e877a7961cdfb1b5b9540a0f51f08d3b715f0717
tdreszer
Wed Mar 9 14:06:54 2011 -0800
For download file lookup, beta should look on hgdownloads-test but in beta/ subdirectory.
diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c
index 70662ab..70aed8a 100644
--- src/hg/lib/fileUi.c
+++ src/hg/lib/fileUi.c
@@ -1,786 +1,830 @@
/* fileUi.c - human genome file downloads common controls. */
#include "common.h"
#include "hash.h"
#include "cheapcgi.h"
#include "jsHelper.h"
#include "cart.h"
#include "hdb.h"
#include "fileUi.h"
#include "hui.h"
#include "obscure.h"
#include "mdb.h"
// FIXME: Move to hui.h since hui.c also needs this
#define ENCODE_DCC_DOWNLOADS "encodeDCC"
void fileDbFree(struct fileDb **pFileList)
// free one or more fileDb objects
{
while (pFileList && *pFileList)
{
struct fileDb *oneFile = slPopHead(pFileList);
freeMem(oneFile->fileName);
freeMem(oneFile->fileType);
freeMem(oneFile->fileDate);
freeMem(oneFile->sortFields);
freeMem(oneFile->reverse);
mdbObjsFree(&(oneFile->mdb));
freeMem(oneFile);
}
}
struct fileDb *fileDbGet(char *db, char *dir, char *subDir, char *fileName)
// Returns NULL or if found a fileDb struct with name, size and date filled in.
{
static char *savedDb = NULL;
static char *savedDir = NULL;
static char *savedSubDir = NULL;
static struct fileDb *foundFiles = NULL;// Use static list to save excess IO
struct fileDb *oneFile = NULL;
if (foundFiles == NULL
|| savedDb == NULL || differentString(savedDb, db)
|| savedDir == NULL || differentString(savedDir,dir)
|| savedSubDir == NULL || differentString(savedSubDir,subDir))
{
// free up any static mem
freeMem(savedDb);
freeMem(savedDir);
freeMem(savedSubDir);
fileDbFree(&foundFiles);
FILE *scriptOutput = NULL;
char buf[1024];
char cmd[512];
char *words[10];
char *server = hDownloadsServer();
- if (sameString(server,"hgdownload-test.cse.ucsc.edu")) // genome-test is different
+
+ boolean useRsync = TRUE;
+ if (hIsPrivateHost())
{
- // Does not work: rsync -avn rsync://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone
+ // For hgwdev (which is the same machine as "hgdownload-test.cse.ucsc.edu") rsync does not work
// Use ls -log --time=ctime --time-style=long-iso /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone
safef(cmd,sizeof(cmd),"ls -log --time-style=long-iso /usr/local/apache/htdocs-hgdownload/goldenPath/%s/%s/%s/", db,dir,subDir);
+ useRsync = FALSE;
+ }
+ else if (hIsBetaHost())
+ {
+ // For hgwbeta, the files are being looked for one test in a "beta/" subdir. Have to rsync
+ server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu"
+ safef(cmd,sizeof(cmd),"rsync -avn rsync://%s/goldenPath/%s/%s/%s/beta/", server, db, dir, subDir);
}
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);
safef(cmd,sizeof(cmd),"rsync -avn rsync://%s/goldenPath/%s/%s/%s/", server, db, dir, subDir);
}
//warn("cmd: %s",cmd);
scriptOutput = popen(cmd, "r");
while(fgets(buf, sizeof(buf), scriptOutput))
{
eraseTrailingSpaces(buf);
if (!endsWith(buf,".md5sum")) // Just ignore these
{
int count = chopLine(buf, words);
- if (count >= 6 && sameString(server,"hgdownload-test.cse.ucsc.edu")) // genome-test is different
+ if (count >= 6 && useRsync == FALSE) // hgwdev is same as hgdownloads-test so can't use rsync
{
//-rw-rw-r-- 5 502826550 2010-10-22 16:51 /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdRawDataRep1.fastq.gz
AllocVar(oneFile);
oneFile->fileSize = sqlUnsignedLong(words[2]);
oneFile->fileDate = cloneString(words[3]);
char *atSlash = strrchr(words[5], '/');
if (atSlash != NULL)
oneFile->fileName = cloneString(atSlash + 1);
else
oneFile->fileName = cloneString(words[5]);
slAddHead(&foundFiles,oneFile);
}
- else if (count == 5 && differentString(server,"hgdownload-test.cse.ucsc.edu"))// genome and hgwbeta can use rsync
+ else if (count == 5 && useRsync == TRUE)// genome and hgwbeta can use rsync because files are on different machine
{
//-rw-rw-r-- 26420982 2009/09/29 14:53:30 wgEncodeBroadChipSeq/wgEncodeBroadChipSeqSignalNhlfH4k20me1.wig.gz
AllocVar(oneFile);
oneFile->fileSize = sqlUnsignedLong(words[1]);
oneFile->fileDate = cloneString(words[2]);
strSwapChar(oneFile->fileDate,'/','-');// Standardize YYYY-MM-DD, no time
oneFile->fileName = cloneString(words[4]);
slAddHead(&foundFiles,oneFile);
}
//warn("File:%s size:%ld",foundFiles->fileName,foundFiles->fileSize);
}
}
pclose(scriptOutput);
+ // mark this as done to avoid excessive io
+ savedDb = cloneString(db);
+ savedDir = cloneString(dir);
+ savedSubDir = cloneString(subDir);
+
if (foundFiles == NULL)
{
AllocVar(oneFile);
oneFile->fileName = cloneString("No files found!");
oneFile->fileDate = cloneString(cmd);
slAddHead(&foundFiles,oneFile);
warn("No files found for command:\n%s",cmd);
return NULL;
}
-
- // 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; // Found means removed from list: shorter list for next file.
slAddHead(&newList,oneFile);
oneFile = NULL;
}
if (newList)
foundFiles = slCat(foundFiles,newList); // Order does not remain the same
if (oneFile != NULL && oneFile->fileType == NULL)
{
char *suffix = strchr(oneFile->fileName, '.');
if (suffix != NULL && strlen(suffix) > 2)
{
oneFile->fileType = cloneString(suffix + 1);
if (endsWith(oneFile->fileType,".gz"))
chopSuffix(oneFile->fileType);
}
}
return oneFile;
}
+
static sortOrder_t *fileSortOrderGet(struct cart *cart,struct trackDb *parentTdb,struct mdbObj *mdbObjs)
/* Parses 'fileSortOrder' trackDb/cart instructions and returns a sort order struct or NULL.
Some trickiness here. sortOrder->sortOrder is from cart (changed by user action), as is sortOrder->order,
But columns are in original tdb order (unchanging)! However, if cart is null, all is from trackDb.ra */
{
int ix;
sortOrder_t *sortOrder = NULL;
char *carveSetting = NULL,*setting = NULL;
if (parentTdb)
setting = trackDbSetting(parentTdb, FILE_SORT_ORDER);
if(setting)
{
sortOrder = needMem(sizeof(sortOrder_t));
sortOrder->setting = cloneString(setting);
carveSetting = sortOrder->setting;
}
else
{
if (mdbObjs != NULL)
{
struct dyString *dySortFields = dyStringNew(512);
struct mdbObj *commonVars = mdbObjsCommonVars(mdbObjs);
// Problem with making common fieds as sorable is that it REQUIRES a fixed sort order
char *sortables[] = {"grant","lab","dataType","cell","strain","age","obtainedBy", "rnaExtract","localization","phase","treatment","antibody","protocol",
"labProtocolId","restrictionEnzyme","control","replicate","expId","labExpId","setType","view","submittedDataVersion","subId",
"dateSubmitted","dateResubmitted","dateUnrestricted","dataVersion","origAssembly"};//"labVersion","softwareVersion",
// Not included: no:not searchable
// accession no, annotation no, bioRep no, composite no, controlId no, dccInternalNotes no, fileIndex no, fileName no,
// fragSize no, fragLength no, freezeDate no, geoSample, geoSeries, insertLength no, labVersion, level no,
// mapAlgorithm, privacy no, rank no, readType, seqPlatform, sex, size no, softwareVersion,
// tableName no, uniqueness no
int ix = 0, count = sizeof(sortables)/sizeof(char *);
for (ix=0;ix<count;ix++)
{
// If sortables[ix] is in common vars then then add it to the settings field
if (mdbObjContains(commonVars,sortables[ix],NULL))
{
// TODO: This would be good, but valuable information slips away. This is especially true in fileSearch
// Maybe another whiteList?
//if (mdbRemoveCommonVar(mdbObjs, sortables[ix])) // Don't bother if all the vals are the same
// continue;
dyStringPrintf(dySortFields,"%s=%s ",sortables[ix],strSwapChar(cloneString(cvLabel(sortables[ix])),' ','_'));
}
}
if (dyStringLen(dySortFields))
{
dyStringAppend(dySortFields,"fileSize=Size fileType=File_Type");
setting = dyStringCannibalize(&dySortFields);
}
else
dyStringFree(&dySortFields);
mdbObjsFree(&commonVars);
}
if(setting == NULL) // Must be in trackDb or not a sortable list of files
{
#define FILE_SORT_ORDER_DEFAULT "cell=Cell_Line lab=Lab view=View replicate=Rep fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until"
setting = FILE_SORT_ORDER_DEFAULT;
}
sortOrder = needMem(sizeof(sortOrder_t));
carveSetting = cloneString(setting);
sortOrder->setting = NULL;
}
if (parentTdb)
{
sortOrder->htmlId = needMem(strlen(parentTdb->track)+20);
safef(sortOrder->htmlId, (strlen(parentTdb->track)+20), "%s.%s", parentTdb->track,FILE_SORT_ORDER);
if(cart != NULL)
sortOrder->sortOrder = cloneString(cartOptionalString(cart, sortOrder->htmlId));
}
sortOrder->count = chopByWhite(carveSetting,NULL,0); // Get size
sortOrder->column = needMem(sortOrder->count*sizeof(char*));
sortOrder->count = chopByWhite(carveSetting,sortOrder->column,sortOrder->count);
sortOrder->title = needMem(sortOrder->count*sizeof(char*));
sortOrder->forward = needMem(sortOrder->count*sizeof(boolean));
sortOrder->order = needMem(sortOrder->count*sizeof(int));
for (ix = 0; ix<sortOrder->count; ix++)
{
// separate out mtaDb var in sortColumn from title
sortOrder->title[ix] = strchr(sortOrder->column[ix],'='); // Could be 'cell=Cell_Line'
if (sortOrder->title[ix] != NULL)
{
sortOrder->title[ix][0] = '\0';
sortOrder->title[ix] = strSwapChar(sortOrder->title[ix]+1,'_',' '); // +1 jumps to next char after '='
}
else
sortOrder->title[ix] = sortOrder->column[ix]; // or could be just 'cell'
// Sort order defaults to forward but may be found in a cart var
sortOrder->order[ix] = ix+1;
sortOrder->forward[ix] = TRUE;
if (sortOrder->sortOrder != NULL)
{
char *pos = stringIn(sortOrder->column[ix], sortOrder->sortOrder);// find tdb substr in cart current order string
if(pos != NULL && pos[strlen(sortOrder->column[ix])] == '=')
{
int ord=1;
char* pos2 = sortOrder->sortOrder;
for(;*pos2 && pos2 < pos;pos2++)
{
if(*pos2 == '=') // Discovering sort order in cart
ord++;
}
sortOrder->forward[ix] = (pos[strlen(sortOrder->column[ix]) + 1] == '+');
sortOrder->order[ix] = ord;
}
}
}
if (sortOrder->sortOrder == NULL)
sortOrder->sortOrder = cloneString(setting); // no order in cart, all power to trackDb
return sortOrder; // NOTE cloneString:words[0]==*sortOrder->column[0] and will be freed when sortOrder is freed
}
static int fileDbSortCmp(const void *va, const void *vb)
// Compare two sortable tdb items based upon sort columns.
{
const struct fileDb *a = *((struct fileDb **)va);
const struct fileDb *b = *((struct fileDb **)vb);
char **fieldsA = a->sortFields;
char **fieldsB = b->sortFields;
int ix=0;
int compared = 0;
while(fieldsA[ix] != NULL && fieldsB[ix] != NULL && compared == 0)
{
compared = strcmp(fieldsA[ix], fieldsB[ix]) * (a->reverse[ix]? -1: 1);
ix++;
}
return compared;
}
static void fileDbSortList(struct fileDb **fileList, sortOrder_t *sortOrder)
{// If sortOrder struct provided, will update sortFields in fileList, then sort it
if (sortOrder && fileList)
{
struct fileDb *oneFile = NULL;
for(oneFile = *fileList;oneFile != NULL;oneFile=oneFile->next)
{
oneFile->sortFields = needMem(sizeof(char *) * (sortOrder->count + 1)); // +1 Null terminated
oneFile->reverse = needMem(sizeof(boolean *) * sortOrder->count);
int ix;
for(ix=0;ix<sortOrder->count;ix++)
{
char *field = NULL;
if (sameString("fileSize",sortOrder->column[ix]))
{
char niceNumber[32];
sprintf(niceNumber, "%.15lu", oneFile->fileSize);
field = cloneString(niceNumber);
}
else if (sameString("fileType",sortOrder->column[ix]))
field = oneFile->fileType;
else
field = mdbObjFindValue(oneFile->mdb,sortOrder->column[ix]);
if (field)
{
oneFile->sortFields[sortOrder->order[ix] - 1] = field;
oneFile->reverse[ sortOrder->order[ix] - 1] = (sortOrder->forward[ix] == FALSE);
}
else
{
oneFile->sortFields[sortOrder->order[ix] - 1] = NULL;
oneFile->reverse[ sortOrder->order[ix] - 1] = FALSE;
}
oneFile->sortFields[sortOrder->count] = NULL;
}
}
slSort(fileList,fileDbSortCmp);
}
}
+static char *removeCommonMdbVarsNotInSortOrder(struct mdbObj *mdbObjs,sortOrder_t *sortOrder)
+{ // Removes varaibles common to all mdbObjs and not found in sortOrder. Returns allocated string oh removed var=val pairs
+if (sortOrder != NULL)
+ {
+ // Remove common vars from mdbs grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std;
+ // However, keep the term if it is in the sortOrder
+ struct dyString *dyCommon = dyStringNew(256);
+ char *commonTerms[] = { "grant", "lab", "dataType", "control", "setType" };
+ int tIx=0,sIx = 0;
+ for(;tIx<ArraySize(commonTerms);tIx++)
+ {
+ for(sIx = 0;
+ sIx<sortOrder->count && differentString(commonTerms[tIx],sortOrder->column[sIx]);
+ sIx++) ;
+ if (sIx<sortOrder->count) // Found in sort Order so leave it in mdbObjs
+ continue;
+
+ char *val = mdbRemoveCommonVar(mdbObjs, commonTerms[tIx]); // All mdbs have it and have the same val for it.
+ if (val)
+ dyStringPrintf(dyCommon,"%s=%s ",commonTerms[tIx],val);
+ }
+ return dyStringCannibalize(&dyCommon);
+ }
+return NULL;
+}
+
static void filesDownloadsPreamble(char *db, struct trackDb *tdb)
{
// Do not bother getting preamble.html
// 1) It isn't on the RR (yet)
// 2) It will likely refer back to the composite for Description info which is included in this page
// 3) The rsync-to-tmp-file hurdle isn't worth the effort.
puts("<p><B>Data is <A HREF='http://genome.ucsc.edu/ENCODE/terms.html'>RESTRICTED FROM USE</a>");
puts("in publication until the restriction date noted for the given data file.</B></p>");
+char *server = hDownloadsServer();
+char *subDir = "";
+if (hIsBetaHost())
+ {
+ server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu"
+ subDir = "/beta";
+ }
+
struct fileDb *oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "supplemental");
if (oneFile != NULL)
{
- printf("<p>\n<B>Supplemental materials</b> may be found <A HREF='http://%s/goldenPath/%s/%s/%s/supplemental/' TARGET=ucscDownloads>here</A>.</p>\n",
- hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track);
+ printf("<p>\n<B>Supplemental materials</b> may be found <A HREF='http://%s/goldenPath/%s/%s/%s%s/supplemental/' TARGET=ucscDownloads>here</A>.</p>\n",
+ server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
}
puts("<p>\nThere are two files within this directory that contain information about the downloads:");
-printf("<BR>• <A HREF='http://%s/goldenPath/%s/%s/%s/files.txt' TARGET=ucscDownloads>files.txt</A> which is a tab-separated file with the name and metadata for each download.</LI>\n",
- hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track);
-printf("<BR>• <A HREF='http://%s/goldenPath/%s/%s/%s/md5sum.txt' TARGET=ucscDownloads>md5sum.txt</A> which is a list of the md5sum output for each download.</LI>\n",
- hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, tdb->track);
+printf("<BR>• <A HREF='http://%s/goldenPath/%s/%s/%s%s/files.txt' TARGET=ucscDownloads>files.txt</A> which is a tab-separated file with the name and metadata for each download.</LI>\n",
+ server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
+printf("<BR>• <A HREF='http://%s/goldenPath/%s/%s/%s%s/md5sum.txt' TARGET=ucscDownloads>md5sum.txt</A> which is a list of the md5sum output for each download.</LI>\n",
+ server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
puts("<P>");
}
static int filesPrintTable(char *db, struct trackDb *parentTdb, struct fileDb *fileList, sortOrder_t *sortOrder)
// Prints filesList as a sortable table. Returns count
{
// Table class=sortable
int columnCount = 0;
int restrictedColumn = 0;
char *nowrap = (sortOrder->setting != NULL ? " nowrap":""); // Sort order trackDb setting found so rely on <BR> in titles for wrapping
printf("<TABLE class='sortable' style='border: 2px outset #006600;'>\n");
printf("<THEAD class='sortable'>\n");
printf("<TR class='sortable' valign='bottom'>\n");
printf("<TD align='center' valign='center'> ");
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++;
/*#define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
#ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
if (parentTdb == NULL)
{
printf("<TD align='center' valign='center'> </TD>");
columnCount++;
}
#endif///def SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
*/
// Now the columns
int curOrder = 0,ix=0;
if (sortOrder)
{
curOrder = sortOrder->count;
for(ix=0;ix<sortOrder->count;ix++)
{
char *align = (sameString("labVersion",sortOrder->column[ix]) || sameString("softwareVersion",sortOrder->column[ix]) ? " align='left'":"");
printf("<TH class='sortable sort%d%s' %s%s%s>%s</TH>\n",
sortOrder->order[ix],(sortOrder->forward[ix]?"":" sortRev"),
(sameString("fileSize",sortOrder->column[ix])?"abbr='use' ":""),
nowrap,align,sortOrder->title[ix]); // keeing track of sortOrder
columnCount++;
if (sameWord(sortOrder->column[ix],"dateUnrestricted"))
restrictedColumn = columnCount;
}
}
//#define INCLUDE_FILENAMES
#ifndef INCLUDE_FILENAMES
else
#endif///defn INCLUDE_FILENAMES
{
printf("<TH class='sortable sort%d' nowrap>File Name</TH>\n",++curOrder);
columnCount++;
}
printf("<TH class='sortable sort%d' align='left' nowrap>Additional Details</TH>\n",++curOrder);
columnCount++;
printf("</TR></THEAD>\n");
// Now the files...
+char *server = hDownloadsServer();
+char *subDir = "";
+if (hIsBetaHost())
+ {
+ server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think it's downloads server is "hgdownload.cse.ucsc.edu"
+ subDir = "/beta";
+ }
struct fileDb *oneFile = fileList;
printf("<TBODY class='sortable sorting'>\n"); // 'sorting' is a fib but it conveniently greys the list till the table is initialized.
for( ;oneFile!= NULL;oneFile=oneFile->next)
{
oneFile->mdb->next = NULL; // mdbs were in list for generating sortOrder, but list no longer needed
char *field = NULL;
printf("<TR valign='top'>"); // TODO: BUILD IN THE CLASSES TO ALLOW FILTERBOXES TO WORK!!!
// Download button
printf("<TD nowrap>");
if (parentTdb)
field = parentTdb->track;
else
field = mdbObjFindValue(oneFile->mdb,"composite");
assert(field != NULL);
- printf("<A HREF='http://%s/goldenPath/%s/%s/%s/%s' title='Download %s ...' TARGET=ucscDownloads>",
- hDownloadsServer(),db,ENCODE_DCC_DOWNLOADS, field, oneFile->fileName, oneFile->fileName);
+ printf("<A HREF='http://%s/goldenPath/%s/%s/%s%s/%s' title='Download %s ...' TARGET=ucscDownloads>",
+ server,db,ENCODE_DCC_DOWNLOADS, field, subDir, oneFile->fileName, oneFile->fileName);
printf("<input type='button' value='Download'>");
printf("</a>");
#define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
#ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
if (parentTdb == NULL)
printf(" <A href='../cgi-bin/hgFileUi?db=%s&g=%s' title='Navigate to downloads page for %s set...'><IMG SRC='../images/folderC.png'></a> ", db,field,field);
#endif///def SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
printf("</TD>\n");
// Each of the pulled out mdb vars
if (sortOrder)
{
for(ix=0;ix<sortOrder->count;ix++)
{
char *align = (sameString("labVersion",sortOrder->column[ix]) || sameString("softwareVersion",sortOrder->column[ix]) ? " align='left'":" align='center'");
if (sameString("fileSize",sortOrder->column[ix]))
{
char niceNumber[128];
sprintWithGreekByte(niceNumber, sizeof(niceNumber), oneFile->fileSize);
field = oneFile->sortFields[sortOrder->order[ix] - 1];
printf("<TD abbr='%s' align='right' nowrap>%s</td>",field,niceNumber);
}
else
{
field = oneFile->sortFields[sortOrder->order[ix] - 1];
if (sameString("dateUnrestricted",sortOrder->column[ix]) && field && dateIsOld(field,"%F"))
printf("<TD%s nowrap style='color: #BBBBBB;'>%s</td>",align,field);
else
printf("<TD%s nowrap>%s</td>",align,field?field:" ");
if (!sameString("fileType",sortOrder->column[ix]))
mdbObjRemoveVars(oneFile->mdb,sortOrder->column[ix]); // Remove this from mdb now so that it isn't displayed in "extras'
}
}
}
#ifndef INCLUDE_FILENAMES
else
#endif///ndef INCLUDE_FILENAMES
{ // fileName
printf("<TD nowrap>%s",oneFile->fileName);
//// FIXME: " The "..." encapsulation could be rebuilt so it could be called here
//printf(" <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 dccInternalNotes"); // 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:" ");
printf("</TR>\n");
}
printf("</TBODY><TFOOT class='bgLevel1'>\n");
printf("<TR valign='top'>");
// Restriction policy link in first column?
if (restrictedColumn == 1)
printf("<TH colspan=%d><A HREF='%s' TARGET=BLANK style='font-size:.9em;'>Restriction Policy</A></TH>", (columnCount - restrictedColumn),ENCODE_DATA_RELEASE_POLICY);
printf("<TD colspan=%d> ",(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");
if (parentTdb == NULL)
printf("<script type='text/javascript'>{$(document).ready(function() {sortTableInitialize($('table.sortable')[0],true,true);});}</script>\n");
return filesCount;
}
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 'fileSortOrder'
// 5) TODO: present filter controls
// 6) Presort of files list
// 7) make table class=sortable
// 8) Final file count
// 9) Use trackDb settings to get at html description
// Nice to have: Make filtering and sorting persistent (saved to cart)
// 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);
// 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]);// All mdbs have it and have the same val for it.
- 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
struct fileDb *fileList = NULL, *oneFile = NULL; // Will contain found files
struct mdbObj *mdbFiles = NULL; // Will caontain a list of mdbs for the found files
while(mdbList)
{
char buf[512];
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;
slAddHead(&mdbFiles,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
if (fileName && endsWith(fileName,".bam")) // Special to fill in missing .bam.bai's
{
safef(buf,sizeof(buf),"%s.bai",fileName);
fileName = buf;
}
else
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;
slAddHead(&mdbFiles,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,mdbFiles);
if (sortOrder != NULL)
{
+ char *vars = removeCommonMdbVarsNotInSortOrder(mdbFiles,sortOrder);
+ if (vars)
+ {
+ if (debug)
+ warn("These terms are common:%s",vars);
+ freeMem(vars);
+ }
+
// Fill in and sort fileList
fileDbSortList(&fileList,sortOrder);
}
+// FilterBoxes ?
+ // Dimensions
+ // cart contents
+ //boolean filterAble = dimensionsExist(tdb);
+ //membersForAll_t* membersForAll = membersForAllSubGroupsGet(tdb,cart);
+
jsIncludeFile("hui.js",NULL);
jsIncludeFile("ajax.js",NULL);
// standard preamble
filesDownloadsPreamble(db,tdb);
// Print table
filesPrintTable(db,tdb,fileList,sortOrder);
//fileDbFree(&fileList); // Why bother on this very long running cgi?
}
int fileSearchResults(char *db, struct sqlConnection *conn, struct slPair *varValPairs, char *fileType)
// Prints list of files in downloads directories matching mdb search terms. Returns count
{
struct sqlConnection *connLocal = conn;
if (conn == NULL)
connLocal = hAllocConn(db);
struct mdbObj *mdbList = mdbObjRepeatedSearch(connLocal,varValPairs,FALSE,TRUE);
if (conn == NULL)
hFreeConn(&connLocal);
if (slCount(mdbList) == 0)
{
printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n");
return 0;
}
// Now sort mdbObjs so that composites will stay together and lookup of files will be most efficient
mdbObjsSortOnVars(&mdbList, "composite");
#define FOUND_FILE_LIMIT 1000
int fileCount = 0;
// Verify file existance and make fileList of those found
struct fileDb *fileList = NULL, *oneFile = NULL; // Will contain found files
struct mdbObj *mdbFiles = NULL; // Will caontain a list of mdbs for the found files
while(mdbList && fileCount < FOUND_FILE_LIMIT)
{
boolean found = FALSE;
struct mdbObj *mdbFile = slPopHead(&mdbList);
char *composite = mdbObjFindValue(mdbFile,"composite");
if (composite != NULL)
{
// First for FileName
char *fileName = mdbObjFindValue(mdbFile,"fileName");
if (fileName != NULL)
{
oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName);
if (oneFile)
{
//warn("%s == %s",fileType,oneFile->fileType);
if (isEmpty(fileType) || sameWord(fileType,"Any")
|| (oneFile->fileType && sameWord(fileType,oneFile->fileType)))
{
slAddHead(&fileList,oneFile);
oneFile->mdb = mdbFile;
slAddHead(&mdbFiles,mdbFile);
fileCount++;
found = TRUE;
continue;
}
}
else
fileDbFree(&oneFile);
}
// Now for FileIndexes
fileName = mdbObjFindValue(mdbFile,"fileIndex");
if (fileName != NULL)
{
// Verify existance first
oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName);
if (oneFile)
{
//warn("%s == %s",fileType,oneFile->fileType);
if (isEmpty(fileType) || sameWord(fileType,"Any")
|| (oneFile->fileType && sameWord(fileType,oneFile->fileType)))
{
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;
slAddHead(&mdbFiles,mdbFile);
}
fileCount++;
found = TRUE;
continue;
}
else
fileDbFree(&oneFile);
}
}
}
if (!found)
mdbObjsFree(&mdbFile);
}
if (slCount(fileList) == 0)
{
printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n");
return 0; // No files so nothing to do.
}
// TODO Could sort on varValPairs by creating a sortOrder struct of them
//// Now update all files with their sortable fields and sort the list
sortOrder_t *sortOrder = fileSortOrderGet(NULL,NULL,mdbFiles); // No cart, no tdb
if (sortOrder != NULL)
{
// Fill in and sort fileList
fileDbSortList(&fileList,sortOrder);
}
mdbObjRemoveVars(mdbFiles,"tableName"); // Remove this from mdb now so that it isn't displayed in "extras'
//jsIncludeFile("hui.js",NULL);
//jsIncludeFile("ajax.js",NULL);
// Print table
printf("<DIV id='filesFound'>");
if (mdbList != NULL)
{
printf("<DIV class='redBox' style='width: 380px;'>Too many files found. Displaying first %d of potentially %d.<BR>Narrow search parameters and try again.</DIV><BR>\n",
fileCount,(fileCount+slCount(mdbList)*2)); // Multiply*2 because of fileIndexes
//warn("Too many files found. Displaying first %d of potentially %d.<BR>Narrow search parameters and try again.\n", fileCount,(fileCount+slCount(mdbList)*2)); // Multiply because of fileIndexes
mdbObjsFree(&mdbList);
}
fileCount = filesPrintTable(db,NULL,fileList,sortOrder);
printf("</DIV><BR>\n");
//fileDbFree(&fileList); // Why bother on this very long running cgi?
return fileCount;
}