4a234f089be336a40604bf7002b3811dc3dad308
kent
  Mon Aug 9 14:58:47 2010 -0700
Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table.  Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
diff --git src/hg/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c
index f63b995..c429a4e 100644
--- src/hg/hgTracks/searchTracks.c
+++ src/hg/hgTracks/searchTracks.c
@@ -1,542 +1,543 @@
 /* Track search code used by hgTracks CGI */
 
 #include "common.h"
 #include "searchTracks.h"
 #include "hCommon.h"
 #include "memalloc.h"
 #include "obscure.h"
 #include "dystring.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "hPrint.h"
 #include "htmshell.h"
 #include "cart.h"
 #include "hgTracks.h"
 #include "web.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "trix.h"
 #include "jsHelper.h"
 
 static char const rcsid[] = "$Id: searchTracks.c,v 1.11 2010/06/11 18:21:40 larrym Exp $";
 
 #define ANYLABEL "Any"
 #define METADATA_NAME_PREFIX "hgt.metadataName"
 #define METADATA_VALUE_PREFIX "hgt.metadataValue"
 
 static int gCmpGroup(const void *va, const void *vb)
 /* Compare groups based on label. */
 {
 const struct group *a = *((struct group **)va);
 const struct group *b = *((struct group **)vb);
 return strcmp(a->label, b->label);
 }
 
 static int gCmpTrack(const void *va, const void *vb)
 /* Compare tracks based on longLabel. */
 {
 const struct slRef *aa = *((struct slRef **)va);
 const struct slRef *bb = *((struct slRef **)vb);
 const struct track *a = ((struct track *) aa->val);
 const struct track *b = ((struct track *) bb->val);
 return strcmp(a->longLabel, b->longLabel);
 }
 
 // XXXX make a matchString function to support "contains", "is" etc. and wildcards in contains
 
 //    ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) ||
 
 static boolean isNameMatch(struct track *track, char *str, char *op)
 {
 return str && strlen(str) &&
     ((sameString(op, "is") && !strcasecmp(track->shortLabel, str)) ||
     (sameString(op, "is") && !strcasecmp(track->longLabel, str)) ||
     (sameString(op, "contains") && containsStringNoCase(track->shortLabel, str) != NULL) ||
     (sameString(op, "contains") && containsStringNoCase(track->longLabel, str) != NULL));
 }
 
 static boolean isDescriptionMatch(struct track *track, 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 = track->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;
 }
 
 static int getTermArray(struct sqlConnection *conn, char ***terms, char *type)
 // Pull out all term fields from ra entries with given type
 // Returns count of items found and items via the terms argument.
 {
 struct sqlResult *sr = NULL;
 char **row = NULL;
 char query[256];
 struct slName *termList = NULL;
 int i, count = 0;
 char **retVal;
 
 safef(query, sizeof(query), "select distinct val from metaDb where var = '%s'", type);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     slNameAddHead(&termList, row[0]);
     count++;
     }
 sqlFreeResult(&sr);
 slSort(&termList, slNameCmpCase);
 count++; // make room for "Any"
 AllocArray(retVal, count);
 retVal[0] = cloneString(ANYLABEL);
 for(i = 1; termList != NULL;termList = termList->next, i++)
     {
     retVal[i] = cloneString(termList->name);
     }
 *terms = retVal;
 return count;
 }
 
 static struct slName *metaDbSearch(struct sqlConnection *conn, char *name, char *val, char *op)
 // Search the assembly's metaDb table for var; If name == NULL, we search every metadata field.
 // Search is via mysql, so it's case-insensitive.
 {
 struct slName *retVal = NULL;
 char query[256];
 struct sqlResult *sr = NULL;
 char **row = NULL;
 
 if(sameString(op, "contains"))
     if(name == NULL)
         safef(query, sizeof(query), "select obj from metaDb where val like  '%%%s%%'", val);
     else
         safef(query, sizeof(query), "select obj from metaDb where var = '%s' and val like  '%%%s%%'", name, val);
 else
     if(name == NULL)
         safef(query, sizeof(query), "select distinct obj from metaDb where val = '%s'", val);
     else
         safef(query, sizeof(query), "select obj from metaDb where var = '%s' and val = '%s'", name, val);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     slNameAddHead(&retVal, row[0]);
     }
 sqlFreeResult(&sr);
 return retVal;
 }
 
 static int metaDbVars(struct sqlConnection *conn, char *** metaValues)
 // Search the assemblies metaDb table; If name == NULL, we search every metadata field.
 {
 char query[256];
 struct sqlResult *sr = NULL;
 char **row = NULL;
 int i;
 struct slName *el, *varList = NULL;
 char **retVal;
 
 safef(query, sizeof(query), "select distinct var from metaDb");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     slNameAddHead(&varList, row[0]);
 sqlFreeResult(&sr);
 retVal = needMem(sizeof(char *) * slCount(varList));
 slNameSort(&varList);
 for (el = varList, i = 0; el != NULL; el = el->next, i++)
     retVal[i] = el->name;
 *metaValues = retVal;
 return i;
 }
 
 void doSearchTracks(struct group *groupList)
 {
 struct group *group;
 char *ops[] = {"is", "contains"};
 char *op_labels[] = {"is", "contains"};
 char *groups[128];
 char *labels[128];
 int numGroups = 1;
 groups[0] = ANYLABEL;
 labels[0] = ANYLABEL;
 char *currentTab = cartUsualString(cart, "hgt.currentSearchTab", "simpleTab");
 char *nameSearch = cartOptionalString(cart, "hgt.nameSearch");
 char *nameOp = cartOptionalString(cart, "hgt.nameOp");
 char *descSearch;
 char *groupSearch = cartOptionalString(cart, "hgt.groupSearch");
 boolean doSearch = sameString(cartOptionalString(cart, searchTracks), "Search");
 struct sqlConnection *conn = hAllocConn(database);
 boolean metaDbExists = sqlTableExists(conn, "metaDb");
 struct slRef *tracks = NULL;
 int numMetadataSelects, tracksFound = 0;
 int numMetadataNonEmpty = 0;
 char **metadataName;
 char **metadataValue;
 struct hash *parents = newHash(4);
 boolean simpleSearch;
 struct trix *trix;
 char trixFile[HDB_MAX_PATH_STRING];
 char **descWords = NULL;
 int descWordCount = 0;
 
 if(sameString(currentTab, "simpleTab"))
     {
     descSearch = cartOptionalString(cart, "hgt.simpleSearch");
     simpleSearch = TRUE;
     freez(&nameSearch);
     freez(&groupSearch);
     }
 else
     {
     descSearch = cartOptionalString(cart, "hgt.descSearch");
     simpleSearch = FALSE;
     }
 
 getSearchTrixFile(database, trixFile, sizeof(trixFile));
 trix = trixOpen(trixFile);
 getTrackList(&groupList, -2);
 slSort(&groupList, gCmpGroup);
 for (group = groupList; group != NULL; group = group->next)
     {
     if (group->trackList != NULL)
         {
         groups[numGroups] = cloneString(group->name);
         labels[numGroups] = cloneString(group->label);
         numGroups++;
         if (numGroups >= ArraySize(groups))
             internalErr();
         }
     }
 
 hPrintf("<form action='%s' name='SearchTracks' id='searchTracks' method='get'>\n\n", hgTracksName());
 
 webStartWrapperDetailedNoArgs(cart, database, "", "Track Search", FALSE, FALSE, FALSE, FALSE);
 
 hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
 hPrintf("<input type='hidden' name='hgt.currentSearchTab' id='currentSearchTab' value='%s'>\n", currentTab);
 
 hPrintf("<div id='tabs'>\n"
         "<ul>\n"
         "<li><a href='#simpleTab'><span>Search</span></a></li>\n"
         "<li><a href='#advancedTab'><span>Advanced Search</span></a></li>\n"
         "</ul>\n"
         "<div id='simpleTab'>\n");
 
 hPrintf("<input type='text' name='hgt.simpleSearch' id='simpleSearch' value='%s' size='80'>\n", descSearch == NULL ? "" : descSearch);
 
 hPrintf("</div>\n"
         "<div id='advancedTab'>\n"
         "<table>\n");
 
 hPrintf("<tr><td></td><td></td><td><b>Description:</b></td><td>contains</td>\n");
 hPrintf("<td><input type='text' name='hgt.descSearch' id='descSearch' value='%s' size='80'></td></tr>\n", descSearch == NULL ? "" : descSearch);
 
 hPrintf("<tr><td></td><td>and</td><td><b>Track Name:</b></td><td>\n");
 cgiMakeDropListFull("hgt.nameOp", op_labels, ops, ArraySize(ops), nameOp == NULL ? "contains" : nameOp, NULL);
 hPrintf("</td>\n<td><input type='text' name='hgt.nameSearch' id='nameSearch' value='%s'></td></tr>\n", nameSearch == NULL ? "" : nameSearch);
 
 hPrintf("<tr><td></td><td>and</td>\n");
 hPrintf("<td><b>Group</b></td><td>is</td>\n<td>\n");
 cgiMakeDropListFull("hgt.groupSearch", labels, groups, numGroups, groupSearch, NULL);
 hPrintf("</td></tr>\n");
 
 // figure out how many metadata selects are visible.
 
 for(numMetadataSelects = 0;;)
     {
     char buf[256];
     safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
     char *str = cartOptionalString(cart, buf);
     if(isEmpty(str))
         break;
     else
         numMetadataSelects++;
     }
 
 if(numMetadataSelects)
     {
     metadataName = needMem(sizeof(char *) * numMetadataSelects);
     metadataValue = needMem(sizeof(char *) * numMetadataSelects);
     int i;
     for(i = 0; i < numMetadataSelects; i++)
         {
         char buf[256];
         safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, i + 1);
         metadataName[i] = cartOptionalString(cart, buf);
         if(!simpleSearch)
             {
             safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, i + 1);
             metadataValue[i] = cartOptionalString(cart, buf);
             if(sameString(metadataValue[i], ANYLABEL))
                 metadataValue[i] = NULL;
             if(!isEmpty(metadataValue[i]))
                 numMetadataNonEmpty++;
             }
         }
     }
 else
     {
     // create defaults
     numMetadataSelects = 2;
     metadataName = needMem(sizeof(char *) * numMetadataSelects);
     metadataValue = needMem(sizeof(char *) * numMetadataSelects);
     metadataName[0] = "cell";
     metadataName[1] = "antibody";
     metadataValue[0] = ANYLABEL;
     metadataValue[1] = ANYLABEL;
     }
 
 if(metaDbExists)
     {
     int i;
     char **metaValues = NULL;
     int count = metaDbVars(conn, &metaValues);
 
     for(i = 0; i < numMetadataSelects; i++)
         {
         char **terms;
         char buf[256];
         int len;
 
         hPrintf("<tr><td>\n");
 
         if(i == 0)
             hPrintf("&nbsp;\n");
         else
             hButtonWithOnClick("hgt.ignoreme", "+", "add a select", "alert('add a select is not yet implemented'); return false;");
 
         hPrintf("</td><td>and</td>\n");
         hPrintf("</td><td>\n");
         safef(buf, sizeof(buf), "%s%i", METADATA_NAME_PREFIX, i + 1);
         cgiMakeDropListClassWithStyleAndJavascript(buf, metaValues, count, metadataName[i], 
                                                    NULL, NULL, "onchange=metadataSelectChanged(this)");
         hPrintf("</td><td>is</td>\n<td>\n");
         len = getTermArray(conn, &terms, metadataName[i]);
         safef(buf, sizeof(buf), "%s%i", METADATA_VALUE_PREFIX, i + 1);
         cgiMakeDropListFull(buf, terms, terms, len, metadataValue[i], NULL);
         hPrintf("</td></tr>\n");
         }
     }
 
 hPrintf("</table>\n");
 
 hPrintf("</div>\n</div>\n");
 
 hPrintf("<input type='submit' name='%s' id='searchSubmit' value='Search'>\n", searchTracks);
 hPrintf("<input type='submit' name='submit' value='Cancel'>\n");
 hPrintf("</form>\n");
 
 if(descSearch != NULL && !strlen(descSearch))
     descSearch = NULL;
 if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
     groupSearch = NULL;
 
 if(!isEmpty(descSearch))
     {
     char *tmp = cloneString(descSearch);
     char *val = nextWord(&tmp);
     struct slName *el, *descList = NULL;
     int i;
 
     while (val != NULL)
         {
         slNameAddTail(&descList, val);
         val = nextWord(&tmp);
         }
     descWordCount = slCount(descList);
     descWords = needMem(sizeof(char *) * descWordCount);
     for(i = 0, el = descList; el != NULL; i++, el = el->next)
         descWords[i] = strLower(el->name);
 
     }
 
 if(doSearch)
     {
     if(simpleSearch)
         {
         struct trixSearchResult *tsList;
         struct hash *trackHash = newHash(0);
 
         // Create a hash of tracks, so we can map the track name into a track struct.
         for (group = groupList; group != NULL; group = group->next)
             {
             struct trackRef *tr;
             for (tr = group->trackList; tr != NULL; tr = tr->next)
                 {
                 struct track *track = tr->track;
                 hashAdd(trackHash, track->track, track);
                 struct track *subTrack = track->subtracks;
                 for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
                     hashAdd(trackHash, subTrack->track, subTrack);
                 }
             }
         for(tsList = trixSearch(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next)
             {
             struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId);
             refAdd(&tracks, track);
             tracksFound++;
             }
         slReverse(&tracks);
         }
     else if(!isEmpty(nameSearch) || descSearch != NULL || groupSearch != NULL || numMetadataNonEmpty)
         {
         // First do the metaDb searches, which can be done quickly for all tracks with db queries.
         struct hash *matchingTracks = newHash(0);
         struct hash *trackMetadata = newHash(0);
         struct slName *el, *metaTracks = NULL;
         int i;
 
         for(i = 0; i < numMetadataSelects; i++)
             {
             if(!isEmpty(metadataValue[i]))
                 {
                 struct slName *tmp = metaDbSearch(conn, metadataName[i], metadataValue[i], "is");
                 if(metaTracks == NULL)
                     metaTracks = tmp;
                 else
                     metaTracks = slNameIntersection(metaTracks, tmp);
                 }
             }
         for (el = metaTracks; el != NULL; el = el->next)
             hashAddInt(matchingTracks, el->name, 1);
 
         if(metaDbExists && !isEmpty(descSearch))
             {
             // Load all metadata words for each track to facilitate metadata search.
             char query[256];
             struct sqlResult *sr = NULL;
             char **row;
             safef(query, sizeof(query), "select obj, val from metaDb");
             sr = sqlGetResult(conn, query);
             while ((row = sqlNextRow(sr)) != NULL)
                 {
                 char *str = cloneString(row[1]);
                 hashAdd(trackMetadata, row[0], str);
                 }
             sqlFreeResult(&sr);
             }
 
         for (group = groupList; group != NULL; group = group->next)
             {
             if(groupSearch == NULL || sameString(group->name, groupSearch))
                 {
                 if (group->trackList != NULL)
                     {
                     struct trackRef *tr;
                     for (tr = group->trackList; tr != NULL; tr = tr->next)
                         {
                         struct track *track = tr->track;
                         if((isEmpty(nameSearch) || isNameMatch(track, nameSearch, nameOp)) && 
                            (isEmpty(descSearch) || isDescriptionMatch(track, descWords, descWordCount)) &&
                            (!numMetadataNonEmpty || hashLookup(matchingTracks, track->track) != NULL))
                             {
                             tracksFound++;
                             refAdd(&tracks, track);
                             }
                         if (track->subtracks != NULL)
                             {
                             struct track *subTrack;
                             for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
                                 {
                                 if((isEmpty(nameSearch) || isNameMatch(subTrack, nameSearch, nameOp)) &&
                                    (isEmpty(descSearch) || isDescriptionMatch(subTrack, descWords, descWordCount)) &&
                                    (!numMetadataNonEmpty || hashLookup(matchingTracks, subTrack->track) != NULL))
                                     {
                                     // XXXX to parent hash. - use tdb->parent instead.
                                     hashAdd(parents, subTrack->track, track);
                                     tracksFound++;
                                     refAdd(&tracks, subTrack);
                                     }
                                 }                        
                             }
                         }
                     }
                 }
             }
         slSort(&tracks, gCmpTrack);
         }
     }
 
 if(tracksFound)
     {
+    struct hash *tdbHash = makeTrackHash(database, chromName);
     hPrintf("<h3><b>%d tracks found:</b></h3>\n", tracksFound);
     hPrintf("<form action='%s' name='SearchTracks' id='searchResultsForm' method='post'>\n\n", hgTracksName());
     hPrintf("<table><tr><td colspan='2'>\n");
     hButton("submit", "View in Browser");
     hPrintf("</td><td align='right'>\n");
     hButtonWithOnClick("hgt.ignoreme", "Select All", "show all found tracks", "changeSearchVisibilityPopups('full'); return false;");
     hButtonWithOnClick("hgt.ignoreme", "Unselect All", "show all found tracks", "changeSearchVisibilityPopups('hide'); return false;");
     hPrintf("</td></tr><tr bgcolor='#666666'><td><br /></td><td><b>Name</b></td><td><b>Description</b></td></tr>\n");
     struct slRef *ptr;
     while((ptr = slPopHead(&tracks)))
         {
         struct track *track = (struct track *) ptr->val;
         // trackDbOutput(track->tdb, stderr, ',', '\n');
         hPrintf("<tr bgcolor='#EEEEEE'>\n");
         hPrintf("<td>\n");
         if (tdbIsSuper(track->tdb))
             {
             superTrackDropDown(cart, track->tdb,
                                superTrackHasVisibleMembers(track->tdb));
             }
         else
             {
             hTvDropDownClassVisOnly(track->track, track->visibility,
                                     track->canPack, (track->visibility == tvHide) ? 
                                     "hiddenText" : "normalText", 
                                     trackDbSetting(track->tdb, "onlyVisibility"));
             }
         hPrintf("</td>\n");
         hPrintf("<td>%s", track->shortLabel);
-        compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE);
+        compositeMetadataToggle(database, track->tdb, "...", TRUE, FALSE, tdbHash);
         hPrintf("</td>\n");
         hPrintf("<td><a target='_top' href='%s'>%s</a></td>\n", trackUrl(track->track, NULL), track->longLabel);
         hPrintf("</tr>\n");
         }
     hPrintf("</table>\n");
     hButton("submit", "View in Browser");
     hPrintf("\n</form>\n");
     } 
 else
     {
     if(doSearch)
         hPrintf("<p>No tracks found</p>\n");
     }
 
 hPrintf("<p><b>Recently Done</b></p><ul>\n"
         "<li>Full descriptions of metadata items are indexed in simple search index (e.g. cell descriptions)</li>"
         "</ul>"
         "<p><b>Known Problems</b></p><ul><li>Menu bar up top doesn't work (clicks are ignored)</li>\n"
         "<li>subtracks often come up with the wrong visibility (but saving visibility for subtracks does work)</li>"
         "</ul>\n");
 
 webEndSectionTables();
 }