748b06ac95ff2a3957be3845bd3594984e3cc3cf chmalee Wed Aug 17 19:21:48 2022 -0700 Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind diff --git src/hg/lib/bigBedFind.c src/hg/lib/bigBedFind.c index f81e4f0..edafd0e 100644 --- src/hg/lib/bigBedFind.c +++ src/hg/lib/bigBedFind.c @@ -76,158 +76,164 @@ bptFileDetach(&bpt); } errCatchEnd(errCatch); if (errCatch->gotError) { // we fail silently if there is a problem e.g. bad index name return NULL; } return posList; } static struct hgPos *doTrixSearch(struct cart *cart, struct trackDb *tdb, char *trixFile, struct slName *indices, struct bbiFile *bbi, char *term, char *description, struct hgFindSpec *hfs) -/* search a trix file in the "searchTrix" field of a bigBed trackDb - * TODO: Get trixSearchResult snippets in here*/ +/* search a trix file in the "searchTrix" field of a bigBed trackDb */ { struct trix *trix = trixOpen(trixFile); int trixWordCount = 0; char *tmp = cloneString(term); char *val = nextWord(&tmp); char *trixWords[128]; while (val != NULL) { trixWords[trixWordCount] = strLower(val); trixWordCount++; if (trixWordCount == sizeof(trixWords)/sizeof(char*)) errAbort("exhausted space for trixWords"); val = nextWord(&tmp); } if (trixWordCount == 0) return NULL; + struct trixSearchResult *tsList = trixSearch(trix, trixWordCount, trixWords, tsmExpand); +char *context = NULL; +if (hfs) + context = hgFindSpecSetting(hfs, "searchTrixContext"); +boolean doSnippets = FALSE; +if (context && sameString(context, "on")) + { + doSnippets = TRUE; + initSnippetIndex(trix); + } struct hgPos *posList = NULL; for ( ; tsList != NULL; tsList = tsList->next) { struct slName *oneIndex = indices; + if (doSnippets) + addSnippetForResult(tsList, trix); for (; oneIndex; oneIndex = oneIndex->next) { struct hgPos *posList2 = getPosFromBigBed(cart, tdb, bbi, oneIndex->name, - tsList->itemId, description, hfs); + tsList->itemId, tsList->snippet, hfs); posList = slCat(posList, posList2); } } return posList; } int posListCompare(const void *va, const void *vb) /* Compare to sort based on name and then position. */ { const struct hgPos *a = *((struct hgPos **)va); const struct hgPos *b = *((struct hgPos **)vb); int diff = strcmp(a->name, b->name); if (diff == 0) { diff = strcmp(a->chrom, b->chrom); if (diff == 0) { diff = a->chromStart - b->chromStart; if (diff == 0) diff = a->chromEnd - b->chromEnd; } } return diff; } -boolean findBigBedPosInTdbList(struct cart *cart, char *db, struct trackDb *tdbList, char *term, struct hgPositions *hgp, struct hgFindSpec *hfs, boolean measureTiming) -/* Given a list of trackDb entries, check each of them for a searchIndex */ + + +boolean findBigBedPosInTdb(struct cart *cart, char *db, struct trackDb *tdb, char *term, struct hgPositions *hgp, struct hgFindSpec *hfs, boolean measureTiming) +/* Find a position in a single trackDb entry */ { +if (startsWith("bigWig", tdb->type) || !startsWith("big", tdb->type)) + return FALSE; +long startTime = clock1000(); +boolean found = FALSE; char *description = NULL; + if (hfs) { char buf[2048]; if (isNotEmpty(hfs->searchDescription)) truncatef(buf, sizeof(buf), "%s", hfs->searchDescription); else safef(buf, sizeof(buf), "%s", hfs->searchTable); description = cloneString(buf); } -struct trackDb *tdb; -boolean found = FALSE; -for(tdb=tdbList; tdb; tdb = tdb->next) - { - long startTime = clock1000(); - if (tdb->subtracks) - { - found = findBigBedPosInTdbList(cart, db, tdb->subtracks, term, hgp, hfs, measureTiming) || found; - continue; - } - if (startsWith("bigWig", tdb->type) || !startsWith("big", tdb->type)) - continue; // Which field(s) to search? Look for searchIndex in search spec, then in trackDb for // backwards compat. char *indexField = NULL; if (hfs) indexField = hgFindSpecSetting(hfs, "searchIndex"); if (!indexField) indexField = trackDbSetting(tdb, "searchIndex"); if (!indexField && !hfs) - continue; + return FALSE; // If !indexField but we do have a non-NULL hfs, then open file to see if it has a name index. char *fileName = trackDbSetting(tdb, "bigDataUrl"); if (!fileName && !trackHubDatabase(db)) { struct sqlConnection *conn = hAllocConnTrack(db, tdb); fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table); hFreeConn(&conn); } if (!fileName) - continue; + return FALSE; // we fail silently if bigBed can't be opened. struct bbiFile *bbi = NULL; struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { bbi = bigBedFileOpen(fileName); } errCatchEnd(errCatch); if (errCatch->gotError) - continue; + return FALSE; // Now (since hfs is non-NULL) check the file to see if it has a name index if we // don't already have indexField. if (!indexField) { struct slName *indexFields = bigBedListExtraIndexes(bbi); if (slNameInList(indexFields, "name")) indexField = "name"; slNameFreeList(&indexFields); } if (!indexField) { bigBedFileClose(&bbi); - continue; + return FALSE; } struct slName *indexList = slNameListFromString(indexField, ','); struct hgPos *posList1 = NULL, *posList2 = NULL; char *trixFile = trackDbSetting(tdb, "searchTrix"); // if there is a trix file, use it to search for the term if (trixFile != NULL) { struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { posList1 = doTrixSearch(cart, tdb, hReplaceGbdb(trixFile), indexList, bbi, term, NULL, hfs); } errCatchEnd(errCatch); @@ -243,41 +249,58 @@ posList2 = getPosFromBigBed(cart, tdb, bbi, oneIndex->name, term, NULL, hfs); posList1 = slCat(posList1, posList2); } // the trix search and the id search may have found the same item so uniqify: slUniqify(&posList1, posListCompare, hgPosFree); if (posList1 != NULL) { struct hgPosTable *table; found = TRUE; AllocVar(table); slAddHead(&hgp->tableList, table); table->description = cloneString(description ? description : tdb->longLabel); table->name = cloneString(tdb->table); + table->searchTime = -1; if (measureTiming) table->searchTime = clock1000() - startTime; table->posList = posList1; } bigBedFileClose(&bbi); - } freeMem(description); return found; } +boolean findBigBedPosInTdbList(struct cart *cart, char *db, struct trackDb *tdbList, char *term, struct hgPositions *hgp, struct hgFindSpec *hfs, boolean measureTiming) +/* Given a list of trackDb entries, check each of them for a searchIndex */ +{ +struct trackDb *tdb; +boolean found = FALSE; +for (tdb = tdbList; tdb; tdb = tdb->next) + { + if (tdb->subtracks) + { + found = findBigBedPosInTdbList(cart, db, tdb->subtracks, term, hgp, hfs, measureTiming) || found; + continue; + } + found = findBigBedPosInTdb(cart, db, tdb, term, hgp, hfs, measureTiming) || found; + } +return found; +} + boolean isTdbSearchable(struct trackDb *tdb) /* Check if a single tdb is searchable */ { if (tdb->subtracks) { boolean searchable = FALSE; struct trackDb *sub; for (sub = tdb->subtracks; sub != NULL; sub = sub->next) searchable |= isTdbSearchable(sub); return searchable; } if (startsWith("bigWig", tdb->type) || !startsWith("big", tdb->type)) return FALSE; char *indexField = NULL;