Examples with StringUtils.isBlank org.apache.commons.lang3.StringUtils.isBlank used on opensource projects

Example 21 with StringUtils.isBlank

use of org.apache.commons.lang3.StringUtils.isBlank in project Gemma by PavlidisLab.

the class SearchServiceImpl method characteristicSearchTerm.

/**
 * Perform a search on a query - it does not have to be one word, it could be "parkinson's disease"
 */
private Collection<SearchResult> characteristicSearchTerm(Collection<Class<?>> classes, String query) {
    if (SearchServiceImpl.log.isDebugEnabled())
        SearchServiceImpl.log.debug("Starting search for " + query);
    StopWatch watch = this.startTiming();
    Collection<Characteristic> cs = new HashSet<>();
    Collection<OntologyIndividual> individuals = ontologyService.findIndividuals(query);
    for (Collection<OntologyIndividual> individualbatch : BatchIterator.batches(individuals, 10)) {
        Collection<String> uris = new HashSet<>();
        for (OntologyIndividual individual : individualbatch) {
            uris.add(individual.getUri());
        }
        Collection<SearchResult> dbhits = this.dbHitsToSearchResult(characteristicService.findByUri(classes, uris), null);
        for (SearchResult crs : dbhits) {
            cs.add((Characteristic) crs.getResultObject());
        }
        if (cs.size() >= SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
            break;
        }
    }
    if (individuals.size() > 0 && watch.getTime() > 1000) {
        SearchServiceImpl.log.info("Found " + individuals.size() + " individuals matching '" + query + "' in " + watch.getTime() + "ms");
    }
    /*
         * Add characteristics that have values matching the query; this pulls in items not associated with ontology
         * terms (free text). We do this here so we can apply the query logic to the matches.
         */
    if (cs.size() < SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
        // note I changed the order of search operations so
        String dbQueryString = query.replaceAll("\\*", "");
        // this might not be wanted.
        Collection<Characteristic> valueMatches = characteristicService.findByValue(classes, dbQueryString);
        if (valueMatches != null && !valueMatches.isEmpty()) {
            cs.addAll(valueMatches);
            if (watch.getTime() > 1000) {
                SearchServiceImpl.log.info("Found " + valueMatches.size() + " characteristics matching value '" + query + "' in " + watch.getTime() + "ms");
            }
            watch.reset();
            watch.start();
        }
    }
    if (cs.size() < SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
        /*
             * Identify initial set of matches to the query.
             */
        Collection<OntologyTerm> matchingTerms = ontologyService.findTerms(query);
        if (watch.getTime() > 1000) {
            SearchServiceImpl.log.info("Found " + matchingTerms.size() + " ontology classes matching '" + query + "' in " + watch.getTime() + "ms");
        }
        /*
             * Search for child terms.
             */
        if (!matchingTerms.isEmpty()) {
            for (OntologyTerm term : matchingTerms) {
                /*
                     * In this loop, each term is a match directly to our query, and we do a depth-first fetch of the
                     * children.
                     */
                String uri = term.getUri();
                if (StringUtils.isBlank(uri))
                    continue;
                int sizeBefore = cs.size();
                this.getCharacteristicsAnnotatedToChildren(classes, term, cs);
                if (SearchServiceImpl.log.isDebugEnabled() && cs.size() > sizeBefore) {
                    SearchServiceImpl.log.debug((cs.size() - sizeBefore) + " characteristics matching children term of " + term);
                }
                if (cs.size() >= SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
                    break;
                }
            }
            if (watch.getTime() > 1000) {
                SearchServiceImpl.log.info("Found " + cs.size() + " characteristics for '" + query + "' including child terms in " + watch.getTime() + "ms");
            }
            watch.reset();
            watch.start();
        }
    }
    /*
         * Retrieve the owner objects
         */
    watch.reset();
    watch.start();
    Collection<SearchResult> matchingEntities = this.getAnnotatedEntities(classes, cs);
    if (watch.getTime() > 1000) {
        SearchServiceImpl.log.info("Retrieved " + matchingEntities.size() + " entities via characteristics for '" + query + "' in " + watch.getTime() + "ms");
    }
    if (SearchServiceImpl.log.isDebugEnabled())
        SearchServiceImpl.log.debug("End search for " + query);
    return matchingEntities;
}

Example 22 with StringUtils.isBlank

use of org.apache.commons.lang3.StringUtils.isBlank in project Gemma by PavlidisLab.

the class SearchServiceImpl method databaseGeneSearch.

/**
 * Search the DB for genes that exactly match the given search string searches geneProducts, gene and bioSequence
 * tables
 */
private Collection<SearchResult> databaseGeneSearch(SearchSettings settings) {
    if (!settings.getUseDatabase())
        return new HashSet<>();
    StopWatch watch = this.startTiming();
    String searchString = StringEscapeUtils.unescapeJava(settings.getQuery());
    if (StringUtils.isBlank(searchString))
        return new HashSet<>();
    Collection<SearchResult> results = new HashSet<>();
    /*
         * First search by accession. If we find it, stop.
         */
    Gene result = null;
    try {
        result = geneService.findByNCBIId(Integer.parseInt(searchString));
    } catch (NumberFormatException e) {
    // 
    }
    if (result != null) {
        results.add(this.dbHitToSearchResult(result));
    } else {
        result = geneService.findByAccession(searchString, null);
        if (result != null) {
            results.add(this.dbHitToSearchResult(result));
        }
    }
    if (results.size() > 0) {
        this.filterByTaxon(settings, results, true);
        watch.stop();
        if (watch.getTime() > 1000)
            SearchServiceImpl.log.info("Gene DB search for " + searchString + " took " + watch.getTime() + " ms and found " + results.size() + " genes");
        return results;
    }
    // replace * at end with % for inexact symbol search
    String inexactString = searchString;
    Pattern pattern = Pattern.compile("\\*$");
    Matcher match = pattern.matcher(inexactString);
    inexactString = match.replaceAll("%");
    // note that at this point, the inexactString might not have a wildcard - only if the user asked for it.
    String exactString = inexactString.replaceAll("%", "");
    // if the query is shortish, always do a wild card search. This gives better behavior in 'live
    // search' situations. If we do wildcards on very short queries we get too many results.
    Collection<Gene> geneSet = new HashSet<>();
    if (searchString.length() <= 2) {
        // case 0: we got no result syet, or user entered a very short string. We search only for exact matches.
        geneSet.addAll(geneService.findByOfficialSymbolInexact(exactString));
    } else if (inexactString.endsWith("%")) {
        // case 1: user explicitly asked for wildcard. We allow this on strings of length 3 or more.
        geneSet.addAll(geneService.findByOfficialSymbolInexact(inexactString));
    } else if (searchString.length() > 3) {
        // case 2: user did not ask for a wildcard, but we add it anyway, if the string is 4 or 5 characters.
        if (!inexactString.endsWith("%")) {
            inexactString = inexactString + "%";
        }
        geneSet.addAll(geneService.findByOfficialSymbolInexact(inexactString));
    } else {
        // case 3: string is long enough, and user did not ask for wildcard.
        geneSet.addAll(geneService.findByOfficialSymbol(exactString));
    }
    /*
         * If we found a match using official symbol or name, don't bother with this
         */
    if (geneSet.isEmpty()) {
        geneSet.addAll(geneService.findByAlias(exactString));
        geneSet.addAll(geneProductService.getGenesByName(exactString));
        geneSet.addAll(geneProductService.getGenesByNcbiId(exactString));
        geneSet.addAll(bioSequenceService.getGenesByAccession(exactString));
        geneSet.addAll(bioSequenceService.getGenesByName(exactString));
        geneSet.add(geneService.findByEnsemblId(exactString));
    }
    watch.stop();
    if (watch.getTime() > 1000)
        SearchServiceImpl.log.info("Gene DB search for " + searchString + " took " + watch.getTime() + " ms and found " + geneSet.size() + " genes");
    results = this.dbHitsToSearchResult(geneSet, null);
    this.filterByTaxon(settings, results, true);
    return results;
}

Example 23 with StringUtils.isBlank

use of org.apache.commons.lang3.StringUtils.isBlank in project Gemma by PavlidisLab.

the class SearchServiceImpl method performSearch.

/**
 * Runs inside Compass transaction
 */
private Collection<SearchResult> performSearch(SearchSettings settings, CompassSession session) {
    StopWatch watch = this.startTiming();
    String enhancedQuery = settings.getQuery().trim();
    // noinspection ConstantConditions // Not obvious to me why that would have to be false.
    if (StringUtils.isBlank(enhancedQuery) || enhancedQuery.length() < SearchServiceImpl.MINIMUM_STRING_LENGTH_FOR_FREE_TEXT_SEARCH || enhancedQuery.equals("*"))
        return new ArrayList<>();
    CompassQuery compassQuery = session.queryBuilder().queryString(enhancedQuery).toQuery();
    SearchServiceImpl.log.debug("Parsed query: " + compassQuery);
    CompassHits hits = compassQuery.hits();
    // highlighting.
    if (((SearchSettingsImpl) settings).getDoHighlighting()) {
        if (session instanceof InternalCompassSession) {
            // always ...
            CompassMapping mapping = ((InternalCompassSession) session).getMapping();
            ResourceMapping[] rootMappings = mapping.getRootMappings();
            // should only be one rootMapping.
            this.process(rootMappings, hits);
        }
    }
    watch.stop();
    if (watch.getTime() > 100) {
        SearchServiceImpl.log.info("Getting " + hits.getLength() + " lucene hits for " + enhancedQuery + " took " + watch.getTime() + " ms");
    }
    if (watch.getTime() > 5000) {
        SearchServiceImpl.log.info("*****Extremely long Lucene Index Search!  " + hits.getLength() + " lucene hits for " + enhancedQuery + " took " + watch.getTime() + " ms");
    }
    return this.getSearchResults(hits);
}

Example 24 with StringUtils.isBlank

use of org.apache.commons.lang3.StringUtils.isBlank in project Gemma by PavlidisLab.

the class GeneOntologyServiceImpl method findTerm.

@Override
public Collection<OntologyTerm> findTerm(String queryString) {
    if (!this.isReady())
        return new HashSet<>();
    if (GeneOntologyServiceImpl.log.isDebugEnabled())
        GeneOntologyServiceImpl.log.debug("Searching Gene Ontology for '" + queryString + "'");
    // make sure we are all-inclusive
    queryString = queryString.trim();
    queryString = queryString.replaceAll("\\s+", " AND ");
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<OntologyResource> rawMatches = new HashSet<>();
    for (SearchIndex index : this.indices) {
        rawMatches.addAll(OntologySearch.matchIndividuals(model, index, queryString));
    }
    if (timer.getTime() > 100) {
        GeneOntologyServiceImpl.log.info("Find " + rawMatches.size() + " raw go terms from " + queryString + ": " + timer.getTime() + " ms");
    }
    timer.reset();
    timer.start();
    /*
         * Required to make sure the descriptions are filled in.
         */
    Collection<OntologyTerm> matches = new HashSet<>();
    for (OntologyResource r : rawMatches) {
        if (StringUtils.isBlank(r.getUri()))
            continue;
        OntologyTerm termForURI = GeneOntologyServiceImpl.getTermForURI(r.getUri());
        if (termForURI == null) {
            GeneOntologyServiceImpl.log.warn("No term for : " + r);
            continue;
        }
        matches.add(termForURI);
    }
    if (timer.getTime() > 100) {
        GeneOntologyServiceImpl.log.info("Convert " + rawMatches.size() + " raw go terms to terms: " + timer.getTime() + " ms");
    }
    return matches;
}

Example 25 with StringUtils.isBlank

use of org.apache.commons.lang3.StringUtils.isBlank in project Gemma by PavlidisLab.

the class GeoFamilyParser method doParse.

private void doParse(BufferedReader dis) {
    if (dis == null) {
        throw new RuntimeException("Null reader");
    }
    this.numWarnings = 0;
    haveReadPlatformHeader = false;
    haveReadSampleDataHeader = false;
    alreadyWarnedAboutClobbering = false;
    alreadyWarnedAboutInconsistentColumnOrder = false;
    alreadyWarnedAboutDuplicateColumnName = false;
    String line;
    parsedLines = 0;
    processedDesignElements.clear();
    StopWatch timer = new StopWatch();
    timer.start();
    try {
        while ((line = dis.readLine()) != null) {
            if (StringUtils.isBlank(line)) {
                continue;
            }
            this.parseLine(line);
            if (++parsedLines % 20000 == 0 && Thread.currentThread().isInterrupted()) {
                // clean up
                dis.close();
                throw new java.util.concurrent.CancellationException("Thread was terminated during parsing. " + this.getClass());
            }
        }
        this.tidyUp();
    } catch (Exception e) {
        GeoFamilyParser.log.error("Parsing failed (Cancelled?) :" + e.getMessage());
        /*
             * This happens if there was a cancellation.
             */
        throw new RuntimeException(e);
    }
    timer.stop();
    if (timer.getTime() > 10000) {
        // 10 s
        GeoFamilyParser.log.info("Parsed total of " + parsedLines + " lines in " + String.format("%.2gs", timer.getTime() / 1000.0));
    }
    GeoFamilyParser.log.debug(this.platformLines + " platform  lines");
    int seriesDataLines = 0;
    GeoFamilyParser.log.debug(seriesDataLines + " series data lines");
    int dataSetDataLines = 0;
    GeoFamilyParser.log.debug(dataSetDataLines + " data set data lines");
    GeoFamilyParser.log.debug(this.sampleDataLines + " sample data lines");
}