9d4635d2821b3d8a73396728cbd9cd56ad842f7c
wisulliv
  Fri Feb 9 15:54:43 2024 -0800
Updated Home and Data Images.

diff --git src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
index 448051a..eee196c 100644
--- src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
+++ src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
@@ -1,2374 +1,2374 @@
 /* cdwWebBrowse - Browse CIRM data warehouse.. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "obscure.h"
 #include "cheapcgi.h"
 #include "sqlSanity.h"
 #include "trix.h"
 #include "htmshell.h"
 #include "fieldedTable.h"
 #include "portable.h"
 #include "paraFetch.h"
 #include "tagStorm.h"
 #include "rql.h"
 #include "intValTree.h"
 #include "cart.h"
 #include "cartDb.h"
 #include "jksql.h"
 #include "cdw.h"
 #include "cdwLib.h"
 #include "cdwValid.h"
 #include "hui.h"
 #include "hgConfig.h"
 #include "hgColors.h"
 #include "rainbow.h"
 #include "web.h"
 #include "tablesTables.h"
 #include "jsHelper.h"
 #include "wikiLink.h"
 #include "cdwFlowCharts.h"
 #include "cdwStep.h"
 #include "facetField.h"
 #include "rqlToSql.h"
 
 /* Global vars */
 struct cart *cart;	// User variables saved from click to click
 struct hash *oldVars;	// Previous cart, before current round of CGI vars folded in
 struct cdwUser *user;	// Our logged in user if any
 static char *accessibleFilesToken = NULL;  // Token for file access if any
 boolean isPublicSite = FALSE;
 
 
 char *excludeVars[] = {"cdwCommand", "submit", "DownloadFormat", NULL};
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "cdwWebBrowse is a cgi script not meant to be run from command line.\n"
   );
 }
 
 void printHash(char *label, struct hash *hash)
 /* Print out keys in hash alphabetically. */
 {
 struct hashEl *list, *el;
 list = hashElListHash(hash);
 slSort(&list, hashElCmp);
 printf("%s:\n", label);
 for (el = list; el != NULL; el = el->next)
     printf("    %s\n", el->name);
 hashElFreeList(&list);
 }
 
 // fields/columns of the browse file table
 char *fileTableFields = NULL;
 char *visibleFacetFields = NULL;
 #define FILEFIELDS "file_name,file_size,ucsc_db"
 #define FILEFACETFIELDS "species,assay,format,lab,data_set_id"
 
 struct dyString *printPopularTags(struct hash *hash, int maxSize)
 /* Get all hash elements, sorted by count, and print all the ones that fit */
 {
 maxSize -= 3;  // Leave room for ...
 struct dyString *dy = dyStringNew(0);
 
 struct hashEl *hel, *helList = hashElListHash(hash);
 slSort(&helList, hashElCmpIntValDesc);
 for (hel = helList; hel != NULL; hel = hel->next)
     {
     int oldSize = dy->stringSize;
     if (oldSize != 0)
         dyStringAppend(dy, ", ");
     dyStringPrintf(dy, "%s (%d)", hel->name, ptToInt(hel->val));
     if (dy->stringSize >= maxSize)
         {
 	dy->string[oldSize] = 0;
 	dy->stringSize = oldSize;
 	dyStringAppend(dy, "...");
 	break;
 	}
     }
 hashElFreeList(&helList);
 return dy;
 }
 
 static long long sumCounts(struct hash *hash)
 /* Figuring hash is integer valued, return sum of all vals in hash */
 {
 long long total = 0;
 struct hashEl *hel, *helList = hashElListHash(hash);
 for (hel = helList; hel != NULL; hel = hel->next)
     {
     int val = ptToInt(hel->val);
     total += val;
     }
 hashElFreeList(&helList);
 return total;
 }
 
 int labCount(struct tagStorm *tags)
 /* Return number of different labs in tags */
 {
 struct hash *hash = tagStormCountTagVals(tags, "lab", "accession");
 int count = hash->elCount;
 hashFree(&hash);
 return count;
 }
 
 
 void wrapFileName(struct fieldedTable *table, struct fieldedRow *row, 
     char *field, char *val, char *shortVal, void *context)
 /* Write out wrapper that links us to metadata display */
 {
 printf("<A HREF=\"../cgi-bin/cdwWebBrowse?cdwCommand=oneFile&cdwFileTag=%s&cdwFileVal=%s&%s\">",
     field, val, cartSidUrlString(cart));
 printf("%s</A>", shortVal);
 }
 
 
 void wrapTagField(struct fieldedTable *table, struct fieldedRow *row, 
     char *field, char *val, char *shortVal, void *context)
 /* Write out wrapper that links us to something nice */
 {
 printf("<A HREF=\"../cgi-bin/cdwWebBrowse?cdwCommand=oneTag&cdwTagName=%s&%s\">",
     val, cartSidUrlString(cart));
 printf("%s</A>", shortVal);
 }
 
 void wrapTagValueInFiles(struct fieldedTable *table, struct fieldedRow *row, 
     char *field, char *val, char *shortVal, void *context)
 /* Write out wrapper that links us to something nice */
 {
 printf("<A HREF=\"../cgi-bin/cdwWebBrowse?cdwCommand=browseFiles&%s&",
     cartSidUrlString(cart));
 char query[2*PATH_LEN];
 safef(query, sizeof(query), "%s = '%s'", field, val);
 char *escapedQuery = cgiEncode(query);
 printf("%s=%s&cdwBrowseFiles_page=1", "cdwBrowseFiles_filter", escapedQuery);
 freez(&escapedQuery);
 printf("\">%s</A>", shortVal);
 }
 
 void wrapFileSize(struct fieldedTable *table, struct fieldedRow *row,
     char * field, char *val, char *shortVal, void *context)
 /* Write out wrapper that displays file sizes in human-readable format */
 {
 if (!isdigit(val[0]))
     warn("Warning: expected a number for file_size, but got %s", val);
 double fVal = atof(val);
 char* valQual = "";
 int intVal = 0;
 if (fVal>=1E12)
     {
     intVal = round(fVal/1E12);
     valQual = "TB";
     }
 else if (fVal>=1E9)
     {
     intVal = round(fVal/1E9);
     valQual = "GB";
     }
 else if (fVal>=1E6)
     {
     intVal = round(fVal/1E6);
     valQual = "MB";
     }
 else if (fVal>=1E3)
     {
     intVal = round(fVal/1E3);
     valQual = "KB";
     }
 else
     {
     intVal = round(fVal);
     valQual = "B";
     }
 printf("%d %s", intVal, valQual);
 }
 
 static char *mustFindFieldInRow(char *field, struct slName *fieldList, char **row)
 /* Assuming field is in list, which is ordered same as row, return row cell
  * corrsepondint to field */
 {
 int fieldIx = 0;
 struct slName *el;
 for (el = fieldList; el != NULL; el = el->next)
     {
     if (sameString(el->name, field))
         {
 	return row[fieldIx];
 	}
     ++fieldIx;
     }
 errAbort("Couldn't find field %s in row", field);
 return NULL;
 }
 
 char *tagDescription(char *tag)
 /* Return tag description given tag name. */
 {
 char *unparsed[] = {
 #include "tagDescriptions.h"
     };
 int unparsedCount = ArraySize(unparsed);
 
 int i;
 for (i=0; i<unparsedCount; ++i)
     {
     char *s = unparsed[i];
     if (startsWithWord(tag, s))
         {
 	int tagLen = strlen(tag);
 	s = skipLeadingSpaces(s + tagLen);
 	return s;
 	}
     }
 return NULL;
 }
 
 void doOneTag(struct sqlConnection *conn)
 /* Put up information on one tag */
 {
 /* Get all tags on user accessible files */
 struct tagStorm *tags = cdwUserTagStorm(conn, user);
 
 /* Look up which tag we're working on from cart, and make summary info hash and report stats */
 char *tag = cartString(cart, "cdwTagName");
 
 /* Print out tag description */
 char *description = tagDescription(tag);
 if (description != NULL)
     printf("<B>%s tag description</B>: %s<BR>\n", tag, description);
 
 /* Print out some summary stats */
 struct hash *hash = tagStormCountTagVals(tags, tag, "accession");
 printf("The <B>%s</B> tag has %d distinct values and is used on %lld files. ", 
     tag, hash->elCount, sumCounts(hash));
 
 /* Initially sort from most popular to least popular */
 struct hashEl *hel, *helList = hashElListHash(hash);
 slSort(&helList, hashElCmpIntValDesc);
 
 /* Create fielded table containing tag values */
 char *labels[] = {"files", tag};
 int fieldCount = ArraySize(labels);
 struct fieldedTable *table = fieldedTableNew("Tag Values", labels, fieldCount);
 for (hel = helList; hel != NULL; hel = hel->next)
     {
     char numBuf[16];
     safef(numBuf, sizeof(numBuf), "%d", ptToInt(hel->val));
     char *row[2] = {numBuf, hel->name};
     fieldedTableAdd(table, row, fieldCount, 0);
     }
 
 /* Draw sortable table */
 char returnUrl[PATH_LEN*2];
 safef(returnUrl, sizeof(returnUrl), "../cgi-bin/cdwWebBrowse?cdwCommand=oneTag&cdwTagName=%s&%s",
     tag, cartSidUrlString(cart) );
 struct hash *outputWrappers = hashNew(0);
 hashAdd(outputWrappers, tag, wrapTagValueInFiles);
 webSortableFieldedTable(cart, table, returnUrl, "cdwOneTag", 0, outputWrappers, NULL);
 fieldedTableFree(&table);
 }
 
 void generateTableRow(struct slName *list,char **row, char *idTag , char *idVal) 
 {
 struct slName *el; 
 static char *outputFields[] = {"tag", "value"};
 struct fieldedTable *table = fieldedTableNew("File Tags", outputFields,ArraySize(outputFields));
 int fieldIx = 0;
 char *accession = NULL;
 for (el = list; el != NULL; el = el->next)
     {
     char *outRow[2];
     char *val = row[fieldIx];
     if (val != NULL)
 	{
 	outRow[0] = el->name;
 	outRow[1] = row[fieldIx];
 
 	// add a link to the accession row
 	if (sameWord(el->name, "accession"))
 	    {
 	    char link[1024];
 	    safef(link, sizeof(link), "%s <a href='cdwGetFile?acc=%s'>download</a>", outRow[1], outRow[1]);
 	    accession = cloneString(outRow[1]);
 	    outRow[1] = cloneString(link);
 	    }
 	// add a link to the submit_file_name row
 	if (sameWord(el->name, "submit_file_name"))
 	    {
 	    char link[1024];
 	    safef(link, sizeof(link), "%s <a href='cdwGetFile?acc=%s&useSubmitFname=1'>download</a>", outRow[1], accession);
 	    outRow[1] = cloneString(link);
 	    }
 	fieldedTableAdd(table, outRow, 2, fieldIx);
 	}
     ++fieldIx;
     }
 char returnUrl[PATH_LEN*2];
 safef(returnUrl, sizeof(returnUrl), 
     "../cgi-bin/cdwWebBrowse?cdwCommand=oneFile&cdwFileTag=%s&cdwFileVal=%s&%s",
     idTag, idVal, cartSidUrlString(cart) );
 struct hash *outputWrappers = hashNew(0);
 hashAdd(outputWrappers, "tag", wrapTagField);
 webSortableFieldedTable(cart, table, returnUrl, "cdwOneFile", 0, outputWrappers, NULL);
 fieldedTableFree(&table);
 freeMem(accession);
 }
 
 char *unquotedCartString(struct cart *cart, char *varName)
 /* Return unquoted cart variable */
 {
 char *val = cartOptionalString(cart, varName);
 if (val == NULL)
     return "";
 stripChar(val, '"');
 stripChar(val, '\'');
 return val;
 }
 
 char *getCdwSetting(char *setting, char *deflt)
 /* Get string cdw.<setting> */
 {
 char cdwSetting[1024];
 safef(cdwSetting, sizeof cdwSetting, "cdw.%s", setting);
 return cfgOptionDefault(cdwSetting, deflt);
 } 
 
 char *getCdwTableSetting(char *setting)
 /* Get string cdw.<setting>
  * Allows us to use non-default settings for tables */
 {
 return getCdwSetting(setting, setting); // table name is its own default
 } 
 
 void doFileFlowchart(struct sqlConnection *conn)
 /* Put up a page with info on one file */
 {
 char *idTag = cartUsualString(cart, "cdwFileTag", "accession");
 char *idVal = cartString(cart, "cdwFileVal");
 char query[512];
 sqlSafef(query, sizeof(query), "select * from %s where %s='%s'", getCdwTableSetting("cdwFileTags"), idTag, idVal);
 struct sqlResult *sr = sqlGetResult(conn, query);
 struct slName  *list = sqlResultFieldList(sr);
 char **row;
 struct dyString *dy = dyStringNew(1024); 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *fileId = mustFindFieldInRow("file_id", list, row);
     printf("Click on a box in the flow chart to navigate to that file."); 
     dy = makeCdwFlowchart(sqlSigned(fileId), cart);
     printf("<a href='cdwWebBrowse?cdwCommand=oneFile");
     printf("&%s", cartSidUrlString(cart));
     printf("&cdwFileTag=%s", idTag);
     printf("&cdwFileVal=%s", idVal);
     printf("'>Remove flow chart</a>"); 
     generateTableRow(list, row, idTag, idVal); 
     }
 jsInline(dy->string);
 dyStringFree(&dy); 
 sqlFreeResult(&sr);
 }
 
 void doOneFile(struct sqlConnection *conn)
 /* Put up a page with info on one file */
 {
 struct sqlConnection *conn2 = cdwConnect();
 char *idTag = cartUsualString(cart, "cdwFileTag", "accession");
 char *idVal = cartString(cart, "cdwFileVal");
 char query[512];
 sqlSafef(query, sizeof(query), "select * from %s where %s='%s'", getCdwTableSetting("cdwFileTags"), idTag, idVal);
 struct sqlResult *sr = sqlGetResult(conn, query);
 struct slName *list = sqlResultFieldList(sr);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *fileName = mustFindFieldInRow("file_name", list, row);
     char *fileSize = mustFindFieldInRow("file_size", list, row);
     char *format = mustFindFieldInRow("format", list, row);
     char *fileId = mustFindFieldInRow("file_id", list, row);
     long long size = sqlLongLongInList(&fileSize);
     printf("Tags associated with %s a %s format file of size ", fileName, format);
     printLongWithCommas(stdout, size);
      
     printf("<BR>\n");
     /* Figure out number of file inputs and outputs, and put up link to flowcharts */
     sqlSafef(query, sizeof(query), "select * from cdwStepIn where fileId = %s", fileId);
     struct cdwStepIn *cSI = cdwStepInLoadByQuery(conn2, query), *stepIter;
     int outFiles = 0, stepRunId;  
     for (stepIter = cSI; stepIter != NULL; stepIter=stepIter->next)
 	{
 	sqlSafef(query, sizeof(query), "select count(*) from cdwStepOut where stepRunId = %i", stepIter->stepRunId);
 	outFiles += sqlQuickNum(conn2, query);
 	}
 
     sqlSafef(query, sizeof(query), "select stepRunId from cdwStepOut where fileId = %s", fileId);
     stepRunId = sqlQuickNum(conn2, query);
     sqlSafef(query, sizeof(query), "select count(*) from cdwStepIn where stepRunId = %i", stepRunId);
     int inFiles = sqlQuickNum(conn2, query);
     if (inFiles > 0 || outFiles > 0)
 	{
 	printf("File relationships: %d inputs, %d outputs ", inFiles, outFiles);
 	printf("<a href='cdwWebBrowse?cdwCommand=doFileFlowchart");
 	printf("&%s", cartSidUrlString(cart));
 	printf("&cdwFileTag=%s", idTag);
 	printf("&cdwFileVal=%s", idVal);
 	printf("'>flow chart</a>"); 
 	} 
     generateTableRow(list, row, idTag, idVal); 
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn2);
 }
 
 struct dyString *customTextForFile(struct sqlConnection *conn, struct cdwTrackViz *viz)
 /* Create custom track text */
 {
 struct dyString *dy = dyStringNew(0);
 dyStringPrintf(dy, "track name=\"%s\" ", viz->shortLabel);
 dyStringPrintf(dy, "description=\"%s\" ", viz->longLabel);
 //char *host = hHttpHost();
 dyStringPrintf(dy, "bigDataUrl=https://localhost/cgi-bin/cdwGetFile?acc=%s", viz->shortLabel);
 if (accessibleFilesToken != NULL)
     dyStringPrintf(dy, "&token=%s", accessibleFilesToken);
 dyStringPrintf(dy, " ");
     
 char *indexExt = NULL;
 if (sameWord(viz->type, "bam"))
     indexExt = ".bai";
 else if (sameWord(viz->type, "vcfTabix"))
     indexExt = ".tbi";
 
 if (indexExt != NULL)
     {
     dyStringPrintf(dy, "bigDataIndex=http://localhost/cgi-bin/cdwGetFile?addExt=%s&acc=%s", indexExt, viz->shortLabel);
     if (accessibleFilesToken != NULL)
         dyStringPrintf(dy, "&token=%s", accessibleFilesToken);
     }
 
 dyStringPrintf(dy, " type=%s", viz->type);
 return dy;
 }
 
 struct cdwTrackViz *cdwTrackVizFromFileId(struct sqlConnection *conn, long long fileId)
 /* Return cdwTrackViz if any associated with file ID */
 {
 char query[256];
 sqlSafef(query, sizeof(query), "select * from cdwTrackViz where fileId=%lld", fileId);
 return cdwTrackVizLoadByQuery(conn, query);
 }
 
 
 void wrapFileVis(struct sqlConnection *conn, char *acc, char *unwrapped)
 /* Wrap hyperlink link to file around unwrapped text.  Link goes to file in vf. */
 {
 char *host = hHttpHost();
 printf("<A HREF=\"");
 printf("http://%s/cgi-bin/cdwGetFile?acc=%s", host, acc);
 if (accessibleFilesToken != NULL)
     printf("&token=%s", accessibleFilesToken);
 printf("\">");
 printf("%s</A>", unwrapped);
 }
 
 boolean wrapTrackVis(struct sqlConnection *conn, struct cdwValidFile *vf, char *unwrapped)
 /* Attempt to wrap genome browser link around unwrapped text.  Link goes to file in vf. */
 {
 if (vf == NULL)
     return FALSE;
 struct cdwTrackViz *viz = cdwTrackVizFromFileId(conn, vf->fileId);
 if (viz == NULL)
     return FALSE;
 struct dyString *track = customTextForFile(conn, viz);
 char *encoded = cgiEncode(track->string);
 printf("<A TARGET=_BLANK HREF=\"../cgi-bin/hgTracks");
 printf("?%s", cartSidUrlString(cart));
 printf("&db=%s", vf->ucscDb);
 printf("&hgt.customText=");
 printf("%s", encoded);
 printf("\">");	       // Finish HREF quote and A tag
 printf("%s</A>", unwrapped);
 freez(&encoded);
 dyStringFree(&track);
 return TRUE;
 }
 
 
 void wrapTrackNearFileName(struct fieldedTable *table, struct fieldedRow *row, char *tag, char *val,
     char *shortVal, void *context)
 /* Construct wrapper to UCSC if row actually is a track */
 {
 struct sqlConnection *conn = context;
 int fileNameIx = stringArrayIx("file_name", table->fields, table->fieldCount);
 boolean printed = FALSE;
 if (fileNameIx >= 0)
     {
     char *fileName = row->row[fileNameIx];
     char acc[FILENAME_LEN];
     safef(acc, sizeof(acc), "%s", fileName);
     char *dot = strchr(acc, '.');
     if (dot != NULL)
         *dot = 0;
     struct cdwValidFile *vf = cdwValidFileFromLicensePlate(conn, acc);
     struct cdwFile *ef = cdwFileFromId(conn, vf->fileId);
     if (cdwCheckAccess(conn, ef, user, cdwAccessRead)) printed = wrapTrackVis(conn, vf, shortVal);
     }
 if (!printed)
     printf("%s", shortVal);
 }
 
 void wrapTrackNearAccession(struct fieldedTable *table, struct fieldedRow *row, 
     char *tag, char *val, char *shortVal, void *context)
 /* Construct wrapper that can link to Genome Browser if any field in table
  * is an accession */
 {
 struct sqlConnection *conn = context;
 int accIx = stringArrayIx("accession", table->fields, table->fieldCount);
 boolean printed = FALSE;
 if (accIx >= 0)
     {
     char *acc = row->row[accIx];
     if (acc != NULL)
 	{
 	struct cdwValidFile *vf = cdwValidFileFromLicensePlate(conn, acc);
 	struct cdwFile *ef = cdwFileFromId(conn, vf->fileId);
 	if (cdwCheckAccess(conn, ef, user, cdwAccessRead))
 	    printed = wrapTrackVis(conn, vf, shortVal);
 	}
     }
 if (!printed)
     printf("%s", shortVal);
 }
 
 boolean isWebBrowsableFormat(char *format)
 /* Return TRUE if it's one of the web-browseable formats */
 {
 char *formats[] = {"html", "jpg", "pdf", "png", "text", "tsv"};
 return stringArrayIx(format, formats, ArraySize(formats)) >= 0;
 }
 
 void wrapFormat(struct fieldedTable *table, struct fieldedRow *row, 
     char *field, char *val, char *shortVal, void *context)
 /* Write out wrapper that links us to something nice */
 {
 struct sqlConnection *conn = context;
 char *format = val;
 if (isWebBrowsableFormat(format))
      {
      /* Get file name out of table */
      int fileNameIx = stringArrayIx("file_name", table->fields, table->fieldCount);
      if (fileNameIx < 0)
         errAbort("Expecting a file_name in this table");
      char *fileName = row->row[fileNameIx];
 
      /* Convert file to accession by chopping off at first dot */
      char *acc = cloneString(fileName);
      char *dot = strchr(acc, '.');
      if (dot != NULL)
          *dot = 0;
 
      struct cdwValidFile *vf = cdwValidFileFromLicensePlate(conn, acc);
      struct cdwFile *ef = cdwFileFromId(conn, vf->fileId);
      if (cdwCheckAccess(conn, ef, user, cdwAccessRead))
 	   wrapFileVis(conn, acc, shortVal);
      freez(&acc);
      }
 else
      printf("%s", format);
 }
 
 void wrapMetaNearAccession(struct fieldedTable *table, struct fieldedRow *row, 
     char *field, char *val, char *shortVal, void *context)
 /* Write out wrapper on a column that looks for accession in same table and uses
  * that to link us to oneFile display. */
 {
 struct sqlConnection *conn = context;
 int accIx = stringArrayIx("accession", table->fields, table->fieldCount);
 boolean wrapped = FALSE;
 if (accIx >= 0)
     {
     char *acc = row->row[accIx];
     if (acc != NULL)
         {
 	struct cdwValidFile *vf = cdwValidFileFromLicensePlate(conn, acc);
 	if (vf != NULL)
 	    {
 	    wrapped = TRUE;
 	    printf("<A HREF=\"../cgi-bin/cdwWebBrowse?cdwCommand=oneFile&cdwFileTag=accession&cdwFileVal=%s&%s\">",
 		acc, cartSidUrlString(cart));
 	    printf("%s</A>", shortVal);
 	    }
 	}
     }
 
 if (!wrapped)
     printf("%s", shortVal);
 }
 
 void wrapExternalUrl(struct fieldedTable *table, struct fieldedRow *row, 
     char *field, char *val, char *shortVal, void *context)
 /* Attempt to wrap genome browser link around unwrapped text.  Link goes to file in vf. */
 {
 printf("<A HREF=\"%s\" target=\"_blank\">%s</A>", val, shortVal);
 }
 
 static void rSumLocalMatching(struct tagStanza *list, char *field, int *pSum)
 /* Recurse through tree adding matches to *pSum */
 {
 struct tagStanza *stanza;
 for (stanza = list; stanza != NULL; stanza = stanza->next)
     {
     if (tagFindLocalVal(stanza, field))
         *pSum += 1;
     if (stanza->children != NULL)
          rSumLocalMatching(stanza->children, field, pSum);
     }
 }
 
 int tagStormCountStanzasWithLocal(struct tagStorm *tags, char *localField)
 /* Return count of all stanzas that include locally a given field */
 {
 int sum = 0;
 rSumLocalMatching(tags->forest, localField, &sum);
 return sum;
 }
 
 int hashElCmpIntValDescNameAsc(const void *va, const void *vb)
 /* Compare two hashEl from a hashInt type hash, with highest integer values
  * comingFirst. */
 {
 struct hashEl *a = *((struct hashEl **)va);
 struct hashEl *b = *((struct hashEl **)vb);
 int diff = b->val - a->val;
 if (diff == 0)
     diff = strcmp(b->name, a->name);
 return diff;
 }
 
 struct suggestBuilder
 /* A structure to help build a list of suggestions for each file */
     {
     struct suggestBuilder *next;
     char *name;		/* Field name */
     struct hash *hash;  /* Keyed by field values, values are # of times seen */
     };
 
 struct hash *accessibleSuggestHash(struct sqlConnection *conn, char *fields, 
     struct cdwFile *efList)
 /* Create hash keyed by field name and with values the distinct values of this
  * field.  Only do this on fields where it looks like suggest would be useful. */
 {
 struct hash *suggestHash = hashNew(0);
 int totalFiles = slCount(efList);
 
 /* Make up list of helper structures */
 struct slName *name, *nameList = slNameListFromComma(fields);
 struct suggestBuilder *field, *fieldList = NULL;
 for (name = nameList; name != NULL; name = name->next)
     {
     AllocVar(field);
     field->name = name->name;
     field->hash = hashNew(0);
     slAddHead(&fieldList, field);
     }
 slReverse(&fieldList);
 
 /* Build up sql query to fetch all our fields */
 struct dyString *query = dyStringNew(0);
 sqlDyStringPrintf(query, "select ");
 for (field = fieldList; field != NULL; field = field->next)
     {
     if (field != fieldList) // not first one
 	sqlDyStringPrintf(query, ",");
     sqlDyStringPrintf(query, "%s", field->name);
     }
 
 /* Put where on it to limit it to accessible files */
 sqlDyStringPrintf(query, " from %s where file_id in (", getCdwTableSetting("cdwFileTags"));
 
 struct cdwFile *ef;
 for (ef = efList; ef != NULL; ef = ef->next)
     {
     if (ef != efList) // not first one
 	sqlDyStringPrintf(query, ",");
     sqlDyStringPrintf(query, "%u", ef->id);
     }
 sqlDyStringPrintf(query, ")");
 
 struct sqlResult *sr = sqlGetResult(conn, query->string);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     int fieldIx = 0;
     for (field = fieldList; field != NULL; field = field->next, ++fieldIx)
         {
 	char *val = row[fieldIx];
 	if (val != NULL)
 	    hashIncInt(field->hash, val);
 	}
     }
 sqlFreeResult(&sr);
 
 /* Loop through fields making suggestion hash entries where appropriate */
 for (field = fieldList; field != NULL; field = field->next)
     {
     struct hash *valHash = field->hash;
     if (valHash->elCount < 20 || valHash->elCount < totalFiles/3)
         {
 	struct hashEl *hel, *helList = hashElListHash(valHash);
 	slSort(&helList, hashElCmpIntValDescNameAsc);
 	struct slName *valList = NULL;
 	int limit = 200;
 	for (hel = helList ; hel != NULL; hel = hel->next)
 	    {
 	    if (--limit < 0)
 	        break;
 	    slNameAddHead(&valList, hel->name);
 	    }
 	slReverse(&valList);
 	hashAdd(suggestHash, field->name, valList);
 	}
     hashFree(&field->hash);
     }
 slFreeList(&fieldList);
 slFreeList(&nameList);
 dyStringFree(&query);
 return suggestHash;
 }
 
 
 static struct hash *sqlHashFields(struct sqlConnection *conn, char *table)
 /* Return a hash containing all fields in table */
 {
 struct slName *field, *fieldList = sqlListFields(conn, table);
 struct hash *hash = hashNew(7);
 for (field = fieldList; field != NULL; field = field->next)
     hashAdd(hash, field->name, NULL);
 slFreeList(&fieldList);
 return hash;
 }
 
 static char *filterFieldsToJustThoseInTable(struct sqlConnection *conn, char *fields, char *table)
 /* Return subset of all fields just containing those that exist in table */
 {
 struct hash *hash = sqlHashFields(conn, table);
 struct slName *name, *nameList = slNameListFromComma(fields);
 struct dyString *dy = dyStringNew(strlen(fields));
 char *separator = "";
 for (name = nameList; name != NULL; name = name->next)
     {
     char *s = name->name;
     if (hashLookup(hash, s))
 	{
         dyStringPrintf(dy, "%s%s", separator, s);
 	separator = ",";
 	}
     }
 hashFree(&hash);
 slFreeList(&nameList);
 return dyStringCannibalize(&dy);
 }
 
 void searchFilesWithAccess(struct sqlConnection *conn, char *searchString, char *allFields, 
     char* initialWhere, struct cdwFile **retList, struct dyString **retWhere, char **retFields,
     boolean securityColumnsInTable)
 {
 /* Get list of files that we are authorized to see and that match searchString in the trix file
  * Returns: retList of matching files, retWhere with sql where expression for these files, retFields
  * If nothing to see, retList is NULL
  * DO NOT Convert to safef V2 since the where clause is checked by gbSanity in tablesTables.c
  * */
 char *fields = filterFieldsToJustThoseInTable(conn, allFields, getCdwTableSetting("cdwFileTags"));
 
 struct cdwFile *efList = NULL;
 if (!securityColumnsInTable)
     efList = cdwAccessibleFileList(conn, user);
 
 struct cdwFile *ef;
 
 if (!securityColumnsInTable && !efList)
     {
     *retList = NULL;
     return;
     }
 
 struct rbTree *searchPassTree = NULL;
 if (!isEmpty(searchString))
     {
     searchPassTree = intValTreeNew(0);
     char *lowered = cloneString(searchString);
     tolowers(lowered);
     char *words[128];
     int wordCount = chopLine(lowered, words);
     char *trixPath = "/gbdb/cdw/cdw.ix";
     struct trix *trix = trixOpen(trixPath);
     struct trixSearchResult *tsr, *tsrList = trixSearch(trix, wordCount, words, tsmExpand);
     for (tsr = tsrList; tsr != NULL; tsr = tsr->next)
         {
 	if (securityColumnsInTable) // creates a list with all found items file ids on it.
 	    {
 	    AllocVar(ef);
 	    ef->id = sqlUnsigned(tsr->itemId);
 	    slAddHead(&efList, ef);
 	    }
 	else
 	    {
 	    intValTreeAdd(searchPassTree, sqlUnsigned(tsr->itemId), tsr);
 	    }
 	}
     if (securityColumnsInTable)
 	slReverse(&efList);
     }
 
 
 /* Loop through all files constructing a SQL where clause that restricts us
  * to just the ones that we're authorized to hit, and that also pass initial where clause
  * if any. */
 struct dyString *where = dyStringNew(0);
 if (!isEmpty(initialWhere))
     sqlDyStringPrintf(where, "(%-s)", initialWhere); // trust
 if (securityColumnsInTable)
     {
     if (user)
 	{
 	// get all groupIds belonging to this user
 	char query[256];
 	if (!user->isAdmin)
 	    {
 	    sqlSafef(query, sizeof(query), 
 		"select groupId from cdwGroupUser "
 		" where cdwGroupUser.userId = %d", user->id);
 	    struct sqlResult *sr = sqlGetResult(conn, query);
 	    char **row;
 	    if (!isEmpty(where->string))
 		sqlDyStringPrintf(where, " and ");
 	    sqlDyStringPrintf(where, "(allAccess > 0");
 	    while ((row = sqlNextRow(sr)) != NULL)
 		{
 		int groupId = sqlUnsigned(row[0]);
 		sqlDyStringPrintf(where, " or FIND_IN_SET('%u', groupIds)", groupId);
 		}
 	    sqlFreeResult(&sr);
 	    sqlDyStringPrintf(where, ")");
 	    }
 	}
     else
 	{
 	if (!isEmpty(where->string))
 	    sqlDyStringPrintf(where, " and ");
 	sqlDyStringPrintf(where, "allAccess > 0");
 	}
     }
 
 if (efList 
     || (securityColumnsInTable && (!isEmpty(searchString)))) // have search terms but nothing was found
     {
     if (!isEmpty(where->string))
 	sqlDyStringPrintf(where, " and ");
     sqlDyStringPrintf(where, "file_id in (0");	 // initial 0 never found, just makes code smaller
     for (ef = efList; ef != NULL; ef = ef->next)
 	{
 	if (searchPassTree == NULL || securityColumnsInTable || intValTreeFind(searchPassTree, ef->id) != NULL)
 	    {
 	    sqlDyStringPrintf(where, ",%u", ef->id);
 	    }
 	}
     sqlDyStringPrintf(where, ")");
     }
 
 rbTreeFree(&searchPassTree);
 
 // return three variables
 *retWhere  = where;
 *retList   = efList;
 *retFields = fields;
 }
 
 struct cdwFile* findDownloadableFiles(struct sqlConnection *conn, struct cart *cart,
     char* initialWhere, char *searchString)
 /* return list of files that we are allowed to see and that match current filters */
 {
 // get query of files that match and where we have access
 struct cdwFile *efList = NULL;
 struct dyString *accWhere;
 char *fields;
 searchFilesWithAccess(conn, searchString, fileTableFields, initialWhere, &efList, &accWhere, &fields, FALSE);
 
 // reduce query to those that match our filters
 struct dyString *dummy;
 struct dyString *filteredWhere;
 char *table = isEmpty(initialWhere) ? getCdwTableSetting("cdwFileFacets") : getCdwTableSetting("cdwFileTags");
 
 webTableBuildQuery(cart, table, accWhere->string, "cdwBrowseFiles", fileTableFields, FALSE, &dummy, &filteredWhere);
 
 // Selected Facet Values Filtering
 char *selectedFacetValues=cartUsualString(cart, "cdwBrowseFiles_facet_selList", "");
 struct facetField *selectedList = deLinearizeFacetValString(selectedFacetValues);
 struct facetField *sff = NULL;
 struct dyString *facetedWhere = dyStringNew(1024);
 for (sff = selectedList; sff; sff=sff->next)
     {
     if (slCount(sff->valList)>0)
 	{
 	sqlDyStringPrintf(facetedWhere, " and ");  // use Frag to prevent NOSQLINJ tag
 	sqlDyStringPrintf(facetedWhere, "ifnull(%s,'n/a') in (", sff->fieldName);
 	struct facetVal *el;
 	for (el=sff->valList; el; el=el->next)
 	    {
 	    sqlDyStringPrintf(facetedWhere, "'%s'", el->val);
 	    if (el->next)
 		sqlDyStringPrintf(facetedWhere, ",");
 	    }
 	sqlDyStringPrintf(facetedWhere, ")");
 	}
     }
 
 
 // get their fileIds
 struct dyString *tagQuery = sqlDyStringCreate("SELECT file_id from %s %-s", table, filteredWhere->string); // trust
 if (!isEmpty(facetedWhere->string))
     sqlDyStringPrintf(tagQuery,  "%-s", facetedWhere->string); // trust because it was created safely
 struct slName *fileIds = sqlQuickList(conn, tagQuery->string);
 
 // retrieve the cdwFiles objects for these
 struct dyString *fileQuery = sqlDyStringCreate("SELECT * FROM cdwFile WHERE id IN (");
 sqlDyStringPrintValuesList(fileQuery, fileIds);
 sqlDyStringPrintf(fileQuery, ")");
 return cdwFileLoadByQuery(conn, fileQuery->string);
 }
 
 static void continueSearchVars()
 /* print out hidden forms variables for the current search */
 {
 cgiContinueHiddenVar("cdwFileSearch");
 char *fieldNames[128];
 char *tempFileTableFields = cloneString(fileTableFields); // cannot modify string literals
 int fieldCount = chopString(tempFileTableFields, ",", fieldNames, ArraySize(fieldNames));
 int i;
 for (i = 0; i<fieldCount; i++)
     {
     char varName[1024];
     safef(varName, sizeof(varName), "cdwBrowseFiles_f_%s", fieldNames[i]);
     cgiContinueHiddenVar(varName);
     }
 }
 
 void makeDownloadAllButtonForm(int count) 
 /* The "download all" button cannot be a form at this place, nested forms are
  * not allowed in html. So create a link instead. */
 {
 if (count<0)
     errAbort("Error: Search results in a negative number of files found");
 printf("<A class='btn btn-secondary' HREF=\"cdwWebBrowse?hgsid=%s&cdwCommand=downloadFiles", cartSessionId(cart));
 
 printf("&cdwFileSearch=%s", unquotedCartString(cart, "cdwFileSearch"));
 printf("&cdwBrowseFiles_filter=%s", cartUsualString(cart, "cdwBrowseFiles_filter", ""));
 printf("\">Download %d File%s</A>", count, count>1?"s":"");
 printf("<br><br>\n");
 }
 
 char *createTokenForUser()
 /* create a random token and add it to the cdwDownloadToken table with the current username.
  * Returns token, should be freed.*/
 {
 struct sqlConnection *conn = hConnectCentral(); // r/w access -> has to be in hgcentral
 char query[4096]; 
 if (!sqlTableExists(conn, "cdwDownloadToken"))
      {
      sqlSafef(query, sizeof(query),
          "CREATE TABLE cdwDownloadToken (token varchar(255) NOT NULL PRIMARY KEY, "
 	 "userId int NOT NULL, createTime datetime DEFAULT NOW())");
      sqlUpdate(conn, query);
      }
 char *token = makeRandomKey(80);
 sqlSafef(query, sizeof(query), "INSERT INTO cdwDownloadToken (token, userId) VALUES ('%s', %d)", token, user->id);
 sqlUpdate(conn, query);
 hDisconnectCentral(&conn);
 return token;
 }
 
 void accessibleFilesTable(struct cart *cart, struct sqlConnection *conn, 
     char *searchString, char *allFields, char *fromTable, char *initialWhere,  
     char *returnUrl, char *varPrefix, int maxFieldWidth, 
     struct hash *tagOutWrappers, void *wrapperContext,
     boolean withFilters, char *itemPlural, int pageSize,
     char *visibleFacetList, boolean securityColumnsInTable)
 {
 struct cdwFile *efList = NULL;
 struct dyString *where;
 char *fields;
 
 searchFilesWithAccess(conn, searchString, allFields, initialWhere, &efList, &where, &fields, securityColumnsInTable);
 
 if (!securityColumnsInTable && !efList)
     {
     if (user != NULL && user->isAdmin)
 	printf("<BR>The file database is empty.");
     else
 	printf("<BR>Unfortunately there are no %s you are authorized to see.", itemPlural);
     return;
     }
 
 if (user!=NULL)
     accessibleFilesToken = createTokenForUser();
 
 /* Let the sql system handle the rest.  Might be one long 'in' clause.... */
 struct hash *suggestHash = NULL;
 if (!securityColumnsInTable)
     suggestHash = accessibleSuggestHash(conn, fields, efList);
 
 webFilteredSqlTable(cart, conn, fields, fromTable, where->string, returnUrl, varPrefix, maxFieldWidth,
     tagOutWrappers, wrapperContext, withFilters, itemPlural, pageSize, 15, suggestHash, visibleFacetList, makeDownloadAllButtonForm);
 
 /* Clean up and go home. */
 cdwFileFreeList(&efList);
 dyStringFree(&where);
 }
 
 char *showSearchControl(char *varName, char *itemPlural)
 /* Put up the search control text and stuff. Returns current search string. */
 {
 /* Get cart variable and clean it up some removing quotes and the like */
 char *varVal = unquotedCartString(cart, varName);
 
 printf("Search <input name=\"%s\" type=\"text\" id=\"%s\" value=\"%s\" size=60>",
         varName, varName, varVal);
 printf("&nbsp;");
 printf("<img src=\"../images/magnify.png\">\n");
 jsInlineF(
     "$(function () {\n"
     "  $('#%s').watermark(\"type in words or starts of words to find specific %s\");\n" 
     "  $('form').delegate('#%s','change keyup paste',function(e){\n"
     "    $('[name=cdwBrowseFiles_page]').val('1');\n"
     "  });\n"
     "});\n",
     varName, itemPlural, varName);
 return varVal;
 }
 
 
 void doDownloadUrls()
 /* serve textfile with file URLs and ask user's internet browser to save it to disk */
 {
 struct sqlConnection *conn = sqlConnect(cdwDatabase);
 user = cdwCurrentUser(conn);
 
 // on non-public cirm (and development vhosts) users must be logged in to use download tokens. 
 if (user==NULL && !isPublicSite)
     {
     // this should never happen through normal UI use
     puts("Content-type: text/html\n\n");
     puts("Error: user is not logged in");
     return;
     }
 
 // on public cirm we have users not logged in. user=NULL and download tokens are not required
 char *token = NULL;
 if (!isPublicSite)
     {
     token = createTokenForUser();
     }
 
 // if we recreate the submission dir structure, we need to create a shell script
 boolean createSubdirs = FALSE;
 if (sameOk(cgiOptionalString("cdwDownloadName"), "subAndDir"))
     createSubdirs = TRUE;
 
 cart = cartAndCookieWithHtml(hUserCookie(), excludeVars, oldVars, FALSE);
 
 if (createSubdirs)
     puts("Content-disposition: attachment; filename=downloadCirm.sh\n");
 else
     puts("Content-disposition: attachment; filename=fileUrls.txt\n");
 
 char *searchString = unquotedCartString(cart, "cdwFileSearch");
 char *initialWhere = cartUsualString(cart, "cdwBrowseFiles_filter", "");
 if (!sameString(initialWhere, ""))
     {
     struct dyString *safeWhere = dyStringNew(0);
     sqlSanityCheckWhere(initialWhere, safeWhere);
     initialWhere = dyStringCannibalize(&safeWhere);
     }
 
 struct cdwFile *efList = findDownloadableFiles(conn, cart, initialWhere, searchString);
 
 char *host = hHttpHost();
 
 // user may want to download with original submitted filename, not with format <accession>.<submittedExtension>
 char *optArg = "";
 if (sameOk(cgiOptionalString("cdwDownloadName"), "sub"))
     optArg = "&useSubmitFname=1";
 
 struct cdwFile *ef;
 for (ef = efList; ef != NULL; ef = ef->next)
     {
     struct cdwValidFile *vf = cdwValidFileFromFileId(conn, ef->id);
 
     if (createSubdirs)
         {
         struct cdwFile *cf = cdwFileFromId(conn, vf->fileId);
         // if we have an absolute pathname in our DB, strip the leading '/'
         // so if someone runs the script as root, it will not start to write
         // files in strange directories
         char* submitFname = cf->submitFileName;
         if ( (submitFname!=NULL) && (!isEmpty(submitFname)) && (*submitFname=='/') )
             submitFname += 1;
 
         printf("curl ");
 	if (!isPublicSite)
 	    printf("--netrc-file cirm_credentials ");
         printf("'https://%s/cgi-bin/cdwGetFile?acc=%s",
             host, vf->licensePlate); 
 	if (!isPublicSite)
 	    printf("&token=%s", token);
 	printf("' --create-dirs -o %s\n", 
 	    submitFname);
         }
     else
 	{
         printf("https://%s/cgi-bin/cdwGetFile?acc=%s", host, vf->licensePlate);
 	if (!isPublicSite)
 	    printf("&token=%s", token);
 	printf("%s\n", optArg);
 	}
     }
 }
 
 void doDownloadFileConfirmation(struct sqlConnection *conn)
 /* show overview page of download files */
 {
 if (user==NULL && !isPublicSite)
     {
     printf("Sorry, you have to log in before you can download files.");
     return;
     }
 
 printf("<FORM ACTION=\"../cgi-bin/cdwWebBrowse\" METHOD=GET>\n");
 cartSaveSession(cart);
 cgiMakeHiddenVar("cdwCommand", "downloadUrls");
 
 continueSearchVars();
 
 char *searchString = unquotedCartString(cart, "cdwFileSearch");
 char *initialWhere = cartUsualString(cart, "cdwBrowseFiles_filter", "");
 if (!sameString(initialWhere, ""))
     {
     struct dyString *safeWhere = dyStringNew(0);
     sqlSanityCheckWhere(initialWhere, safeWhere);
     initialWhere = dyStringCannibalize(&safeWhere);
     }
 
 struct cdwFile *efList = findDownloadableFiles(conn, cart, initialWhere, searchString);
 
 // get total size
 struct cdwFile *ef;
 long long size = 0;
 for (ef = efList; ef != NULL; ef = ef->next)
     size += ef->size;
 int fCount = slCount(efList);
 
 char sizeStr[4096];
 sprintWithGreekByte(sizeStr, sizeof(sizeStr), size);
 
 printf("<h4>Data Download Options</h4>\n");
 printf("<b>Number of files:</b> %d<br>\n", fCount);
 printf("<b>Total size:</b> %s<p>\n", sizeStr);
 
 puts("<input class='urlListButton' type=radio name='cdwDownloadName' VALUE='acc' checked>\n");
 //cgiMakeRadioButton("cdwDownloadName", "acc", TRUE);
 puts("Name files by accession, one single directory<br>");
 //cgiMakeRadioButton("cdwDownloadName", "sub", FALSE);
 puts("<input class='urlListButton' type=radio name='cdwDownloadName' VALUE='sub'>\n");
 puts("Name files as submitted, one single directory<br>");
 //cgiMakeRadioButton("cdwDownloadName", "subAndDir", FALSE);
 puts("<input class='scriptButton' type=radio name='cdwDownloadName' VALUE='subAndDir'>\n");
 puts("Name files as submitted and put into subdirectories<p>");
 
 printf("<input class='btn btn-secondary' type='submit' name='Submit' id='Submit' value='Submit'>\n");
 printf("</FORM>\n");
 
 jsInline 
     (
     "$('.scriptButton').change( function() {$('#urlListDoc').hide(); $('#scriptDoc').show()} );\n"
     "$('.urlListButton').change( function() {$('#urlListDoc').show(); $('#scriptDoc').hide()} );\n"
     );
 puts("<div id='urlListDoc'>\n");
 puts("When you click 'submit', a text file with the URLs of the files will get downloaded.\n");
 puts("The URLs are valid for one week.<p>\n");
 puts("To download the files:\n");
 puts("<ul>\n");
 puts("<li>With Firefox and <a href=\"https://addons.mozilla.org/en-US/firefox/addon/downthemall/\">DownThemAll</a>: Click Tools - DownThemAll! - Manager. Right click - Advanced - Import from file. Right-click - Select All. Right-click - Toogle All\n");
 
 if (isPublicSite)
     {
     puts("<li>OSX/Linux: With curl and a single thread: <tt>xargs -n1 curl -JO < fileUrls.txt</tt>\n");
     puts("<li>Linux: With wget and a single thread: <tt>wget --content-disposition -i fileUrls.txt</tt>\n");
     puts("<li>With wget and 4 threads: <tt>xargs -n 1 -P 4 wget --content-disposition -q < fileUrls.txt</tt>\n");
     puts("<li>With aria2c, 16 threads and two threads per file: <tt>aria2c -x 16 -s 2 -i fileUrls.txt</tt>\n");
     }
 else 
     {
     puts("<li>OSX/Linux: With curl and a single thread: <tt>xargs -n1 curl -JO --user YOUREMAIL:YOURPASS < fileUrls.txt</tt>\n");
     puts("<li>Linux: With wget and a single thread: <tt>wget --content-disposition -i fileUrls.txt --user YOUREMAIL --password YOURPASS</tt>\n");
     puts("<li>With wget and 4 threads: <tt>xargs -n 1 -P 4 wget --content-disposition -q --user YOUREMAIL --password YOURPASS < fileUrls.txt</tt>\n");
     puts("<li>With aria2c, 16 threads and two threads per file: <tt>aria2c --http-user YOUREMAIL --http-password YOURPASS -x 16 -s 2 -i fileUrls.txt</tt>\n");
     }
 
 puts("</ul>\n");
 puts("</div>\n");
 
 puts("<div id='scriptDoc' style='display:none'>\n");
 puts("When you click 'submit', a shell script that runs curl will get downloaded.\n");
 puts("The URLs are valid for one week.<p>\n");
 if (!isPublicSite)
     {
     puts("Before you start the download, create a file called cirm_credentials with your username and password like this:<br>\n");
     puts("<tt>echo 'default login <i>user@university.edu</i> password <i>mypassword</i>' > cirm_credentials</tt><p>\n");
     }
 puts("Then, to download the files:\n");
 puts("<ul>\n");
 puts("<li>Linux/OSX: With curl and a single thread: <tt>sh downloadCirm.sh</tt>\n");
 puts("<li>Linux/OSX: With curl and four threads: <tt>parallel -j4 :::: downloadCirm.sh</tt>\n");
 puts("</ul>\n");
 puts("<div>\n");
 cdwFileFreeList(&efList);
 }
 
 void doBrowseFiles(struct sqlConnection *conn)
 /* Print list of files */
 {
 printf("<FORM ACTION=\"../cgi-bin/cdwWebBrowse\" METHOD=GET>\n");
 cartSaveSession(cart);
 cgiMakeHiddenVar("cdwCommand", "browseFiles");
 
 cgiMakeHiddenVar("clearRestriction", "0");
 char *clearRestriction = cartOptionalString(cart, "clearRestriction");
 if (clearRestriction && sameString(clearRestriction,"1"))
     {
     cartSetString(cart, "cdwBrowseFiles_filter", "");  // reset file filter to empty string
     cartRemove(cart, "clearRestriction");
     }
 
 // DEBUG REMOVE
 //char *varName = "cdwBrowseFiles_facet_selList";
 //char *varVal = cartUsualString(cart, varName, "");
 //warn("varName=[%s] varVal=[%s]", varName, varVal); // DEBUG REMOVE
 
 //warn("getCdwTableSetting(cdwFileFacets)=%s", getCdwTableSetting("cdwFileFacets")); // DEBUG REMOVE
 
 char *selOp = cartOptionalString(cart, "cdwBrowseFiles_facet_op");
 if (selOp)
     {
     char *selFieldName = cartOptionalString(cart, "cdwBrowseFiles_facet_fieldName");
     char *selFieldVal = cartOptionalString(cart, "cdwBrowseFiles_facet_fieldVal");
     if (selFieldName && selFieldVal)
 	{
 	char *selectedFacetValues=cartUsualString(cart, "cdwBrowseFiles_facet_selList", "");
 	//warn("selectedFacetValues=[%s] selFieldName=%s selFieldVal=%s selOp=%s", 
 	    //selectedFacetValues, selFieldName, selFieldVal, selOp); // DEBUG REMOVE
 	struct facetField *selList = deLinearizeFacetValString(selectedFacetValues);
 	selectedListFacetValUpdate(&selList, selFieldName, selFieldVal, selOp);
 	char *newSelectedFacetValues = linearizeFacetVals(selList);
 	//warn("newSelectedFacetValues=[%s]", newSelectedFacetValues); // DEBUG REMOVE
 	cartSetString(cart, "cdwBrowseFiles_facet_selList", newSelectedFacetValues);
 	cartRemove(cart, "cdwBrowseFiles_facet_op");
 	cartRemove(cart, "cdwBrowseFiles_facet_fieldName");
 	cartRemove(cart, "cdwBrowseFiles_facet_fieldVal");
 	}
     }
 
 printf("Click on file's name to see full metadata.");
 printf(" Links in ucsc_db go to the Genome Browser. <BR>\n");
 char *searchString = showSearchControl("cdwFileSearch", "files");
 
 /* Put up big filtered table of files */
 char returnUrl[PATH_LEN*2];
 safef(returnUrl, sizeof(returnUrl), "../cgi-bin/cdwWebBrowse?cdwCommand=browseFiles&%s",
     cartSidUrlString(cart) );
 char *where = cartUsualString(cart, "cdwBrowseFiles_filter", "");
 if (!sameString(where, ""))
     {
     struct dyString *safeWhere = dyStringNew(0);
     sqlSanityCheckWhere(where, safeWhere);
     where = dyStringCannibalize(&safeWhere);
     }
 
 
 struct hash *wrappers = hashNew(0);
 hashAdd(wrappers, "file_name", wrapFileName);
 hashAdd(wrappers, "ucsc_db", wrapTrackNearFileName);
 hashAdd(wrappers, "format", wrapFormat);
 hashAdd(wrappers, "file_size", wrapFileSize);
 
 accessibleFilesTable(cart, conn, searchString,
   fileTableFields,
   isEmpty(where) ? getCdwTableSetting("cdwFileFacets") : getCdwTableSetting("cdwFileTags"),
   where, 
   returnUrl, "cdwBrowseFiles",
   18, wrappers, conn, FALSE, "files", 100, visibleFacetFields, TRUE);
 printf("</FORM>\n");
 }
 
 char *getBrowseTracksTables()
 {
 char tables[1024];
 safef(tables, sizeof tables, "%s,cdwTrackViz", getCdwTableSetting("cdwFileTags"));
 return cloneString(tables);
 }
 
 void doBrowseTracks(struct sqlConnection *conn)
 /* Print list of files */
 {
 printf("<FORM ACTION=\"../cgi-bin/cdwWebBrowse\" METHOD=GET>\n");
 cartSaveSession(cart);
 cgiMakeHiddenVar("cdwCommand", "browseTracks");
 cgiMakeHiddenVar("clearSearch", "0");
 
 printf("<B>Tracks</B> - Click on ucsc_db to open Genome Browser. ");
 printf("The accession link shows more metadata.<BR>");
 char returnUrl[PATH_LEN*2];
 safef(returnUrl, sizeof(returnUrl), "../cgi-bin/cdwWebBrowse?cdwCommand=browseTracks&%s",
     cartSidUrlString(cart) );
 struct dyString *where = sqlDyStringCreate("fileId=file_id and format in ('bam','bigBed', 'bigWig', 'vcf', 'narrowPeak', 'broadPeak')");
 struct hash *wrappers = hashNew(0);
 hashAdd(wrappers, "accession", wrapMetaNearAccession);
 hashAdd(wrappers, "ucsc_db", wrapTrackNearAccession);
 char *searchString = showSearchControl("cdwTrackSearch", "tracks");
 accessibleFilesTable(cart, conn, searchString,
     "ucsc_db,chrom,accession,format,file_size,lab,assay,data_set_id,output,"
     "enriched_in,sample_label,submit_file_name",
     getBrowseTracksTables(), where->string, 
     returnUrl, "cdw_track_filter", 
     22, wrappers, conn, TRUE, "tracks", 100, NULL, FALSE);
 printf("</FORM>\n");
 dyStringFree(&where);
 }
 
 struct hash* loadDatasetDescs(struct sqlConnection *conn)
 /* Load cdwDataset table and return hash with name -> cdwDataset */
 {
 char query[256];
 sqlSafef(query, sizeof query, "SELECT * FROM cdwDataset");
 struct sqlResult *sr = sqlGetResult(conn, query);
 struct hash *descs = hashNew(7);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct cdwDataset *dataset = cdwDatasetLoad(row);
     hashAdd(descs, dataset->name, dataset);
     }
 sqlFreeResult(&sr);
 return descs;
 }
 
 static boolean cdwCheckAccessFromFileId(struct sqlConnection *conn, int fileId, struct cdwUser *user, int accessType)
 /* Determine if user can access file given a file ID */
 {
 struct cdwFile *ef = cdwFileFromId(conn, fileId);
 boolean ok = cdwCheckAccess(conn, ef, user, accessType);
 cdwFileFree(&ef);
 return ok;
 }
 
 static boolean cdwCheckFileAccess(struct sqlConnection *conn, int fileId, struct cdwUser *user)
 /* Determine if the user can see the specified file. Return True if they can and False otherwise. */ 
 {
 return cdwCheckAccessFromFileId(conn, fileId, user, cdwAccessRead);
 }
 
 void doServeTagStorm(struct sqlConnection *conn, char *dataSet)
 /* Put up meta data tree associated with data set. */
 {
 printf(", <A HREF=\"cdwServeTagStorm?format=text&cdwDataSet=%s&%s\"",
 	dataSet, cartSidUrlString(cart)); 
 printf(">text</A>");
 printf(", <A HREF=\"cdwServeTagStorm?format=tsv&cdwDataSet=%s&%s\"",
 	dataSet, cartSidUrlString(cart)); 
 printf(">tsv</A>");
 printf(", <A HREF=\"cdwServeTagStorm?format=csv&cdwDataSet=%s&%s\"",
 	dataSet, cartSidUrlString(cart)); 
 printf(">csv</A>)"); 
 }
 
 int getRecentSubmitFileId(struct sqlConnection *conn, int submitDirId, char *submitFileName)
 /* Get the file ID of the most recent index.html file for dataset. */
 {
 char query[PATH_LEN]; 
 sqlSafef(query, sizeof(query), "select max(id) from cdwFile where submitFileName='%s' and submitDirId=%d", submitFileName,
     submitDirId);
 return sqlQuickNum(conn, query);  // returns 0 if none found
 }
 
 void doBrowseDatasets(struct sqlConnection *conn)
 /* Show datasets and links to dataset summary pages. */
 {
 printf("<ul class='list-group'>\n");
 char query[PATH_LEN]; 
 sqlSafef(query, sizeof(query), "SELECT * FROM cdwDataset ORDER BY label "); 
 struct cdwDataset *dataset, *datasetList = cdwDatasetLoadByQuery(conn, query);
 // Go through the cdwDataset table and generate an entry for each dataset. 
 for (dataset = datasetList; dataset != NULL; dataset = dataset->next)
     {
     char *label = dataset->label;
     char *desc = dataset->description;
     char *datasetId = dataset->name;
     sqlSafef(query, sizeof(query), "select id from cdwSubmitDir where url='/data/cirm/wrangle/%s'", datasetId);
     int submitDirId = sqlQuickNum(conn, query);
 
     // If the ID exists and the user has access print a link to the page.  
     int fileId = getRecentSubmitFileId(conn, submitDirId, "summary/index.html");
     boolean haveAccess = ((fileId > 0) && cdwCheckFileAccess(conn, fileId, user));
     if (haveAccess)
 	{
 	printf("<li class='list-group-item'><b><a href=\"cdwGetFile/%s/summary/index.html\">%s (%s)</a></b><br>\n", 
 	    datasetId, label, datasetId);
 	
 	// Print out file count and descriptions. 
 	sqlSafef(query, sizeof(query), 
 	    "select count(*) from %s where data_set_id='%s'", getCdwTableSetting("cdwFileTags"), datasetId);  
 	long long fileCount = sqlQuickLongLong(conn, query);
 //	printf("%s (<A HREF=\"cdwWebBrowse?cdwCommand=browseFiles&cdwBrowseFiles_filter=data_set_id%%3D+%%27%s%%27&%s\"",
 //		desc, datasetId, cartSidUrlString(cart)); 
 	char varEqVal[256];
 	safef(varEqVal, sizeof(varEqVal), "data_set_id='%s'", datasetId);
 	printf("%s (<A HREF=\"cdwWebBrowse?cdwCommand=browseFiles&cdwBrowseFiles_filter=%s&%s\"",
 		desc, cgiEncode(varEqVal), cartSidUrlString(cart)); 
 	printf(">%lld files</A>)",fileCount);
 
 	int fileId = getRecentSubmitFileId(conn, submitDirId, "meta.txt");
 	if ((fileId > 0) && cdwCheckFileAccess(conn, fileId, user))
 	    {
 	    printf(" (metadata: <A HREF=\"cdwWebBrowse?cdwCommand=dataSetMetaTree&cdwDataSet=%s&%s\"",
 		    datasetId, cartSidUrlString(cart)); 
 	    printf(">html</A>");
 	    doServeTagStorm(conn, datasetId);
 	    }
 	}
     else // Otherwise print a label and description. 
 	{
 	printf("<li class='list-group-item'><B>%s (%s)</B><BR>\n", label, datasetId);
 	printf("%s\n", desc);
 	}
     printf("</li>\n");
     }
 cdwDatasetFree(&datasetList);
 }
 
 
 void doDataSetMetaTree(struct sqlConnection *conn)
 /* Put up meta data tree associated with data set. */
 {
 char *dataSet = cartString(cart, "cdwDataSet");
 char metaFileName[PATH_LEN];
 safef(metaFileName, sizeof(metaFileName), "%s/%s", dataSet, "meta.txt");
 int fileId = cdwFileIdFromPathSuffix(conn, metaFileName);
 if (!cdwCheckFileAccess(conn, fileId, user))
     errAbort("Unauthorized access to %s", metaFileName);
 printf("<H2>Metadata tree for %s</H2>\n", dataSet);
 char *path = cdwPathForFileId(conn, fileId);
 char command[3*PATH_LEN];
 fflush(stdout);
 safef(command, sizeof(command), "./tagStormToHtml -embed %s -nonce=%s stdout", path, getNonce());
 mustSystem(command);
 }
 
 void doBrowseFormat(struct sqlConnection *conn)
 /* Browse through available formats */
 {
 static char *labels[] = {"count", "format", "description"};
 int fieldCount = ArraySize(labels);
 char *row[fieldCount];
 struct fieldedTable *table = fieldedTableNew("Data formats", labels, fieldCount);
 struct slPair *format, *formatList = cdwFormatList();
 
 for (format = formatList; format != NULL; format = format->next)
     {
     char countString[16];
     char query[256];
     sqlSafef(query, sizeof(query), "select count(*) from %s where format='%s'", 
 	getCdwTableSetting("cdwFileTags"), format->name);
     sqlQuickQuery(conn, query, countString, sizeof(countString));
     row[0] = countString;
     row[1] = format->name;
     row[2] = format->val;
     fieldedTableAdd(table, row, fieldCount, 0);
     }
 char returnUrl[PATH_LEN*2];
 safef(returnUrl, sizeof(returnUrl), "../cgi-bin/cdwWebBrowse?cdwCommand=browseFormats&%s",
     cartSidUrlString(cart) );
 webSortableFieldedTable(cart, table, returnUrl, "cdwFormats", 0, NULL, NULL);
 fieldedTableFree(&table);
 }
 
 void doBrowseLabs(struct sqlConnection *conn)
 /* Put up information on labs */
 {
 static char *labels[] = {"name", "files", "PI", "institution", "web page"};
 int fieldCount = ArraySize(labels);
 char *row[fieldCount];
 struct fieldedTable *table = fieldedTableNew("Data contributing labs", labels, fieldCount);
 
 printf("Here is a table of labs that have contributed data<BR>\n");
 char query[256];
 sqlSafef(query, sizeof(query), "select * from cdwLab");
 struct cdwLab *lab, *labList = cdwLabLoadByQuery(conn, query);
 int i = 0;
 for (lab = labList; lab != NULL; lab = lab->next)
     {
     row[0] = lab->name;
     char countString[16];
     sqlSafef(query, sizeof(query), "select count(*) from %s where lab='%s'", 
 	getCdwTableSetting("cdwFileTags"), lab->name);
     sqlQuickQuery(conn, query, countString, sizeof(countString));
     row[1] = countString;
     row[2] = lab->pi;
     row[3] = lab->institution;
     row[4] = lab->url;
     fieldedTableAdd(table, row, fieldCount, ++i);
     }
 char returnUrl[PATH_LEN*2];
 safef(returnUrl, sizeof(returnUrl), "../cgi-bin/cdwWebBrowse?cdwCommand=browseLabs&%s",
     cartSidUrlString(cart) );
 struct hash *outputWrappers = hashNew(0);
 hashAdd(outputWrappers, "web page", wrapExternalUrl);
 webSortableFieldedTable(cart, table, returnUrl, "cdwLab", 0, outputWrappers, NULL);
 fieldedTableFree(&table);
 }
 
 
 void doAnalysisQuery(struct sqlConnection *conn)
 /* Print up query page */
 {
 if (cartNonemptyString(cart, "cdwQueryReset"))
     {
     cartRemovePrefix(cart, "cdwQuery");
     }
 
 /* Do stuff that keeps us here after a routine submit */
 printf("Enter a SQL-like query below. ");
 printf("In the box after 'select' you can put in a list of tag names including wildcards. ");
 printf("In the box after 'where' you can put in filters <BR> based on boolean operations between ");
 printf("fields and constants. Select one of the four formats and press view to see the matching data on ");
 printf("this page. <BR> The limit can be set lower to increase the query speed. <BR><BR>");
 printf("<FORM class = \"inlineBlock\" ACTION=\"../cgi-bin/cdwWebBrowse\" METHOD=GET>\n");
 cartSaveSession(cart);
 cgiMakeHiddenVar("cdwCommand", "analysisQuery");
 
 /* Get values from text inputs and make up an RQL query string out of fields, where, limit
  * clauses */
 /* Fields clause */
 char *fieldsVar = "cdwQueryFields";
 char *fields = cartUsualString(cart, fieldsVar, "*");
 struct dyString *rqlQuery = dyStringCreate("select %s from files", fields);
 
 /* Where clause */
 char *whereVar = "cdwQueryWhere";
 char *where = cartUsualString(cart, whereVar, "");
 if (!isEmpty(where))
     dyStringPrintf(rqlQuery, " where %s", where);
 
 struct rqlStatement *rql = rqlStatementParseString(rqlQuery->string);
 
 /* Limit clause */
 char *limitVar = "cdwQueryLimit";
 int limit = cartUsualInt(cart, limitVar, 10);
 
 /* Write out select [  ] from files where [  ] limit [ ] <submit> **/
 printf("select ");
 cgiMakeTextVar(fieldsVar, fields, 40);
 printf("from files ");
 printf("where ");
 cgiMakeTextVar(whereVar, where, 40);
 printf(" limit ");
 cgiMakeIntVar(limitVar, limit, 7);
 char *menu[3];
 menu[0] = "ra";
 menu[1] = "tsv";
 menu[2] = "csv";
 
 char *formatVar = "cdwQueryFormat";
 char *format = cartUsualString(cart, formatVar, menu[0]);
 printf("  "); 
 cgiMakeDropList(formatVar, menu, ArraySize(menu), format);
 printf("  "); 
 printf("<input class='btn btn-secondary' type='submit' name='cdwQueryView' id='View' value='View'>\n");
 printf("<input class='btn btn-secondary' type='submit' name='cdwQueryReset' id='View' value='Reset'>\n");
 printf("</FORM>\n\n");
 
 
 printf("<BR>Clicking the download button will take you to a new page with all of the matching data in "); 
 printf("the selected format.<BR>");
 printf("<FORM class=\"inlineBlock\" ACTION=\"../cgi-bin/cdwGetMetadataAsFile\" METHOD=GET>\n");
 cartSaveSession(cart);
 cgiMakeHiddenVar("cdwCommand", "analysisQuery");
 cgiMakeHiddenVar("Download format", format); 
 printf("<input class='btn btn-secondary' type='submit' name='%s' id='%s' value='Download All Matching'>\n", format, format);
 printf("</FORM>\n\n");
 
 // Get field list for the cdwFileTags table, leaving out things we don't want to display on the site
 // (allAccess and groupIds).
 struct dyString *descQuery = dyStringNew(0);
 sqlDyStringPrintf(descQuery, "desc cdwFileTags");
 struct sqlResult *sr = sqlGetResult(conn, descQuery->string);
 char **row;
 struct slName *allFieldList = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if (sameString(row[0], "allAccess") || sameString(row[0], "groupIds"))
         continue;
     slNameAddHead(&allFieldList, row[0]);
     }
 sqlFreeResult(&sr);
 slReverse(&allFieldList);
 
 // Verify the query restrictions are on existing fields
 cdwCheckRqlFields(rql, allFieldList);
 
 // Obtain the list of fields to be returned by the query
 struct slName *returnedFieldList = wildExpandList(allFieldList, rql->fieldList, TRUE);
 
 // Retrieve results from the server
 struct dyString *sqlQuery = dyStringNew(0);
 sqlDyStringPrintf(sqlQuery, "select ");
 struct slName *l = returnedFieldList;
 sqlDyStringPrintf(sqlQuery, "%s", l->name);
 l = l->next;
 while (l != NULL)
     {
     sqlDyStringPrintf(sqlQuery, ",%s", l->name);
     l = l->next;
     }
 sqlDyStringPrintf(sqlQuery, " from cdwFileTags");
 
 int whereClauseStarted = 0;
 if (!isEmpty(where))
     {
     // Can't use sqlDyString functions due to the possible presence of valid wildcards, but
     // the while clause has already been validated by passing through the more restrictive
     // rql parser anyway.
 
     // Note currently unable to use sqlSafefV2 inside /src/lib/rqlParse* since it needs functions in /src/hg/lib/jksql.c
     // and things in /src/lib are not supposed to use and depend on stuff under /src/hg/lib.
     char *rqlWhere = rqlParseToSqlWhereClause(rql->whereClause, FALSE);
     char trustedQuery[strlen(rqlWhere) + NOSQLINJ_SIZE + 1];
     safef(trustedQuery, sizeof trustedQuery, NOSQLINJ "%s", rqlWhere);
     sqlDyStringPrintf(sqlQuery, " where %-s", trustedQuery);
     whereClauseStarted = 1;
     }
 
 // Ensure the user has access to the data.  Access means either it's a public set (allAccess = 1) or one of the user's
 // associated group IDs appears in the groupIds field (or they're an admin).
 if ((user == NULL) || (!user->isAdmin))
     {
     if (whereClauseStarted == 0)
         {
         sqlDyStringPrintf(sqlQuery, " where ");
         whereClauseStarted = 1;
         }
     else
         sqlDyStringPrintf(sqlQuery, " and ");
     sqlDyStringPrintf(sqlQuery, "(allAccess = 1");
     if (user != NULL)
         {
         // Handle group-based access for this user
         struct dyString *groupQuery = dyStringNew(0);
         sqlDyStringPrintf(groupQuery, "select groupId from cdwGroupUser where userId = %u\n", user->id);
         sr = sqlGetResult(conn, groupQuery->string);
         while ((row = sqlNextRow(sr)) != NULL)
             {
             sqlDyStringPrintf(sqlQuery, " or find_in_set(\"%s\", groupIds) > 0", row[0]);
             }
         sqlFreeResult(&sr);
         }
     sqlDyStringPrintf(sqlQuery, ")");
     }
 // limit
 sqlDyStringPrintf(sqlQuery, " limit %d", limit);
 
 // Now to actually fetch the data!
 sr = sqlGetResult(conn, sqlQuery->string);
 struct slName *fieldNames = sqlResultFieldList(sr);
 struct slRef *resultData = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct slPair *fieldList = NULL;
     struct slName *fieldName = fieldNames;
     int fieldIdx = 0;
     while (fieldName != NULL)
         {
         char *val = NULL;
         if (!isEmpty(row[fieldIdx]))
             val = cloneString(row[fieldIdx]);
         slPairAdd(&fieldList, fieldName->name, val);
         fieldIdx++;
         fieldName = fieldName->next;
         }
     slReverse(&fieldList);
     refAdd(&resultData, fieldList);
     }
 
 slReverse(&resultData);
 // Now, resultData is an slRef list of results, and each result contains an slPair list of field name/value pairs.
 int matchCount = slCount(resultData);
 printf("<PRE><TT>");
 printLongWithCommas(stdout, matchCount);
 printf(" files match\n\n");
 cdwPrintSlRefList(resultData, fieldNames, format, limit);
 printf("</TT></PRE>\n");
 rqlStatementFree(&rql);
 }
 
 void doAnalysisJointPages(struct sqlConnection *conn)
 /* Show datasets and links to dataset summary pages. */
 {
 printf("<UL>\n");
 char query[PATH_LEN]; 
 sqlSafef(query, sizeof(query), "SELECT * FROM cdwJointDataset ORDER BY label ");
 struct cdwJointDataset *jointDataset, *datasetList = cdwJointDatasetLoadByQuery(conn, query);
 // Go through the cdwDataset table and generate an entry for each dataset. 
 for (jointDataset = datasetList; jointDataset != NULL; jointDataset = jointDataset->next)
     {
     char *label = jointDataset->label;
     char *desc = jointDataset->description;
     char *datasetId = jointDataset->name;
 
     // Check if we have a dataset summary page in the CDW and store its ID. The file must have passed validation.  
     char summFname[8000];
     safef(summFname, sizeof(summFname), "%s/summary/index.html", datasetId);
     int fileId = cdwFileIdFromPathSuffix(conn, summFname);
     // If the ID exists and the user has access print a link to the page.  
     boolean haveAccess = ((fileId > 0) && cdwCheckFileAccess(conn, fileId, user));
     if (haveAccess)
 	{
 	printf("<LI><B><A href=\"cdwGetFile/%s/summary/index.html\">%s (%s)</A></B><BR>\n", 
 	    datasetId, label, datasetId);
 	// Print out file count and descriptions. 
 	sqlSafef(query, sizeof(query), 
 	    "select count(*) from %s where data_set_id='%s'", 
 		getCdwTableSetting("cdwFileTags"), datasetId);  
 	//long long fileCount = sqlQuickLongLong(conn, query);
 	printf("%s", desc); 
 	char metaFileName[PATH_LEN];
 	safef(metaFileName, sizeof(metaFileName), "%s/%s", datasetId, "meta.txt");
 	int fileId = cdwFileIdFromPathSuffix(conn, metaFileName);
 	if ((fileId > 0) && cdwCheckFileAccess(conn, fileId, user))
 	    {
 	    printf(" (metadata: <A HREF=\"cdwWebBrowse?cdwCommand=dataSetMetaTree&cdwDataSet=%s&%s\"",
 		    datasetId, cartSidUrlString(cart)); 
 	    printf(">html</A>");
 	    doServeTagStorm(conn, datasetId);
 	    }
 	    
 	struct slName *dataset, *dataSetNames=charSepToSlNames(jointDataset->childrenNames, *",");
 	printf("("); 
 	int totFileCount = 0; 
 	// Go through each sub dataset, print a link into the search files and count total files.  
 	for (dataset = dataSetNames; dataset != NULL; dataset=dataset->next)
 	    {
 	    sqlSafef(query, sizeof(query), "select count(*) from %s where data_set_id='%s'", 
 		getCdwTableSetting("cdwFileTags"), dataset->name); 
 	    totFileCount += sqlQuickNum(conn, query); 
 	    printf("<A HREF=\"cdwWebBrowse?cdwCommand=browseFiles&cdwBrowseFiles_f_data_set_id=%s&%s\">%s",
 			    dataset->name, cartSidUrlString(cart), dataset->name);
 	    if (dataset->next != NULL) printf(",");
 	    
 	    printf("</A>\n"); 
 	}
     printf(") (Total files: %i)",totFileCount); 
     printf("</LI>\n");
 
 	}
     else // Otherwise print a label and description. 
 	{
 	printf("<LI><B>%s (%s)</B><BR>\n", label, datasetId);
 	printf("%s\n", desc);
 	}
     printf("</LI>\n");
     }
 cdwJointDatasetFree(&datasetList);
 }
 
 void facetSummaryRow(struct fieldedTable *table, struct facetField *ff)
 /* Print out row in a high level tag counting table */
 {
 struct facetVal *fv;
 int total = 0; // Col 4, 'files'
 char valValueString[PATH_LEN], valCountString[32]; // Col 3, 'popular values (files)...' and col 2, 'vals' 
 valValueString[0]= '\0'; 
 strcat(valValueString, " "); 
 safef(valCountString, sizeof(valCountString), "%d", slCount(ff->valList)); 
 bool hairpin = TRUE; 
 for (fv = ff->valList; fv != NULL; fv = fv->next)
     {
     total += fv->useCount;
     if (hairpin == FALSE) continue; 
 
     char temp[4*1024]; 
     // Make a new name value pair which may get added to the existing string. 
     safef(temp, sizeof(temp),"%s (%d)", fv->val, fv->useCount); 
     int newStringLen = ((int) strlen(valValueString))+((int) strlen(temp));
     if (newStringLen >= 107) // Check if the new string is acceptable size. 
 	{
 	// The hairpin is set to false once the full line is made, this stops the line from growing. 
 	if (hairpin) 
 	    //Remove the comma and append '...'.
 	    {
 	    valValueString[strlen(valValueString)-2] = '\0';
 	    strcat(valValueString, "..."); 
 	    hairpin = FALSE;
 	    }
 	}
     else{ // Append the name:value pair to the string.  
 	strcat(valValueString, temp); 
 	if (fv->next != NULL)
 	    strcat(valValueString, ", "); 
 	}
     }
 char trueTotal[PATH_LEN]; 
 safef(trueTotal, sizeof(trueTotal), "%d", total); 
 
 /* Add data to fielded table */
 char *row[4];
 row[0] = cloneString(ff->fieldName);
 row[1] = cloneString(valCountString);
 row[2] = cloneString(valValueString);
 row[3] = cloneString(trueTotal);
 fieldedTableAdd(table, row, ArraySize(row), 0);
 }
 
 void tagSummaryRow(struct fieldedTable *table, struct sqlConnection *conn, char *tag)
 /* Print out row in a high level tag counting table */
 {
 // These will become the values for our columns. 
 int total = 0; // Col 4, 'files'
 char valValueString[PATH_LEN], valCountString[32]; // Col 3, 'popular values (files)...' and col 2, 'vals' 
 
 // Get the necessary data via SQL and load into a slPair. 
 char query[PATH_LEN];
 sqlSafef(query, sizeof(query),"select %s, count(*) as count from %s where %s is not NULL group by %s order by count desc",
   getCdwTableSetting("cdwFileTags"), tag, tag, tag); 
 struct slPair *iter = NULL, *pairList = sqlQuickPairList(conn, query);
 
 safef(valCountString, sizeof(valCountString), "%d", slCount(&pairList)-1); 
 bool hairpin = TRUE; 
 valValueString[0]= '\0'; 
 strcat(valValueString, " "); 
 //Go through the pair list and generate the 'popular values (files)...' column and the 'files' column
 for (iter = pairList; iter != NULL; iter = iter->next)
     {
     total += sqlSigned( ((char*) iter->val)); // Calculate the total of the values for files column.
     if (hairpin == FALSE) continue; 
 
     char temp[4*1024]; 
     // Make a new name value pair which may get added to the existing string. 
     safef(temp, sizeof(temp),"%s (%s)", iter->name, (char *)iter->val); 
     int newStringLen = ((int) strlen(valValueString))+((int) strlen(temp));
     if (newStringLen >= 107) // Check if the new string is acceptable size. 
 	{
 	// The hairpin is set to false once the full line is made, this stops the line from growing. 
 	if (hairpin) 
 	    //Remove the comma and append '...'.
 	    {
 	    valValueString[strlen(valValueString)-2] = '\0';
 	    strcat(valValueString, "..."); 
 	    hairpin = FALSE;
 	    }
 	}
     else{ // Append the name:value pair to the string.  
 	strcat(valValueString, temp); 
 	if (iter->next != NULL)
 	    strcat(valValueString, ", "); 
 	}
     }
 char trueTotal[PATH_LEN]; 
 safef(trueTotal, sizeof(trueTotal), "%d", total); 
 
 /* Add data to fielded table */
 char *row[4];
 row[0] = cloneString(tag);
 row[1] = cloneString(valCountString);
 row[2] = cloneString(valValueString);
 row[3] = cloneString(trueTotal);
 fieldedTableAdd(table, row, ArraySize(row), 0);
 }
 
 struct tagCount
 /* A tag name and how many things are associated with it. */
     {
     struct tagCount *next;
     char *tag;
     long count;	
     };
 
 struct tagCount *tagCountNew(char *tag, int count)
 /* Return fresh new tag */
 {
 struct tagCount *tc;
 AllocVar(tc);
 tc->tag = cloneString(tag);
 tc->count = count;
 return tc;
 }
 
 void drawPrettyPieGraph(struct facetVal *fvList, char *id, char *title, char *subtitle)
 /* Draw a pretty pie graph using D3. Import D3 and D3pie before use. */
 {
 // Some D3 administrative stuff, the title, subtitle, sizing etc. 
 struct dyString *dy = dyStringNew(1024);
 
 dyStringPrintf(dy,"var pie = new d3pie(\"%s\", {\n\"header\": {", id);
 if (title != NULL)
     {
     dyStringPrintf(dy,"\"title\": { \"text\": \"%s\",", title);
     dyStringPrintf(dy,"\"fontSize\": 16,");
     dyStringPrintf(dy,"\"font\": \"open sans\",},");
     }
 if (subtitle != NULL)
     {
     dyStringPrintf(dy,"\"subtitle\": { \"text\": \"%s\",", subtitle);
     dyStringPrintf(dy,"\"color\": \"#999999\",");
     dyStringPrintf(dy,"\"fontSize\": 10,");
     dyStringPrintf(dy,"\"font\": \"open sans\",},");
     }
 dyStringPrintf(dy,"\"titleSubtitlePadding\":9 },\n");
 dyStringPrintf(dy,"\"footer\": {\"color\": \"#999999\",");
 dyStringPrintf(dy,"\"fontSize\": 10,");
 dyStringPrintf(dy,"\"font\": \"open sans\",");
 dyStringPrintf(dy,"\"location\": \"bottom-left\",},\n");
 dyStringPrintf(dy,"\"size\": { \"canvasWidth\": 330, \"canvasHeight\": 220},\n");
 dyStringPrintf(dy,"\"data\": { \"sortOrder\": \"value-desc\", \"content\": [\n");
 struct facetVal *fv = NULL;
 float colorOffset = 1;
 int totalFields =  slCount(fvList);
 for (fv=fvList; fv!=NULL; fv=fv->next)
     {
     float currentColor = colorOffset/totalFields;
     struct rgbColor color = saturatedRainbowAtPos(currentColor);
     dyStringPrintf(dy,"\t{\"label\": \"%s\",\n\t\"value\": %d,\n\t\"color\": \"rgb(%i,%i,%i)\"}", 
 	fv->val, fv->useCount, color.r, color.b, color.g);
     if (fv->next!=NULL) 
 	dyStringPrintf(dy,",\n");
     ++colorOffset;
     }
 dyStringPrintf(dy,"]},\n\"labels\": {");
 dyStringPrintf(dy,"\"outer\":{\"pieDistance\":20},");
 dyStringPrintf(dy,"\"inner\":{\"hideWhenLessThanPercentage\":5},");
 dyStringPrintf(dy,"\"mainLabel\":{\"fontSize\":11},");
 dyStringPrintf(dy,"\"percentage\":{\"color\":\"#ffffff\", \"decimalPlaces\": 0},");
 dyStringPrintf(dy,"\"value\":{\"color\":\"#adadad\", \"fontSize\":11},");
 dyStringPrintf(dy,"\"lines\":{\"enabled\":true},},\n");
 dyStringPrintf(dy,"\"effects\":{\"pullOutSegmentOnClick\":{");
 dyStringPrintf(dy,"\"effect\": \"linear\",");
 dyStringPrintf(dy,"\"speed\": 400,");
 dyStringPrintf(dy,"\"size\": 8}},\n");
 dyStringPrintf(dy,"\"misc\":{\"gradient\":{");
 dyStringPrintf(dy,"\"enabled\": true,");
 dyStringPrintf(dy,"\"percentage\": 100}}});");
 jsInline(dy->string);
 dyStringFree(&dy);
 }
 
 #ifdef OLD
 struct tagCount *tagCountListFromQuery(struct sqlConnection *conn, char *query)
 /* Return a tagCount list from a query that had tag/count values */
 {
 struct tagCount *list = NULL, *tc;
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     tc = tagCountNew(row[0], sqlUnsigned(row[1]));
     slAddHead(&list, tc);
     }
 sqlFreeResult(&sr);
 slReverse(&list);
 return list;
 }
 #endif /* OLD */
 
 void pieOnFacet(struct facetField *ff, char *divId)
 /* Write a pie chart base on the values of given tag in storm */
 {
 struct facetVal *majorTags = facetValMajorPlusOther(ff->valList, 0.01);
 drawPrettyPieGraph(majorTags, divId, ff->fieldName, NULL);
 }
 
 void printFile(char *fname) 
 /* print file to stdout. Do nothing if file does not exist. */
 {
 FILE *fh = fopen(fname, "r");
 if (fh==NULL)
     return;
 char buf[1000];
 while (fgets(buf, 1000, fh) != NULL)
     puts(buf);
 }
 
 char *tagPopularityFields[] = { "tag name", "vals", "popular values (files)...", "files",};
 
 void doHome(struct sqlConnection *conn)
 /* Put up home/summary page */
 {
 printf("<table><tr><td>");
-printf("<img src=\"../images/freeStemCell.jpg\" width=%d height=%d>\n", 200, 275);
+printf("<img src=\"../images/sspsygene_data_portal_data_img.jpg\" width=%d height=%d>\n", 200, 275);
 printf("</td><td>");
 
 /* Print sentence with summary of bytes, files, and labs */
 char query[256];
 printf("The SSPsyGene Staging Portal contains ");
 sqlSafef(query, sizeof(query),
     "select sum(size) from cdwFile,cdwValidFile where cdwFile.id=cdwValidFile.id "
     " and (errorMessage = '' or errorMessage is null)"
     );
 long long totalBytes = sqlQuickLongLong(conn, query);
 printWithGreekByte(stdout, totalBytes);
 printf(" of data in ");
 #ifdef OLD
 sqlSafef(query, sizeof(query),
     "select count(*) from cdwFile,cdwValidFile where cdwFile.id=cdwValidFile.fileId "
     " and (errorMessage = '' or errorMessage is null)"
     );
 #endif /* OLD */
 
 /* Using a query that is faster than the table join but gives the same result 
  * (0.2 sec vs. 0.8 sec) */
 sqlSafef(query, sizeof(query), 
     "select count(*) from cdwFile where (errorMessage = '' || errorMessage is null)"
     " and cdwFileName like '%%/%s%%'",  cdwLicensePlateHead(conn) );
 
 long long fileCount = sqlQuickLongLong(conn, query);
 printLongWithCommas(stdout, fileCount);
 printf(" files");
 sqlSafef(query, sizeof(query),
     "select count(*) from cdwLab "
     );
 #ifdef OLD
 long long labCount = sqlQuickLongLong(conn, query);  
 printf(" from %llu labs.<BR>\n", labCount); 
 #endif /* OLD */
 printf(".<BR>\n");
 
 printf("Try using the browse menu on files or tracks. ");
 printf("The query link allows simple SQL-like queries of the metadata.");
 printf("<BR>\n");
 
 
 /* Print out some pie charts on important fields */
 static char *pieTags[] = 
   {"lab", "format", "assay", "species",};
 struct facetField *pieFacetList = facetFieldsFromSqlTable(conn, getCdwTableSetting("cdwFileFacets"), 
 						    pieTags, ArraySize(pieTags), "N/A", NULL, NULL, NULL);
 struct facetField *ff;
 int i;
 printf("<TABLE style=\"display:inline\"><TR>\n");
 for (i=0, ff = pieFacetList; i<ArraySize(pieTags); ++i, ff = ff->next)
     {
     char pieDivId[64];
     safef(pieDivId, sizeof(pieDivId), "pie_%d", i);
     printf("<TD id=\"%s\"><TD>", pieDivId);
     pieOnFacet(ff, pieDivId); 
     }
 printf("</TR></TABLE>\n");
 printf("<CENTER><I>charts are based on proportion of files in each category</I></CENTER>\n");
 printf("</td></tr></table>\n");
 
 }
 
 #ifdef OLD
 void doBrowseTags(struct sqlConnection *conn)
 /* Put up browse tags page */
 {
 struct tagStorm *tags = cdwUserTagStorm(conn, user);
 struct slName *tag, *tagList = tagStormFieldList(tags);
 slSort(&tagList, slNameCmp);
 printf("This is a list of all tags and their most popular values.");
 struct fieldedTable *table = fieldedTableNew("Important tags", tagPopularityFields, 
     ArraySize(tagPopularityFields));
 for (tag = tagList; tag != NULL; tag = tag->next)
     tagSummaryRow(table, conn, tag->name);
 char returnUrl[PATH_LEN*2];
 safef(returnUrl, sizeof(returnUrl), "../cgi-bin/cdwWebBrowse?cdwCommand=browseTags&%s",
     cartSidUrlString(cart) );
 struct hash *outputWrappers = hashNew(0);
     hashAdd(outputWrappers, "tag name", wrapTagField);
 webSortableFieldedTable(cart, table, returnUrl, "cdwBrowseTags", 0, outputWrappers, NULL);
 tagStormFree(&tags);
 }
 #endif /* OLD */
 
 void doHelp(struct sqlConnection *conn)
 /* Put up help page */
 {
 puts(
 #include "cdwHelp.h"
 );
 }
 
 void doTestPage(struct sqlConnection *conn)
 /* Put up test page */
 {
 printf("testing 1 2 3...<BR>\n");
 }
 
 void dispatch(struct sqlConnection *conn)
 /* Dispatch page after to routine depending on cdwCommand variable */
 {
 char *command = cartOptionalString(cart, "cdwCommand");
 if (command == NULL)
     {
     doHome(conn);
     }
 else if (sameString(command, "home"))
     {
     doHome(conn);
     }
 else if (sameString(command, "analysisQuery"))
     {
     doAnalysisQuery(conn);
     }
 else if (sameString(command, "analysisJointPages"))
     {
     doAnalysisJointPages(conn);
     }
 else if (sameString(command, "downloadFiles"))
     {
     doDownloadFileConfirmation(conn);
     }
 else if (sameString(command, "browseFiles"))
     {
     doBrowseFiles(conn);
     }
 else if (sameString(command, "doFileFlowchart"))
     {
     doFileFlowchart(conn);
     }
 else if (sameString(command, "browseTracks"))
     {
     doBrowseTracks(conn);
     }
 #ifdef OLD
 else if (sameString(command, "browseTags"))
     {
     doBrowseTags(conn);
     }
 #endif /* OLD */
 else if (sameString(command, "browseLabs"))
     {
     doBrowseLabs(conn);
     }
 else if (sameString(command, "browseDataSets"))
     {
     doBrowseDatasets(conn);
     }
 else if (sameString(command, "browseFormats"))
     {
     doBrowseFormat(conn);
     }
 else if (sameString(command, "oneFile"))
     {
     doOneFile(conn);
     }
 else if (sameString(command, "oneTag"))
     {
     doOneTag(conn);
     }
 else if (sameString(command, "help"))
     {
     doHelp(conn);
     }
 else if (sameString(command, "dataSetMetaTree"))
     {
     doDataSetMetaTree(conn);
     }
 else if (sameString(command, "test"))
     {
     doTestPage(conn);
     }
 else
     {
     printf("unrecognized command %s<BR>\n", command);
     }
 }
 
 void doMiddle()
 /* Menu bar has been drawn.  We are in the middle of first section. */
 {
 struct sqlConnection *conn = sqlConnect(cdwDatabase);
 user = cdwCurrentUser(conn);
 dispatch(conn);
 sqlDisconnect(&conn);
 }
 
 static void doSendMenubar()
 /* print http header and menu bar string */
 {
 oldVars = hashNew(0);
 cart = cartAndCookieWithHtml(hUserCookie(), excludeVars, oldVars, TRUE);
 puts("Content-Type: text/html\n\n");
 char* mb = cdwLocalMenuBar(cart, TRUE);
 puts(mb);
 }
 
 static void doSendUserName()
 /* send username and authentication method info in a tiny JSON block */
 {
 oldVars = hashNew(0);
 cart = cartAndCookieWithHtml(hUserCookie(), excludeVars, oldVars, TRUE);
 printf("{\n");
 int firstEntry = 1;
 if (loginUseBasicAuth())
     {
     if (!firstEntry)
         printf(",");
     else
         firstEntry = 0;
     printf ("\"auth\": \"basic\"\n");
     }
 else
     {
     if (!firstEntry)
         printf(",");
     else
         firstEntry = 0;
     printf ("\"auth\": \"hgLogin\"\n");
     }
 
 char *userName = wikiLinkUserName();
 if (userName != NULL)
     {
     if (!firstEntry)
         printf(",");
     else
         firstEntry = 0;
     printf("\"username\": \"%s\"\n", userName);
     }
 printf("}\n");
 }
 
 void localWebStartWrapper(char *titleString)
 /* Output a HTML header with the given title.  Start table layout.  Draw menu bar. */
 {
 /* Do html header. We do this a little differently than web.c routines, mostly
  * in that we are strict rather than transitional HTML 4.01 */
     {
     printf("<!DOCTYPE html>\n");
     printf("<html>\n\t<head>\n");
     webCirmPragmasEtc();
     puts(getCspMetaHeader());
     printf("<TITLE>%s</TITLE>\n", titleString);
     printf("\t\t<link rel=\"shortcut icon\" href=\"../images/schub.ico\" type=\"image/png\" />\n");
     printf("\t\t<script src=\"https://cdnjs.cloudflare.com/ajax/libs/jquery/1.12.1/jquery.min.js\"></script>");
     webIncludeResourceFile("cirmStyle.css");
 
     printf("\t\t<link rel=\"stylesheet\" href=\"https://use.fontawesome.com/releases/v5.7.2/css/all.css\"\n"
         "\t\t integrity=\"sha384-fnmOCqbTlWIlj8LyTjo7mOUStjsKC4pOpQbqyi7RrhN7udi9RwhKkMHpvLbHG9Sr\"\n"
         "\t\t crossorigin=\"anonymous\">\n"
         "\n"
         "\t\t<!-- Latest compiled and minified CSS -->\n"
         "\t\t<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css\"\n"
         "\t\t integrity=\"sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm\"\n"
         "\t\t crossorigin=\"anonymous\">\n"
         "\n"
         "\t\t<!-- Latest compiled and minified JavaScript -->\n"
         "\t\t<script src=\"https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js\"\n"
         "\t\t  integrity=\"sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q\"\n"
         "\t\t crossorigin=\"anonymous\"></script>\n"
         "\t\t<script src=\"https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js\"\n"
         "\t\t integrity=\"sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl\"\n"
         "\t\t crossorigin=\"anonymous\"></script>\n"
         );
 
     jsIncludeFile("jquery.watermark.js", NULL);
     jsIncludeFile("d3pie.min.js", NULL);
     jsIncludeFile("dagre-d3.js", NULL);
     printf("<script src=\"//cdnjs.cloudflare.com/ajax/libs/d3/3.4.4/d3.min.js\"></script>");
     printf("<script src=\"//cdnjs.cloudflare.com/ajax/libs/bowser/1.6.1/bowser.min.js\"></script>");
     printf("</HEAD>\n");
     printBodyTag(stdout);
     }
 
 puts(cdwPageHeader(cart, FALSE));
 
 printf("<div class=\"cirm-page-body\">\n");
 puts(cdwLocalMenuBar(cart, FALSE));	    // Menu bar after tables open but before first section
 webPushErrHandlers();	    // Now can do improved error handler
 }
 
 
 void localWebWrap(struct cart *theCart)
 /* We got the http stuff handled, and a cart.  Now wrap a web page around it. */
 {
 cart = theCart;
 localWebStartWrapper("SSPsyGene Staging Portal");
 pushWarnHandler(htmlVaWarn);
 doMiddle();
 jsInlineFinish();
 printf("</div> <!-- cirm-page-body -->\n");
 puts(cdwPageFooter(cart, FALSE));
 printf("</BODY></HTML>\n");
 }
 
 void initFields()
 /* initialize fields */
 {
 visibleFacetFields = getCdwSetting("cdwFacetFields", FILEFACETFIELDS);
 char temp[1024];
 safef(temp, sizeof temp, "%s,%s", FILEFIELDS, visibleFacetFields);
 fileTableFields = cloneString(temp);
 
 // filter fields against fields in current facet table
 struct sqlConnection *conn = sqlConnect(cdwDatabase);
 struct slName *fNames = sqlFieldNames(conn, getCdwTableSetting("cdwFileFacets"));
 sqlDisconnect(&conn);
 
 struct dyString *dy = dyStringNew(128);
 char *fieldNames[128];
 char *tempFileTableFields = cloneString(fileTableFields);
 int fieldCount = chopString(tempFileTableFields, ",", fieldNames, ArraySize(fieldNames));
 int i;
 for (i = 0; i<fieldCount; i++)
     {
     if (slNameInList(fNames, fieldNames[i]))
 	{
 	if (dy->stringSize > 0)
 	    dyStringAppendC(dy, ',');
 	dyStringAppend(dy, fieldNames[i]);
 	}
     }
 freeMem(fileTableFields);
 fileTableFields = dyStringCannibalize(&dy);
 
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 long enteredMainTime = clock1000();
 boolean isFromWeb = cgiIsOnWeb();
 if (!isFromWeb && !cgiSpoof(&argc, argv))
     usage();
 dnaUtilOpen();
 oldVars = hashNew(0);
 char *cdwCmd = cgiOptionalString("cdwCommand");
 isPublicSite = cfgOptionBooleanDefault("cdw.siteIsPublic", FALSE);
 
 initFields();
 
 if (sameOk(cdwCmd, "downloadUrls"))
     doDownloadUrls();
 else if (sameOk(cdwCmd, "menubar"))
     doSendMenubar();
 else if (sameOk(cdwCmd, "userName"))
     doSendUserName();
 else
     cartEmptyShell(localWebWrap, hUserCookie(), excludeVars, oldVars);
 cgiExitTime("cdwWebBrowse", enteredMainTime);
 return 0;
 }