70ef68d210fa4b76c16f7b8e8142a8180f75052a
tdreszer
  Fri Jun 17 20:14:06 2011 -0700
Big checkin of jquery 1.5.1, jquery-ui 1.8 and ui-dropdownchecklist 1.3.  Needs more testing and CSS work.  DDCL is working on FF, Chrome and IE.  Both Chrome and IE support required tiny changes to the DDCL wigit code.  DDCL may still have problems with IE.  Other jquery wigits have been tested at a cursory level and work fine.  Ajax calls may need an extrat dataType: html param.  Dialog (popup) needs CSS tuning.
diff --git src/hg/hgFileSearch/hgFileSearch.c src/hg/hgFileSearch/hgFileSearch.c
index a305083..1eaa456 100644
--- src/hg/hgFileSearch/hgFileSearch.c
+++ src/hg/hgFileSearch/hgFileSearch.c
@@ -1,471 +1,476 @@
 #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)
 {
 if (!advancedJavascriptFeaturesEnabled(cart))
     {
     warn("Requires advanced javascript features.");
     return;
     }
 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='findTracksSearchButtonsEnable(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='findTracksClear();'>\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&nbsp;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='findTracksSearchButtonsEnable(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&nbsp;</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='findTracksSearchButtonsEnable(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&nbsp;</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&nbsp;</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,selectedTab, 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='findTracksClear();'>\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");
 
 
 #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);
         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.core.js",NULL);   // NOTE: This appears to be not needed as long as jquery-ui.js comes before ui.dropdownchecklist.js
 jsIncludeFile("ui.dropdownchecklist.js",NULL);
 jsIncludeFile("utils.js",NULL);
 
 // This line is needed to get the multi-selects initialized
-//printf("<script type='text/javascript'>$(document).ready(function() { setTimeout('updateMetaDataHelpLinks(0);',50);  $('.filterBy').each( function(i) { $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true, maxDropHeight: filterByMaxHeight(this) });});});</script>\n");
+#ifdef NEW_JQUERY
+printf("<script type='text/javascript'>var newJQuery=true;</script>\n");
+printf("<script type='text/javascript'>$(document).ready(function() { updateMetaDataHelpLinks(0);  $('.filterBy').each( function(i) { ddclSetup(this,'noneIsAll') });});</script>\n");
+#else///ifndef NEW_JQUERY
+printf("<script type='text/javascript'>var newJQuery=false;</script>\n");
 printf("<script type='text/javascript'>$(document).ready(function() { updateMetaDataHelpLinks(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?
 
 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