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("<div style='max-width:1080px;'>"); // FIXME: Do we need a form at all? printf("<form action='../cgi-bin/hgFileSearch' name='%s' id='%s' method='get'>\n\n", FILE_SEARCH_FORM,FILE_SEARCH_FORM); cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo printf("<input type='hidden' name='db' value='%s'>\n", db); printf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW); printf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW); #ifdef USE_TABS printf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", FILE_SEARCH_CURRENT_TAB, currentTab); printf("<div id='tabs' style='display:none; %s'>\n" "<ul>\n" "<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n" "<li><a href='#filesTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Files</B></a></li>\n" "</ul>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;"); // Files tab printf("<div id='simpleTab' style='max-width:inherit;'>\n"); printf("<table id='simpleTable' style='width:100%%; font-size:.9em;'><tr><td colspan='2'>"); printf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracks.searchButtonsEnable(true);'>\n", TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch); if (selectedTab==simpleTab && descSearch) searchTermsExist = TRUE; printf("</td></tr><td style='max-height:4px;'></td></tr></table>"); printf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", FILE_SEARCH); printf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracks.clear();'>\n"); printf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n"); printf("</div>\n"); #endif///def USE_TABS // Files tab printf("<div id='filesTab' style='width:inherit;'>\n" "<table id='filesTable' cellSpacing=0 style='width:inherit; font-size:.9em;'>\n"); cols = 8; // Track Name contains printf("<tr><td colspan=3></td>"); printf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>"); printf("<td align='right'>contains</td>\n"); printf("<td colspan='%d'>", cols - 4); printf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracks.searchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>", TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch); printf("</td></tr>\n"); // Description contains printf("<tr><td colspan=2></td><td align='right'>and </td>"); printf("<td><b style='max-width:100px;'>Description:</b></td>"); printf("<td align='right'>contains</td>\n"); printf("<td colspan='%d'>", cols - 4); printf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracks.searchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>", TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch); printf("</td></tr>\n"); if (selectedTab==filesTab && descSearch) searchTermsExist = TRUE; // Set up Group dropdown struct grp *grps = hLoadGrps(db); grps = groupsFilterForTdbList(&grps,tdbList); int numGroups = slCount(grps) + 1; // Add Any char **groups = needMem(sizeof(char *) * numGroups); char **labels = needMem(sizeof(char *) * numGroups); groups[0] = ANYLABEL; labels[0] = ANYLABEL; int ix=1; struct grp *grp = grps; for (; grp != NULL; grp = grp->next,ix++) { groups[ix] = cloneString(grp->name); labels[ix] = cloneString(grp->label); } printf("<tr><td colspan=2></td><td align='right'>and </td>\n"); printf("<td><b style='max-width:100px;'>Group:</b></td>"); printf("<td align='right'>is</td>\n"); printf("<td colspan='%d'>", cols - 4); char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP); cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'"); printf("</td></tr>\n"); if (selectedTab==filesTab && groupSearch) searchTermsExist = TRUE; // Track Type is (drop down) printf("<tr><td colspan=2></td><td align='right'>and </td>\n"); printf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>"); printf("<td align='right'>is</td>\n"); printf("<td colspan='%d'>", cols - 4); char *dropDownHtml = fileFormatSelectHtml(FILE_SEARCH_ON_FILETYPE,fileTypeSearch,"style='min-width:40%; font-size:.9em;'"); if (dropDownHtml) { puts(dropDownHtml); freeMem(dropDownHtml); } printf("</td></tr>\n"); if (selectedTab==filesTab && fileTypeSearch) searchTermsExist = TRUE; // mdb selects struct slPair *mdbSelects = NULL; if(metaDbExists) { struct slPair *mdbVars = mdbVarsSearchable(conn,FALSE,TRUE); // Not tables, just files mdbSelects = mdbSelectPairs(cart, mdbVars); char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,TRUE); // restricted to file search if (output) { puts(output); freeMem(output); } slPairFreeList(&mdbVars); } printf("</table>\n"); printf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", FILE_SEARCH); printf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracks.clear();'>\n"); printf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n"); //printf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n"); printf("</div>\n"); #ifdef USE_TABS printf("</div>\n"); // End tabs div #endif///def USE_TABS if(nameSearch != NULL && !strlen(nameSearch)) nameSearch = NULL; if(descSearch != NULL && !strlen(descSearch)) descSearch = NULL; if(groupSearch != NULL && sameString(groupSearch, ANYLABEL)) groupSearch = NULL; printf("</form>\n"); printf("</div>"); // 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("<DIV id='filesFound'><BR>No files found.<BR></DIV><BR>\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("<BR><a target='_blank' href='../goldenPath/help/fileSearch.html'>more help</a>\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("<style type='text/css'>body {background-image:url('%s');}</style>",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("<script type='text/javascript'>var newJQuery=true;</script>\n"); printf("<script type='text/javascript'>$(document).ready(function() { findTracks.updateMdbHelp(0); });</script>\n"); #else///ifndef NEW_JQUERY printf("<script type='text/javascript'>var newJQuery=false;</script>\n"); printf("<script type='text/javascript'>$(document).ready(function() { findTracks.updateMdbHelp(0); $('.filterBy').each( function(i) { $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });});});</script>\n"); #endif///ndef NEW_JQUERY doFileSearch(db,organism,cart,tdbList); printf("<BR>\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