ac1262a2edecf9f0b499bdec42602e4f8d5c2711
tdreszer
  Mon Dec 20 15:18:51 2010 -0800
Minor css change
diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c
index 0620a63..b6ccda2 100644
--- src/hg/lib/fileUi.c
+++ src/hg/lib/fileUi.c
@@ -1,521 +1,521 @@
 /* fileUi.c - human genome file downloads common controls. */
 
 #include "common.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "jsHelper.h"
 #include "cart.h"
 #include "fileUi.h"
 #include "hui.h"
 #include "obscure.h"
 #include "mdb.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->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();
     if (sameString(server,"hgdownload-test.cse.ucsc.edu")) // genome-test is different
         {
         // Does not work: rsync -avn rsync://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone
         // 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);
         }
     else  // genome and hgwbeta can use rsync
         {
         // Works:         rsync -avn rsync://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq
         safef(cmd,sizeof(cmd),"rsync -avn rsync://%s/goldenPath/%s/%s/%s/%s | grep %s", server, db, subDir,dir,fileName,fileName);
         }
     //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 && sameString(server,"hgdownload-test.cse.ucsc.edu")) // genome-test is different
                 {
                 //-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 && differentString(server,"hgdownload-test.cse.ucsc.edu"))// genome and hgwbeta can use rsync
                 {
                 //-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);
     //warn("found %d files",slCount(foundFiles));
 
     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;
         }
 
     // mark this as done to avoid excessive io
     savedDb     = cloneString(db);
     savedDir    = cloneString(dir);
     savedSubDir = cloneString(subDir);
     }
 
 // 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;
 
     slAddHead(&newList,oneFile);
     oneFile = NULL;
     }
 if (newList)
     foundFiles = slCat(newList,foundFiles);
 
 return oneFile;
 }
 
 sortOrder_t *fileSortOrderGet(struct cart *cart,struct trackDb *parentTdb)
 /* 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;
 char *setting = trackDbSetting(parentTdb, FILE_SORT_ORDER);
 if(setting == NULL) // Must be in trackDb or not a sortable list of files
     return NULL;
 
 sortOrder_t *sortOrder = needMem(sizeof(sortOrder_t));
 sortOrder->setting = cloneString(setting);
 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(sortOrder->setting,NULL,0);  // Get size
 sortOrder->column  = needMem(sortOrder->count*sizeof(char*));
 sortOrder->count = chopByWhite(sortOrder->setting,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 = cloneString(oneFile->fileName + strlen(oneFile->mdb->obj) + 1);
                 if (endsWith(field,".gz"))
                     chopSuffix(field);
                 }
             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);
     }
 }
 
 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.
 {
     // The basic idea:
     // 1) tdb of composite or type=downloadsOnly tableless track
     // 2) All mdb Objs associated with "composite=tdb->track" and having fileName
     // 3) Verification of each file in its discovered location
     // 4) Lookup of filters (tdb dimensions?) and filterComposite style controls
     // 5) Presort of files list
     // 6) make table class=sortable
     // 7) Final file count
     // Get preamble from dir ??
     // Use trackDb settings to get at html description, long and short labels
     // Recommend different color background to get the point across that these are files, not tracks
 
 // FIXME: Trick while developing:
 if (tdb->table != NULL)
     tdb->track = tdb->table;
 
 boolean debug = cartUsualBoolean(cart,"debug",FALSE);
 int ix;
 
 struct sqlConnection *conn = sqlConnect(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);
 
 struct fileDb *fileList = NULL, *oneFile = NULL;
 
 // Get an mdbObj list of all that belong to this track and have a fileName
 char buf[256];
 safef(buf,sizeof(buf),"composite=%s fileName=?",tdb->track);
 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),"composite=%s fileIndex= fileName!=",tdb->track);
 mdbVars = mdbByVarsLineParse(buf);
 mdbList = slCat(mdbList, mdbObjsQueryByVars(conn,mdbTable,mdbVars));
 sqlDisconnect(&conn);
 
 if (slCount(mdbList) == 0)
     {
     warn("No files specified in metadata for: %s\n%s",tdb->track,tdb->longLabel);
     return;
     }
 
 // Remove common vars from mdbs grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std;
 char *commonTerms[] = { "grant", "lab", "dataType", "control", "setType" };
 struct dyString *dyCommon = dyStringNew(256);
 for(ix=0;ix<ArraySize(commonTerms);ix++)
     {
     char *val = mdbRemoveCommonVar(mdbList, commonTerms[ix]);
     if (val)
         dyStringPrintf(dyCommon,"%s=%s ",commonTerms[ix],val);
     }
 if (debug && dyStringLen(dyCommon))
     warn("These terms are common:%s",dyStringContents(dyCommon));
 dyStringFree(&dyCommon);
 
 // Verify file existance and make fileList of those found
 while(mdbList)
     {
     boolean found = FALSE;
     struct mdbObj *mdbFile = slPopHead(&mdbList);
     // First for FileName
     char *fileName = mdbObjFindValue(mdbFile,"fileName");
     if (fileName != NULL)
         {
         oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, fileName);
         if (oneFile)
             {
             slAddHead(&fileList,oneFile);
             oneFile->mdb = mdbFile;
             found = TRUE;
             }
         else if (debug)
             warn("goldenPath/%s/%s/%s/%s    in mdb but not found in directory",db,ENCODE_DCC_DOWNLOADS, tdb->track,fileName);
         }
     // Now for FileIndexes
     fileName = mdbObjFindValue(mdbFile,"fileIndex");
     if (fileName != NULL)
         {
         // Verify existance first
         oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, fileName);
         if (oneFile)
             {
             slAddHead(&fileList,oneFile);
             if (found) // if already found then need two mdbObjs (assertable but then this is metadata)
                 oneFile->mdb = mdbObjClone(mdbFile);  // Do we really need to clone this?
             else
                 oneFile->mdb = mdbFile;
             found = TRUE;
             }
         else if (debug)
             warn("goldenPath/%s/%s/%s/%s    in mdb but not found in directory",db,ENCODE_DCC_DOWNLOADS, tdb->track,fileName);
         }
     if (!found)
         mdbObjsFree(&mdbFile);
     }
 
 if (slCount(fileList) == 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");
     }
 
 // FilterBoxes ?
     // Dimensions
     // cart contents
     //boolean filterAble = dimensionsExist(tdb);
     //membersForAll_t* membersForAll = membersForAllSubGroupsGet(tdb,cart);
 
 // Now update all files with their sortable fields and sort the list
 sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb);
 if (sortOrder != NULL)
     {
     // Fill in and sort fileList
     fileDbSortList(&fileList,sortOrder);
     }
 
 jsIncludeFile("hui.js",NULL);
 jsIncludeFile("ajax.js",NULL);
 
 // Table class=sortable
 int columnCount = 0;
 int restrictedColumn = 0;
 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("<i>%d files</i>",filesCount);    //puts("<FONT class='subCBcount'></font>"); // Use this style when filterboxes are up and running
 //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++;
 
 // Now the columns
 int curOrder = 0;
 if (sortOrder)
     {
     curOrder = sortOrder->count;
     for(ix=0;ix<sortOrder->count;ix++)
         {
         printf("<TH class='sortable sort%d%s' %snowrap>%s</TH>\n",
             sortOrder->order[ix],(sortOrder->forward[ix]?"":" sortRev"),
             (sameString("fileSize",sortOrder->column[ix])?"abbr='use' ":""),
             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...
 printf("<TBODY class='sortable sorting'>\n"); // 'sorting' is a fib but it conveniently greys the list till the table is initialized.
 for(oneFile = fileList;oneFile!= NULL;oneFile=oneFile->next)
     {
     char *field = NULL;
 
     printf("<TR valign='top'>");   // TODO: BUILD IN THE CLASSES TO ALLOW FILTERBOXES TO WORK!!!
 
     // Download button
     printf("<TD>");
     printf("<A HREF='http://%s/goldenPath/%s/%s/%s/%s' title='Download %s ...' TARGET=ucscDownloads>",
                 hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track, oneFile->fileName, oneFile->fileName);
     printf("<input type='button' value='Download'>");
     printf("</a></TD>\n");
 
     // Each of the pulled out mdb vars
     if (sortOrder)
         {
         for(ix=0;ix<sortOrder->count;ix++)
             {
             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];
                 printf("<TD align='center' nowrap>%s</td>",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,"fileName fileIndex composite project"); // Remove this from mdb now so that it isn't displayed in "extras'
     mdbObjReorderVars(oneFile->mdb,"grant lab dataType cell treatment antibody protocol replicate view",FALSE); // Bring to front
     mdbObjReorderVars(oneFile->mdb,"subId submittedDataVersion dateResubmitted dataVersion setType inputType controlId tableName",TRUE); // Send to back
     field = mdbObjVarValPairsAsLine(oneFile->mdb,TRUE);
     printf("<TD nowrap>%s</td>",field?field:" &nbsp;");
 
     printf("</TR>\n");
     }
 
-printf("</TBODY><TFOOT class='bgLevel3'>\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("<i>%d files</i>\n",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");
 
 // Free mem?
 }