70ef68d210fa4b76c16f7b8e8142a8180f75052a
tdreszer
  Fri Jun 17 20:14:06 2011 -0700
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3.  Needs more testing and CSS work.  DDCL is working on FF, Chrome and IE.  Both Chrome and IE support required tiny changes to the DDCL wigit code.  DDCL may still have problems with IE.  Other jquery wigits have been tested at a cursory level and work fine.  Ajax calls may need an extrat dataType: html param.  Dialog (popup) needs CSS tuning.
diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c
index a931b59..72167c6 100644
--- src/hg/lib/fileUi.c
+++ src/hg/lib/fileUi.c
@@ -1,974 +1,984 @@
 /* fileUi.c - human genome file downloads common controls. */
 
 #include "common.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "jsHelper.h"
 #include "cart.h"
 #include "hdb.h"
 #include "fileUi.h"
 #include "hui.h"
 #include "obscure.h"
 #include "mdb.h"
 #include "jsHelper.h"
 #include "web.h"
 
 // FIXME: Move to hui.h since hui.c also needs this
 #define ENCODE_DCC_DOWNLOADS "encodeDCC"
 
 
 void fileDbFree(struct fileDb **pFileList)
 // free one or more fileDb objects
 {
 while (pFileList && *pFileList)
     {
     struct fileDb *oneFile = slPopHead(pFileList);
 
     freeMem(oneFile->fileName);
     freeMem(oneFile->fileType);
     freeMem(oneFile->fileDate);
     freeMem(oneFile->sortFields);
     freeMem(oneFile->reverse);
     mdbObjsFree(&(oneFile->mdb));
     freeMem(oneFile);
     }
 }
 
 struct fileDb *fileDbGet(char *db, char *dir, char *subDir, char *fileName)
 // Returns NULL or if found a fileDb struct with name, size and date filled in.
 {
 static char *savedDb     = NULL;
 static char *savedDir    = NULL;
 static char *savedSubDir = NULL;
 static struct fileDb *foundFiles = NULL;// Use static list to save excess IO
 struct fileDb *oneFile = NULL;
 if (foundFiles == NULL
 ||  savedDb  == NULL    || differentString(savedDb, db)
 ||  savedDir == NULL    || differentString(savedDir,dir)
 ||  savedSubDir == NULL || differentString(savedSubDir,subDir))
     {
     // free up any static mem
     freeMem(savedDb);
     freeMem(savedDir);
     freeMem(savedSubDir);
     fileDbFree(&foundFiles);
 
     FILE *scriptOutput = NULL;
     char buf[1024];
     char cmd[512];
     char *words[10];
     char *server = hDownloadsServer();
 
     boolean useRsync = TRUE;
     // Works:         rsync -avn rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/
     if (hIsBetaHost())
         safef(cmd,sizeof(cmd),"rsync -n rsync://hgdownload-test.cse.ucsc.edu/goldenPath/%s/%s/%s/beta/",  db, dir, subDir); // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu"
     else
         safef(cmd,sizeof(cmd),"rsync -n rsync://%s/goldenPath/%s/%s/%s/", server, db, dir, subDir);
 
     scriptOutput = popen(cmd, "r");
     while(fgets(buf, sizeof(buf), scriptOutput))
         {
         eraseTrailingSpaces(buf);
         if (!endsWith(buf,".md5sum")) // Just ignore these
             {
             int count = chopLine(buf, words);
             if (count >= 6 && useRsync == FALSE) // hgwdev is same as hgdownloads-test so can't use rsync
                 {
                 //-rw-rw-r-- 5  502826550 2010-10-22 16:51 /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdRawDataRep1.fastq.gz
                 AllocVar(oneFile);
                 oneFile->fileSize = sqlUnsignedLong(words[2]);
                 oneFile->fileDate = cloneString(words[3]);
                 char *atSlash = strrchr(words[5], '/');
                 if (atSlash != NULL)
                     oneFile->fileName = cloneString(atSlash + 1);
                 else
                     oneFile->fileName = cloneString(words[5]);
                 slAddHead(&foundFiles,oneFile);
                 }
             else if (count == 5 && useRsync == TRUE)// genome and hgwbeta can use rsync because files are on different machine
                 {
                 //-rw-rw-r--    26420982 2009/09/29 14:53:30 wgEncodeBroadChipSeq/wgEncodeBroadChipSeqSignalNhlfH4k20me1.wig.gz
                 AllocVar(oneFile);
                 oneFile->fileSize = sqlUnsignedLong(words[1]);
                 oneFile->fileDate = cloneString(words[2]);
                 strSwapChar(oneFile->fileDate,'/','-');// Standardize YYYY-MM-DD, no time
                 oneFile->fileName = cloneString(words[4]);
                 slAddHead(&foundFiles,oneFile);
                 }
             //warn("File:%s  size:%ld",foundFiles->fileName,foundFiles->fileSize);
             }
         }
     pclose(scriptOutput);
 
     // mark this as done to avoid excessive io
     savedDb     = cloneString(db);
     savedDir    = cloneString(dir);
     savedSubDir = cloneString(subDir);
 
     if (foundFiles == NULL)
         {
         AllocVar(oneFile);
         oneFile->fileName = cloneString("No files found!");
         oneFile->fileDate = cloneString(cmd);
         slAddHead(&foundFiles,oneFile);
         warn("No files found for command:\n%s",cmd);
         return NULL;
         }
     }
 
 // special code that only gets called in debug mode
 if (sameString(fileName,"listAll"))
     {
     for(oneFile=foundFiles;oneFile;oneFile=oneFile->next)
         warn("%s",oneFile->fileName);
     return NULL;
     }
 // Look up the file and return it
 struct fileDb *newList = NULL;
 while (foundFiles)
     {
     oneFile = slPopHead(&foundFiles);
     if (sameString(fileName,oneFile->fileName))
         break;  // Found means removed from list: shorter list for next file.
 
     slAddHead(&newList,oneFile);
     oneFile = NULL;
     }
 if (newList)
     foundFiles = slCat(foundFiles,newList);  // Order does not remain the same
 
 if (oneFile != NULL && oneFile->fileType == NULL)
     {
     char *suffix = strchr(oneFile->fileName, '.');
     if (suffix != NULL && strlen(suffix) > 2)
         {
         oneFile->fileType = cloneString(suffix + 1);
         if (endsWith(oneFile->fileType,".gz"))
             chopSuffix(oneFile->fileType);
         }
     }
 return oneFile;
 }
 
 
 static sortOrder_t *fileSortOrderGet(struct cart *cart,struct trackDb *parentTdb,struct mdbObj *mdbObjs)
 /* Parses 'fileSortOrder' trackDb/cart instructions and returns a sort order struct or NULL.
    Some trickiness here.  sortOrder->sortOrder is from cart (changed by user action), as is sortOrder->order,
    But columns are in original tdb order (unchanging)!  However, if cart is null, all is from trackDb.ra */
 {
 int ix;
 sortOrder_t *sortOrder = NULL;
 char *carveSetting = NULL,*setting = NULL;
 if (parentTdb)
     setting = trackDbSetting(parentTdb, FILE_SORT_ORDER);
 if(setting)
     {
     sortOrder = needMem(sizeof(sortOrder_t));
     sortOrder->setting = cloneString(setting);
     carveSetting = sortOrder->setting;
     }
 else
     {
     if (mdbObjs != NULL)
         {
         struct dyString *dySortFields = dyStringNew(512);
         struct mdbObj *commonVars = mdbObjsCommonVars(mdbObjs);
         // common vars are already in cv defined order, searchable is also sortable
         struct mdbVar *var = commonVars->vars;
         for( ;var != NULL; var = var->next)
             {
             if (differentWord(var->var,MDB_VAR_LAB_VERSION)     // Exclude certain vars
             &&  differentWord(var->var,MDB_VAR_SOFTWARE_VERSION)
             &&  cvSearchMethod(var->var) != cvNotSearchable)   // searchable is also sortable
                 {
                 if (mdbObjsHasCommonVar(mdbObjs, var->var,TRUE)) // Don't bother if all the vals are the same (missing okay)
                     continue;
                 dyStringPrintf(dySortFields,"%s=%s ",var->var,strSwapChar(cloneString(cvLabel(var->var)),' ','_'));
                 }
             }
         if (dyStringLen(dySortFields))
             {
             dyStringAppend(dySortFields,"fileSize=Size fileType=File_Type");
             setting = dyStringCannibalize(&dySortFields);
             }
         else
             dyStringFree(&dySortFields);
         mdbObjsFree(&commonVars);
         }
     if(setting == NULL) // Must be in trackDb or not a sortable list of files
         {
         #define FILE_SORT_ORDER_DEFAULT "cell=Cell_Line lab=Lab view=View replicate=Rep fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until"
         setting = FILE_SORT_ORDER_DEFAULT;
         }
     sortOrder = needMem(sizeof(sortOrder_t));
     carveSetting = cloneString(setting);
     sortOrder->setting = NULL;
     }
 
 if (parentTdb)
     {
     sortOrder->htmlId = needMem(strlen(parentTdb->track)+20);
     safef(sortOrder->htmlId, (strlen(parentTdb->track)+20), "%s.%s", parentTdb->track,FILE_SORT_ORDER);
     if(cart != NULL)
         sortOrder->sortOrder = cloneString(cartOptionalString(cart, sortOrder->htmlId));
     }
 
 sortOrder->count = chopByWhite(carveSetting,NULL,0);  // Get size
 sortOrder->column  = needMem(sortOrder->count*sizeof(char*));
 sortOrder->count = chopByWhite(carveSetting,sortOrder->column,sortOrder->count);
 sortOrder->title   = needMem(sortOrder->count*sizeof(char*));
 sortOrder->forward = needMem(sortOrder->count*sizeof(boolean));
 sortOrder->order   = needMem(sortOrder->count*sizeof(int));
 for (ix = 0; ix<sortOrder->count; ix++)
     {
     // separate out mtaDb var in sortColumn from title
     sortOrder->title[ix] = strchr(sortOrder->column[ix],'='); // Could be 'cell=Cell_Line'
     if (sortOrder->title[ix] != NULL)
         {
         sortOrder->title[ix][0] = '\0';
         sortOrder->title[ix]   = strSwapChar(sortOrder->title[ix]+1,'_',' '); // +1 jumps to next char after '='
         }
     else
         sortOrder->title[ix] = sortOrder->column[ix];         // or could be just 'cell'
 
     // Sort order defaults to forward but may be found in a cart var
     sortOrder->order[ix] = ix+1;
     sortOrder->forward[ix] = TRUE;
     if (sortOrder->sortOrder != NULL)
         {
         char *pos = stringIn(sortOrder->column[ix], sortOrder->sortOrder);// find tdb substr in cart current order string
         if(pos != NULL && pos[strlen(sortOrder->column[ix])] == '=')
             {
             int ord=1;
             char* pos2 = sortOrder->sortOrder;
             for(;*pos2 && pos2 < pos;pos2++)
                 {
                 if(*pos2 == '=') // Discovering sort order in cart
                     ord++;
                 }
             sortOrder->forward[ix] = (pos[strlen(sortOrder->column[ix]) + 1] == '+');
             sortOrder->order[ix] = ord;
             }
         }
     }
 if (sortOrder->sortOrder == NULL)
     sortOrder->sortOrder = cloneString(setting);      // no order in cart, all power to trackDb
 return sortOrder;  // NOTE cloneString:words[0]==*sortOrder->column[0] and will be freed when sortOrder is freed
 }
 
 static int fileDbSortCmp(const void *va, const void *vb)
 // Compare two sortable tdb items based upon sort columns.
 {
 const struct fileDb *a = *((struct fileDb **)va);
 const struct fileDb *b = *((struct fileDb **)vb);
 char **fieldsA = a->sortFields;
 char **fieldsB = b->sortFields;
 int ix=0;
 int compared = 0;
 while(fieldsA[ix] != NULL && fieldsB[ix] != NULL && compared == 0)
     {
     compared = strcmp(fieldsA[ix], fieldsB[ix]) * (a->reverse[ix]? -1: 1);
     ix++;
     }
 return compared;
 }
 
 static void fileDbSortList(struct fileDb **fileList, sortOrder_t *sortOrder)
 {// If sortOrder struct provided, will update sortFields in fileList, then sort it
 if (sortOrder && fileList)
     {
     struct fileDb *oneFile = NULL;
     for(oneFile = *fileList;oneFile != NULL;oneFile=oneFile->next)
         {
         oneFile->sortFields = needMem(sizeof(char *)    * (sortOrder->count + 1)); // +1 Null terminated
         oneFile->reverse    = needMem(sizeof(boolean *) *  sortOrder->count);
         int ix;
         for(ix=0;ix<sortOrder->count;ix++)
             {
             char *field = NULL;
             if (sameString("fileSize",sortOrder->column[ix]))
                 {
                 char niceNumber[32];
                 sprintf(niceNumber, "%.15lu", oneFile->fileSize);
                 field = cloneString(niceNumber);
                 }
             else if (sameString("fileType",sortOrder->column[ix]))
                 field = oneFile->fileType;
             else
                 field = mdbObjFindValue(oneFile->mdb,sortOrder->column[ix]);
 
             if (field)
                 {
                 oneFile->sortFields[sortOrder->order[ix] - 1] = field;
                 oneFile->reverse[   sortOrder->order[ix] - 1] = (sortOrder->forward[ix] == FALSE);
                 }
             else
                 {
                 oneFile->sortFields[sortOrder->order[ix] - 1] = NULL;
                 oneFile->reverse[   sortOrder->order[ix] - 1] = FALSE;
                 }
             oneFile->sortFields[sortOrder->count] = NULL;
             }
         }
     slSort(fileList,fileDbSortCmp);
     }
 }
 
 static char *removeCommonMdbVarsNotInSortOrder(struct mdbObj *mdbObjs,sortOrder_t *sortOrder)
 {  // Removes varaibles common to all mdbObjs and not found in sortOrder. Returns allocated string oh removed var=val pairs
 if (sortOrder != NULL)
     {
     // Remove common vars from mdbs grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std;
     // However, keep the term if it is in the sortOrder
     struct dyString *dyCommon = dyStringNew(256);
     char *commonTerms[] = { "grant", "lab", "dataType", "control", "setType" };
     int tIx=0,sIx = 0;
     for(;tIx<ArraySize(commonTerms);tIx++)
         {
         for(sIx = 0;
             sIx<sortOrder->count && differentString(commonTerms[tIx],sortOrder->column[sIx]);
             sIx++) ;
         if (sIx<sortOrder->count) // Found in sort Order so leave it in mdbObjs
             continue;
 
         char *val = mdbRemoveCommonVar(mdbObjs, commonTerms[tIx]); // All mdbs have it and have the same val for it.
         if (val)
             dyStringPrintf(dyCommon,"%s=%s ",commonTerms[tIx],val);
         }
     return dyStringCannibalize(&dyCommon);
     }
 return NULL;
 }
 
 static char *labelWithVocabLink(char *var,char *title,struct slPair *valsAndLabels,boolean tagsNotVals)
 /* If the parentTdb has a controlledVocabulary setting and the vocabType is found,
    then label will be wrapped with the link to all relevent terms.  Return string is cloned. */
 {
 // Determine if the var is cvDefined.  If not, simple link
 boolean cvDefined = FALSE;
 struct hash *cvTypesOfTerms = (struct hash *)cvTermTypeHash();
 if (cvTypesOfTerms != NULL)
     {
     struct hash *cvTermDef = hashFindVal(cvTypesOfTerms,var);
     if (cvTermDef)
         cvDefined = SETTING_IS_ON(hashFindVal(cvTermDef,"cvDefined"));
     }
 
 struct dyString *dyLink = dyStringNew(256);
 if (!cvDefined)
     dyStringPrintf(dyLink,"<A HREF='hgEncodeVocab?type=%s' title='Click for details of \"%s\"' TARGET=ucscVocab>%s</A>",
                    var,title,title);
 else
     {
     dyStringPrintf(dyLink,"<A HREF='hgEncodeVocab?%s=",tagsNotVals?"tag":"term");
     struct slPair *oneVal = valsAndLabels;
     for(;oneVal!=NULL;oneVal=oneVal->next)
         {
         if (oneVal != valsAndLabels)
             dyStringAppendC(dyLink,',');
         dyStringAppend(dyLink,mdbPairVal(oneVal));
         }
     dyStringPrintf(dyLink,"' title='Click for details of each \"%s\"' TARGET=ucscVocab>%s</A>",title,title);
     }
 return dyStringCannibalize(&dyLink);
 }
 
 static int filterBoxesForFilesList(char *db,struct mdbObj *mdbObjs,sortOrder_t *sortOrder)
 {  // Will create filterBoxes for each sortOrder field.  Returns count of filterBoxes made
 int count = 0;
 if (sortOrder != NULL)
     {
     struct dyString *dyFilters = dyStringNew(256);
     int sIx=0;
     for(sIx = 0;sIx<sortOrder->count;sIx++)
         {
         char *var = sortOrder->column[sIx];
         enum cvSearchable searchBy = cvSearchMethod(var);
         if (searchBy != cvSearchBySingleSelect && searchBy != cvSearchByMultiSelect)
             continue; // Only single selects and multi-select make good candidates for filtering
 
         // get all vals for var, then convert to tag/label pairs for filterBys
         struct slName *vals = mdbObjsFindAllVals(mdbObjs, var);
         struct slPair *tagLabelPairs = NULL;
         while(vals != NULL)
             {
             struct slName *term = slPopHead(&vals);
             char *tag = (char *)cvTag(var,term->name);
             if (tag == NULL)
                 tag = term->name;
             slPairAdd(&tagLabelPairs,tag,cloneString((char *)cvLabel(term->name)));
             slNameFree(&term);
             }
 
         // If there is more than one val for this var then create filterBy box for it
         if (slCount(tagLabelPairs) > 1)
             {
             slPairValSortCase(&tagLabelPairs); // should have a list sorted on the label
             char extraClasses[256];
             safef(extraClasses,sizeof extraClasses,"filterTable %s",var);
+        #ifdef NEW_JQUERY
+            char *dropDownHtml = cgiMakeMultiSelectDropList(var,tagLabelPairs,NULL,"All",extraClasses,"onchange='filterTable();' onclick='filterTableExclude(this);' style='font-size:.9em;'");
+        #else///ifndef NEW_JQUERY
             char *dropDownHtml = cgiMakeMultiSelectDropList(var,tagLabelPairs,NULL,"All",extraClasses,"onchange='filterTable();' onclick='filterTableExclude(this);'");
+        #endif///ndef NEW_JQUERY
             // Note filterBox has classes: filterBy & {var}
             if (dropDownHtml)
                 {
                 dyStringPrintf(dyFilters,"<td align='left'>\n<B>%s</B>:<BR>\n%s</td><td width=10>&nbsp;</td>\n",
                                labelWithVocabLink(var,sortOrder->title[sIx],tagLabelPairs,TRUE),dropDownHtml);  // TRUE were sending tags, not values
                 freeMem(dropDownHtml);
                 count++;
                 }
             }
         if (slCount(tagLabelPairs) > 0)
             slPairFreeValsAndList(&tagLabelPairs);
         }
 
     // Finally ready to print the filterBys out
     if (count)
         {
         webIncludeResourceFile("ui.dropdownchecklist.css");
         jsIncludeFile("ui.dropdownchecklist.js",NULL);
         #define FILTERBY_HELP_LINK  "<A HREF=\"../goldenPath/help/multiView.html\" TARGET=ucscHelp>help</A>"
         cgiDown(0.9);
         printf("<B>Filter files by:</B> (select multiple %sitems - %s)\n<table><tr valign='bottom'>\n",
                (count >= 1 ? "categories and ":""),FILTERBY_HELP_LINK);
         printf("%s\n",dyStringContents(dyFilters));
         printf("</tr></table>\n");
+    #ifdef NEW_JQUERY
+        printf("<script type='text/javascript'>var newJQuery=true;</script>\n");
+        printf("<script type='text/javascript'>$(document).ready(function() { $('.filterBy').each( function(i) { ddclSetup(this,'noneIsAll') });});</script>\n");
+    #else///ifndef NEW_JQUERY
+        printf("<script type='text/javascript'>var newJQuery=false;</script>\n");
         printf("<script type='text/javascript'>$(document).ready(function() { $('.filterBy').each( function(i) { $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });});});</script>\n");
+    #endif///ndef NEW_JQUERY
         }
     dyStringFree(&dyFilters);
     }
 return count;
 }
 
 static void filesDownloadsPreamble(char *db, struct trackDb *tdb)
 {
 // Do not bother getting preamble.html
 // 1) It isn't on the RR (yet)
 // 2) It will likely refer back to the composite for Description info which is included in this page
 // 3) The rsync-to-tmp-file hurdle isn't worth the effort.
 cgiDown(0.7);
 puts("<B>Data is <A HREF='http://genome.ucsc.edu/ENCODE/terms.html'>RESTRICTED FROM USE</a>");
 puts("in publication  until the restriction date noted for the given data file.</B>");
 
 char *server = hDownloadsServer();
 char *subDir = "";
 if (hIsBetaHost())
     {
     server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu"
     subDir = "/beta";
     }
 
 cgiDown(0.7);
 puts("Supporting documents:");
 printf("<BR>&#149;&nbsp;<B><A HREF='http://%s/goldenPath/%s/%s/%s%s/files.txt' TARGET=ucscDownloads>files.txt</A></B> is a tab-separated file with the name and metadata for each download.</LI>\n",
                 server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
 printf("<BR>&#149;&nbsp;<B><A HREF='http://%s/goldenPath/%s/%s/%s%s/md5sum.txt' TARGET=ucscDownloads>md5sum.txt</A></B> is a list of the md5sum output for each download.</LI>\n",
                 server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
 
 struct fileDb *oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "supplemental");
 if (oneFile != NULL)
     {
     printf("<BR>&#149;&nbsp;<B><A HREF='http://%s/goldenPath/%s/%s/%s%s/supplemental/' TARGET=ucscDownloads>Supplemental materials</A></B> contains additional files provided by the laboratory related to these downloads.</LI>\n",
           server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
     }
 }
 
 static int filesPrintTable(char *db, struct trackDb *parentTdb, struct fileDb *fileList, sortOrder_t *sortOrder,boolean filterable)
 // Prints filesList as a sortable table. Returns count
 {
 // Table class=sortable
 int columnCount = 0;
 int restrictedColumn = 0;
 char *nowrap = (sortOrder->setting != NULL ? " nowrap":""); // Sort order trackDb setting found so rely on <BR> in titles for wrapping
 printf("<TABLE class='sortable' style='border: 2px outset #006600;'>\n");
 printf("<THEAD class='sortable'>\n");
 printf("<TR class='sortable' valign='bottom'>\n");
 printf("<TD align='center' valign='center'>&nbsp;");
 int filesCount = slCount(fileList);
 if (filesCount > 5)
     printf("<em><span class='filesCount'></span>%d files</em>",filesCount);
 
 //if (sortOrder) // NOTE: This could be done to preserve sort order   FIXME: However hgFileUi would need form OR changes would need to be ajaxed over AND hgsid would be needed.
 //    printf("<INPUT TYPE=HIDDEN NAME='%s' class='sortOrder' VALUE=\"%s\">",sortOrder->htmlId, sortOrder->sortOrder);
 printf("</TD>\n");
 columnCount++;
 
 /*#define SHOW_FOLDER_FOR_COMPOSITE_DOWNLOADS
 #ifdef SHOW_FOLDER_FOR_COMPOSITE_DOWNLOADS
 if (parentTdb == NULL)
     {
     printf("<TD align='center' valign='center'>&nbsp;</TD>");
     columnCount++;
     }
 #endif///def SHOW_FOLDER_FOR_COMPOSITE_DOWNLOADS
 */
 // Now the columns
 int curOrder = 0,ix=0;
 if (sortOrder)
     {
     curOrder = sortOrder->count;
     for(ix=0;ix<sortOrder->count;ix++)
         {
         char *align = (sameString("labVersion",sortOrder->column[ix]) || sameString("softwareVersion",sortOrder->column[ix]) ? " align='left'":"");
         printf("<TH class='sortable sort%d%s' %s%s%s>%s</TH>\n",
             sortOrder->order[ix],(sortOrder->forward[ix]?"":" sortRev"),
             (sameString("fileSize",sortOrder->column[ix])?"abbr='use' ":""),
             nowrap,align,sortOrder->title[ix]); // keeing track of sortOrder
         columnCount++;
         if (sameWord(sortOrder->column[ix],"dateUnrestricted"))
             restrictedColumn = columnCount;
         }
     }
 //#define INCLUDE_FILENAMES
 #ifndef INCLUDE_FILENAMES
 else
 #endif///defn INCLUDE_FILENAMES
     {
     printf("<TH class='sortable sort%d' nowrap>File Name</TH>\n",++curOrder);
     columnCount++;
     }
 printf("<TH class='sortable sort%d' align='left' nowrap>Additional Details</TH>\n",++curOrder);
 columnCount++;
 printf("</TR></THEAD>\n");
 
 // Now the files...
 char *server = hDownloadsServer();
 char *subDir = "";
 if (hIsBetaHost())
     {
     server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu"
     subDir = "/beta";
     }
 struct fileDb *oneFile = fileList;
 printf("<TBODY class='sortable sorting'>\n"); // 'sorting' is a fib but it conveniently greys the list till the table is initialized.
 for( ;oneFile!= NULL;oneFile=oneFile->next)
     {
     oneFile->mdb->next = NULL; // mdbs were in list for generating sortOrder, but list no longer needed
     char *field = NULL;
 
     printf("<TR valign='top'%s>",filterable?" class='filterable'":"");
     // Download button
     printf("<TD nowrap>");
     if (parentTdb)
         field = parentTdb->track;
     else
         field = mdbObjFindValue(oneFile->mdb,"composite");
     assert(field != NULL);
 
     printf("<input type='button' value='Download' onclick=\"window.location='http://%s/goldenPath/%s/%s/%s%s/%s';\" title='Download %s ...'>",
           server,db,ENCODE_DCC_DOWNLOADS, field, subDir, oneFile->fileName, oneFile->fileName);
 
 #define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
 #ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
     if (parentTdb == NULL)
         printf("&nbsp;<A href='../cgi-bin/hgFileUi?db=%s&g=%s' title='Navigate to downloads page for %s set...'><IMG SRC='../images/folderC.png'></a>&nbsp;", db,field,field);
 #endif///def SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
     printf("</TD>\n");
 
     // Each of the pulled out mdb vars
     if (sortOrder)
         {
         for(ix=0;ix<sortOrder->count;ix++)
             {
             char *align = (sameString("labVersion",sortOrder->column[ix]) || sameString("softwareVersion",sortOrder->column[ix]) ? " align='left'":" align='center'");
             if (sameString("fileSize",sortOrder->column[ix]))
                 {
                 char niceNumber[128];
                 sprintWithGreekByte(niceNumber, sizeof(niceNumber), oneFile->fileSize);
                 field = oneFile->sortFields[sortOrder->order[ix] - 1];
                 printf("<TD abbr='%s' align='right' nowrap>%s</td>",field,niceNumber);
                 }
             else
                 {
                 field = oneFile->sortFields[sortOrder->order[ix] - 1];
                 boolean isFieldEmpty = cvTermIsEmpty(sortOrder->column[ix],field);
                 char class[128];
                 class[0] = '\0';
                 if (filterable)
                     {
                     enum cvSearchable searchBy = cvSearchMethod(sortOrder->column[ix]);
                     if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
                         {
                         char *cleanClass = NULL;
                         if (isFieldEmpty)
                             cleanClass = "None";
                         else
                             {
                             cleanClass = (char *)cvTag(sortOrder->column[ix],field); // class should be tag
                             if (cleanClass == NULL)
                                 cleanClass = field;
                             }
                         safef(class,sizeof class," class='%s %s'",sortOrder->column[ix],cleanClass);
                         }
                     }
 
                 if (sameString("dateUnrestricted",sortOrder->column[ix]) && field && dateIsOld(field,"%F"))
                     printf("<TD%s nowrap style='color: #BBBBBB;'%s>%s</td>",align,class,field);
                 else
                     printf("<TD%s nowrap%s>%s</td>",align,class,isFieldEmpty?" &nbsp;":field);
                 if (!sameString("fileType",sortOrder->column[ix]))
                     mdbObjRemoveVars(oneFile->mdb,sortOrder->column[ix]); // Remove this from mdb now so that it isn't displayed in "extras'
                 }
             }
         }
 #ifndef INCLUDE_FILENAMES
     else
 #endif///ndef INCLUDE_FILENAMES
         { // fileName
         printf("<TD nowrap>%s",oneFile->fileName);
         //// FIXME: " The "..." encapsulation could be rebuilt so it could be called here
         //printf("&nbsp;<A HREF='#a_meta_%s' onclick='return metadataShowHide(\"%s\",true,true);' title='Show metadata details...'>...</A>",
         //    oneFile->mdb->obj,oneFile->mdb->obj);
         //printf("<DIV id='div_%s_meta' style='display:none;'></div></td>",oneFile->mdb->obj);
         }
 
     // Extras  grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std;
     mdbObjRemoveVars(oneFile->mdb,MDB_VAR_FILENAME " " MDB_VAR_FILEINDEX " " MDB_VAR_COMPOSITE " " MDB_VAR_PROJECT); // Remove this from mdb now so that it isn't displayed in "extras'
     field = mdbObjVarValPairsAsLine(oneFile->mdb,TRUE);
     printf("<TD nowrap>%s</td>",field?field:" &nbsp;");
 
     printf("</TR>\n");
     }
 
 printf("</TBODY><TFOOT class='bgLevel1'>\n");
 printf("<TR valign='top'>");
 
 // Restriction policy link in first column?
 if (restrictedColumn == 1)
     printf("<TH colspan=%d><A HREF='%s' TARGET=BLANK style='font-size:.9em;'>Restriction Policy</A></TH>", (columnCount - restrictedColumn),ENCODE_DATA_RELEASE_POLICY);
 
 printf("<TD colspan=%d>&nbsp;&nbsp;&nbsp;&nbsp;",(restrictedColumn > 1 ? (restrictedColumn - 1) : columnCount));
 
 // Total
 if (filesCount > 5)
     printf("<em><span class='filesCount'></span>%d files</em>",filesCount);
 
 // Restriction policy link in later column?
 if (restrictedColumn > 1)
     printf("</TD><TH colspan=%d align='left'><A HREF='%s' TARGET=BLANK style='font-size:.9em;'>Restriction Policy</A>", columnCount,ENCODE_DATA_RELEASE_POLICY);
 
 printf("</TD></TR>\n");
 printf("</TFOOT></TABLE>\n");
 
 if (parentTdb == NULL)
     printf("<script type='text/javascript'>{$(document).ready(function() {sortTableInitialize($('table.sortable')[0],true,true);});}</script>\n");
 
 return filesCount;
 }
 
 
 static int filesFindInDir(char *db, struct mdbObj **pmdbFiles, struct fileDb **pFileList, char *fileType, int limit,boolean *exceededLimit)
 // Prints list of files in downloads directories matching mdb search terms. Returns count
 {
 int fileCount = 0;
 // Verify file existance and make fileList of those found
 struct fileDb *fileList = NULL, *oneFile = NULL; // Will contain found files
 struct mdbObj *mdbFiles = NULL; // Will caontain a list of mdbs for the found files
 struct mdbObj *mdbList = *pmdbFiles;
 while (mdbList && (limit == 0 || fileCount < limit))
     {
     boolean found = FALSE;
     struct mdbObj *mdbFile = slPopHead(&mdbList);
     char *composite = mdbObjFindValue(mdbFile,MDB_VAR_COMPOSITE);
     if (composite == NULL)
         {
         mdbObjsFree(&mdbFile);
         continue;
         }
 
     // First for FileName
     char *fileName = mdbObjFindValue(mdbFile,MDB_VAR_FILENAME);
     if (fileName == NULL)
         {
         mdbObjsFree(&mdbFile);
         continue;
         }
 
 //#define NO_FILENAME_LISTS
 #ifdef NO_FILENAME_LISTS
     oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName);
     if (oneFile == NULL)
         {
         mdbObjsFree(&mdbFile);
         continue;
         }
 
     //warn("%s == %s",fileType,oneFile->fileType);
     if (isEmpty(fileType) || sameWord(fileType,"Any")
     || (oneFile->fileType && sameWord(fileType,oneFile->fileType)))
         {
         slAddHead(&fileList,oneFile);
         oneFile->mdb = mdbFile;
         slAddHead(&mdbFiles,oneFile->mdb);
         found = TRUE;
         fileCount++;
         if (limit > 0 && fileCount >= limit)
             break;
         }
     else
         fileDbFree(&oneFile);
 
 #else///ifndef NO_FILENAME_LISTS
 
     struct slName *fileSet = slNameListFromComma(fileName);
     struct slName *md5Set = NULL;
     char *md5sums = mdbObjFindValue(mdbFile,MDB_VAR_MD5SUM);
     if (md5sums != NULL)
         md5Set = slNameListFromComma(md5sums);
     while (fileSet != NULL)
         {
         struct slName *file = slPopHead(&fileSet);
         struct slName *md5 = NULL;
         if (md5Set)
             md5 = slPopHead(&md5Set);
         oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, file->name);
         if (oneFile == NULL)
             {
             slNameFree(&file);
             if (md5)
                 slNameFree(&md5);
             continue;
             }
 
         //warn("%s == %s",fileType,oneFile->fileType);
         if (isEmpty(fileType) || sameWord(fileType,"Any")
         || (oneFile->fileType && startsWithWordByDelimiter(fileType,'.',oneFile->fileType))) // Starts with!  This ensures both bam and bam.bai are found.
             {
             slAddHead(&fileList,oneFile);
             if (found) // if already found then need two mdbObjs (assertable but then this is metadata)
                 oneFile->mdb = mdbObjClone(mdbFile);  // Yes clone this as differences will occur
             else
                 oneFile->mdb = mdbFile;
             if (md5 != NULL)
                 mdbObjSetVar(oneFile->mdb,MDB_VAR_MD5SUM,md5->name);
             else
                 mdbObjRemoveVars(oneFile->mdb,MDB_VAR_MD5SUM);
             slAddHead(&mdbFiles,oneFile->mdb);
             found = TRUE;
             fileCount++;
             if (limit > 0 && fileCount >= limit)
                 {
                 slNameFreeList(&fileSet);
                 if (md5Set)
                     slNameFreeList(&md5Set);
                 break;
                 }
             }
         else
             fileDbFree(&oneFile);
 
         slNameFree(&file);
         if (md5)
             slNameFree(&md5);
         }
 #endif///ndef NO_FILENAME_LISTS
 
     // FIXME: This support of fileIndex and implicit bam.bai's should be removed when mdb is cleaned up.
     // Now for FileIndexes
     if (limit == 0 || fileCount < limit)
         {
         char buf[512];
         if (strchr(fileName,',') == NULL && endsWith(fileName,".bam")) // Special to fill in missing .bam.bai's
             {
             safef(buf,sizeof(buf),"%s.bai",fileName);
             fileName = buf;
             }
         else
             {
             fileName = mdbObjFindValue(mdbFile,MDB_VAR_FILEINDEX);   // This mdb var should be going away.
             if (fileName == NULL)
                 continue;
             }
 
         // Verify existance first
         oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName);  // NOTE: won't be found if already found in comma delimited fileName!
         if (oneFile == NULL)
             continue;
 
         //warn("%s == %s",fileType,oneFile->fileType);
         if (isEmpty(fileType) || sameWord(fileType,"Any")
         || (oneFile->fileType && sameWord(fileType,oneFile->fileType))
         || (oneFile->fileType && sameWord(fileType,"bam") && sameWord("bam.bai",oneFile->fileType))) // TODO: put fileType matching into search.c lib code to segregate index logic.
             {
             slAddHead(&fileList,oneFile);
             if (found) // if already found then need two mdbObjs (assertable but then this is metadata)
                 oneFile->mdb = mdbObjClone(mdbFile);
             else
                 oneFile->mdb = mdbFile;
             mdbObjRemoveVars(oneFile->mdb,MDB_VAR_MD5SUM);
             slAddHead(&mdbFiles,oneFile->mdb);
             fileCount++;
             found = TRUE;
             continue;
             }
         else
             fileDbFree(&oneFile);
         }
 
     if (!found)
         mdbObjsFree(&mdbFile);
     }
 *pmdbFiles = mdbFiles;
 *pFileList = fileList;
 if (exceededLimit != NULL)
     *exceededLimit = FALSE;
 if (mdbList != NULL)
     {
     if (exceededLimit != NULL)
         *exceededLimit = TRUE;
     mdbObjsFree(&mdbList);
     }
 return fileCount;
 }
 
 void filesDownloadUi(char *db, struct cart *cart, struct trackDb *tdb)
 // UI for a "composite like" track: This will list downloadable files associated with
 // a single trackDb entry (composite or of type "downloadsOnly". The list of files
 // will have links to their download and have metadata information associated.
 // The list will be a sortable table and there may be filtering controls.
 {
 boolean debug = cartUsualBoolean(cart,"debug",FALSE);
 
 struct sqlConnection *conn = hAllocConn(db);
 char *mdbTable = mdbTableName(conn,TRUE); // Look for sandBox name first
 if(mdbTable == NULL)
     errAbort("TABLE NOT FOUND: '%s.%s'.\n",db,MDB_DEFAULT_NAME);
 
 // Get an mdbObj list of all that belong to this track and have a fileName
 char buf[256];
 safef(buf,sizeof(buf),"%s=%s %s=?",MDB_VAR_COMPOSITE,tdb->track,MDB_VAR_FILENAME);
 struct mdbByVar *mdbVars = mdbByVarsLineParse(buf);
 struct mdbObj *mdbList = mdbObjsQueryByVars(conn,mdbTable,mdbVars);
 
 // Now get Indexes  But be sure not to duplicate entries in the list!!!
 safef(buf,sizeof(buf),"%s=%s %s= %s!=",MDB_VAR_COMPOSITE,tdb->track,MDB_VAR_FILEINDEX,MDB_VAR_FILENAME);
 mdbVars = mdbByVarsLineParse(buf);
 mdbList = slCat(mdbList, mdbObjsQueryByVars(conn,mdbTable,mdbVars));
 mdbObjRemoveHiddenVars(mdbList);
 hFreeConn(&conn);
 
 if (slCount(mdbList) == 0)
     {
     warn("No files specified in metadata for: %s\n%s",tdb->track,tdb->longLabel);
     return;
     }
 
 // Verify file existance and make fileList of those found
 struct fileDb *fileList = NULL; // Will contain found files
 
 int fileCount = filesFindInDir(db, &mdbList, &fileList, NULL, 0, NULL);
 assert(fileCount == slCount(fileList));
 
 if (fileCount == 0)
     {
     warn("No downloadable files currently available for: %s\n%s",tdb->track,tdb->longLabel);
     return;  // No files so nothing to do.
     }
 if (debug)
     {
     warn("The following files are in goldenPath/%s/%s/%s/ but NOT in the mdb:",db,ENCODE_DCC_DOWNLOADS, tdb->track);
     fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "listAll");
     }
 
 jsIncludeFile("hui.js",NULL);
 jsIncludeFile("ajax.js",NULL);
 
 // standard preamble
 filesDownloadsPreamble(db,tdb);
 
 // Now update all files with their sortable fields and sort the list
 mdbObjReorderByCv(mdbList,FALSE);// Start with cv defined order for visible vars. NOTE: will not need to reorder during print!
 sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb,mdbList);
 boolean filterable = FALSE;
 if (sortOrder != NULL)
     {
     char *vars = removeCommonMdbVarsNotInSortOrder(mdbList,sortOrder);
     if (vars)
         {
         if (debug)
             warn("These terms are common:%s",vars);
         freeMem(vars);
         }
 
     // Fill in and sort fileList
     fileDbSortList(&fileList,sortOrder);
 
     // FilterBoxes
     filterable = (filterBoxesForFilesList(db,mdbList,sortOrder) > 0);
     }
 
 // Print table
 filesPrintTable(db,tdb,fileList,sortOrder,filterable);
 
 //fileDbFree(&fileList); // Why bother on this very long running cgi?
 //mdbObjsFree(&mdbList);
 }
 
 int fileSearchResults(char *db, struct sqlConnection *conn, struct slPair *varValPairs, char *fileType)
 // Prints list of files in downloads directories matching mdb search terms. Returns count
 {
 struct sqlConnection *connLocal = conn;
 if (conn == NULL)
     connLocal = hAllocConn(db);
 struct mdbObj *mdbList = mdbObjRepeatedSearch(connLocal,varValPairs,FALSE,TRUE);
 if (conn == NULL)
     hFreeConn(&connLocal);
 if (slCount(mdbList) == 0)
     {
     printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n");
     return 0;
     }
 
 // Now sort mdbObjs so that composites will stay together and lookup of files will be most efficient
 mdbObjsSortOnVars(&mdbList, MDB_VAR_COMPOSITE);
 mdbObjRemoveHiddenVars(mdbList);
 
 #define FOUND_FILE_LIMIT 1000
 struct fileDb *fileList = NULL; // Will contain found files
 int filesExpected = slCount(mdbList);
 boolean exceededLimit = FALSE;
 int fileCount = filesFindInDir(db, &mdbList, &fileList, fileType, FOUND_FILE_LIMIT, &exceededLimit);
 assert(fileCount == slCount(fileList));
 
 if (fileCount == 0)
     {
     printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n");
     return 0;  // No files so nothing to do.
     }
 
 // TODO Could sort on varValPairs by creating a sortOrder struct of them
 //// Now update all files with their sortable fields and sort the list
 mdbObjReorderByCv(mdbList,FALSE);// Start with cv defined order for visible vars. NOTE: will not need to reorder during print!
 sortOrder_t *sortOrder = fileSortOrderGet(NULL,NULL,mdbList); // No cart, no tdb
 if (sortOrder != NULL)
     {
     // Fill in and sort fileList
     fileDbSortList(&fileList,sortOrder);
     }
 
 mdbObjRemoveVars(mdbList,"tableName"); // Remove this from mdb now so that it isn't displayed in "extras'
 
 //jsIncludeFile("hui.js",NULL);
 //jsIncludeFile("ajax.js",NULL);
 
 // Print table
 printf("<DIV id='filesFound'>");
 if (exceededLimit)
     {
     // What is the expected count?  Difficult to say because of comma delimited list in fileName.
     if (filesExpected <= FOUND_FILE_LIMIT)
         filesExpected = FOUND_FILE_LIMIT + 1;
 
     printf("<DIV class='redBox' style='width: 380px;'>Too many files found.  Displaying first %d of at least %d.<BR>Narrow search parameters and try again.</DIV><BR>\n",
            fileCount,filesExpected);
     //warn("Too many files found.  Displaying first %d of at least %d.<BR>Narrow search parameters and try again.\n", fileCount,filesExpected);
     }
 
 fileCount = filesPrintTable(db,NULL,fileList,sortOrder,FALSE); // FALSE=Don't offer more filtering on the file search page
 printf("</DIV><BR>\n");
 
 //fileDbFree(&fileList); // Why bother on this very long running cgi?
 //mdbObjsFree(&mdbList);
 
 return fileCount;
 }