26cebe44005d181116b3a85bc8d999aadbd606dc
angie
  Mon Mar 14 16:10:48 2011 -0700
Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
diff --git src/hg/hgFileSearch/hgFileSearch.c src/hg/hgFileSearch/hgFileSearch.c
index 226e8ae..952f499 100644
--- src/hg/hgFileSearch/hgFileSearch.c
+++ src/hg/hgFileSearch/hgFileSearch.c
@@ -1,472 +1,472 @@
 #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 "searchTracks.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              "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
 //#define SUPPORT_COMPOSITE_SEARCH
 
 #ifdef OMIT_SUPPORT_COMPOSITE_SEARCH
 // make a matchString function to support "contains", "is" etc. and wildcards in contains
 
 //    ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) ||
 
 static boolean isNameMatch(struct trackDb *tdb, char *str, char *op)
 {
 return str && strlen(str) &&
     ((sameString(op, "is") && !strcasecmp(tdb->shortLabel, str)) ||
     (sameString(op, "is") && !strcasecmp(tdb->longLabel, str)) ||
     (sameString(op, "contains") && containsStringNoCase(tdb->shortLabel, str) != NULL) ||
     (sameString(op, "contains") && containsStringNoCase(tdb->longLabel, str) != NULL));
 }
 
 static boolean isDescriptionMatch(struct trackDb *tdb, char **words, int wordCount)
 // We parse str and look for every word at the start of any word in track description (i.e. google style).
 {
 if(words)
     {
     // We do NOT lookup up parent hierarchy for html descriptions.
     char *html = tdb->html;
     if(!isEmpty(html))
         {
         // This probably could be made more efficient by parsing the html into some kind of b-tree, but I am assuming
         // that the inner html loop while only happen for 1-2 words for vast majority of the tracks.
 
         int i, numMatches = 0;
         html = stripRegEx(html, "<[^>]*>", REG_ICASE);
         for(i = 0; i < wordCount; i++)
             {
             char *needle = words[i];
             char *haystack, *tmp = cloneString(html);
             boolean found = FALSE;
             while((haystack = nextWord(&tmp)))
                 {
                 char *ptr = strstrNoCase(haystack, needle);
                 if(ptr != NULL && ptr == haystack)
                     {
                     found = TRUE;
                     break;
                     }
                 }
             if(found)
                 numMatches++;
             else
                 break;
             }
         if(numMatches == wordCount)
             return TRUE;
         }
     }
 return FALSE;
 }
 #endif///def SUPPORT_COMPOSITE_SEARCH
 
 #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 movedf 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;
 }
 
 void doSearch(char *db,char *organism,struct cart *cart,struct trackDb *tdbList)
 {
 if (!advancedJavascriptFeaturesEnabled(cart))
     {
     warn("Requires advanced javascript features.");
     return;
     }
 #ifdef SUPPORT_COMPOSITE_SEARCH
 char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
 #endif///def SUPPORT_COMPOSITE_SEARCH
 char *fileTypeSearch = cartOptionalString(cart, FILE_SEARCH_ON_FILETYPE);
 char *descSearch=FALSE;
 boolean doSearch = sameWord(cartUsualString(cart, FILE_SEARCH,"no"), "search");
 struct sqlConnection *conn = hAllocConn(db);
 boolean metaDbExists = sqlTableExists(conn, "metaDb");
 #ifdef ONE_FUNC
 struct hash *parents = newHash(4);
 #endif///def ONE_FUNC
 char **descWords = NULL;
 int descWordCount = 0;
 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);
     #ifdef SUPPORT_COMPOSITE_SEARCH
     freez(&nameSearch);
     #endif///def SUPPORT_COMPOSITE_SEARCH
     }
 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
 
 if(descSearch)
     stripChar(descSearch, '"');
 
 #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='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),FILE_SEARCH_FORM,FILE_SEARCH_FORM);
 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
 //safef(buf, sizeof(buf), "%lu", clock1());
 //cgiMakeHiddenVar("hgt_", buf);  // timestamps page to avoid browser cache
 
 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("</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");
 //#else///ifndef USE_TABS
 //printf("<div id='noTabs' style='width:1060px;'>\n");//,cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
 #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;
 
 #ifdef SUPPORT_COMPOSITE_SEARCH
 //// 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;
 #endif///def SUPPORT_COMPOSITE_SEARCH
 
 // Track Type is (drop down)
 #ifdef SUPPORT_COMPOSITE_SEARCH
 printf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>\n");
 #else///ifndef SUPPORT_COMPOSITE_SEARCH
 printf("<tr><td colspan=2></td><td align='right'>&nbsp;</td>\n");
 #endif///ndef SUPPORT_COMPOSITE_SEARCH
 //printf("<tr><td colspan=2></td><td align='right'>and&nbsp;</td>\n"); // Bring back "and" if using "Track Name,Description or Group
 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 = mdbVarsRelevant(conn);
     mdbSelects = mdbSelectPairs(cart,selectedTab, mdbVars);
     char *output = mdbSelectsHtmlRows(conn,mdbSelects,mdbVars,cols);
     if (output)
         {
-        printf(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
 
 printf("</form>\n");
 printf("</div>"); // Restricts to max-width:1000px;
 
 if (measureTiming)
     uglyTime("Rendered tabs");
 
 if(descSearch != NULL && !strlen(descSearch))
     descSearch = NULL;
 #ifdef SUPPORT_COMPOSITE_SEARCH
 if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
     groupSearch = NULL;
 #endif///def SUPPORT_COMPOSITE_SEARCH
 
 if(!isEmpty(descSearch))
     {
     char *tmp = cloneString(descSearch);
     char *val = nextWord(&tmp);
     struct slName *el, *descList = NULL;
     int i;
     while (val != NULL)
         {
         slNameAddTail(&descList, val);
         descWordCount++;
         val = nextWord(&tmp);
         }
     descWords = needMem(sizeof(char *) * descWordCount);
     for(i = 0, el = descList; el != NULL; i++, el = el->next)
         descWords[i] = strLower(el->name);
     }
 if (doSearch && selectedTab==simpleTab && descWordCount <= 0)
     doSearch = FALSE;
 
 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
         {
         fileSearchResults(db, conn, mdbSelects, fileTypeSearch);
         if (measureTiming)
             uglyTime("Searched for files");
         }
 
     slPairFreeList(&mdbSelects);
     }
 hFreeConn(&conn);
 
 webNewSection("About Downloadable Files Search");
 if(metaDbExists)
     printf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
             "metadata.  If multiple terms are entered, only tracks with all terms "
             "will be part of the results.");
 else
     printf("<p>Search for terms in track descriptions, groups, and names. "
             "If multiple terms are entered, only tracks with all terms "
             "will be part of the results.");
 printf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\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 Downloadable Files 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.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) { $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true });});});</script>\n");
 printf("<script type='text/javascript'>$(document).ready(function() { updateMetaDataHelpLinks(0);  $('.filterBy').each( function(i) { $(this).dropdownchecklist({ firstItemChecksAll: true, noneIsAll: true });});});</script>\n");
 
 doSearch(db,organism,cart,tdbList);
 
 
 printf("<BR>\n");
 webEnd();
 }
 
 char *excludeVars[] = { "submit", "Submit", "g", NULL, "ajax", NULL,};  // 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) SORT OF: Work out strangeness with dropdownchecklist and use in hgTracks (By some miracle multiselect is working in my hgTracks)
 // 3) Work out support for selecting composites and limiting search to those
 // 4) Work out simple verses advanced tabs
 // 5) work out support for non-encode downloads
 // 6) Make an hgTrackSearch to replces hgTracks track search ??   Silpler code, but may not be good idea.