8fdc86ea29f656cf7efee9954fdae6b573190fb3
tdreszer
  Fri May 6 17:23:22 2011 -0700
Standardized replacement for <P> with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi.
diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c
index eefb10d..eaf276f 100644
--- src/hg/lib/fileUi.c
+++ src/hg/lib/fileUi.c
@@ -1,988 +1,989 @@
 /* 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;
 //#define RSYNC_DONT_WORK_ON_HGWDEV
 #ifdef RSYNC_DONT_WORK_ON_HGWDEV
     if (hIsPrivateHost() || hIsPreviewHost())
         {
         // For hgwdev (which is the same machine as "hgdownload-test.cse.ucsc.edu") rsync does not work
         // Use ls -log --time=ctime --time-style=long-iso /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone
         safef(cmd,sizeof(cmd),"ls -log --time-style=long-iso /usr/local/apache/htdocs-hgdownload/goldenPath/%s/%s/%s/", db,dir,subDir);
         useRsync = FALSE;
         }
     else if (hIsBetaHost())
         {
         // For hgwbeta, the files are being looked for one test in a "beta/" subdir.  Have to rsync
         //server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu"
         //safef(cmd,sizeof(cmd),"rsync -avn rsync://%s/goldenPath/%s/%s/%s/beta/", server, db, dir, subDir);
         // FIXME: Need cluster-admins help to get rsync solution
         safef(cmd,sizeof(cmd),"ls -log --time-style=long-iso /hive/groups/encode/dcc/pipeline/downloads/%s/%s/beta/", db,subDir);
         useRsync = FALSE;
         }
     else  // genome and hgwbeta can use rsync
 #endif///def RSYNC_DONT_WORK_ON_HGWDEV
         {
         // Works:         rsync -avn rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/
         if (hIsBetaHost())
             safef(cmd,sizeof(cmd),"rsync -avn 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 -avn rsync://%s/goldenPath/%s/%s/%s/", server, db, dir, subDir);
         }
     //warn("cmd: %s",cmd);
     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 == cvSearchByDateRange || searchBy == cvSearchByIntegerRange) // dates and numbers probably not good for filtering. FIXME: Should cvsNotSearchable be filterable??
         if (searchBy != cvSearchBySingleSelect && searchBy != cvSearchByMultiSelect)
             continue; // Only single selects and multi-select make good candidates for filtering
 
         struct sqlConnection *conn = hAllocConn(db);
         struct slPair *valsAndLabels = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE, FALSE, TRUE); // not tags, not tables, just files
         hFreeConn(&conn);
         // Need to verify that each val exists in an object for these files
         struct slPair *relevantVals = NULL;
         while(valsAndLabels != NULL)
             {
             struct slPair *oneVal = slPopHead(&valsAndLabels);
             if(mdbObjsContainAltleastOneMatchingVar(mdbObjs,var,mdbPairVal(oneVal)))
                 {
                 eraseNonAlphaNum(mdbPairVal(oneVal));   // Have to squeeze out uglies from val to ensure filter by class works
                 slAddHead(&relevantVals,oneVal);
                 }
             else
                 slPairFreeValsAndList(&oneVal);
             }
         if (slCount(relevantVals) > 1)
             {
             slReverse(&relevantVals);
             char extraClasses[256];
             safef(extraClasses,sizeof extraClasses,"filterTable %s",var);
             char *dropDownHtml = cgiMakeMultiSelectDropList(var,relevantVals,NULL,"All",extraClasses,"onchange='filterTable();' onclick='filterTableExclude(this);'");
             // 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],relevantVals,TRUE),dropDownHtml);  // TRUE were sending tags, not values
                 freeMem(dropDownHtml);
                 count++;
                 }
             }
         if (slCount(relevantVals) > 0)
             slPairFreeValsAndList(&relevantVals);
         }
     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");
         printf("<script type='text/javascript'>$(document).ready(function() { $('.filterBy').each( function(i) { $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });});});</script>\n");
         }
     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.
-puts("<p><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></p>");
+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";
     }
 
 struct fileDb *oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "supplemental");
 if (oneFile != NULL)
     {
-    printf("<p>\n<B>Supplemental materials</b> may be found <A HREF='http://%s/goldenPath/%s/%s/%s%s/supplemental/' TARGET=ucscDownloads>here</A>.</p>\n",
+    cgiDown(0.7);
+    printf("<B>Supplemental materials</b> may be found <A HREF='http://%s/goldenPath/%s/%s/%s%s/supplemental/' TARGET=ucscDownloads>here</A>.\n",
           server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
     }
-puts("<p>\nThere are two files within this directory that contain information about the downloads:");
+cgiDown(0.7);
+puts("There are two files within this directory that contain information about the downloads:");
 printf("<BR>&#149;&nbsp;<A HREF='http://%s/goldenPath/%s/%s/%s%s/files.txt' TARGET=ucscDownloads>files.txt</A> which 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;<A HREF='http://%s/goldenPath/%s/%s/%s%s/md5sum.txt' TARGET=ucscDownloads>md5sum.txt</A> which is a list of the md5sum output for each download.</LI>\n",
                 server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
-
-
-puts("<P>");
 }
 
 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_FRO_COMPOSITE_DOWNLOADS
 #ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
 if (parentTdb == NULL)
     {
     printf("<TD align='center' valign='center'>&nbsp;</TD>");
     columnCount++;
     }
 #endif///def SHOW_FOLDER_FRO_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];
                 char class[128];
                 class[0] = '\0';
                 if (filterable)
                     {
                     enum cvSearchable searchBy = cvSearchMethod(sortOrder->column[ix]);
                     if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
                         {
                         char *cleanClass = cloneString(field?field:"None");     // FIXME: Only none if none is a fliter choice.
                         eraseNonAlphaNum(cleanClass);
                         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,field?field:" &nbsp;");
                 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><BR>\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;
 }