d781bc31ad6c4a86a3b8e1f0e78827a08c544128
tdreszer
  Fri Oct 1 11:05:56 2010 -0700
Fixing git mess (I hope) created from an accidental 'git add .'
diff --git src/hg/hgTracks/searchTracks.c.fxit src/hg/hgTracks/searchTracks.c.fxit
deleted file mode 100644
index eeff438..0000000
--- src/hg/hgTracks/searchTracks.c.fxit
+++ /dev/null
@@ -1,861 +0,0 @@
-/* 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 FINDTRACKS_SORT
-#ifdef FINDTRACKS_SORT
-#define SORT_BY_VAR           "findTracksSortBy"
-#define SORT_BY_ABC           "abc"
-#define SORT_BY_HIER          "hier"
-#define SORT_BY_REL           "rel"
-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 gCmpTrackReverseHierarchy(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 ( tdbIsContainerChild(a->tdb) && !tdbIsContainerChild(b->tdb))
-//        return -1;
-//else if (!tdbIsContainerChild(a->tdb) &&  tdbIsContainerChild(b->tdb))
-//        return 1;
-//     if ( tdbIsContainer(a->tdb) && !tdbIsContainer(b->tdb))
-//        return -1;
-//else if (!tdbIsContainer(a->tdb) &&  tdbIsContainer(b->tdb))
-//        return 1;
-//     if (!tdbIsFolder(a->tdb) &&  tdbIsFolder(b->tdb))
-//        return -1;
-//else if ( tdbIsFolder(a->tdb) && !tdbIsFolder(b->tdb))
-//        return 1;
-//return strcasecmp(a->longLabel, b->longLabel);
-//}
-#endif///def FINDTRACKS_SORT
-
-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)
-{
-#ifdef FINDTRACKS_SORT
-if (sortBy == sbHierarchy)
-    slSort(pTrack, gCmpTrackHierarchy);
-else if (sortBy == sbAbc)
-    slSort(pTrack, gCmpTrack);
-else //if(simpleSearch)
-    slReverse(pTrack);
-//else
-//    slSort(pTrack, gCmpTrackReverseHierarchy);
-#else///ifndef FINDTRACKS_SORT
-if (simpleSearch)
-    slReverse(pTrack);
-else
-    slSort(&tracks, gCmpTrack);
-#endif///ndef FINDTRACKS_SORT
-}
-
-
-// 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 ***terms, 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 i, count = 0;
-char **retVal;
-struct slName *termList = mdbValSearch(conn, type, MDB_VAL_STD_TRUNCATION, TRUE, FALSE); // Tables not files
-count = slCount(termList) + 1; // make room for "Any"
-AllocArray(retVal, count);
-retVal[0] = cloneString(ANYLABEL);
-for(i = 1; termList != NULL;termList = termList->next, i++)
-    {
-    retVal[i] = cloneString(termList->name);
-    }
-*terms = retVal;
-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"},
-    {"accession",        "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
-}
-
-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;
-
-if(sameString(currentTab, "simpleTab"))
-    {
-    descSearch = cartOptionalString(cart, "hgt.simpleSearch");
-    simpleSearch = TRUE;
-    freez(&nameSearch);
-    freez(&groupSearch);
-    }
-else
-    {
-    descSearch = cartOptionalString(cart, "hgt.descSearch");
-    simpleSearch = FALSE;
-    }
-
-getSearchTrixFile(database, trixFile, sizeof(trixFile));
-trix = trixOpen(trixFile);
-//#define DO_RESHAPING
-// Do shaping was meant to handle shaping supertracks after * configuring contained composite.
-// HOWEVER, this will not work since supertrack reshaping relies upon the temporary "_sel" cart var.
-// What to do?  Alter hgTrackUi to set "_sel" when necessary?  Probably.  Then doReshaping will be needed.
-// Possibly need doReshaping anyway, if it relies upon old/new cart!
-#ifdef DO_RESHAPING
-struct track *trackList = getTrackList(&groupList, -2);
-#else///ifndef DO_RESHAPING
-(void)getTrackList(&groupList, -2);
-#endif///ndef DO_RESHAPING
-slSort(&groupList, gCmpGroup);
-for (group = groupList; group != NULL; group = group->next)
-    {
-#define FIND_SUPERS_TOO
-#ifdef FIND_SUPERS_TOO
-    groupTrackListAddSuper(cart, group);
-#endif///def FIND_SUPERS_TOO
-    if (group->trackList != NULL)
-        {
-        groups[numGroups] = cloneString(group->name);
-        labels[numGroups] = cloneString(group->label);
-        numGroups++;
-        if (numGroups >= ArraySize(groups))
-            internalErr();
-        }
-    }
-#ifdef DO_RESHAPING
-// NOTE: Is this buying me anything??   It should buy composite/view override when subtrack specific vis exists.
-// FIXME: Crashes when superTrackChild "_sel" is found
-parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
-#endif///def DO_RESHAPING
-
-webStartWrapperDetailedNoArgs(cart, database, "", "Search for Tracks", 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
-
-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("<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;'>\n");
-hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a></td></tr></table>\n");
-//hPrintf("</td><td align='right'><a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a></td></tr></table>\n");
-hPrintf("</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;
-        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, &terms, mdbVar[i]);
-        safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1);
-        cgiMakeDropListFull(buf, terms, 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("<tr><td colspan='%d'>\n", cols);
-hPrintf("<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;'>\n");
-hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a></td></tr>\n");
-hPrintf("</table>\n");
-hPrintf("</div>\n</div>\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;
-
-#ifdef FINDTRACKS_SORT
-enum sortBy sortBy = cartUsualInt(cart,SORT_BY_VAR,sbRelevance);
-//boolean sortByHierarchy = sameString(cartUsualString(cart,SORT_BY_VAR,SORT_BY_HIER),SORT_BY_HIER);
-#endif///def FINDTRACKS_SORT
-if(doSearch)
-    {
-    if(simpleSearch)
-        {
-        struct trixSearchResult *tsList;
-        struct hash *trackHash = newHash(0);
-
-        // Create a hash of tracks, so we can map the track name into a track struct.
-        for (group = groupList; group != NULL; group = group->next)
-            {
-            struct trackRef *tr;
-            for (tr = group->trackList; tr != NULL; tr = tr->next)
-                {
-                struct track *track = tr->track;
-                hashAdd(trackHash, track->track, track);
-                struct track *subTrack = track->subtracks;
-                for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
-                    hashAdd(trackHash, subTrack->track, subTrack);
-                }
-            }
-        for(tsList = trixSearch(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next)
-            {
-            struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId);
-            if (track != NULL)
-                {
-                refAdd(&tracks, track);
-                tracksFound++;
-                }
-            //else // FIXME: Should get to the bottom of why some of these are null
-            //    warn("found trix track is NULL.");
-            }
-        }
-    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 hash *trackMetadata = 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);
-
-        if(metaDbExists && !isEmpty(descSearch))
-            {
-            // Load all metadata words for each track to facilitate metadata search.
-            char query[256];
-            struct sqlResult *sr = NULL;
-            char **row;
-            safef(query, sizeof(query), "select obj, val from metaDb");
-            sr = sqlGetResult(conn, query);
-            while ((row = sqlNextRow(sr)) != NULL)
-                {
-                char *str = cloneString(row[1]);
-                hashAdd(trackMetadata, row[0], str);
-                }
-            sqlFreeResult(&sr);
-            }
-
-        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
-    #define MAX_FOUND_TRACKS 100
-    if(tracksFound > MAX_FOUND_TRACKS)
-        {
-        hPrintf("<table class='redBox'><tr><td>Found %d tracks, but only the first %d are displayed.",tracksFound,MAX_FOUND_TRACKS);
-        hPrintf("<BR><B><I>Please narrow search criteria to find fewer tracks.</I></B></div></td></tr></table>\n");
-        }
-
-    #define ENOUGH_FOUND_TRACKS 10
-    if(tracksFound >= ENOUGH_FOUND_TRACKS)
-        {
-        hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='View in Browser' class='viewBtn'>");
-        hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<FONT class='selCbCount'></font>\n");
-        }
-
-    // Set up json for js functionality
-    struct dyString *jsonTdbVars = NULL;
-
-    hPrintf("<table id='foundTracks'><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");
-    if(tracksFound >= ENOUGH_FOUND_TRACKS)
-        {
-        #ifdef FINDTRACKS_SORT
-        hPrintf("<span style='float:right;'>Sort:");
-        cgiMakeOnClickRadioButton(SORT_BY_VAR, "0", (sortBy == sbRelevance),"onchange=\"findTracksSortNow(this);\""); // FIXME: var is in wrong form!
-        hPrintf("by Relevance");
-        cgiMakeOnClickRadioButton(SORT_BY_VAR, "1", (sortBy == sbAbc),"onchange=\"findTracksSortNow(this);\""); // FIXME: var is in wrong form!
-        //cgiMakeOnClickRadioButton(SORT_BY_VAR, SORT_BY_ABC, !sortByHierarchy,"onchange=\"findTracksSortNow(this);\""); // FIXME: var is in wrong form!
-        hPrintf("Alphabetically");
-        cgiMakeOnClickRadioButton(SORT_BY_VAR, "2",(sortBy == sbHierarchy), "onchange=\"findTracksSortNow(this);\"");
-        //cgiMakeOnClickRadioButton(SORT_BY_VAR, SORT_BY_HIER,sortByHierarchy, "onchange=\"findTracksSortNow(this);\"");
-        hPrintf("by Hierarchy&nbsp;&nbsp;</span>\n");
-        #endif///def FINDTRACKS_SORT
-        }
-    hPrintf("</td></tr>\n");
-
-    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);
-
-        #ifdef FINDTRACKS_SORT
-        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
-        #endif///def FINDTRACKS_SORT
-            hPrintf("<tr bgcolor='%s' valign='top' class='found'>\n",COLOR_TRACKLIST_LEVEL2);
-
-        hPrintf("<td align='center'>\n");
-
-        // Determine visibility and checked state
-        track->visibility = tdbVisLimitedByAncestry(cart, track->tdb, FALSE);
-        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))
-            {
-            // FIXME, I haven't seen a single supertrack from simple search
-            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("</td>\n");
-        //if(tdbIsContainer(track->tdb) || tdbIsFolder(track->tdb))
-        //    hPrintf("<td><a target='_top' href='%s' title='Configure track...'>%s</a></td>\n", trackUrl(track->track, NULL), track->shortLabel);
-        //else
-            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");
-    if(containerTrackCount > 0)
-        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>\n");
-    hPrintf("<INPUT TYPE=SUBMIT NAME='submit' VALUE='View in Browser' class='viewBtn'>");
-    hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<FONT class='selCbCount'></font>");
-    hPrintf("\n</form>\n");
-
-    // be done with json
-    hWrites(jsonTdbSettingsUse(&jsonTdbVars));
-    }
-
-if(!doSearch)
-    {
-    hPrintf("<p><b>Recently Done</b><ul>\n"
-        #ifdef FINDTRACKS_SORT
-        "<li>Added sort toggle: Relevance, Alphabetically or by Hierarchy.</li>"
-        //"<li>Added sort toggle: Alphabetically or by Hierarchy.</li>"
-        #endif///def FINDTRACKS_SORT
-        "<li>Composite/view visibilites in hgTrackUi get reshaped to reflect found/selected subtracks.  (In demo1: only default state composites; demo2: all composites.)</li>"
-        "<li>Metadata variables have been 'white-listed' to only include vetted items.  Short text descriptions and vetted list should be reviewed.</li>"
-        "<li>Clicking on shortLabel for found track will popup the description text.  Subtracks should show their composite description.</li>"
-        "<li>Non-data 'container' tracks (composites and supertracks) have '*' to mark them, and can be configured before displaying.  Better suggestions?</li>"
-        "<li>Found track list shows only the first 100 tracks with warning to narrow search.  Larry suggests this could be done by pages of results in v2.0.</li>\n"
-        "</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");
-    }
-hPrintf("</div"); // This div allows the clear button to empty it
-webEndSectionTables();
-}