d33d422222f6846b3eb05e49242e9d764d4c4aea tdreszer Tue Nov 23 14:17:17 2010 -0800 Missing comma in whitelist of formats caused a problem diff --git src/hg/hgTracks/searchTracks.c src/hg/hgTracks/searchTracks.c index 7448d2b..1d362bb 100644 --- src/hg/hgTracks/searchTracks.c +++ src/hg/hgTracks/searchTracks.c @@ -163,85 +163,83 @@ ix++; labels[ix] = pair->name; values[ix] = pair->val; freeMem(pair); } *pLabels = labels; *pTerms = values; return count; } #ifdef TRACK_SEARCH_ON_TYPE static int getFormatTypes(char ***pLabels, char ***pTypes) { char *crudeTypes[] = { ANYLABEL, - //"altGraphX", "bam", "psl", "chain", "netAlign", "maf", "bed", "bigBed", "ctgPos", "expRatio", "genePred", "broadPeak", "narrowPeak", "rmsk", "bedGraph", "bigWig", "wig", - "wigMaf", + "wigMaf" }; // Non-standard: // type altGraphX // type axt // type bed5FloatScore // type bed5FloatScoreWithFdr // type chromGraph // type clonePos // type coloredExon // type encodeFiveC // type factorSource // type ld2 // type logo // type maf // type sample // type wigMafProt 0.0 1.0 char *nicerTypes[] = { ANYLABEL, - //"altGraphX", "Alignment binary (bam) - binary SAM", "Alignment Blast (psl) - Blast output", "Alignment Chains (chain) - Pairwise alignment", "Alignment Nets (netAlign) - Net alignments", "Alignments (maf) - multiple alignment format", "bed - browser extensible data", "bigBed - self index, often remote bed format", "ctgPos - Contigs", "expRatio - Expression ratios", "Genes (genePred) - Gene prediction and annotation", "Peaks Broad (broadPeak) - ENCODE large region peak format", "Peaks Narrow (narrowPeak) - ENCODE small region peak format", "Repeats (rmsk) - Repeat masking", "Signal (bedGraph) - graphically represented bed data", "Signal (bigWig) - self index, often remote wiggle format", - "Signal (wig) - wiggle format" - "Signal (wigMaf) - multiple alignment wiggle", + "Signal (wig) - wiggle format", + "Signal (wigMaf) - multiple alignment wiggle" }; #endif///def TRACK_SEARCH_ON_TYPE int ix = 0, count = sizeof(crudeTypes)/sizeof(char *); char **labels; char **values; AllocArray(labels, count); AllocArray(values, count); for(ix=0;ix<count;ix++) { labels[ix] = cloneString(nicerTypes[ix]); values[ix] = cloneString(crudeTypes[ix]); } *pLabels = labels; *pTypes = values; @@ -524,79 +522,72 @@ for (el = metaTracks; el != NULL; el = el->next) hashAddInt(matchingTracks, el->name, 1); struct group *group; 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; #ifdef TRACK_SEARCH_ON_TYPE - char *trackType = cloneFirstWord(track->tdb->type); + char *trackType = cloneFirstWord(track->tdb->type); // will be spilled #endif///def TRACK_SEARCH_ON_TYPE if((isEmpty(nameSearch) || isNameMatch(track, nameSearch, "contains")) && #ifdef TRACK_SEARCH_ON_TYPE (isEmpty(typeSearch) || (sameWord(typeSearch, trackType) && !tdbIsComposite(track->tdb))) && - //(isEmpty(typeSearch) || sameWord(typeSearch, trackType)) && #endif///def TRACK_SEARCH_ON_TYPE (isEmpty(descSearch) || isDescriptionMatch(track, descWords, descWordCount)) && (!numMetadataNonEmpty || hashLookup(matchingTracks, track->track) != NULL)) { if (track != NULL) { tracksFound++; refAdd(&tracks, track); } else warn("found group track is NULL."); } - #ifdef TRACK_SEARCH_ON_TYPE - freeMem(trackType); - #endif///def TRACK_SEARCH_ON_TYPE if (track->subtracks != NULL) { struct track *subTrack; for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next) { #ifdef TRACK_SEARCH_ON_TYPE - trackType = cloneFirstWord(subTrack->tdb->type); + trackType = cloneFirstWord(subTrack->tdb->type); // will be spilled #endif///def TRACK_SEARCH_ON_TYPE if((isEmpty(nameSearch) || isNameMatch(subTrack, nameSearch, "contains")) && #ifdef TRACK_SEARCH_ON_TYPE (isEmpty(typeSearch) || sameWord(typeSearch, trackType)) && #endif///def TRACK_SEARCH_ON_TYPE (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); if (track != NULL) { tracksFound++; refAdd(&tracks, subTrack); } else warn("found subtrack is NULL."); } - #ifdef TRACK_SEARCH_ON_TYPE - freeMem(trackType); - #endif///def TRACK_SEARCH_ON_TYPE } } } } } } } return tracks; } #define MAX_FOUND_TRACKS 100 static void findTracksPageLinks(int tracksFound, int startFrom) { if (tracksFound <= MAX_FOUND_TRACKS) @@ -838,30 +829,32 @@ if (!advancedJavascriptFeaturesEnabled(cart)) { warn("Requires advanced javascript features."); return; } struct group *group; char *groups[128]; char *labels[128]; int numGroups = 1; groups[0] = ANYLABEL; labels[0] = ANYLABEL; char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab"); char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME); #ifdef TRACK_SEARCH_ON_TYPE char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE); +#else///ifndef TRACK_SEARCH_ON_TYPE +char *typeSearch = NULL; #endif///def TRACK_SEARCH_ON_TYPE char *descSearch; char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP); boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0; struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); int numMetadataSelects, tracksFound = 0; int numMetadataNonEmpty = 0; char **mdbVar = NULL; char **mdbVal = NULL; #ifdef ONE_FUNC struct hash *parents = newHash(4); #endif///def ONE_FUNC boolean simpleSearch; struct trix *trix; @@ -1035,35 +1028,31 @@ } descWords = needMem(sizeof(char *) * descWordCount); for(i = 0, el = descList; el != NULL; i++, el = el->next) descWords[i] = strLower(el->name); } if (doSearch && simpleSearch && descWordCount <= 0) doSearch = FALSE; if(doSearch) { // Now search struct slRef *tracks = NULL; if(simpleSearch) tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount); else -#ifdef TRACK_SEARCH_ON_TYPE tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal); -#else///ifndef TRACK_SEARCH_ON_TYPE - tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,NULL,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal); -#endif///ndef TRACK_SEARCH_ON_TYPE // Sort and Print results enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance); tracksFound = slCount(tracks); if(tracksFound > 1) findTracksSort(&tracks,simpleSearch,sortBy); displayFoundTracks(cart,tracks,tracksFound,sortBy); } hFreeConn(&conn); webNewSection("About Track Search"); if(metaDbExists) hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE " "metadata. If multiple terms are entered, only tracks with all terms "