2b91bbbfc4cf6c21f4160e769fde58f6a5af3d1b
kate
Fri Oct 5 10:53:42 2012 -0700
Remove links to preview browser. #9264
diff --git src/hg/lib/fileUi.c src/hg/lib/fileUi.c
index 012130f..5ac7cee 100644
--- src/hg/lib/fileUi.c
+++ src/hg/lib/fileUi.c
@@ -1,1191 +1,1182 @@
/* fileUi.c - human genome file downloads common controls. */
#include "common.h"
#include "hash.h"
#include "cheapcgi.h"
#include "jsHelper.h"
#include "cart.h"
#include "hdb.h"
#include "fileUi.h"
#include "hui.h"
#include "obscure.h"
#include "mdb.h"
#include "jsHelper.h"
#include "web.h"
#include "trashDir.h"
static boolean timeIt = FALSE; // Can remove when satisfied with timing.
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);
}
}
static struct fileDb *fileDbReadFromBackup(char *db, char *dir, char *subDir)
{
struct tempName buFile;
boolean exists = trashDirReusableFile(&buFile, dir, subDir, db); // encodeDCC/composite.db
if (!exists)
return NULL;
struct fileDb *fileList = NULL;
struct fileDb *oneFile = NULL;
struct lineFile *lf = lineFileOpen(buFile.forCgi, TRUE);
char *words[4];
while (lineFileChop(lf, words) >= 3)
{
AllocVar(oneFile);
oneFile->fileName = cloneString(words[0]);
oneFile->fileSize = sqlUnsignedLong(words[1]);
oneFile->fileDate = cloneString(words[2]);
slAddHead(&fileList,oneFile);
}
lineFileClose(&lf);
if (fileList == NULL)
unlink(buFile.forCgi); // remove empty file
return fileList;
}
// Cache is not faster, so just use it as a backup
#define CACHE_IS_FASTER_THAN_RSYNC
#ifdef CACHE_IS_FASTER_THAN_RSYNC
static boolean fileDbBackupAvailable(char *db, char *dir, char *subDir)
// Checks if there is a recent enough cache file
{
if (cgiVarExists("clearCache")) // Trick to invalidate cache at will.
return FALSE;
struct tempName buFile;
boolean exists = trashDirReusableFile(&buFile, dir, subDir, db); // encodeDCC/composite.db
if (exists)
{
struct stat mystat;
ZeroVar(&mystat);
if (stat(buFile.forCgi,&mystat)==0)
{
// how old is old?
int secs = (clock1() - mystat.st_ctime); // seconds since created
if (secs < (24 * 60 * 60)) // one date
return TRUE;
}
}
return FALSE;
}
#endif///def CACHE_IS_FASTER_THAN_RSYNC
static void fileDbWriteToBackup(char *db, char *dir, char *subDir,struct fileDb *fileList)
{
struct tempName buFile;
(void)trashDirReusableFile(&buFile, dir, subDir, db); // encodeDCC/composite.db
FILE *fd = NULL;
if ((fd = fopen(buFile.forCgi, "w")) != NULL)
{
struct fileDb *oneFile = fileList;
for (;oneFile != NULL;oneFile=oneFile->next)
{
char buf[1024];
safef(buf,sizeof buf,"%s %ld %s\n",oneFile->fileName,oneFile->fileSize,oneFile->fileDate);
fwrite(buf, strlen(buf), 1, fd);
}
fclose(fd);
}
}
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);
#ifdef CACHE_IS_FASTER_THAN_RSYNC
if (fileDbBackupAvailable(db, dir, subDir)) // check backup first
foundFiles = fileDbReadFromBackup(db, dir, subDir);
else
#endif///def CACHE_IS_FASTER_THAN_RSYNC
{
FILE *scriptOutput = NULL;
char buf[1024];
char cmd[512];
char *words[10];
char *server = hDownloadsServer();
// Always uses rsync, even when same server, to ensure testability
if (hIsBetaHost())
{
// NOTE: Force this case because beta may think it's downloads server is
// "hgdownload.cse.ucsc.edu"
safef(cmd,sizeof(cmd),"rsync -n rsync://hgdownload-test.cse.ucsc.edu/goldenPath/"
"%s/%s/%s/beta/", db, dir, subDir);
}
else
safef(cmd,sizeof(cmd),"rsync -n rsync://%s/goldenPath/%s/%s/%s/",
server, db, dir, subDir);
scriptOutput = popen(cmd, "r");
while (fgets(buf, sizeof(buf), scriptOutput))
{
eraseTrailingSpaces(buf);
if (!endsWith(buf,".md5sum")) // Just ignore these
{
int count = chopLine(buf, words);
if (count == 5)
{
//-rw-rw-r-- 26420982 2009/09/29 14:53:30 wgEncodeBroadChipSeq/wgEncode...
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);
}
}
}
pclose(scriptOutput);
if (foundFiles == NULL)
{
foundFiles = fileDbReadFromBackup(db, dir, 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);
}
}
else
{
fileDbWriteToBackup(db, dir, subDir,foundFiles);
if (timeIt)
uglyTime("Successful rsync found %d files",slCount(foundFiles));
}
}
// mark this as done to avoid excessive io
savedDb = cloneString(db);
savedDir = cloneString(dir);
savedSubDir = cloneString(subDir);
if (foundFiles == NULL)
return NULL;
}
// special code that only gets called in debug mode
if (sameString(fileName,"listAll"))
{
for (oneFile=foundFiles;oneFile;oneFile=oneFile->next)
warn("%s",oneFile->fileName);
return NULL;
}
// Look up the file and return it
struct fileDb *newList = NULL;
while (foundFiles)
{
oneFile = slPopHead(&foundFiles);
if (sameString(fileName,oneFile->fileName))
break; // Found means removed from list: shorter list for next file.
slAddHead(&newList,oneFile);
oneFile = NULL;
}
if (newList)
foundFiles = slCat(foundFiles,newList); // Order does not remain the same
if (oneFile != NULL && oneFile->fileType == NULL)
{
char *suffix = strchr(oneFile->fileName, '.');
if (suffix != NULL && strlen(suffix) > 2)
{
oneFile->fileType = cloneString(suffix + 1);
if (endsWith(oneFile->fileType,".gz"))
chopSuffix(oneFile->fileType);
}
}
return oneFile;
}
static sortOrder_t *fileSortOrderGet(struct cart *cart,struct trackDb *parentTdb,
struct mdbObj *mdbObjs)
// Parses 'fileSortOrder' trackDb/cart instructions and returns a sort order struct or NULL.
// Some trickiness here. sortOrder->sortOrder is from cart (changed by user action),
// as is sortOrder->order, but columns are in original tdb order (unchanging)!
// However, if cart is null, all is from trackDb.ra.
{
int ix;
sortOrder_t *sortOrder = NULL;
char *carveSetting = NULL,*setting = NULL;
if (parentTdb)
setting = trackDbSetting(parentTdb, FILE_SORT_ORDER);
if (setting)
{
sortOrder = needMem(sizeof(sortOrder_t));
sortOrder->setting = cloneString(setting);
carveSetting = sortOrder->setting;
}
else
{
if (mdbObjs != NULL)
{
struct dyString *dySortFields = dyStringNew(512);
struct mdbObj *commonVars = mdbObjsCommonVars(mdbObjs);
// common vars are already in cv defined order, searchable is also sortable
struct mdbVar *var = commonVars->vars;
for (;var != NULL; var = var->next)
{
if (differentWord(var->var,MDB_VAR_LAB_VERSION) // Exclude certain vars
&& differentWord(var->var,MDB_VAR_SOFTWARE_VERSION)
&& cvSearchMethod(var->var) != cvNotSearchable) // searchable is also sortable
{
if (mdbObjsHasCommonVar(mdbObjs, var->var,TRUE)) // Don't bother if all the vals
continue; // are the same (missing okay)
dyStringPrintf(dySortFields,"%s=%s ",var->var,
strSwapChar(cloneString(cvLabel(NULL,var->var)),' ','_'));
}
}
if (dyStringLen(dySortFields))
{
dyStringAppend(dySortFields,"fileSize=Size fileType=File_Type");
setting = dyStringCannibalize(&dySortFields);
}
else
dyStringFree(&dySortFields);
mdbObjsFree(&commonVars);
}
if (setting == NULL) // Must be in trackDb or not a sortable list of files
{
#define FILE_SORT_ORDER_DEFAULT "cell=Cell_Line lab=Lab view=View replicate=Rep " \
"fileSize=Size fileType=File_Type dateSubmitted=Submitted " \
"dateUnrestricted=RESTRICTED<BR>Until"
setting = FILE_SORT_ORDER_DEFAULT;
}
sortOrder = needMem(sizeof(sortOrder_t));
carveSetting = cloneString(setting);
sortOrder->setting = NULL;
}
if (parentTdb)
{
sortOrder->htmlId = needMem(strlen(parentTdb->track)+20);
safef(sortOrder->htmlId, (strlen(parentTdb->track)+20), "%s.%s",
parentTdb->track,FILE_SORT_ORDER);
if (cart != NULL)
sortOrder->sortOrder = cloneString(cartOptionalString(cart, sortOrder->htmlId));
}
sortOrder->count = chopByWhite(carveSetting,NULL,0); // Get size
sortOrder->column = needMem(sortOrder->count*sizeof(char*));
sortOrder->count = chopByWhite(carveSetting,sortOrder->column,sortOrder->count);
sortOrder->title = needMem(sortOrder->count*sizeof(char*));
sortOrder->forward = needMem(sortOrder->count*sizeof(boolean));
sortOrder->order = needMem(sortOrder->count*sizeof(int));
for (ix = 0; ix<sortOrder->count; ix++)
{
// separate out mtaDb var in sortColumn from title
sortOrder->title[ix] = strchr(sortOrder->column[ix],'='); // Could be 'cell=Cell_Line'
if (sortOrder->title[ix] != NULL)
{
sortOrder->title[ix][0] = '\0'; // +1 jumps to next char after '='
sortOrder->title[ix] = strSwapChar(sortOrder->title[ix]+1,'_',' ');
}
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)
{
// find tdb substr in cart current order string
char *pos = stringIn(sortOrder->column[ix], sortOrder->sortOrder);
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]
} // 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 = strcmp(fieldsA[ix], fieldsB[ix]);
if (compared != 0)
{
if (a->reverse[ix])
compared *= -1;
break;
}
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)
{ // + 1 Null terminated
oneFile->sortFields = needMem(sizeof(char *) * (sortOrder->count + 1));
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 int removeCommonMdbVarsNotInSortOrder(struct mdbObj *mdbObjs,sortOrder_t *sortOrder)
// Removes varaibles common to all mdbObjs and not found in sortOrder.
// Returns count of vars removed
{
if (sortOrder != NULL)
{
// Remove common vars from mdbs grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp;
// However, keep the term if it is in the sortOrder
int count = 0;
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;
if (mdbObjsHasCommonVar(mdbObjs, commonTerms[tIx], TRUE)) // val the same or missing
{
count++;
dyStringPrintf(dyCommon,"%s ",commonTerms[tIx]);
}
}
if (count > 0)
mdbObjRemoveVars(mdbObjs,dyStringContents(dyCommon)); // removes from full list of mdbs
dyStringFree(&dyCommon);
return count;
}
return 0;
}
static char *labelWithVocabLink(char *var,char *title,struct slPair *valsAndLabels,
boolean tagsNotVals)
// If the parentTdb has a controlledVocabulary setting and the vocabType is found,
// then label will be wrapped with the link to all relevent terms. Return string is cloned.
{
// Determine if the var is cvDefined. If not, simple link
boolean cvDefined = FALSE;
struct hash *cvTypesOfTerms = (struct hash *)cvTermTypeHash();
if (cvTypesOfTerms != NULL)
{
struct hash *cvTermDef = hashFindVal(cvTypesOfTerms,var);
if (cvTermDef)
cvDefined = SETTING_IS_ON(hashFindVal(cvTermDef,"cvDefined"));
}
struct dyString *dyLink = dyStringNew(256);
if (!cvDefined)
dyStringPrintf(dyLink,"<A HREF='hgEncodeVocab?type=%s' title='Click for details of \"%s\"'"
" TARGET=ucscVocab>%s</A>",var,title,title);
else
{
dyStringPrintf(dyLink,"<A HREF='hgEncodeVocab?%s=",tagsNotVals?"tag":"term");
struct slPair *oneVal = valsAndLabels;
for (;oneVal!=NULL;oneVal=oneVal->next)
{
if (oneVal != valsAndLabels)
dyStringAppendC(dyLink,',');
dyStringAppend(dyLink,mdbPairVal(oneVal));
}
dyStringPrintf(dyLink,"' title='Click for details of each \"%s\"' TARGET=ucscVocab>%s</A>",
title,title);
}
return dyStringCannibalize(&dyLink);
}
static int filterBoxesForFilesList(char *db,struct mdbObj *mdbObjs,sortOrder_t *sortOrder)
// Will create filterBoxes for each sortOrder field. Returns bitmask of sortOrder colums included
{
int count = 0;
int filterableBits = 0;
if (sortOrder != NULL)
{
struct dyString *dyFilters = dyStringNew(256);
int sIx=0;
for (sIx = 0;sIx<sortOrder->count;sIx++)
{
char *var = sortOrder->column[sIx];
enum cvSearchable searchBy = cvSearchMethod(var);
if (searchBy == cvNotSearchable || searchBy == cvSearchByFreeText)
continue; // Free text is not good candidate for filters. Best is single word/date/int.
// get all vals for var, then convert to tag/label pairs for filterBys
struct slName *vals = mdbObjsFindAllVals(mdbObjs, var, CV_LABEL_EMPTY_IS_NONE);
if (searchBy != cvSearchByMultiSelect && searchBy != cvSearchBySingleSelect)
{
// We can't be too ambitious about creating filterboxes on the fly so some limitations:
// If there are more than 80 options, the filterBy is way too large and of limited use
// If there is a distinct val for each file in the table, then the filterBy is the
// same size as the table and of no help. Really the number of options should be
// half the number of rows but we are being lenient and cutting off at 0.8 not 0.5
// If there is any non-alphanum char in a value then the filterBy will fail in js code.
// Those filterBy's are abandoned a but further down.
int valCount = slCount(vals);
if (valCount > 80 || valCount > (slCount(mdbObjs) * 0.8))
{
slNameFreeList(&vals);
continue;
}
}
struct slPair *tagLabelPairs = NULL;
while (vals != NULL)
{
char buf[256];
struct slName *term = slPopHead(&vals);
char *tag = (char *)cvTag(var,term->name);
if (tag == NULL) // Does not require cv defined!
{
safecpy(buf,sizeof buf,term->name);
tag = buf; // Bad news if tag has special chars,
eraseNonAlphaNum(tag); // unfortunately this does not pretect us from dups
// filtering by terms not in cv or regularized should be
// abandanded at the first sign of trouble!
if (searchBy != cvSearchByMultiSelect
&& searchBy != cvSearchBySingleSelect
&& searchBy != cvSearchByDateRange)
{
if (strlen(term->name) > strlen(tag))
{
slNameFreeList(&vals);
slNameFree(&term);
break;
}
}
}
slPairAdd(&tagLabelPairs,tag,cloneString((char *)cvLabel(var,term->name)));
slNameFree(&term);
}
// If there is more than one val for this var then create filterBy box for it
if (slCount(tagLabelPairs) > 1)
{
// should have a list sorted on the label
enum cvDataType eCvDataType = cvDataType(var);
if (eCvDataType == cvInteger)
slPairValAtoiSort(&tagLabelPairs);
else
slPairValSortCase(&tagLabelPairs);
char extraClasses[256];
safef(extraClasses,sizeof extraClasses,"filterTable %s",var);
char *dropDownHtml = cgiMakeMultiSelectDropList(var,tagLabelPairs,NULL,"All",
extraClasses,"onchange='filterTable.filter(this);' style='font-size:.9em;'");
// Note filterBox has classes: filterBy & {var}
if (dropDownHtml)
{
dyStringPrintf(dyFilters,
"<td align='left'>\n<B>%s</B>:<BR>\n%s</td><td width=10> </td>\n",
labelWithVocabLink(var,sortOrder->title[sIx],tagLabelPairs,TRUE),
dropDownHtml); // TRUE were sending tags, not values
freeMem(dropDownHtml);
count++;
if (sIx < 32) // avoid bit overflow but 32 filterBoxes? I don't think so
filterableBits |= (0x1<<(sIx));
}
}
if (tagLabelPairs != NULL)
slPairFreeValsAndList(&tagLabelPairs);
}
// Finally ready to print the filterBys out
if (count)
{
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("ui.dropdownchecklist.js",NULL);
#define FILTERBY_HELP_LINK "<A HREF=\"../goldenPath/help/multiView.html\" " \
"TARGET=ucscHelp>help</A>"
cgiDown(0.9);
printf("<B>Filter files by:</B> (select multiple %sitems - %s)\n"
"<table><tr valign='bottom'>\n",
(count >= 1 ? "categories and ":""),FILTERBY_HELP_LINK);
printf("%s\n",dyStringContents(dyFilters));
printf("</tr></table>\n");
jsIncludeFile("ddcl.js",NULL);
}
dyStringFree(&dyFilters);
}
return filterableBits;
}
static void filesDownloadsPreamble(char *db, struct trackDb *tdb)
// Replacement for preamble.html which should expose parent dir, files.txt and supplemental, but
// not have any specialized notes per composite. Specialized notes belong in track description.
{
char *server = hDownloadsServer();
char *subDir = "";
if (hIsBetaHost())
{
server = "hgdownload-test.cse.ucsc.edu"; // NOTE: Force this case because beta may think
subDir = "/beta"; // it's downloads server is "hgdownload.cse.ucsc.edu"
}
cgiDown(0.9);
puts("<B>Data is <A HREF='../ENCODE/terms.html' TARGET='_BLANK'>RESTRICTED FROM USE</a>");
puts("in publication until the restriction date noted for the given data file.</B>");
cgiDown(0.7);
puts("Additional resources:");
printf("<BR>• <B><A HREF='http://%s/goldenPath/%s/%s/%s%s/files.txt' "
"TARGET=ucscDownloads>files.txt</A></B> - lists the name and metadata for each download.\n",
server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
printf("<BR>• <B><A HREF='http://%s/goldenPath/%s/%s/%s%s/md5sum.txt' "
"TARGET=ucscDownloads>md5sum.txt</A></B> - lists the md5sum output for each download.\n",
server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
printf("<BR>• <B><A HREF='http://%s/goldenPath/%s/%s/%s%s'>downloads server</A></B> - "
"alternative access to downloadable files (may include obsolete data).\n",
server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
struct fileDb *oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "supplemental");
if (oneFile != NULL)
{
printf("<BR>• <B><A HREF='http://%s/goldenPath/%s/%s/%s%s/supplemental/' "
"TARGET=ucscDownloads>supplemental materials</A></B> - "
"any related files provided by the laboratory.\n",
server,db,ENCODE_DCC_DOWNLOADS, tdb->track, subDir);
}
-if (hIsPreviewHost())
- printf("<BR><b>WARNING</b>: This data is provided for early access via the Preview Browser -- "
- "it is unreviewed and subject to change. For high quality reviewed annotations, "
- "see the <a target=_blank href='http://%s/cgi-bin/hgTracks?db=%s'>Genome Browser</a>.",
- "genome.ucsc.edu", db);
-else
- printf("<BR><b>NOTE</b>: Early access to additional track data may be available on the "
- "<a target=_blank href='http://%s/cgi-bin/hgFileUi?db=%s&g=%s'>Preview Browser</A>.",
- "genome-preview.ucsc.edu", db, tdb->track);
}
static int filesPrintTable(char *db, struct trackDb *parentTdb, struct fileDb *fileList,
sortOrder_t *sortOrder,int filterable)
// Prints filesList as a sortable table. Returns count
{
if (timeIt)
uglyTime("Start table");
// 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("<em><span class='filesCount'></span>%d files</em>",filesCount);
// NOTE: This could be done to preserve sort order in cart.
// However hgFileUi would need form OR changes would need to be ajaxed over
// AND hgsid would be needed.
//if (sortOrder)
// printf("<INPUT TYPE=HIDDEN NAME='%s' class='sortOrder' VALUE=\"%s\">",
// sortOrder->htmlId, sortOrder->sortOrder);
printf("</TD>\n");
columnCount++;
// 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
subDir = "/beta"; // it's downloads server is "hgdownload.cse.ucsc.edu"
}
struct fileDb *oneFile = fileList;
printf("<TBODY class='sortable sorting'>\n"); // 'sorting' is a fib but it conveniently greys
if (timeIt) // the list till the table is initialized.
uglyTime("Finished column headers");
for (;oneFile!= NULL;oneFile=oneFile->next)
{
oneFile->mdb->next = NULL; // mdbs were in list for generating sortOrder,
char *field = NULL; // but list no longer needed
printf("<TR valign='top'%s>",(filterable != 0) ?" class='filterable'":"");
// Download button
printf("<TD nowrap>");
if (parentTdb)
field = parentTdb->track;
else
{
field = cloneString(mdbObjFindValue(oneFile->mdb,MDB_VAR_COMPOSITE));
mdbObjRemoveOneVar(oneFile->mdb,MDB_VAR_COMPOSITE,NULL);
}
assert(field != NULL);
printf("<input type='button' value='Download' onclick=\"window.location="
"'http://%s/goldenPath/%s/%s/%s%s/%s';\" title='Download %s ...'>",
server,db,ENCODE_DCC_DOWNLOADS, field, subDir, oneFile->fileName, oneFile->fileName);
#define SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
#ifdef SHOW_FOLDER_FRO_COMPOSITE_DOWNLOADS
if (parentTdb == NULL)
printf(" <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++)
{
if (sameString("fileSize",sortOrder->column[ix]))
{
char niceNumber[128];
sprintWithGreekByte(niceNumber, sizeof(niceNumber), oneFile->fileSize);
field = oneFile->sortFields[sortOrder->order[ix] - 1];
printf("<TD abbr='%s' align='right' nowrap>%s</td>",field,niceNumber);
}
else
{
field = oneFile->sortFields[sortOrder->order[ix] - 1];
boolean isFieldEmpty = isEmpty(field);
struct hash *termHash = NULL;
if (!isFieldEmpty)
{
termHash = (struct hash *)cvOneTermHash(sortOrder->column[ix],field);
if (termHash && sameString(field,MDB_VAL_ENCODE_EDV_NONE))
isFieldEmpty = cvTermIsEmpty(sortOrder->column[ix],field);
}
char class[128];
class[0] = '\0';
if (filterable & (0x1<<ix))
{
char *cleanClass = NULL;
char buf[256];
if (isFieldEmpty)
cleanClass = CV_LABEL_EMPTY_IS_NONE;
else
{
if (termHash)
cleanClass = (char *)hashFindVal((struct hash *)termHash,CV_TAG);
if (cleanClass == NULL)
{
// This may not be needed because the filterBy code
// already eliminated these.
safecpy(buf,sizeof buf,field);
cleanClass = buf;
eraseNonAlphaNum(cleanClass);
}
}
safef(class,sizeof class," class='%s %s'",sortOrder->column[ix],cleanClass);
}
char *align = (sameString("labVersion",sortOrder->column[ix])
|| sameString("softwareVersion",sortOrder->column[ix]) ?
" align='left'":" align='center'");
if (sameString("dateUnrestricted",sortOrder->column[ix])
&& field
&& dateIsOld(field,"%F"))
printf("<TD%s nowrap style='color: #BBBBBB;'%s>%s</td>",align,class,field);
else
{
// use label
if (!isFieldEmpty && termHash)
{
char *label = hashFindVal(termHash,CV_LABEL);
if (label != NULL)
field = label;
}
printf("<TD%s nowrap%s>%s</td>",align,class,isFieldEmpty?" ":field);
}
if (!sameString("fileType",sortOrder->column[ix]))
mdbObjRemoveOneVar(oneFile->mdb,sortOrder->column[ix],NULL);
}
}
}
#ifndef INCLUDE_FILENAMES
else
#endif///ndef INCLUDE_FILENAMES
{ // fileName
printf("<TD nowrap>%s",oneFile->fileName);
}
// Extras grant=Bernstein; lab=Broad; dataType=ChipSeq; setType=exp; control=std;
field = mdbObjVarValPairsAsLine(oneFile->mdb,TRUE,FALSE);
printf("<TD nowrap>%s</td>",field?field:" ");
printf("</TR>\n");
}
if (timeIt)
uglyTime("Finished files");
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("<em><span class='filesCount'></span>%d files</em>",filesCount);
// Restriction policy link in later column?
if (restrictedColumn > 1)
printf("</TD><TH colspan=%d align='left'><A HREF='%s' TARGET=BLANK style='font-size:.9em;'>"
"Restriction Policy</A>", columnCount,ENCODE_DATA_RELEASE_POLICY);
printf("</TD></TR>\n");
printf("</TFOOT></TABLE>\n");
if (parentTdb == NULL)
printf("<script type='text/javascript'>{$(document).ready(function() {"
"sortTable.initialize($('table.sortable')[0],true,true);});}</script>\n");
if (timeIt)
uglyTime("Finished table");
return filesCount;
}
static int filesFindInDir(char *db, struct mdbObj **pmdbFiles, struct fileDb **pFileList,
char *fileType, int limit,boolean *exceededLimit)
// Prints list of files in downloads directories matching mdb search terms. Returns count
{
int fileCount = 0;
// Verify file existance and make fileList of those found
struct fileDb *fileList = NULL, *oneFile = NULL; // Will contain found files
struct mdbObj *mdbFiles = NULL; // Will caontain a list of mdbs for the found files
struct mdbObj *mdbList = *pmdbFiles;
while (mdbList && (limit == 0 || fileCount < limit))
{
boolean found = FALSE;
struct mdbObj *mdbFile = slPopHead(&mdbList);
char *composite = mdbObjFindValue(mdbFile,MDB_VAR_COMPOSITE);
if (composite == NULL)
{
mdbObjsFree(&mdbFile);
continue;
}
// First for FileName
char *fileName = mdbObjFindValue(mdbFile,MDB_VAR_FILENAME);
if (fileName == NULL)
{
mdbObjsFree(&mdbFile);
continue;
}
struct slName *fileSet = slNameListFromComma(fileName);
struct slName *md5Set = NULL;
char *md5sums = mdbObjFindValue(mdbFile,MDB_VAR_MD5SUM);
if (md5sums != NULL)
md5Set = slNameListFromComma(md5sums);
// Could be that "bai" is implicit with "bam"
if ((slCount(fileSet) == 1) && endsWith(fileSet->name,".bam"))
{
char buf[512];
safef(buf,sizeof(buf),"%s.bai",fileSet->name);
slNameAddTail(&fileSet, buf);
}
while (fileSet != NULL)
{
struct slName *file = slPopHead(&fileSet);
struct slName *md5 = NULL;
if (md5Set)
md5 = slPopHead(&md5Set);
oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, file->name);
if (oneFile == NULL)
{
slNameFree(&file);
if (md5)
slNameFree(&md5);
continue;
}
//warn("%s == %s",fileType,oneFile->fileType);
if (isEmpty(fileType)
|| sameWord(fileType,"Any")
|| ( oneFile->fileType
&& startsWithWordByDelimiter(fileType,'.',oneFile->fileType)))
// Starts with! This ensures both bam and bam.bai are found.
{
slAddHead(&fileList,oneFile);
if (found) // if already found then need two mdbObjs (assertable but this is metadata)
oneFile->mdb = mdbObjClone(mdbFile); // Yes clone this as differences will occur
else
oneFile->mdb = mdbFile;
if (md5 != NULL)
mdbObjSetVar(oneFile->mdb,MDB_VAR_MD5SUM,md5->name);
else
mdbObjRemoveOneVar(oneFile->mdb,MDB_VAR_MD5SUM,NULL);
slAddHead(&mdbFiles,oneFile->mdb);
found = TRUE;
fileCount++;
if (limit > 0 && fileCount >= limit)
{
slNameFreeList(&fileSet);
if (md5Set)
slNameFreeList(&md5Set);
break;
}
}
else
fileDbFree(&oneFile);
slNameFree(&file);
if (md5)
slNameFree(&md5);
}
// FIXME: This support of fileIndex should be removed when mdb is cleaned up.
// Now for FileIndexes
if (limit == 0 || fileCount < limit)
{
fileName = mdbObjFindValue(mdbFile,MDB_VAR_FILEINDEX);// This mdb var should be going away.
if (fileName == NULL)
continue;
// Verify existance first
oneFile = fileDbGet(db, ENCODE_DCC_DOWNLOADS, composite, fileName);
if (oneFile == NULL) // NOTE: won't be found if already found in comma delimited fileName!
continue;
if (isEmpty(fileType) || sameWord(fileType,"Any")
|| (oneFile->fileType && sameWord(fileType,oneFile->fileType))
|| (oneFile->fileType && sameWord(fileType,"bam") && sameWord("bam.bai",oneFile->fileType)))
{ // TODO: put fileType matching into search.c lib code to segregate index logic.
slAddHead(&fileList,oneFile);
if (found) // if already found then need two mdbObjs (assertable but this is metadata)
oneFile->mdb = mdbObjClone(mdbFile);
else
oneFile->mdb = mdbFile;
mdbObjRemoveOneVar(oneFile->mdb,MDB_VAR_MD5SUM,NULL);
slAddHead(&mdbFiles,oneFile->mdb);
fileCount++;
found = TRUE;
continue;
}
else
fileDbFree(&oneFile);
}
// FIXME: This support of fileIndex should be removed when mdb is cleaned up.
if (!found)
mdbObjsFree(&mdbFile);
}
*pmdbFiles = mdbFiles;
*pFileList = fileList;
if (exceededLimit != NULL)
*exceededLimit = FALSE;
if (mdbList != NULL)
{
if (exceededLimit != NULL)
*exceededLimit = TRUE;
mdbObjsFree(&mdbList);
}
return fileCount;
}
void filesDownloadUi(char *db, struct cart *cart, struct trackDb *tdb)
// UI for a "composite like" track: This will list downloadable files associated with
// a single trackDb entry (composite or of type "downloadsOnly". The list of files
// will have links to their download and have metadata information associated.
// The list will be a sortable table and there may be filtering controls.
{
timeIt = cartUsualBoolean(cart, "measureTiming",FALSE); // static to file
if (timeIt)
uglyTime("Starting file search");
boolean debug = cartUsualBoolean(cart,"debug",FALSE);
struct sqlConnection *conn = hAllocConn(db);
char *mdbTable = mdbTableName(conn,TRUE); // Look for sandBox name first
if (mdbTable == NULL)
errAbort("TABLE NOT FOUND: '%s.%s'.\n",db,MDB_DEFAULT_NAME);
// Get an mdbObj list of all that belong to this track and have a fileName
char buf[256];
safef(buf,sizeof(buf),"%s=%s %s=?",MDB_VAR_COMPOSITE,tdb->track,MDB_VAR_FILENAME);
struct mdbByVar *mdbVars = mdbByVarsLineParse(buf);
struct mdbObj *mdbList = mdbObjsQueryByVars(conn,mdbTable,mdbVars);
// Now get Indexes But be sure not to duplicate entries in the list!!!
safef(buf,sizeof(buf),"%s=%s %s= %s!=",MDB_VAR_COMPOSITE,tdb->track,
MDB_VAR_FILEINDEX,MDB_VAR_FILENAME);
mdbVars = mdbByVarsLineParse(buf);
mdbList = slCat(mdbList, mdbObjsQueryByVars(conn,mdbTable,mdbVars));
mdbObjRemoveHiddenVars(mdbList);
hFreeConn(&conn);
if (mdbList)
(void)mdbObjsFilter(&mdbList,"objStatus","re*",TRUE); // revoked, replaced, renamed
if (slCount(mdbList) == 0)
{
warn("No files specified in metadata for: %s\n%s",tdb->track,tdb->longLabel);
return;
}
if (timeIt)
uglyTime("Found %d mdb objects",slCount(mdbList));
// Verify file existance and make fileList of those found
struct fileDb *fileList = NULL; // Will contain found files
int fileCount = filesFindInDir(db, &mdbList, &fileList, NULL, 0, NULL);
if (timeIt)
uglyTime("Found %d files in dir",fileCount);
assert(fileCount == slCount(fileList));
if (fileCount == 0)
{
warn("No downloadable files currently available for: %s\n%s",tdb->track,tdb->longLabel);
return; // No files so nothing to do.
}
if (debug)
{
warn("The following files are in goldenPath/%s/%s/%s/ but NOT in the mdb:",
db,ENCODE_DCC_DOWNLOADS, tdb->track);
fileDbGet(db, ENCODE_DCC_DOWNLOADS, tdb->track, "listAll");
}
jsIncludeFile("hui.js",NULL);
jsIncludeFile("ajax.js",NULL);
// standard preamble
filesDownloadsPreamble(db,tdb);
// remove these now to get them out of the way
mdbObjRemoveVars(mdbList,MDB_VAR_FILENAME " " MDB_VAR_FILEINDEX " "
MDB_VAR_COMPOSITE " " MDB_VAR_PROJECT);
if (timeIt)
uglyTime("<BR>Removed 4 unwanted vars");
// Now update all files with their sortable fields and sort the list
mdbObjReorderByCv(mdbList,FALSE);// Start with cv defined order for visible vars.
// NOTE: will not need to reorder during print!
sortOrder_t *sortOrder = fileSortOrderGet(cart,tdb,mdbList);
int filterable = 0;
if (sortOrder != NULL)
{
int removed = removeCommonMdbVarsNotInSortOrder(mdbList,sortOrder);
if (removed && debug)
warn("%d terms are common and were removed",removed);
if (timeIt)
uglyTime("Removed %d common vars",removed);
// Fill in and sort fileList
fileDbSortList(&fileList,sortOrder);
if (timeIt)
uglyTime("Sorted %d files on %d columns",fileCount,sortOrder->count);
// FilterBoxes
filterable = filterBoxesForFilesList(db,mdbList,sortOrder);
if (timeIt && filterable)
uglyTime("Created filter boxes");
}
// Print table
filesPrintTable(db,tdb,fileList,sortOrder,filterable);
//fileDbFree(&fileList); // Why bother on this very long running cgi?
//mdbObjsFree(&mdbList);
}
int fileSearchResults(char *db, struct sqlConnection *conn, struct cart *cart,
struct slPair *varValPairs, char *fileType)
// Prints list of files in downloads directories matching mdb search terms. Returns count
{
timeIt = cartUsualBoolean(cart, "measureTiming",FALSE); // static to file
if (timeIt)
uglyTime("Starting file search");
struct sqlConnection *connLocal = conn;
if (conn == NULL)
connLocal = hAllocConn(db);
struct mdbObj *mdbList = mdbObjRepeatedSearch(connLocal,varValPairs,FALSE,TRUE);
if (conn == NULL)
hFreeConn(&connLocal);
mdbObjRemoveHiddenVars(mdbList);
if (mdbList)
(void)mdbObjsFilter(&mdbList,"objStatus","re*",TRUE); // revoked, replaced, renamed
if (slCount(mdbList) == 0)
{
printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n");
return 0;
}
if (timeIt)
uglyTime("Found %d mdb objects",slCount(mdbList));
// Now sort mdbObjs so that composites will stay together & lookup of files will be most efficient
mdbObjsSortOnVars(&mdbList, MDB_VAR_COMPOSITE);
#define FOUND_FILE_LIMIT 1000
struct fileDb *fileList = NULL; // Will contain found files
int filesExpected = slCount(mdbList);
boolean exceededLimit = FALSE;
int fileCount = filesFindInDir(db, &mdbList, &fileList, fileType, FOUND_FILE_LIMIT, &exceededLimit);
if (timeIt)
uglyTime("Found %d files in dir",fileCount);
assert(fileCount == slCount(fileList));
if (fileCount == 0)
{
printf("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\n");
return 0; // No files so nothing to do.
}
// remove these now to get them out of the way
mdbObjRemoveVars(mdbList,MDB_VAR_FILENAME " " MDB_VAR_FILEINDEX " "
MDB_VAR_PROJECT " " MDB_VAR_TABLENAME);
if (timeIt)
uglyTime("Removed 4 unwanted vars");
// Now update all files with their sortable fields and sort the list
mdbObjReorderByCv(mdbList,FALSE);// Start with cv defined order for visible vars.
// NOTE: will not need to reorder during print!
sortOrder_t *sortOrder = fileSortOrderGet(NULL,NULL,mdbList); // No cart, no tdb
if (sortOrder != NULL)
{
// Fill in and sort fileList
fileDbSortList(&fileList,sortOrder);
if (timeIt)
uglyTime("Sorted %d files on %d columns",fileCount,sortOrder->count);
}
// Print table
printf("<DIV id='filesFound'>");
if (exceededLimit)
{
// What is the expected count? Difficult to say because of comma delimited list in fileName.
if (filesExpected <= FOUND_FILE_LIMIT)
filesExpected = FOUND_FILE_LIMIT + 1;
printf("<DIV class='redBox' style='width: 380px;'>Too many files found. Displaying first "
"%d of at least %d.<BR>Narrow search parameters and try again.</DIV><BR>\n",
fileCount,filesExpected);
}
// 0=No columns 'filtered' on file search page
fileCount = filesPrintTable(db,NULL,fileList,sortOrder,0);
printf("</DIV><BR>\n");
//fileDbFree(&fileList); // Why bother on this very long running cgi?
//mdbObjsFree(&mdbList);
return fileCount;
}