static void visiGeneMatchDescription(struct visiSearcher *searcher,
struct sqlConnection *conn, struct slName *wordList)
/* Fold in matches to description - using full text index. */
{
struct trix *trix = NULL;
struct slName *word;
int wordIx;
if (!fileExists("visiGeneData/visiGene.ix"))
{
safef(titleMessage,sizeof(titleMessage),
" - visiGene.ix not found, run vgGetText");
fprintf(stderr,"%s\n",titleMessage);
return;
}
trix = trixOpen("visiGeneData/visiGene.ix");
for (word=wordList, wordIx=0; word != NULL; word = word->next, ++wordIx)
{
char *s = cloneString(word->name);
struct trixSearchResult *tsr, *tsrList;
tolowers(s);
tsrList = trixSearch(trix, 1, &s, FALSE);
for (tsr = tsrList; tsr != NULL; tsr = tsr->next)
visiSearcherAdd(searcher, sqlUnsigned(tsr->itemId), 1.0, wordIx, 1);
trixSearchResultFreeList(&tsrList);
freez(&s);
}
trixClose(&trix);
}
static struct slRef *simpleSearchForTracksstruct(struct trix *trix,char **descWords,int descWordCount)
// Performs the simple search and returns the found tracks.
{
struct slRef *tracks = NULL;
struct trixSearchResult *tsList;
for(tsList = trixSearch(trix, descWordCount, descWords, TRUE); tsList != NULL; tsList = tsList->next)
{
struct track *track = (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(&tracks, track);
}
}
return tracks;
}
static struct slRef *simpleSearchForTracksstruct(char *simpleEntry)
// Performs the simple search and returns the found tracks.
{
struct slRef *tracks = NULL;
// Prepare for trix search
if (!isEmpty(simpleEntry))
{
int trixWordCount = 0;
char *tmp = cloneString(simpleEntry);
char *val = nextWord(&tmp);
struct slName *el, *trixList = NULL;
while (val != NULL)
{
slNameAddTail(&trixList, val);
trixWordCount++;
val = nextWord(&tmp);
}
if (trixWordCount > 0)
{
// Unfortunately trixSearch can't handle the slName list
int i;
char **trixWords = needMem(sizeof(char *) * trixWordCount);
for (i = 0, el = trixList; el != NULL; i++, el = el->next)
trixWords[i] = strLower(el->name);
// Now open the trix file
char trixFile[HDB_MAX_PATH_STRING];
getSearchTrixFile(database, trixFile, sizeof(trixFile));
struct trix *trix = trixOpen(trixFile);
struct trixSearchResult *tsList = trixSearch(trix, trixWordCount, trixWords, TRUE);
for ( ; tsList != NULL; tsList = tsList->next)
{
struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId);
if (track != NULL) // It is expected that this is NULL
{ // (e.g. when trix references trackDb tracks which have no tables)
refAdd(&tracks, track);
}
}
//trixClose(trix); // don't bother (this is a CGI that is about to end)
}
}
return tracks;
}
static struct aHubMatch *searchPublicHubs(struct dbDb *dbDbList, char *term)
/* Search for term in public hub trix files -- return a list of matches to assembly hubs
* (i.e. hubs that host an assembly with 2bit etc as opposed to only providing tracks.) */
{
struct aHubMatch *aHubMatchList = NULL;
char *trixFile = cfgOptionEnvDefault("HUBSEARCHTRIXFILE", "hubSearchTrixFile",
hReplaceGbdb("/gbdb/hubs/public.ix"));
if (fileExists(trixFile))
{
struct trix *trix = trixOpen(trixFile);
char termCopy[strlen(term)+1];
safecpy(termCopy, sizeof(termCopy), term);
tolowers(termCopy);
char *words[512];
int wordCount = chopByWhite(termCopy, words, ArraySize(words));
struct trixSearchResult *tsrList = trixSearch(trix, wordCount, words, tsmFirstFive);
aHubMatchList = filterTrixSearchMatches(dbDbList, tsrList);
trixClose(&trix);
}
return aHubMatchList;
}
struct visiMatch *visiSearch(struct sqlConnection *conn, char *searchString)
/* visiSearch - return list of images that match searchString sorted
* by how well they match. This will search most fields in the
* database. */
{
char *dupe = cloneString(searchString);
struct trix *trix = trixOpen("visiGeneData/visiGene.ix");
struct trixSearchResult *tsrList, *tsr;
struct visiMatch *matchList = NULL, *match;
int wordCount = chopByWhite(dupe, NULL, 0);
char **words;
boolean hasWild;
struct hash *privateHash = makePrivateHash(conn);
tolowers(dupe);
hasWild = (strchr(searchString, '*') != NULL);
if (hasWild)
stripChar(dupe, '*');
AllocArray(words, wordCount);
chopByWhite(dupe, words, wordCount);
/* if (wordCount != 1 ||
(matchList = matchGeneName(conn, words[0],privateHash)) == NULL) */
{
tsrList = trixSearch(trix, wordCount, words, hasWild);
for (tsr = tsrList; tsr != NULL; tsr = tsr->next)
{
if (!isPrivate(conn, privateHash, tsr->itemId))
{
AllocVar(match);
match->imageId = sqlUnsigned(tsr->itemId);
slAddHead(&matchList, match);
}
}
trixSearchResultFreeList(&tsrList);
trixClose(&trix);
slReverse(&matchList);
}
freeMem(dupe);
return matchList;
}
