBy sortBy)
 {
 if (sortBy == sbHierarchy)
     slSort(pTrack, gCmpTrackHierarchy);
 else if (sortBy == sbAbc)
     slSort(pTrack, gCmpTrack);
 else
     slReverse(pTrack);
 }
 
 
 // XXXX make a matchString function to support "contains", "is" etc. and wildcards in contains
 
 //    ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) ||
 
 static boolean isNameMatch(struct track *track, char *str, char *op)
 {
 return str && strlen(str) &&
     ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) ||
     (sameString(op, "is") && !strcasecmp(track->longLabel, str)) ||
     (sameString(op, "contains") && containsStringNoCase(track->shortLabel, str) != NULL) ||
     (sameString(op, "contains") && containsStringNoCase(track->longLabel, str) != NULL));
 }
 
 static boolean isDescriptionMatch(struct track *track, char **words, int wordCount)
 // We parse str and look for every word at the start of any word in track description (i.e. google style).
 {
 if(words)
     {
     // We do NOT lookup up parent hierarchy for html descriptions.
     char *html = track->tdb->html;
     if(!isEmpty(html))
         {
         /* This probably could be made more efficient by parsing the html into some kind of b-tree, but I am assuming
            that the inner html loop while only happen for 1-2 words for vast majority of the tracks. */
 
         int i, numMatches = 0;
         html = stripRegEx(html, "<[^>]*>", REG_ICASE);
         for(i = 0; i < wordCount; i++)
             {
             char *needle = words[i];
             char *haystack, *tmp = cloneString(html);
             boolean found = FALSE;
             while((haystack = nextWord(&tmp)))
                 {
                 char *ptr = strstrNoCase(haystack, needle);
                 if(ptr != NULL && ptr == haystack)
                     {
                     found = TRUE;
                     break;
                     }
                 }
             if(found)
                 numMatches++;
             else
                 break;
             }
         if(numMatches == wordCount)
             return TRUE;
         }
     }
 return FALSE;
 }
 
 static int getTermArray(struct sqlConnection *conn, char ***pLabels, char ***pTerms, char *type)
 // Pull out all term fields from ra entries with given type
 // Returns count of items found and items via the terms argument.
 {
 int ix = 0, count = 0;
 char **labels;
 char **values;
 struct slPair *pairs = mdbValLabelSearch(conn, type, MDB_VAL_STD_TRUNCATION, TRUE, FALSE); // Tables not files
 count = slCount(pairs) + 1; // make room for "Any"
 AllocArray(labels, count);
 AllocArray(values, count);
 labels[ix] = cloneString(ANYLABEL);
 values[ix] = cloneString(ANYLABEL);
 struct slPair *pair = NULL;
 while((pair = slPopHead(&pairs)) != NULL)
     {
     ix++;
     labels[ix] = pair->name;
     values[ix] = pair->val;
     freeMem(pair);
     }
 *pLabels = labels;
 *pTerms = values;
 return count;
 }
 
 static int metaDbVars(struct sqlConnection *conn, char *** metaVars, char *** metaLabels)
 // Search the assemblies metaDb table; If name == NULL, we search every metadata field.
 {
 char query[256];
 #define WHITE_LIST_COUNT 35
 #ifdef WHITE_LIST_COUNT
 #define WHITE_LIST_VAR 0
 #define WHITE_LIST_LABEL 1
 char *whiteList[WHITE_LIST_COUNT][2] = {
     {"age",              "Age of experimental organism"},
     {"antibody",         "Antibody or target protein"},
     {"origAssembly",     "Assembly originally mapped to"},
     {"cell",             "Cell, tissue or DNA sample"},
     {"localization",     "Cell compartment"},
     {"control",          "Control or Input for ChIPseq"},
     //{"controlId",        "ControlId - explicit relationship"},
     {"dataType",         "Experiment type"},
     {"dataVersion",      "ENCODE release"},
     //{"fragLength",       "Fragment Length for ChIPseq"},
     //{"freezeDate",       "Gencode freeze date"},
     //{"level",            "Gencode level"},
     //{"annotation",       "Gencode annotation"},
     {"geoSample",        "GEO accession"},
     {"growthProtocol",   "Growth Protocol"},
     {"lab",              "Lab producing data"},
     {"labVersion",       "Lab specific details"},
     {"labExpId",         "Lab specific identifier"},
     {"softwareVersion",  "Lab specific informatics"},
     {"protocol",         "Library Protocol"},
     {"mapAlgorithm",     "Mapping algorithm"},
     {"readType",         "Paired/Single reads lengths"},
     {"grant",            "Principal Investigator"},
     {"replicate",        "Replicate number"},
     //{"restrictionEnzyme","Restriction Enzyme used"},
     //{"ripAntibody",      "RIP Antibody"},
     //{"ripTgtProtein",    "RIP Target Protein"},
     {"rnaExtract",       "RNA Extract"},
     {"seqPlatform",      "Sequencing Platform"},
     {"setType",          "Experiment or Input"},
     {"sex",              "Sex of organism"},
     {"strain",           "Strain of organism"},
     {"subId",            "Submission Id"},
     {"treatment",        "Treatment"},
     {"view",             "View - Peaks or Signals"},
 };
 // FIXME: The whitelist should be a table or ra
 // FIXME: The whitelist should be in list order
 // FIXME: Should read in list, then verify that an mdb val exists.
 
 char **retVar = needMem(sizeof(char *) * WHITE_LIST_COUNT);
 char **retLab = needMem(sizeof(char *) * WHITE_LIST_COUNT);
 int ix,count;
 for(ix=0,count=0;ix<WHITE_LIST_COUNT;ix++)
     {
     safef(query, sizeof(query), "select count(*) from metaDb where var = '%s'",whiteList[ix][WHITE_LIST_VAR]);
     if(sqlQuickNum(conn,query) > 0)
         {
         retVar[count] = whiteList[ix][WHITE_LIST_VAR];
         retLab[count] = whiteList[ix][WHITE_LIST_LABEL];
         count++;
         }
     }
 if(count == 0)
     {
     freez(&retVar);
     freez(&retLab);
     }
 *metaVars = retVar;
 *metaLabels = retLab;
 return count;
 
 #else///ifndef WHITE_LIST_COUNT
 
 char **retVar;
 char **retLab;
 struct slName *el, *varList = NULL;
 struct sqlResult *sr = NULL;
 char **row = NULL;
 
 safef(query, sizeof(query), "select distinct var from metaDb order by var");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     slNameAddHead(&varList, row[0]);
 sqlFreeResult(&sr);
 retVar = needMem(sizeof(char *) * slCount(varList));
 retLab = needMem(sizeof(char *) * slCount(varList));
 slReverse(&varList);
 //slNameSort(&varList);
 int count = 0;
 for (el = varList; el != NULL; el = el->next)
     {
     retVar[count] = el->name;
     retLab[count] = el->name;
     count++;
     }
 *metaVars = retVar;
 *whiteLabels = retLab;
 return count;
 #endif///ndef WHITE_LIST_COUNT
 }
 
 #define MAX_FOUND_TRACKS 100
 #define FOUND_TRACKS_PAGING "hgt_startFrom"
 void findTracksPageLinks(int tracksFound, int startFrom)
 {
 if (tracksFound <= MAX_FOUND_TRACKS)
     return;
 
 // Opener
 int curPage  = (startFrom/MAX_FOUND_TRACKS) + 1;
 int endAt = startFrom+MAX_FOUND_TRACKS;
 if (endAt > tracksFound)
     endAt = tracksFound;
 hPrintf("<em>Listing %d - %d of %d tracks</em>&nbsp;&nbsp;&nbsp;",startFrom+1,endAt,tracksFound);
 
 // << and <
 hPrintf("<a href='' title='First page of found tracks' onclick='return findTracksPage(\"%s\",%d);'>&lt;&lt;</a>&nbsp;",FOUND_TRACKS_PAGING,0);
 if (startFrom >= MAX_FOUND_TRACKS)
     hPrintf("&nbsp;<a href='' title='Previous page of found tracks' onclick='return findTracksPage(\"%s\",%d);'>&lt;</a>&nbsp;",FOUND_TRACKS_PAGING,startFrom - MAX_FOUND_TRACKS);
 else
     hPrintf("&nbsp;<em>&lt;</em>&nbsp;");
 
 // page number links
 int lastPage = (tracksFound/MAX_FOUND_TRACKS);
 if ((tracksFound % MAX_FOUND_TRACKS) > 0)
     lastPage++;
 
 int thisPage = curPage - 3; // Window of 3 pages above and below
 if (thisPage < 1)
     thisPage = 1;
 for (;thisPage <= lastPage && thisPage <= curPage + 3; thisPage++)
     {
     if (thisPage != curPage)
         {
         int willStartAt = ((thisPage - 1) * MAX_FOUND_TRACKS);
         endAt = willStartAt+ MAX_FOUND_TRACKS;
         if (endAt > tracksFound)
             endAt = tracksFound;
         hPrintf("&nbsp;<a href='' title='Page %d (%d - %d) tracks' onclick='return findTracksPage(\"%s\",%d);'>%d</a>&nbsp;",
                 thisPage,willStartAt+1,endAt,FOUND_TRACKS_PAGING,((thisPage - 1) * MAX_FOUND_TRACKS),thisPage);
         }
     else
         hPrintf("&nbsp;<em>%d</em>&nbsp;",thisPage);
     }
 
 // > and >>
 if ((startFrom + MAX_FOUND_TRACKS) < tracksFound)
     hPrintf("&nbsp;<a href='' title='Next page of found tracks' onclick='return findTracksPage(\"%s\",%d);'>&gt;</a>&nbsp;",FOUND_TRACKS_PAGING,(startFrom + MAX_FOUND_TRACKS));
 else
     hPrintf("&nbsp;<em>&gt;</em>&nbsp;");
 thisPage =  tracksFound - (tracksFound % MAX_FOUND_TRACKS);
 if (thisPage == tracksFound)
     thisPage -= MAX_FOUND_TRACKS;
 hPrintf("&nbsp;<a href='' title='Last page of found tracks' onclick='return findTracksPage(\"%s\",%d);'>&gt;&gt;</a>\n",FOUND_TRACKS_PAGING,thisPage);
 }
 
 void doSearchTracks(struct group *groupList)
 {
 struct group *group;
 char *groups[128];
 char *labels[128];
 int numGroups = 1;
 groups[0] = ANYLABEL;
 labels[0] = ANYLABEL;
 char *currentTab = cartUsualString(cart, "hgt.currentSearchTab", "simpleTab");
 char *nameSearch = cartOptionalString(cart, "hgt.nameSearch");
 char *descSearch;
 char *groupSearch = cartOptionalString(cart, "hgt.groupSearch");
 boolean doSearch = sameString(cartOptionalString(cart, searchTracks), "Search") || cartUsualInt(cart, "hgt.forceSearch", 0) == 1;
 struct sqlConnection *conn = hAllocConn(database);
 boolean metaDbExists = sqlTableExists(conn, "metaDb");
 struct slRef *tracks = NULL;
 int numMetadataSelects, tracksFound = 0;
 int numMetadataNonEmpty = 0;
 char **mdbVar;
 char **mdbVal;
 struct hash *parents = newHash(4);
 boolean simpleSearch;
 struct trix *trix;
 char trixFile[HDB_MAX_PATH_STRING];
 char **descWords = NULL;
 int descWordCount = 0;
 boolean searchTermsExist = FALSE;
 int cols;
 char buf[64];
 
 if(sameString(currentTab, "simpleTab"))
     {
     descSearch = cartOptionalString(cart, "hgt.simpleSearch");
     simpleSearch = TRUE;
     freez(&nameSearch);
     freez(&groupSearch);
     }
 else
     {
     descSearch = cartOptionalString(cart, "hgt.descSearch");
     simpleSearch = FALSE;
     }
 
 trackList = getTrackList(&groupList, -2); // global
 makeGlobalTrackHash(trackList);
 
 // NOTE: This is necessary when container cfg by '*' results in vis changes
 // This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping.
 #ifdef SUBTRACKS_HAVE_VIS
 parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
 #endif///def SUBTRACKS_HAVE_VIS
 
 getSearchTrixFile(database, trixFile, sizeof(trixFile));
 trix = trixOpen(trixFile);
 slSort(&groupList, gCmpGroup);
 for (group = groupList; group != NULL; group = group->next)
     {
     groupTrackListAddSuper(cart, group);
     if (group->trackList != NULL)
         {
         groups[numGroups] = cloneString(group->name);
         labels[numGroups] = cloneString(group->label);
         numGroups++;
         if (numGroups >= ArraySize(groups))
             internalErr();
         }
     }
 
 safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database));
 webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
 
 hPrintf("<div style='max-width:1080px;'>");
 hPrintf("<form action='%s' name='SearchTracks' id='searchTracks' method='get'>\n\n", hgTracksName());
 cartSaveSession(cart);  // Creates hidden var of hgsid to avoid bad voodoo
 safef(buf, sizeof(buf), "%lu", clock1());
 cgiMakeHiddenVar("hgt_", buf);  // timestamps page to avoid browser cache
 
 
 hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
 hPrintf("<input type='hidden' name='hgt.currentSearchTab' id='currentSearchTab' value='%s'>\n", currentTab);
 hPrintf("<input type='hidden' name='hgt.delRow' value=''>\n");
 hPrintf("<input type='hidden' name='hgt.addRow' value=''>\n");
 hPrintf("<input type='hidden' name='hgt.forceSearch' value=''>\n");
 
 hPrintf("<div id='tabs' style='display:none; %s'>\n"
         "<ul>\n"
         "<li><a href='#simpleTab'><span>Search</span></a></li>\n"
         "<li><a href='#advancedTab'><span>Advanced</span></a></li>\n"
         "</ul>\n"
         "<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
 
 hPrintf("<table style='width:100%%;'><tr><td colspan='2'>");
 hPrintf("<input type='text' name='hgt.simpleSearch' id='simpleSearch' value='%s' style='max-width:1000px; width:100%%' onkeyup='findTracksSearchButtonsEnable(true);'>\n", descSearch == NULL ? "" : descSearch);
 hPrintf("</td></tr><tr><td>");
 if (simpleSearch && descSearch)
     searchTermsExist = TRUE;
 
 hPrintf("</table></div>\n"
         "<div id='advancedTab' style='width:inherit;'>\n"
         "<table cellSpacing=0 style='width:inherit;'>\n");
 
 cols = 7;
 
 // Track Name contains
 hPrintf("<tr><td colspan=3></td>");
 hPrintf("<td nowrap><b style='max-width:100px;'>Track&nbsp;Name:</b></td>");
 hPrintf("<td align='right'>contains</td>\n");
 hPrintf("<td colspan='%d'>", cols - 4);
 hPrintf("<input type='text' name='hgt.nameSearch' id='nameSearch' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px;'>", nameSearch == NULL ? "" : nameSearch);
 hPrintf("</td></tr>\n");
 
 
 // Description contains
 hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>");
 hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
 hPrintf("<td align='right'>contains</td>\n");
 hPrintf("<td colspan='%d'>", cols - 4);
 hPrintf("<input type='text' name='hgt.descSearch' id='descSearch' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px;'>",
         descSearch == NULL ? "" : descSearch);
 hPrintf("</td></tr>\n");
 if (!simpleSearch && descSearch)
     searchTermsExist = TRUE;
 
 hPrintf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>\n");
 hPrintf("<td><b style='max-width:100px;'>Group</b></td>");
 hPrintf("<td align='right'>is</td>\n");
 hPrintf("<td colspan='%d'>", cols - 4);
 cgiMakeDropListFull("hgt.groupSearch", labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%%;'");
 hPrintf("</td></tr>\n");
 if (!simpleSearch && groupSearch)
     searchTermsExist = TRUE;
 
 // figure out how many metadata selects are visible.
 int delSearchSelect = cartUsualInt(cart, "hgt.delRow", 0);   // 1-based row to delete
 int addSearchSelect = cartUsualInt(cart, "hgt.addRow", 0);   // 1-based row to insert after
 
 for(numMetadataSelects = 0;;)
     {
     char buf[256];
     safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
     char *str = cartOptionalString(cart, buf);
     if(isEmpty(str))
         break;
     else
         numMetadataSelects++;
     }
 
 if(delSearchSelect)
     numMetadataSelects--;
 if(addSearchSelect)
     numMetadataSelects++;
 
 if(numMetadataSelects)
     {
     mdbVar = needMem(sizeof(char *) * numMetadataSelects);
     mdbVal = needMem(sizeof(char *) * numMetadataSelects);
     int i;
     for(i = 0; i < numMetadataSelects; i++)
         {
         char buf[256];
         int offset;   // used to handle additions/deletions
         if(addSearchSelect > 0 && i >= addSearchSelect)
             offset = 0; // do nothing to offset (i.e. copy data from previous row)
         else if(delSearchSelect > 0 && i + 1 >= delSearchSelect)
             offset = 2;
         else
             offset = 1;
         safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, i + offset);
         mdbVar[i] = cloneString(cartOptionalString(cart, buf));
         if(!simpleSearch)
             {
             safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, i + offset);
             mdbVal[i] = cloneString(cartOptionalString(cart, buf));
             if(sameString(mdbVal[i], ANYLABEL))
                 mdbVal[i] = NULL;
             if(!isEmpty(mdbVal[i]))
                 numMetadataNonEmpty++;
             }
         }
     if(delSearchSelect > 0)
         {
         char buf[255];
         safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
         cartRemove(cart, buf);
         safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, numMetadataSelects + 1);
         cartRemove(cart, buf);
         }
     }
 else
     {
     // create defaults
     numMetadataSelects = 2;
     mdbVar = needMem(sizeof(char *) * numMetadataSelects);
     mdbVal = needMem(sizeof(char *) * numMetadataSelects);
     mdbVar[0] = "cell";
     mdbVar[1] = "antibody";
     mdbVal[0] = ANYLABEL;
     mdbVal[1] = ANYLABEL;
     }
 
 if(metaDbExists)
     {
     int i;
     char **mdbVars = NULL;
     char **mdbVarLabels = NULL;
     int count = metaDbVars(conn, &mdbVars,&mdbVarLabels);
 
     hPrintf("<tr><td colspan='%d' align='right' class='lineOnTop' style='height:20px; max-height:20px;'><em style='color:%s; width:200px;'>ENCODE terms</em></td></tr>", cols,COLOR_DARKGREY);
     for(i = 0; i < numMetadataSelects; i++)
         {
         char **terms = NULL, **labels = NULL;
         char buf[256];
         int len;
 
         hPrintf("<tr><td>\n");
         if(numMetadataSelects > 2 || i >= 2)
             {
             safef(buf, sizeof(buf), "return delSearchSelect(this, %d);", i + 1);
             hButtonWithOnClick(searchTracks, "-", "delete this row", buf);
             }
         else
             hPrintf("&nbsp;");
         hPrintf("</td><td>\n");
         safef(buf, sizeof(buf), "return addSearchSelect(this, %d);", i + 1);
         hButtonWithOnClick(searchTracks, "+", "add another row after this row", buf);
 
         hPrintf("</td><td>and&nbsp;</td><td colspan=3 nowrap>\n");
         safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, i + 1);
         cgiDropDownWithTextValsAndExtra(buf, mdbVarLabels, mdbVars,count,mdbVar[i],"class='mdbVar' onchange=findTracksMdbVarChanged(this)");
         hPrintf("</td><td nowrap style='max-width:600px;'>is\n");
         len = getTermArray(conn, &labels, &terms, mdbVar[i]);
         safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1);
         cgiMakeDropListFull(buf, labels, terms, len, mdbVal[i], "class='mdbVal' style='min-width:200px;' onchange='findTracksSearchButtonsEnable(true)'");
         if (!simpleSearch && mdbVal[i])
             searchTermsExist = TRUE;
         hPrintf("<span id='helpLink%d'>help</span></td>\n", i + 1);
         hPrintf("</tr>\n");
         }
     }
 
 hPrintf("</table>\n");
 hPrintf("</div>\n</div>\n");
 
 hPrintf("<p><input type='submit' name='%s' id='searchSubmit' value='Search' style='font-size:14px;'>\n", searchTracks);
 hPrintf("<input type='button' name='clear' value='Clear' class='clear' style='font-size:14px;' onclick='findTracksClear();'>\n");
 hPrintf("<input type='submit' name='submit' value='Cancel' class='cancel' style='font-size:14px;'></p>\n");
 
 hPrintf("</form>\n");
 hPrintf("</div"); // Restricts to max-width:1000px;
 
 if(descSearch != NULL && !strlen(descSearch))
     descSearch = NULL;
 if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
     groupSearch = NULL;
 
 if(!isEmpty(descSearch))
     {
     char *tmp = cloneString(descSearch);
     char *val = nextWord(&tmp);
     struct slName *el, *descList = NULL;
     int i;
     while (val != NULL)
         {
         slNameAddTail(&descList, val);
         descWordCount++;
         val = nextWord(&tmp);
         }
     descWords = needMem(sizeof(char *) * descWordCount);
     for(i = 0, el = descList; el != NULL; i++, el = el->next)
         descWords[i] = strLower(el->name);
     }
 if (doSearch && simpleSearch && descWordCount <= 0)
     doSearch = FALSE;
 
 enum sortBy sortBy = cartUsualInt(cart,SORT_BY_VAR,sbRelevance);
 if(doSearch)
     {
     if(simpleSearch)
         {
         struct trixSearchResult *tsList;
         for(tsList = trixSearch(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next)
             {
             struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId);
             if (track != NULL)  // It is expected that this is NULL (e.g. when the trix references trackDb tracks which have no tables)
                 {
                 refAdd(&tracks, track);
                 tracksFound++;
                 }
             }
         }
     else if(!isEmpty(nameSearch) || descSearch != NULL || groupSearch != NULL || numMetadataNonEmpty)
         {
         // First do the metaDb searches, which can be done quickly for all tracks with db queries.
         struct hash *matchingTracks = newHash(0);
         struct slName *el, *metaTracks = NULL;
         int i;
 
         for(i = 0; i < numMetadataSelects; i++)
             {
             if(!isEmpty(mdbVal[i]))
                 {
                 struct slName *tmp = mdbObjSearch(conn, mdbVar[i], mdbVal[i], "is", MDB_VAL_STD_TRUNCATION, TRUE, FALSE);
                 if(metaTracks == NULL)
                     metaTracks = tmp;
                 else
                     metaTracks = slNameIntersection(metaTracks, tmp);
                 }
             }
         for (el = metaTracks; el != NULL; el = el->next)
             hashAddInt(matchingTracks, el->name, 1);
         for (group = groupList; group != NULL; group = group->next)
             {
             if(groupSearch == NULL || sameString(group->name, groupSearch))
                 {
                 if (group->trackList != NULL)
                     {
                     struct trackRef *tr;
                     for (tr = group->trackList; tr != NULL; tr = tr->next)
                         {
                         struct track *track = tr->track;
                         if((isEmpty(nameSearch) || isNameMatch(track, nameSearch, "contains")) &&
                            (isEmpty(descSearch) || isDescriptionMatch(track, descWords, descWordCount)) &&
                           (!numMetadataNonEmpty || hashLookup(matchingTracks, track->track) != NULL))
                             {
                             if (track != NULL)
                                 {
                                 tracksFound++;
                                 refAdd(&tracks, track);
                                 }
                             else
                                 warn("found group track is NULL.");
                             }
                         if (track->subtracks != NULL)
                             {
                             struct track *subTrack;
                             for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
                                 {
                                 if((isEmpty(nameSearch) || isNameMatch(subTrack, nameSearch, "contains")) &&
                                    (isEmpty(descSearch) || isDescriptionMatch(subTrack, descWords, descWordCount)) &&
                                    (!numMetadataNonEmpty || hashLookup(matchingTracks, subTrack->track) != NULL))
                                     {
                                     // XXXX to parent hash. - use tdb->parent instead.
                                     hashAdd(parents, subTrack->track, track);
                                     if (track != NULL)
                                         {
                                         tracksFound++;
                                         refAdd(&tracks, subTrack);
                                         }
                                     else
                                         warn("found subtrack is NULL.");
                                     }
                                 }
                             }
                         }
                     }
                 }
             }
         }
     if(tracksFound > 1)
         findTracksSort(&tracks,simpleSearch,sortBy);
     }
 
 hPrintf("<div id='found' style='display:none;'>\n"); // This div allows the clear button to empty it
 if(tracksFound < 1)
     {
     if(doSearch)
         hPrintf("<p>No tracks found</p>\n");
     }
 else
     {
     struct hash *tdbHash = makeTrackHash(database, chromName);
     hPrintf("<form action='%s' name='SearchTracks' id='searchResultsForm' method='post'>\n\n", hgTracksName());
     cartSaveSession(cart);  // Creates hidden var of hgsid to avoid bad voodoo
 
     int startFrom = 0;
     hPrintf("<table id='foundTracks'>\n");
 
     // Opening view in browser button and foundTracks count
     #define ENOUGH_FOUND_TRACKS 10
     if(tracksFound >= ENOUGH_FOUND_TRACKS)
         {
         hPrintf("<tr><td nowrap colspan=3>\n");
         hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn'>");
         hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<FONT class='selCbCount'></font>\n");
 
         startFrom = cartUsualInt(cart,FOUND_TRACKS_PAGING,0);
         if (startFrom > 0 && startFrom < tracksFound)
             {
             int countUp = 0;
             for(countUp=0; countUp < startFrom;countUp++)
                 {
                 if (slPopHead(&tracks) == NULL) // memory waste
                     break;
                 }
             }
         hPrintf("</td><td align='right'>\n");
         findTracksPageLinks(tracksFound,startFrom);
         hPrintf("</td></tr>\n");
         }
 
     // Begin foundTracks table
     //hPrintf("<table id='foundTracks'><tr><td colspan='2'>\n");
     hPrintf("<tr><td colspan='2'>\n");
     hPrintf("</td><td align='right'>\n");
     #define PM_BUTTON "<IMG height=18 width=18 onclick=\"return findTracksCheckAllWithWait(%s);\" id='btn_%s' src='../images/%s' title='%s all found tracks'>"
     hPrintf("</td></tr><tr bgcolor='#%s'><td>",HG_COL_HEADER);
     hPrintf(PM_BUTTON,"true",  "plus_all",   "add_sm.gif",  "Select");
     hPrintf(PM_BUTTON,"false","minus_all","remove_sm.gif","Unselect");
     hPrintf("</td><td><b>Visibility</b></td><td colspan=2>&nbsp;&nbsp;<b>Track Name</b>\n");
 
     // Sort options?
     if(tracksFound >= ENOUGH_FOUND_TRACKS)
         {
         hPrintf("<span style='float:right;'>Sort:");
         cgiMakeOnClickRadioButton(SORT_BY_VAR, "0", (sortBy == sbRelevance),"onchange=\"findTracksSortNow(this);\"");
         hPrintf("by Relevance");
         cgiMakeOnClickRadioButton(SORT_BY_VAR, "1", (sortBy == sbAbc),      "onchange=\"findTracksSortNow(this);\"");
         hPrintf("Alphabetically");
         cgiMakeOnClickRadioButton(SORT_BY_VAR, "2",(sortBy == sbHierarchy), "onchange=\"findTracksSortNow(this);\"");
         hPrintf("by Hierarchy&nbsp;&nbsp;</span>\n");
         }
     hPrintf("</td></tr>\n");
 
     // Set up json for js functionality
     struct dyString *jsonTdbVars = NULL;
 
     int trackCount=0;
     boolean containerTrackCount = 0;
     struct slRef *ptr;
     while((ptr = slPopHead(&tracks)))
         {
         if(++trackCount > MAX_FOUND_TRACKS)
             break;
 
         struct track *track = (struct track *) ptr->val;
         jsonTdbSettingsBuild(&jsonTdbVars, track);
 
         if (tdbIsFolder(track->tdb)) // supertrack
             hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n","#EED5B7");//"#DEB887");//"#E6B426");//#FCECC0//COLOR_LTGREY);//COLOR_LTGREEN);//COLOR_TRACKLIST_LEVEL1);
         else if (tdbIsContainer(track->tdb))
             hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL3);
         else
             hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL2);
 
         hPrintf("<td align='center'>\n");
 
         // Determine visibility and checked state
-        track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, FALSE);
+        track->visibility = tdbVisLimitedByAncestors(cart, track->tdb, TRUE, TRUE);
         boolean checked = ( track->visibility != tvHide );
         if(tdbIsContainerChild(track->tdb))
             {
             //track->visibility = limitedVisFromComposite(track);
             checked = fourStateVisible(subtrackFourStateChecked(track->tdb,cart)); // Don't need all 4 states here.  Visible=checked&&enabled
             checked = (checked && ( track->visibility != tvHide )); // Checked is only if subtrack level vis is also set!
             }
 
         // Setup the check box
         #define CB_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s_sel' VALUE='%s'>"
         if (tdbIsContainerChild(track->tdb) || tdbIsFolderContent(track->tdb))  // subtracks and folder children get "_sel" var.  ("_sel" var is temporary on folder children)
             hPrintf(CB_HIDDEN_VAR,track->track,checked?"1":CART_VAR_EMPTY);
         #define CB_SEEN "<INPUT TYPE=CHECKBOX id='%s_sel_id' VALUE='on' class='selCb' onclick='findTracksClickedOne(this,true);'%s>"
         hPrintf(CB_SEEN,track->track,(checked?" CHECKED":""));
         hPrintf("</td><td>\n");
 
         // Setup the visibility drop down
         #define VIS_HIDDEN_VAR "<INPUT TYPE=HIDDEN disabled=true NAME='%s' VALUE='%s'>"
         hPrintf(VIS_HIDDEN_VAR,track->track,CART_VAR_EMPTY); // All tracks get vis hidden var
         char extra[512];
         if (tdbIsFolder(track->tdb))
             {
             safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track);
             hideShowDropDownWithClassAndExtra(track->track, (track->visibility != tvHide), "normalText visDD",extra);
-
             }
         else
             {
             safef(extra,sizeof(extra),"id='%s_id' onchange='findTracksChangeVis(this)'",track->track);
             hTvDropDownClassWithJavascript(NULL, track->visibility,track->canPack,"normalText seenVis",extra);
             }
 
         // If this is a container track, allow configuring...
         if (tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
             {
             containerTrackCount++;
             //hPrintf("&nbsp;<a href='hgTrackUi?db=%s&g=%s&hgt_searchTracks=1&hgt_searchTracks=Search' title='Configure this container track...'>*</a>&nbsp;",database,track->track);
             hPrintf("&nbsp;<a href='hgTrackUi?db=%s&g=%s&hgt_searchTracks=1&hgt_searchTracks=Search' title='Configure this container track...'><IMG SRC='../images/folderWrench.png'></a>&nbsp;",database,track->track);
             }
         hPrintf("</td>\n");
 
         // shortLabel has description popup and longLabel has "..." metadata
         hPrintf("<td><a target='_top' onclick=\"hgTrackUiPopUp('%s',true); return false;\" href='%s' title='Display track details'>%s</a></td>\n", track->track, trackUrl(track->track, NULL), track->shortLabel);
         hPrintf("<td>%s", track->longLabel);
         compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE, tdbHash);
         hPrintf("</td></tr>\n");
         }
     //hPrintf("</table>\n");
 
     // Closing view in browser button and foundTracks count
     hPrintf("<tr><td nowrap colspan=3>");
     hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='Return to Browser' class='viewBtn'>");
     hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<FONT class='selCbCount'></font>");
     if(tracksFound >= ENOUGH_FOUND_TRACKS)
         {
         hPrintf("</td><td align='right'>\n");
         findTracksPageLinks(tracksFound,startFrom);
         hPrintf("</td></tr>\n");
         }
     hPrintf("</table>\n");
 
     if(containerTrackCount > 0)
         hPrintf("<BR><IMG SRC='../images/folderWrench.png'>&nbsp;Tracks so marked are containers which group related data tracks.  Containers may need additional configuration (by clicking on the <IMG SRC='../images/folderWrench.png'> icon) before they can be viewed in the browser.<BR>\n");
         //hPrintf("* Tracks so marked are containers which group related data tracks.  These may not be visible unless further configuration is done.  Click on the * to configure these.<BR><BR>\n");
     hPrintf("\n</form>\n");
 
     // be done with json
     hWrites(jsonTdbSettingsUse(&jsonTdbVars));
     }
 
 #ifdef OMIT
 if(!doSearch)
     {
     hPrintf("<p><b>Recently Done</b><ul>\n"
         "<li>Can now page through found tracks 100 at a time.</li>"
         "<li>Added <IMG SRC='../images/folderWrench.png'> icon for contqainers with a configuration link.  Is this okay?</li>"
         "<li>SuperTracks can now be found.</li>"
         "<li>Configuration of superTrack children's vis should result in proper superTrack reshaping. (This is really an hgTrackUi feature.)</li>"
         "<li>Added sort toggle: Relevance, Alphabetically or by Hierarchy.</li>"
         "<li>Composite/view visibilites in hgTrackUi get reshaped to reflect found/selected subtracks.  (In demo1: only default state composites; demo2: all composites.)</li>"
         "<li>Non-data 'container' tracks (composites and supertracks) have '*' to mark them, and can be configured before displaying.  Better suggestions?</li>"
         "</ul></p>"
         "<p><b>Suggested improvments:</b><ul>\n"
         "<li>The metadata values will not be white-listed, but it would be nice to have more descriptive text for them.  A short label added to cv.ra?</li>"
         "<li>Look and feel of found track list (here) and composite subtrack list (hgTrackUi) should converge.  Jim suggests look and feel of hgTracks 'Configure Tracks...' list instead.</li>"
         "<li>Drop-down list of terms (cells, antibodies, etc.) should be multi-select with checkBoxes as seen in filterComposites. Perhaps saved for v2.0.</li>"
         "</ul></p>\n");
     }
 #endif///def OMIT
 hPrintf("</div"); // This div allows the clear button to empty it
 hFreeConn(&conn);
 webNewSection("About Track Search");
 if(metaDbExists)
     hPrintf("<p>Search for terms in track descriptions, groups, names, and ENCODE "
             "metadata.  If multiple terms are entered, only tracks with all terms "
             "will be part of the results.</p>");
 else
     hPrintf("<p>Search for terms in track descriptions, groups, and names. "
             "If multiple terms are entered, only tracks with all terms "
             "will be part of the results.</p>");
 hPrintf("<p><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
 
 webEndSectionTables();
 }