7466d1654758a960990796f5c049e09e475f7766
tdreszer
Thu Dec 1 17:12:06 2011 -0800
More timing in hgFileUi and hgFileSearch led to important efficiency changes. Most notable, I am relying upon cached rsync results now to improve speed.
diff --git src/hg/hgFileSearch/hgFileSearch.c src/hg/hgFileSearch/hgFileSearch.c
index 2fc6832..0b33da2 100644
--- src/hg/hgFileSearch/hgFileSearch.c
+++ src/hg/hgFileSearch/hgFileSearch.c
@@ -1,471 +1,471 @@
#include "common.h"
#include "hash.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "jsHelper.h"
#include "trackDb.h"
#include "hdb.h"
#include "web.h"
#include "mdb.h"
#include "hCommon.h"
#include "hui.h"
#include "fileUi.h"
#include "search.h"
#include "cart.h"
#include "grp.h"
#define FAKE_MDB_MULTI_SELECT_SUPPORT
struct hash *trackHash = NULL; // Is this needed?
boolean measureTiming = FALSE; /* DON'T EDIT THIS -- use CGI param "&measureTiming=." . */
#define FILE_SEARCH_WHAT "Downloadable ENCODE Files"
#define FILE_SEARCH_NAME FILE_SEARCH_WHAT " Search"
#define FILE_SEARCH "hgfs_Search"
#define FILE_SEARCH_FORM "fileSearch"
#define FILE_SEARCH_CURRENT_TAB "fsCurTab"
#define FILE_SEARCH_ON_FILETYPE "fsFileType"
// These are common with trackSearch. Should they be?
#define TRACK_SEARCH_SIMPLE "tsSimple"
#define TRACK_SEARCH_ON_NAME "tsName"
#define TRACK_SEARCH_ON_GROUP "tsGroup"
#define TRACK_SEARCH_ON_DESCR "tsDescr"
#define TRACK_SEARCH_SORT "tsSort"
//#define USE_TABS
static struct trackDb *tdbFilterBy(struct trackDb **pTdbList, char *name, char *description, char *group)
// returns tdbs that match supplied criterion, leaving unmatched in list passed in
{
// Set the word lists up once
struct slName *nameList = NULL;
if (name)
nameList = slNameListOfUniqueWords(cloneString(name),TRUE); // TRUE means respect quotes
struct slName *descList = NULL;
if (description)
descList = slNameListOfUniqueWords(cloneString(description),TRUE);
struct trackDb *tdbList = *pTdbList;
struct trackDb *tdbRejects = NULL;
struct trackDb *tdbMatched = NULL;
while (tdbList != NULL)
{
struct trackDb *tdb = slPopHead(&tdbList);
if (!tdbIsComposite(tdb))
slAddHead(&tdbRejects,tdb);
else if (group && differentString(tdb->grp,group))
slAddHead(&tdbRejects,tdb);
else if (name && !searchNameMatches(tdb, nameList))
slAddHead(&tdbRejects,tdb);
else if (description && !searchDescriptionMatches(tdb, descList))
slAddHead(&tdbRejects,tdb);
else
slAddHead(&tdbMatched,tdb);
}
*pTdbList = tdbRejects;
//warn("matched %d tracks",slCount(tdbMatched));
return tdbMatched;
}
static boolean mdbSelectsAddFoundComposites(struct slPair **pMdbSelects,struct trackDb *tdbsFound)
// Adds a composite mdbSelect (if found in tdbsFound) to the head of the pairs list.
// If tdbsFound is NULL, then add dummy composite search criteria
{
// create comma separated list of composites
struct dyString *dyComposites = dyStringNew(256);
struct trackDb *tdb = tdbsFound;
for(;tdb != NULL; tdb = tdb->next)
{
if (tdbIsComposite(tdb))
dyStringPrintf(dyComposites,"%s,",tdb->track);
else if (tdbIsCompositeChild(tdb))
{
struct trackDb *composite = tdbGetComposite(tdb);
dyStringPrintf(dyComposites,"%s,",composite->track);
}
}
if (dyStringLen(dyComposites) > 0)
{
char *composites = dyStringCannibalize(&dyComposites);
composites[strlen(composites) - 1] = '\0'; // drop the last ','
//warn("Found composites: %s",composites);
slPairAdd(pMdbSelects,MDB_VAR_COMPOSITE,composites); // Composite should not already be in the list, because it is only indirectly sortable
return TRUE;
}
//warn("No composites found");
dyStringFree(&dyComposites);
return FALSE;
}
#ifdef USE_TABS
static struct slRef *simpleSearchForTdbs(struct trix *trix,char **descWords,int descWordCount)
// Performs the simple search and returns the found tracks.
{
struct slRef *foundTdbs = NULL;
struct trixSearchResult *tsList;
for(tsList = trixSearch(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next)
{
struct trackDb *tdb = (struct track *) hashFindVal(trackHash, tsList->itemId);
if (track != NULL) // It is expected that this is NULL (e.g. when the trix references trackDb tracks which have no tables)
{
refAdd(&foundTdbs, tdb);
}
}
return foundTdbs;
}
#endif///def USE_TABS
struct slName *tdbListGetGroups(struct trackDb *tdbList)
// Returns a list of groups found in the tdbList
// FIXME: Should be moved to trackDbCustom and shared
{
struct slName *groupList = NULL;
char *lastGroup = "[]";
struct trackDb *tdb = tdbList;
for(;tdb!=NULL;tdb=tdb->next)
{
if (differentString(lastGroup,tdb->grp))
lastGroup = slNameStore(&groupList, tdb->grp);
}
return groupList;
}
struct grp *groupsFilterForTdbList(struct grp **grps,struct trackDb *tdbList)
{
struct grp *grpList = *grps;
*grps = NULL;
struct slName *tdbGroups = tdbListGetGroups(tdbList);
if (tdbList == NULL)
return *grps;
while (grpList != NULL)
{
struct grp *grp = slPopHead(&grpList);
if (slNameInList(tdbGroups,grp->name))
slAddHead(grps,grp);
}
slNameFreeList(&tdbGroups);
slReverse(grps);
return *grps;
}
static void doFileSearch(char *db,char *organism,struct cart *cart,struct trackDb *tdbList)
{
struct sqlConnection *conn = hAllocConn(db);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (!sqlTableExists(conn, "metaDb"))
{
warn("Assembly %s %s does not support Downloadable Files search.", organism, hFreezeFromDb(db));
hFreeConn(&conn);
return;
}
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
char *descSearch=NULL;
char *fileTypeSearch = cartOptionalString(cart, FILE_SEARCH_ON_FILETYPE);
boolean doSearch = sameWord(cartUsualString(cart, FILE_SEARCH,"no"), "search");
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean searchTermsExist = FALSE; // FIXME: Why is this needed?
int cols;
#ifdef USE_TABS
enum searchTab selectedTab = simpleTab;
char *currentTab = cartUsualString(cart, FILE_SEARCH_CURRENT_TAB, "simpleTab");
if(sameString(currentTab, "simpleTab"))
{
selectedTab = simpleTab;
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
freez(&nameSearch);
}
else if(sameString(currentTab, "filesTab"))
{
selectedTab = filesTab;
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
}
#else///ifndef USE_TABS
enum searchTab selectedTab = filesTab;
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
#endif///ndef USE_TABS
#ifdef USE_TABS
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
getSearchTrixFile(db, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
#endif///def USE_TABS
printf("
");
// FIXME: Do we need a form at all?
printf("\n");
printf("
"); // Restricts to max-width:1000px;
cgiDown(0.8);
if (measureTiming)
- uglyTime("Rendered tabs");
+ uglyTime("Generated search controls");
#ifdef USE_TABS
if (doSearch && selectedTab==simpleTab && isEmpty(descSearch))
doSearch = FALSE;
#endif///def USE_TABS
if(doSearch)
{
// Now search
#ifdef USE_TABS
struct slRef *foundTdbs = NULL;
if(selectedTab==simpleTab)
{
foundTdbs = simpleSearchForTdbs(trix,descWords,descWordCount);
// What to do now?
if (measureTiming)
uglyTime("Searched for tracks");
// Sort and Print results
if(selectedTab!=filesTab)
{
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
int tracksFound = slCount(foundTdbs);
if(tracksFound > 1)
findTracksSort(&tracks,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
if (measureTiming)
uglyTime("Displayed found files");
}
}
else if(selectedTab==filesTab && mdbPairs != NULL)
#endif///def USE_TABS
{
if (nameSearch || descSearch || groupSearch)
{ // Use nameSearch, descSearch and groupSearch to narrow down the list of composites.
if (isNotEmpty(nameSearch) || isNotEmpty(descSearch) || isNotEmpty(groupSearch))
{
struct trackDb *tdbList = hTrackDb(db);
struct trackDb *tdbsMatch = tdbFilterBy(&tdbList, nameSearch, descSearch, groupSearch);
// Now we have a list of tracks, so we need a unique list of composites to add to mdbSelects
doSearch = mdbSelectsAddFoundComposites(&mdbSelects,tdbsMatch);
}
}
if (doSearch && mdbSelects != NULL && isNotEmpty(fileTypeSearch))
- fileSearchResults(db, conn, mdbSelects, fileTypeSearch);
+ fileSearchResults(db, conn, cart, mdbSelects, fileTypeSearch);
else
printf("
No files found.
\n");
if (measureTiming)
uglyTime("Searched for files");
}
slPairFreeList(&mdbSelects);
}
hFreeConn(&conn);
webNewSection("About " FILE_SEARCH_NAME);
printf("Search for downloadable ENCODE files by entering search terms in "
"the Track name or Description fields and/or by making selections with "
"the group, data format, and/or ENCODE metadata drop-downs.");
printf(" more help\n");
webEndSectionTables();
}
void doMiddle(struct cart *cart)
/* Write body of web page. */
{
struct trackDb *tdbList = NULL;
char *organism = NULL;
char *db = NULL;
getDbAndGenome(cart, &db, &organism, NULL);
char *chrom = cartUsualString(cart, "c", hDefaultChrom(db));
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
// QUESTION: Do We need track list ??? trackHash ??? Can't we just get one track and no children
trackHash = trackHashMakeWithComposites(db,chrom,&tdbList,FALSE);
cartWebStart(cart, db, "Search for " FILE_SEARCH_WHAT " in the %s %s Assembly", organism, hFreezeFromDb(db));
// This cleverness allows us to have the background image like "Track Search" does, without all the hgTracks overhead
printf("",hBackgroundImage());
webIncludeResourceFile("HGStyle.css");
webIncludeResourceFile("jquery-ui.css");
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("ui.dropdownchecklist.js",NULL);
jsIncludeFile("utils.js",NULL);
// This line is needed to get the multi-selects initialized
#ifdef NEW_JQUERY
jsIncludeFile("ddcl.js",NULL);
printf("\n");
printf("\n");
#else///ifndef NEW_JQUERY
printf("\n");
printf("\n");
#endif///ndef NEW_JQUERY
doFileSearch(db,organism,cart,tdbList);
printf(" \n");
webEnd();
}
-char *excludeVars[] = { "submit", "Submit", "g", "ajax", FILE_SEARCH,TRACK_SEARCH_ADD_ROW,TRACK_SEARCH_DEL_ROW}; // HOW IS 'ajax" going to be supported?
+char *excludeVars[] = { "submit", "Submit", "g", "ajax", "clearCache", FILE_SEARCH,TRACK_SEARCH_ADD_ROW,TRACK_SEARCH_DEL_ROW}; // HOW IS 'ajax" going to be supported?
int main(int argc, char *argv[])
/* Process command line. */
{
cgiSpoof(&argc, argv);
htmlSetBackground(hBackgroundImage());
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, NULL);
return 0;
}
// TODO:
// 1) Done: Limit to first 1000
// 2) Work out simple verses advanced tabs
// 3) work out support for non-encode downloads
// 4) Make an hgTrackSearch to replace hgTracks track search ?? Simlpler code, but may not be good idea because of composite reshaping in cart vars