Example usage for org.apache.solr.client.solrj.util ClientUtils escapeQueryChars

Introduction

In this page you can find the example usage for org.apache.solr.client.solrj.util ClientUtils escapeQueryChars.

Prototype

public static String escapeQueryChars(String s) 

Source Link

Document

See: <a href="https://www.google.com/?gws_rd=ssl#q=lucene+query+parser+syntax">Lucene query parser syntax</a> for more information on Escaping Special Characters

Usage

From source file:org.phenotips.data.indexing.internal.SolrPatientIndexer.java

License:Open Source License

@Override
public void delete(Patient patient) {
    try {// w  w  w.  ja  va 2 s  . c  o  m
        this.server.deleteByQuery("document:" + ClientUtils.escapeQueryChars(patient.getDocument().toString()));
        this.server.commit();
    } catch (SolrServerException ex) {
        this.logger.warn("Failed to delete from Solr: {}", ex.getMessage());
    } catch (IOException ex) {
        this.logger.warn("Error occurred while deleting Solr documents: {}", ex.getMessage());
    }
}

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From source file:org.phenotips.data.indexing.internal.SolrPatientIndexerTest.java

License:Open Source License

@Test
public void deleteDefaultBehaviourTest() throws IOException, SolrServerException {
    doReturn(this.patientDocReference).when(this.patient).getDocument();
    this.patientIndexer.delete(this.patient);
    verify(this.server)
            .deleteByQuery("document:" + ClientUtils.escapeQueryChars(this.patientDocReference.toString()));
    verify(this.server).commit();
}

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From source file:org.phenotips.ontology.internal.GeneNomenclature.java

License:Open Source License

private StringBuilder processQueryPart(StringBuilder query, Map.Entry<String, ?> field,
        boolean includeOperator) {
    if (Collection.class.isInstance(field.getValue()) && ((Collection<?>) field.getValue()).isEmpty()) {
        return query;
    }//from  w w w .  ja  v a  2  s  .  co  m
    if (Map.class.isInstance(field.getValue())) {
        if (QUERY_OPERATORS.containsKey(field.getKey())) {
            @SuppressWarnings("unchecked")
            Map.Entry<String, Map<String, ?>> subquery = (Map.Entry<String, Map<String, ?>>) field;
            return processSubquery(query, subquery);
        } else {
            this.logger.warn("Invalid subquery operator: {}", field.getKey());
            return query;
        }
    }
    query.append(' ');
    if (includeOperator) {
        query.append(QUERY_OPERATORS.get(DEFAULT_OPERATOR));
    }

    query.append(ClientUtils.escapeQueryChars(field.getKey()));
    query.append(":(");
    if (Collection.class.isInstance(field.getValue())) {
        for (Object value : (Collection<?>) field.getValue()) {
            String svalue = String.valueOf(value);
            if (svalue.endsWith(WILDCARD)) {
                svalue = ClientUtils.escapeQueryChars(StringUtils.removeEnd(svalue, WILDCARD)) + WILDCARD;
            } else {
                svalue = ClientUtils.escapeQueryChars(svalue);
            }
            query.append(svalue);
            query.append(' ');
        }
    } else {
        String svalue = String.valueOf(field.getValue());
        if (svalue.endsWith(WILDCARD)) {
            svalue = ClientUtils.escapeQueryChars(StringUtils.removeEnd(svalue, WILDCARD)) + WILDCARD;
        } else {
            svalue = ClientUtils.escapeQueryChars(svalue);
        }
        query.append(svalue);
    }
    query.append(')');
    return query;

}

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From source file:org.phenotips.ontology.internal.solr.AbstractSolrOntologyService.java

License:Open Source License

@Override
public OntologyTerm getTerm(String id) {
    OntologyTerm result = this.externalServicesAccess.getCache().get(id);
    if (result == null) {
        ModifiableSolrParams params = new ModifiableSolrParams();
        params.set(CommonParams.Q, ID_FIELD_NAME + ':' + ClientUtils.escapeQueryChars(id));
        SolrDocumentList allResults = this.search(params);
        if (allResults != null && !allResults.isEmpty()) {
            result = new SolrOntologyTerm(allResults.get(0), this);
            this.externalServicesAccess.getCache().set(id, result);
        } else {/*from  w  w  w  .  jav  a2 s.c  o  m*/
            this.externalServicesAccess.getCache().set(id, EMPTY_MARKER);
        }
    }
    return (result == EMPTY_MARKER) ? null : result;
}

---

From source file:org.phenotips.ontology.internal.solr.AbstractSolrOntologyService.java

License:Open Source License

@Override
public Set<OntologyTerm> getTerms(Collection<String> ids) {
    Set<OntologyTerm> result = new LinkedHashSet<OntologyTerm>();
    StringBuilder query = new StringBuilder("id:(");
    for (String id : ids) {
        OntologyTerm cachedTerm = this.externalServicesAccess.getCache().get(id);
        if (cachedTerm != null) {
            if (cachedTerm != EMPTY_MARKER) {
                result.add(cachedTerm);//from  ww  w .  j a  va 2 s  .  c  o m
            }
        } else {
            query.append(ClientUtils.escapeQueryChars(id));
            query.append(' ');
        }
    }
    query.append(')');

    // There's at least one more term not found in the cache
    if (query.length() > 5) {
        for (SolrDocument doc : this.search(SolrQueryUtils.transformQueryToSolrParams(query.toString()))) {
            result.add(new SolrOntologyTerm(doc, this));
        }
    }
    return result;
}

---

From source file:org.phenotips.ontology.internal.solr.AbstractSolrOntologyService.java

License:Open Source License

/**
 * Generate a Lucene query from a map of parameters, to be used in the "q" parameter for Solr.
 *
 * @param fieldValues a map with term meta-property values that must be matched by the returned terms; the keys are
 *            property names, like {@code id}, {@code description}, {@code is_a}, and the values can be either a
 *            single value, or a collection of values that can (OR) be matched by the term;
 * @return the String representation of the equivalent Lucene query
 *//*from  w  w  w.jav a 2 s  .c  o m*/
protected String generateLuceneQuery(Map<String, ?> fieldValues) {
    StringBuilder query = new StringBuilder();
    for (Map.Entry<String, ?> field : fieldValues.entrySet()) {
        if (Collection.class.isInstance(field.getValue()) && ((Collection<?>) field.getValue()).isEmpty()) {
            continue;
        }
        query.append("+");
        query.append(ClientUtils.escapeQueryChars(field.getKey()));
        query.append(":(");
        if (Collection.class.isInstance(field.getValue())) {
            for (Object value : (Collection<?>) field.getValue()) {
                query.append(ClientUtils.escapeQueryChars(String.valueOf(value)));
                query.append(' ');
            }
        } else {
            String value = String.valueOf(field.getValue());
            if ("*".equals(value)) {
                query.append(value);
            } else {
                query.append(ClientUtils.escapeQueryChars(value));
            }
        }
        query.append(')');
    }
    return query.toString();
}

---

From source file:org.phenotips.similarity.internal.SolrSimilarPatientsFinder.java

License:Open Source License

/**
 * Generates a Solr query that tries to match patients similar to the reference.
 *
 * @param referencePatient the reference patient
 * @return a query populated with terms from the patient phenotype
 *//*from  w  w  w .  j  a v a 2 s  . c  om*/
private SolrQuery generateQuery(Patient referencePatient, boolean prototypes) {
    SolrQuery query = new SolrQuery();
    StringBuilder q = new StringBuilder();
    // FIXME This is a very basic implementation, to be revisited
    for (Feature phenotype : referencePatient.getFeatures()) {
        if (StringUtils.isNotBlank(phenotype.getId())) {
            q.append(phenotype.getType() + ":" + ClientUtils.escapeQueryChars(phenotype.getId()) + " ");
        }
    }
    // Ignore the reference patient itself (unless reference patient is a temporary in-memory only
    // patient, e.g. a RemoteMatchingPatient created from remote patient data obtained via remote-matching API)
    if (referencePatient.getDocument() != null) {
        q.append("-document:" + ClientUtils.escapeQueryChars(referencePatient.getDocument().toString()));
    }
    q.append(prototypes ? " +" : " -").append("document:xwiki\\:data.MIM*");
    query.add(CommonParams.Q, q.toString());
    //logger.error("SOLRQUERY generated: {}", query.toString());
    return query;
}

---

From source file:org.phenotips.termrequester.db.solr.SolrDatabaseService.java

License:Open Source License

@Override
public Phenotype getPhenotype(Phenotype other) throws IOException {
    checkUp();/*w  w w  .java  2  s  .c  om*/
    Set<String> names = other.getSynonyms();
    names.add(other.getName());
    List<String> queryPieces = new ArrayList<>(names.size() * 2 + 2);
    if (other.getId().isPresent()) {
        queryPieces.add(String.format(FIELD_IS, Schema.ID, ClientUtils.escapeQueryChars(other.getId().get())));
    }
    if (other.getIssueNumber().isPresent()) {
        queryPieces.add(String.format(FIELD_IS, Schema.ISSUE_NUMBER,
                ClientUtils.escapeQueryChars(other.getIssueNumber().get())));
    }
    for (String name : names) {
        queryPieces.add(String.format(FIELD_IS, Schema.NAME_EXACT, ClientUtils.escapeQueryChars(name)));
        queryPieces.add(String.format(FIELD_IS, Schema.SYNONYM_EXACT, ClientUtils.escapeQueryChars(name)));
    }
    String queryString = OR_QUERY_JOINER.join(queryPieces);
    SolrQuery q = new SolrQuery().setQuery(queryString).setRows(1);
    return runQuery(q);
}

---

From source file:org.phenotips.termrequester.db.solr.SolrDatabaseService.java

License:Open Source License

@Override
public List<Phenotype> searchPhenotypes(String text) throws IOException {
    checkUp();/*from ww  w  .  j av a2  s  .co m*/
    try {
        SolrQuery q = new SolrQuery();
        String escaped = ClientUtils.escapeQueryChars(text);
        q.add(CommonParams.Q, escaped);
        q.add(SpellingParams.SPELLCHECK_Q, text);
        q.add(DisMaxParams.PF,
                String.format("%s^20 %s^36 %s^100 %s^30 %s^15 %s^25 %s^70 %s^20 %s^3 %s^5", Schema.NAME,
                        Schema.NAME_SPELL, Schema.NAME_EXACT, Schema.NAME_PREFIX, Schema.SYNONYM,
                        Schema.SYNONYM_SPELL, Schema.SYNONYM_EXACT, Schema.SYNONYM_PREFIX, Schema.TEXT,
                        Schema.TEXT_SPELL));
        String qstring = String.format("%s^10 %s^18 %s^5 %s^6 %s^10 %s^3 %s^1 %s^2 %s^0.5", Schema.NAME,
                Schema.NAME_SPELL, Schema.NAME_STUB, Schema.SYNONYM, Schema.SYNONYM_SPELL, Schema.SYNONYM_STUB,
                Schema.TEXT, Schema.TEXT, Schema.TEXT_SPELL, Schema.TEXT_STUB);
        qstring = addStatusFilter(qstring, Phenotype.Status.SYNONYM);
        q.add(DisMaxParams.QF, qstring);
        q.add("spellcheck", Boolean.toString(true));
        q.add(SpellingParams.SPELLCHECK_COLLATE, Boolean.toString(true));
        q.add(SpellingParams.SPELLCHECK_COUNT, "100");
        q.add(SpellingParams.SPELLCHECK_MAX_COLLATION_TRIES, "3");
        q.add("lowercaseOperators", Boolean.toString(false));
        q.add("defType", "edismax");
        QueryResponse resp = server.query(q);
        List<SolrDocument> results = resp.getResults();
        List<Phenotype> retval = new ArrayList<>(results.size());
        for (SolrDocument doc : results) {
            retval.add(mapper.fromDoc(doc));
        }
        return retval;
    } catch (SolrServerException e) {
        throw new IOException(e);
    }
}

---

From source file:org.phenotips.variantstore.db.solr.SolrController.java

License:Open Source License

@Override
public List<GAVariant> getTopHarmfulWithGene(String id, int n, String gene, List<String> variantEffects,
        Map<String, Double> alleleFrequencies) {

    List<GAVariant> list = new ArrayList<>();

    checkNotNull(id);// w  w w .  j  ava2  s.  co  m
    checkArgument(!"".equals(id));

    checkArgument(n != 0);

    checkNotNull(gene);
    checkArgument(!"".equals(gene));

    checkNotNull(variantEffects);
    checkArgument(variantEffects.size() != 0);

    checkNotNull(alleleFrequencies);
    checkArgument(alleleFrequencies.size() != 0);

    /** Build Query String **/

    String effectQuery = "";
    for (String effect : variantEffects) {
        effectQuery += String.format("%s:%s OR ", VariantsSchema.GENE_EFFECT,
                ClientUtils.escapeQueryChars(effect));
    }
    // Strip final ' OR '
    effectQuery = effectQuery.substring(0, effectQuery.length() - 4);

    // Find ExAC AF under the specified frequency, or where ExAC is null.
    String exacQuery = String.format("(-%s:[* TO *] AND *:*) OR %s:[0 TO %s] ", VariantsSchema.EXAC_AF,
            VariantsSchema.EXAC_AF,
            ClientUtils.escapeQueryChars(String.valueOf(alleleFrequencies.get(EXAC_FREQUENCY_FIELD))));

    String queryString = String.format("s:%s AND %s:%s AND (%s) AND (%s)", VariantsSchema.CALLSET_IDS,
            ClientUtils.escapeQueryChars(id), VariantsSchema.GENE, ClientUtils.escapeQueryChars(gene),
            effectQuery, exacQuery);

    SolrQuery q = new SolrQuery().setRows(n).setQuery(queryString);

    QueryResponse resp = null;

    try {
        resp = server.query(q);
    } catch (SolrServerException | IOException e) {
        logger.error("Error getting individuals with variants", e);
        return list;
    }
    Map<String, List<GAVariant>> map = SolrVariantUtils
            .variantListToCallsetMap(SolrVariantUtils.documentListToMapList(resp.getResults()));

    if (map.containsKey(id)) {
        list = map.get(id);
    }
    return list;
}

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