Example usage for org.apache.solr.client.solrj SolrQuery setSort

List of usage examples for org.apache.solr.client.solrj SolrQuery setSort

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Introduction

In this page you can find the example usage for org.apache.solr.client.solrj SolrQuery setSort.

Prototype

public SolrQuery setSort(String field, ORDER order)

Source Link

Document

Replaces the current sort information with a single sort clause

Usage

From source file:org.mousephenotype.cda.solr.service.ExpressionService.java

License:Apache License

/**
 *
 * @param mgiAccession/*  w  w  w  .  j a v  a2  s  .  c o m*/
 *            if mgi accesion null assume a request for control data
 * @param fields
 * @return
 * @throws SolrServerException, IOException
 */
private QueryResponse getCategoricalAdultLacZData(String mgiAccession, boolean embryo, String... fields)
        throws SolrServerException, IOException {
    // e.g.
    // http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/experiment/select?q=gene_accession_id:%22MGI:1351668%22&facet=true&facet.field=parameter_name&facet.mincount=1&fq=(procedure_name:%22Adult%20LacZ%22)&rows=10000
    SolrQuery solrQuery = new SolrQuery();
    if (mgiAccession != null) {
        solrQuery.setQuery(ImageDTO.GENE_ACCESSION_ID + ":\"" + mgiAccession + "\"");
    } else {
        // http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/impc_images/select?q=biological_sample_group:control&facet=true&facet.field=ma_term&facet.mincount=1&fq=(parameter_name:%22LacZ%20Images%20Section%22%20OR%20parameter_name:%22LacZ%20Images%20Wholemount%22)&rows=100000
        solrQuery.setQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":\"" + "control" + "\"");
    }
    if (embryo) {
        solrQuery.addFilterQuery(ImageDTO.PROCEDURE_NAME + ":\"Embryo LacZ\"");
        solrQuery.addFilterQuery("-" + ImageDTO.PARAMETER_NAME + ":\"LacZ images section\"");
        solrQuery.addFilterQuery("-" + ImageDTO.PARAMETER_NAME + ":\"LacZ images wholemount\"");
        solrQuery.addFilterQuery(ObservationDTO.OBSERVATION_TYPE + ":\"categorical\"");
    } else {
        solrQuery.addFilterQuery(ImageDTO.PROCEDURE_NAME + ":\"Adult LacZ\"");
        solrQuery.addFilterQuery("-" + ImageDTO.PARAMETER_NAME + ":\"LacZ Images Section\"");
        solrQuery.addFilterQuery("-" + ImageDTO.PARAMETER_NAME + ":\"LacZ Images Wholemount\"");
        solrQuery.addFilterQuery(ObservationDTO.OBSERVATION_TYPE + ":\"categorical\"");
    }

    solrQuery.addSort(ImageDTO.ID, SolrQuery.ORDER.asc);
    solrQuery.setFields(fields);
    solrQuery.setRows(Integer.MAX_VALUE);
    solrQuery.setSort(ObservationDTO.ID, SolrQuery.ORDER.asc);

    QueryResponse response = experimentCore.query(solrQuery);
    return response;
}

From source file:org.mousephenotype.cda.solr.service.ExpressionService.java

License:Apache License

private QueryResponse getEmbryoLaczImageFacetsForGene(String mgiAccession, String parameterStableId,
        String... fields) throws SolrServerException, IOException {
    //solrQuery.addFilterQuery(ImageDTO.PARAMETER_STABLE_ID + ":IMPC_ELZ_064_001" + " OR "
    //+ ImageDTO.PARAMETER_STABLE_ID + ":IMPC_ELZ_063_001");
    // e.g.//from  w w  w. java  2 s  .  com
    // http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/impc_images/select?q=gene_accession_id:%22MGI:1920455%22&facet=true&facet.field=selected_top_level_ma_term&fq=(parameter_name:%22LacZ%20Images%20Section%22%20OR%20parameter_name:%22LacZ%20Images%20Wholemount%22)
    // for embryo data the fields would be like this
    // "parameter_name": "LacZ images section",
    // "procedure_name": "Embryo LacZ",

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(ImageDTO.GENE_ACCESSION_ID + ":\"" + mgiAccession + "\"");
    solrQuery.addFilterQuery(ImageDTO.PARAMETER_STABLE_ID + ":" + parameterStableId);// reduce
    // the number to image parameters only as we are talking about images not expression data here
    solrQuery.setFacetMinCount(1);
    solrQuery.setFacet(true);
    solrQuery.setFields(fields);
    solrQuery.addFacetField(ImageDTO.SELECTED_TOP_LEVEL_ANATOMY_TERM);
    solrQuery.setRows(Integer.MAX_VALUE);
    solrQuery.setSort(ObservationDTO.ID, SolrQuery.ORDER.asc);
    QueryResponse response = impcImagesCore.query(solrQuery);
    return response;
}

From source file:org.mousephenotype.cda.solr.service.GenotypePhenotypeService.java

License:Apache License

public SolrDocumentList getPhenotypesForTopLevelTerm(String gene, String mpID, ZygosityType zygosity)
        throws SolrServerException, IOException {

    String query;/*  w  w w. j a  v  a2  s . co m*/
    if (gene.equalsIgnoreCase("*")) {
        query = GenotypePhenotypeDTO.MARKER_ACCESSION_ID + ":" + gene + " AND ";
    } else {
        query = GenotypePhenotypeDTO.MARKER_ACCESSION_ID + ":\"" + gene + "\" AND ";

    }

    SolrQuery solrQuery = new SolrQuery();
    solrQuery.setQuery(query + "(" + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID + ":\"" + mpID + "\" OR "
            + GenotypePhenotypeDTO.MP_TERM_ID + ":\"" + mpID + "\")");
    solrQuery.setRows(1000000);
    solrQuery.setSort(StatisticalResultDTO.P_VALUE, ORDER.asc);
    solrQuery.setFields(GenotypePhenotypeDTO.P_VALUE, GenotypePhenotypeDTO.SEX, GenotypePhenotypeDTO.ZYGOSITY,
            GenotypePhenotypeDTO.MARKER_ACCESSION_ID, GenotypePhenotypeDTO.MARKER_SYMBOL,
            GenotypePhenotypeDTO.MP_TERM_ID, GenotypePhenotypeDTO.MP_TERM_NAME,
            GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID, GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME);

    if (zygosity != null) {
        solrQuery.setFilterQueries(GenotypePhenotypeDTO.ZYGOSITY + ":" + zygosity.getName());
    }

    SolrDocumentList result = genotypePhenotypeCore.query(solrQuery).getResults();

    return result;
}

From source file:org.mousephenotype.cda.solr.service.GenotypePhenotypeService.java

License:Apache License

public PhenotypeFacetResult getMPByGeneAccessionAndFilter(String accId, List<String> topLevelMpTermName,
        List<String> resourceFullname) throws IOException, URISyntaxException, JSONException {

    String solrUrl = SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select?";
    SolrQuery q = new SolrQuery();

    q.setQuery(GenotypePhenotypeDTO.MARKER_ACCESSION_ID + ":\"" + accId + "\"");
    q.setRows(10000000);/*  ww  w . j a  va 2  s . c  om*/
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    q.addFacetField(GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME);
    //q.addFacetField(GenotypePhenotypeDTO.RESOURCE_FULLNAME);
    q.set("wt", "json");
    q.setSort(GenotypePhenotypeDTO.P_VALUE, ORDER.asc);

    if (topLevelMpTermName != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME + ":(\""
                + StringUtils.join(topLevelMpTermName, "\" OR \"") + "\")");
    }

    solrUrl += q;

    return createPhenotypeResultFromSolrResponse(solrUrl);
}

From source file:org.mousephenotype.cda.solr.service.GenotypePhenotypeService.java

License:Apache License

public PhenotypeFacetResult getMPCallByMPAccessionAndFilter(String phenotype_id, List<String> procedureName,
        List<String> markerSymbol, List<String> mpTermName, Map<String, Synonym> synonyms)
        throws IOException, URISyntaxException, JSONException {

    String url = SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select/?";
    SolrQuery q = new SolrQuery();

    q.setQuery("*:*");
    q.addFilterQuery("(" + GenotypePhenotypeDTO.MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.INTERMEDIATE_MP_TERM_ID + ":\"" + phenotype_id + "\")");
    q.setRows(10000000);/*from  w w  w .  j ava  2  s.c om*/
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    q.addFacetField(GenotypePhenotypeDTO.PROCEDURE_NAME);
    q.addFacetField(GenotypePhenotypeDTO.MARKER_SYMBOL);
    q.addFacetField(GenotypePhenotypeDTO.MP_TERM_NAME);
    q.set("wt", "json");
    q.setSort(GenotypePhenotypeDTO.P_VALUE, ORDER.asc);

    q.setFields(GenotypePhenotypeDTO.MP_TERM_NAME, GenotypePhenotypeDTO.MP_TERM_ID,
            GenotypePhenotypeDTO.MPATH_TERM_NAME, GenotypePhenotypeDTO.MPATH_TERM_ID,
            GenotypePhenotypeDTO.EXTERNAL_ID, GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID,
            GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME, GenotypePhenotypeDTO.ALLELE_SYMBOL,
            GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ALLELE_ACCESSION_ID,
            GenotypePhenotypeDTO.MARKER_SYMBOL, GenotypePhenotypeDTO.MARKER_ACCESSION_ID,
            GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ZYGOSITY, GenotypePhenotypeDTO.SEX,
            GenotypePhenotypeDTO.LIFE_STAGE_NAME, GenotypePhenotypeDTO.RESOURCE_NAME,
            GenotypePhenotypeDTO.PARAMETER_STABLE_ID, GenotypePhenotypeDTO.PARAMETER_NAME,
            GenotypePhenotypeDTO.PIPELINE_STABLE_ID, GenotypePhenotypeDTO.PROJECT_NAME,
            GenotypePhenotypeDTO.PROJECT_EXTERNAL_ID, GenotypePhenotypeDTO.P_VALUE,
            GenotypePhenotypeDTO.EFFECT_SIZE, GenotypePhenotypeDTO.PROCEDURE_STABLE_ID,
            GenotypePhenotypeDTO.PROCEDURE_NAME, GenotypePhenotypeDTO.PIPELINE_NAME);

    if (procedureName != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.PROCEDURE_NAME + ":(\""
                + StringUtils.join(procedureName, "\" OR \"") + "\")");
    }
    if (markerSymbol != null) {
        q.addFilterQuery(GenotypePhenotypeDTO.MARKER_SYMBOL + ":(\""
                + StringUtils.join(markerSymbol, "\" OR \"") + "\")");
    }
    if (mpTermName != null) {
        q.addFilterQuery(
                GenotypePhenotypeDTO.MP_TERM_NAME + ":(\"" + StringUtils.join(mpTermName, "\" OR \"") + "\")");
    }

    url += q;

    return createPhenotypeResultFromSolrResponse(url, synonyms);

}

From source file:org.mousephenotype.cda.solr.service.GenotypePhenotypeService.java

License:Apache License

/**
 * Get a list of gene symbols for this phenotype
 * @param phenotype_id//from   w  ww  . j a va2 s  .c  o  m
 * @return
 * @throws IOException
 * @throws URISyntaxException
 * @throws SolrServerException
 */
public List<String> getGenesForMpId(String phenotype_id)
        throws IOException, URISyntaxException, SolrServerException {
    List<String> results = new ArrayList<>();
    String url = SolrUtils.getBaseURL(genotypePhenotypeCore) + "/select/?";
    SolrQuery q = new SolrQuery();

    q.setQuery("*:*");
    q.addFilterQuery("(" + GenotypePhenotypeDTO.MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID + ":\"" + phenotype_id + "\" OR "
            + GenotypePhenotypeDTO.INTERMEDIATE_MP_TERM_ID + ":\"" + phenotype_id + "\")");
    q.setRows(10000000);
    q.setFacet(true);
    q.setFacetMinCount(1);
    q.setFacetLimit(-1);
    //q.addFacetField(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
    q.addFacetField(GenotypePhenotypeDTO.MARKER_SYMBOL);
    // q.addFacetField(GenotypePhenotypeDTO.MP_TERM_NAME );
    q.set("wt", "json");
    q.setSort(GenotypePhenotypeDTO.P_VALUE, ORDER.asc);
    q.setFields(GenotypePhenotypeDTO.MARKER_SYMBOL);
    //               q.setFields(GenotypePhenotypeDTO.MP_TERM_NAME, GenotypePhenotypeDTO.MP_TERM_ID, GenotypePhenotypeDTO.MPATH_TERM_NAME, GenotypePhenotypeDTO.MPATH_TERM_ID, GenotypePhenotypeDTO.EXTERNAL_ID,
    //                     GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID, GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME, GenotypePhenotypeDTO.ALLELE_SYMBOL, 
    //                     GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ALLELE_ACCESSION_ID, GenotypePhenotypeDTO.MARKER_SYMBOL,
    //                     GenotypePhenotypeDTO.MARKER_ACCESSION_ID, GenotypePhenotypeDTO.PHENOTYPING_CENTER, GenotypePhenotypeDTO.ZYGOSITY, 
    //                     GenotypePhenotypeDTO.SEX, GenotypePhenotypeDTO.LIFE_STAGE_NAME, GenotypePhenotypeDTO.RESOURCE_NAME, GenotypePhenotypeDTO.PARAMETER_STABLE_ID, GenotypePhenotypeDTO.PARAMETER_NAME,
    //                     GenotypePhenotypeDTO.PIPELINE_STABLE_ID, GenotypePhenotypeDTO.PROJECT_NAME, GenotypePhenotypeDTO.PROJECT_EXTERNAL_ID,
    //                     GenotypePhenotypeDTO.P_VALUE, GenotypePhenotypeDTO.EFFECT_SIZE, GenotypePhenotypeDTO.PROCEDURE_STABLE_ID,
    //                     GenotypePhenotypeDTO.PROCEDURE_NAME, GenotypePhenotypeDTO.PIPELINE_NAME);

    QueryResponse response = genotypePhenotypeCore.query(q);
    for (Count facet : response.getFacetField(GenotypePhenotypeDTO.MARKER_SYMBOL).getValues()) {
        //System.out.println("facet="+facet.getName());
        results.add(facet.getName());
    }
    return results;
}

From source file:org.mousephenotype.cda.solr.service.ImageService.java

License:Apache License

/**
*
* @param metadataGroup/* ww w . j a  va  2 s .  com*/
* @param center
* @param strain
* @param procedure_name
* @param parameter
* @param date
* @param numberOfImagesToRetrieve
* @param sex
* @return
* @throws SolrServerException, IOException
*/
public QueryResponse getControlImagesForProcedure(String metadataGroup, String center, String strain,
        String procedure_name, String parameter, Date date, int numberOfImagesToRetrieve, SexType sex)
        throws SolrServerException, IOException {

    SolrQuery solrQuery = new SolrQuery();

    solrQuery.setQuery("*:*");

    solrQuery.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":control",
            ObservationDTO.PHENOTYPING_CENTER + ":\"" + center + "\"",
            ObservationDTO.STRAIN_NAME + ":" + strain, ObservationDTO.PARAMETER_STABLE_ID + ":" + parameter,
            ObservationDTO.PROCEDURE_NAME + ":\"" + procedure_name + "\"");

    solrQuery.setSort(ObservationDTO.DATE_OF_EXPERIMENT, SolrQuery.ORDER.asc);
    solrQuery.setRows(numberOfImagesToRetrieve);

    if (StringUtils.isNotEmpty(metadataGroup)) {
        solrQuery.addFilterQuery(ObservationDTO.METADATA_GROUP + ":" + metadataGroup);
    }
    if (sex != null) {
        solrQuery.addFilterQuery(ObservationDTO.SEX + ":" + sex.name());
    }

    QueryResponse response = impcImagesCore.query(solrQuery);

    return response;
}

From source file:org.mousephenotype.cda.solr.service.ObservationService.java

License:Apache License

public List<ObservationDTO> getObservationsByParameterStableId(String parameterStableId)
        throws SolrServerException, IOException {

    SolrQuery query = new SolrQuery();
    query.setQuery(String.format("%s:\"%s\"", ObservationDTO.PARAMETER_STABLE_ID, parameterStableId));
    query.setRows(Integer.MAX_VALUE);
    query.setSort(ObservationDTO.ID, SolrQuery.ORDER.asc);
    logger.info("getObservationsByParameterStableId Url: " + SolrUtils.getBaseURL(experimentCore) + "/select?"
            + query);//w  w  w .j a va2s.  c o m

    return experimentCore.query(query).getBeans(ObservationDTO.class);
}

From source file:org.mousephenotype.cda.solr.service.ObservationService.java

License:Apache License

public Set<String> getViabilityForGene(String acc) throws SolrServerException, IOException {

    SolrQuery query = new SolrQuery();
    query.setQuery(ObservationDTO.PARAMETER_STABLE_ID + ":IMPC_VIA_001_001");
    query.setFilterQueries(ObservationDTO.GENE_ACCESSION_ID + ":\"" + acc + "\"");
    query.addField(ObservationDTO.GENE_SYMBOL);
    query.addField(ObservationDTO.GENE_ACCESSION_ID);
    query.addField(ObservationDTO.CATEGORY);
    query.setSort(ObservationDTO.ID, SolrQuery.ORDER.asc);
    query.setRows(100000);//  w  w w .ja  v  a 2  s .c  o  m

    logger.info("getViabilityForGene Url" + SolrUtils.getBaseURL(experimentCore) + "/select?" + query);

    HashSet<String> viabilityCategories = new HashSet<>();

    for (SolrDocument doc : experimentCore.query(query).getResults()) {
        viabilityCategories.add(doc.getFieldValue(ObservationDTO.CATEGORY).toString());
    }

    return viabilityCategories;
}

From source file:org.mousephenotype.cda.solr.service.ObservationService.java

License:Apache License

/**
 * Returns a <code>QueryResponse</code> of data found using the given resources, parameter stable ids, and category
 * comprising geneSymbol, geneAccessionId, colonyId, and category.
 *
 * @param resources//from   w w w  .j  a  va  2  s  .  com
 * @param parameterStableIds A list of parameter stable ids that is "or'd" together to produce the result (e.g. IMPC_VIA_001_001)
 * @param categories         A list of categories that is "or'd" together to produce the result (e.g. Viable, Lethal, Male, Fertile)
 * @return a <code>QueryResponse</code> of data found using the given resources, parameter stable ids, and category,
 * comprising geneSymbol, geneAccessionId, colonyId, and category.
 * @throws SolrServerException, IOException
 */
public QueryResponse getData(List<String> resources, List<String> parameterStableIds, List<String> categories)
        throws SolrServerException, IOException {
    SolrQuery query = new SolrQuery();
    if ((resources != null) && (!resources.isEmpty())) {
        query.setFilterQueries(ObservationDTO.DATASOURCE_NAME + ":"
                + StringUtils.join(resources, " OR " + ObservationDTO.DATASOURCE_NAME + ":"));
    }
    if ((categories != null) && (!categories.isEmpty())) {
        query.setFilterQueries(ObservationDTO.CATEGORY + ":"
                + StringUtils.join(categories, " OR " + ObservationDTO.CATEGORY + ":"));
    }
    if ((parameterStableIds != null) && (!parameterStableIds.isEmpty())) {
        query.setQuery(ObservationDTO.PARAMETER_STABLE_ID + ":"
                + StringUtils.join(parameterStableIds, " OR " + ObservationDTO.PARAMETER_STABLE_ID + ":"));
    }

    query.addField(ObservationDTO.GENE_SYMBOL);
    query.addField(ObservationDTO.GENE_ACCESSION_ID);
    query.addField(ObservationDTO.ALLELE_SYMBOL);
    query.addField(ObservationDTO.ALLELE_ACCESSION_ID);
    query.addField(ObservationDTO.PHENOTYPING_CENTER);
    query.addField(ObservationDTO.COLONY_ID);
    query.addField(ObservationDTO.CATEGORY);
    query.addField(ObservationDTO.SEX);
    query.addField(ObservationDTO.ZYGOSITY);
    query.setSort(ObservationDTO.ID, SolrQuery.ORDER.asc);
    query.setRows(1000000);

    logger.info("getData Url: " + SolrUtils.getBaseURL(experimentCore) + "/select?" + query);

    return experimentCore.query(query);
}