8705123ad669501646271bdd1e341af235dcb1fd chmalee Fri Jul 22 09:37:38 2022 -0700 Fix subtle duplicated item bug in bigBed trix searching diff --git src/hg/lib/bigBedFind.c src/hg/lib/bigBedFind.c index 9ffd17f..e3c5862 100644 --- src/hg/lib/bigBedFind.c +++ src/hg/lib/bigBedFind.c @@ -1,243 +1,247 @@ #include "common.h" #include "bPlusTree.h" #include "bbiFile.h" #include "bigBed.h" #include "hgFind.h" #include "trix.h" #include "trackHub.h" #include "hubConnect.h" #include "hdb.h" #include "errCatch.h" #include "bigBedLabel.h" #include "bigBedFind.h" static struct hgPos *bigBedIntervalListToHgPositions(struct cart *cart, struct trackDb *tdb, struct bbiFile *bbi, char *term, struct bigBedInterval *intervalList, char *description, struct hgFindSpec *hfs) /* Given an open bigBed file, and an interval list, return a pointer to a list of hgPos structures. */ { struct hgPos *posList = NULL; char chromName[bbi->chromBpt->keySize+1]; int lastChromId = -1; struct bigBedInterval *interval; struct slInt *labelColumns = NULL; bigBedLabelCalculateFields(cart, tdb, bbi, &labelColumns ); for (interval = intervalList; interval != NULL; interval = interval->next) { struct hgPos *hgPos; AllocVar(hgPos); slAddHead(&posList, hgPos); bbiCachedChromLookup(bbi, interval->chromId, lastChromId, chromName, sizeof(chromName)); lastChromId = interval->chromId; hgPos->chrom = cloneString(chromName); hgPos->chromStart = interval->start; hgPos->chromEnd = interval->end; hgPos->name = bigBedMakeLabel(tdb, labelColumns, interval, chromName); hgPos->browserName = cloneString(term); hgPos->description = cloneString(description); if (hfs) { char *paddingStr = hgFindSpecSetting(hfs, "padding"); int padding = isEmpty(paddingStr) ? 0 : atoi(paddingStr); if (padding > 0) { // highlight the item bases only, to distinguish from padding hgPos->highlight = addHighlight(cartString(cart, "db"), hgPos->chrom, hgPos->chromStart, hgPos->chromEnd); hgPos->chromStart -= padding; hgPos->chromEnd += padding; if (hgPos->chromStart < 0) hgPos->chromStart = 0; } } } return posList; } static struct hgPos *getPosFromBigBed(struct cart *cart, struct trackDb *tdb, struct bbiFile *bbi, char *indexField, char *term, char *description, struct hgFindSpec *hfs) /* Given a bigBed file with a search index, check for term. */ { struct errCatch *errCatch = errCatchNew(); struct hgPos *posList = NULL; if (errCatchStart(errCatch)) { int fieldIx; struct bptFile *bpt = bigBedOpenExtraIndex(bbi, indexField, &fieldIx); struct lm *lm = lmInit(0); struct bigBedInterval *intervalList; intervalList = bigBedNameQuery(bbi, bpt, fieldIx, term, lm); posList = bigBedIntervalListToHgPositions(cart, tdb, bbi, term, intervalList, description, hfs); 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 */ { 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); struct hgPos *posList = NULL; for ( ; tsList != NULL; tsList = tsList->next) { struct slName *oneIndex = indices; for (; oneIndex; oneIndex = oneIndex->next) { struct hgPos *posList2 = getPosFromBigBed(cart, tdb, bbi, oneIndex->name, tsList->itemId, description, hfs); posList = slCat(posList, posList2); } } return posList; } boolean findBigBedPosInTdbList(struct cart *cart, char *db, struct trackDb *tdbList, char *term, struct hgPositions *hgp, struct hgFindSpec *hfs) /* Given a list of trackDb entries, check each of them for a searchIndex */ { 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) { if (tdb->subtracks) { found = findBigBedPosInTdbList(cart, db, tdb->subtracks, term, hgp, hfs) || 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; // 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; // 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; // 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; } 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); if (errCatch->gotError) warn("trix search failure for %s: %s", tdb->table, dyStringContents(errCatch->message)); errCatchFree(&errCatch); } + // if no trix file or we didn't find anything from a trix search + if (!posList1) + { // now search for the raw id's struct slName *oneIndex=indexList; for (; oneIndex; oneIndex = oneIndex->next) { posList2 = getPosFromBigBed(cart, tdb, bbi, oneIndex->name, term, NULL, hfs); posList1 = slCat(posList1, posList2); } + } 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->posList = posList1; } bigBedFileClose(&bbi); } freeMem(description); return found; }