e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/hgFileSearch/hgFileSearch.c src/hg/hgFileSearch/hgFileSearch.c
index 8591658..09feb6c 100644
--- src/hg/hgFileSearch/hgFileSearch.c
+++ src/hg/hgFileSearch/hgFileSearch.c
@@ -1,485 +1,488 @@
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #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 ','
     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&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='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&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='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&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, mdbVars);
     char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols,TRUE); // just for fileSearch
     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("</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("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
                 doSearch = mdbSelectsAddFoundComposites(&mdbSelects,tdbsMatch);
                 }
             }
 
         if (doSearch && mdbSelects != NULL && isNotEmpty(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");
 }
 
 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));
 
 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
 jsIncludeFile("ddcl.js",NULL);
 printf("<script type='text/javascript'>$(document).ready(function() "
        "{ findTracks.updateMdbHelp(0); });</script>\n");
 
 doFileSearch(db,organism,cart,tdbList);
 
 
 printf("<BR>\n");
 webEnd();
 }
 
 char *excludeVars[] = { "submit", "Submit", "g", "ajax", "clearCache", 
                         FILE_SEARCH,TRACK_SEARCH_ADD_ROW,TRACK_SEARCH_DEL_ROW};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 long enteredMainTime = clock1000();
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, NULL);
 cgiExitTime("hgFileSearch", enteredMainTime);
 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 ??   
 //    Simpler code, but may not be good idea because of composite reshaping in cart vars