List of usage examples for org.apache.solr.client.solrj SolrQuery addFacetField
public SolrQuery addFacetField(String... fields)
From source file:org.mousephenotype.cda.solr.service.GenotypePhenotypeService.java
License:Apache License
/** * The query differs depending on topLevelMpTerms. If at least one term is passed, we need to find out the list of * genes that have the required phenotypes and use them in the query. We can't use the list of MP terms themselves * as t will filter out the other phenotype associations for the genese we're interested in. * @param topLevelMpTerms/*from www. j a v a 2 s. c o m*/ * @author ilinca * @return Solr query for g-p associations of genes that have all phenotypes passed in topLevelMpTerms. * @throws IOException * @throws SolrServerException */ private SolrQuery getPleiotropyQuery(List<String> topLevelMpTerms, Boolean idg, String idgClass) throws IOException, SolrServerException, SQLException { String pivot = GenotypePhenotypeDTO.MARKER_SYMBOL + "," + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME; SolrQuery query = new SolrQuery().setQuery("*:*").setFacet(true).setFacetLimit(-1); query.add("facet.pivot", pivot); query.addFacetField(GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME); if (idg != null && idg) { Set<GenesSecondaryProject> projectBeans = genesSecondaryProjectRepository .getAllBySecondaryProjectIdAndGroupLabel("idg", idgClass); query.addFilterQuery( GenotypePhenotypeDTO.MARKER_ACCESSION_ID + ":(\"" + projectBeans.stream().map(gene -> { return gene.getMgiGeneAccessionId(); }).collect(Collectors.joining("\" OR \"")) + "\")"); } if (topLevelMpTerms != null) { // We want data for genes that have ALL top level phenotypes in the list String interimPivot = GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME + "," + GenotypePhenotypeDTO.MARKER_SYMBOL; SolrQuery interimQuery = new SolrQuery().setFacet(true).setFacetLimit(-1).setQuery("*:*") .addFilterQuery(topLevelMpTerms.stream().collect(Collectors.joining("\" OR \"", GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_NAME + ":(\"", "\")"))); interimQuery.add("facet.pivot", interimPivot); // Filter out the pivot facets for un-wanted MP top level terms. We can get other top levels in the facets due to multiple parents. Map<String, Set<String>> genesByMpTopLevel = getFacetPivotResultsKeepCount( genotypePhenotypeCore.query(interimQuery), interimPivot).entrySet().stream() .filter(entry -> topLevelMpTerms.contains(entry.getKey())) .collect(Collectors.toMap(entry -> entry.getKey(), entry -> entry.getValue().keySet())); // Instantiate commonGenes with itself as it will work as identity on first set intersection (intersection of same sets) Set<String> commonGenes = genesByMpTopLevel.values().iterator().next(); // Keep only genes that are present in all top level mp groups commonGenes = genesByMpTopLevel.values().stream().reduce(commonGenes, (a, b) -> { a.retainAll(b); return a; }); query.addFilterQuery(commonGenes.stream() .collect(Collectors.joining(" OR ", GenotypePhenotypeDTO.MARKER_SYMBOL + ":(", ")"))); } return query; }
From source file:org.mousephenotype.cda.solr.service.GenotypePhenotypeService.java
License:Apache License
Map<String, Long> getDocumentCountByMgiGeneAccessionId() {
SolrQuery query = new SolrQuery();
query.setQuery("*:*");
query.setRows(0);//from w w w . ja v a2 s. c om
query.setFacet(true);
query.addFacetField(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
query.setFacetLimit(-1);
query.setFacetMinCount(1);
try {
return getFacets(genotypePhenotypeCore.query(query)).get(GenotypePhenotypeDTO.MARKER_ACCESSION_ID);
} catch (SolrServerException | IOException e) {
e.printStackTrace();
}
return new HashMap<>();
}
From source file:org.mousephenotype.cda.solr.service.GenotypePhenotypeService.java
License:Apache License
/** * * @param mpId// ww w. j a va2 s. c om * @param filterOnAccessions list of marker accessions to restrict the results by e.g. for the hearing page we only want results for the 67 genes for the paper * @return * @throws JSONException */ public JSONArray getTopLevelPhenotypeIntersection(String mpId, Set<String> filterOnAccessions) throws JSONException { String pivot = GenotypePhenotypeDTO.MARKER_ACCESSION_ID + "," + GenotypePhenotypeDTO.MARKER_SYMBOL; SolrQuery query = new SolrQuery(); query.setQuery(mpId == null ? "*:*" : GenotypePhenotypeDTO.MP_TERM_ID + ":\"" + mpId + "\" OR " + GenotypePhenotypeDTO.INTERMEDIATE_MP_TERM_ID + ":\"" + mpId + "\" OR " + GenotypePhenotypeDTO.TOP_LEVEL_MP_TERM_ID + ":\"" + mpId + "\""); query.setRows(0); query.setFacet(true); query.addFacetField(GenotypePhenotypeDTO.MARKER_ACCESSION_ID); query.setFacetLimit(-1); query.setFacetMinCount(1); query.add("facet.pivot", pivot); try { QueryResponse response = genotypePhenotypeCore.query(query); Map<String, Long> countByGene = getFacets(response).get(GenotypePhenotypeDTO.MARKER_ACCESSION_ID); Map<String, List<String>> geneAccSymbol = getFacetPivotResults(response, pivot); Set<String> jitter = new HashSet<>(); JSONArray array = new JSONArray(); for (String markerAcc : countByGene.keySet()) { JSONObject obj = new JSONObject(); Double y = new Double(countByGene.get(markerAcc)); Double x = (getDocumentCountByMgiGeneAccessionId().get(markerAcc) - y); obj = addJitter(x, y, jitter, obj); obj.accumulate("markerAcc", markerAcc); obj.accumulate("markerSymbol", geneAccSymbol.get(markerAcc).get(0)); if (filterOnAccessions != null && filterOnAccessions.contains(markerAcc)) { array.put(obj); } else if (filterOnAccessions == null) { array.put(obj); } } return array; } catch (SolrServerException | IOException e) { e.printStackTrace(); } return null; }
From source file:org.mousephenotype.cda.solr.service.ImageService.java
License:Apache License
public Map<String, Set<String>> getFacets(String anatomyId) throws SolrServerException, IOException { Map<String, Set<String>> res = new HashMap<>(); SolrQuery query = new SolrQuery(); query.setQuery(ImageDTO.PROCEDURE_NAME + ":*LacZ"); if (anatomyId != null) { query.addFilterQuery("(" + ImageDTO.ANATOMY_ID + ":\"" + anatomyId + "\" OR " + ImageDTO.INTERMEDIATE_ANATOMY_ID + ":\"" + anatomyId + "\" OR " + ImageDTO.SELECTED_TOP_LEVEL_ANATOMY_ID + ":\"" + anatomyId + "\")"); }/* w ww. j a v a2 s. c o m*/ query.addFilterQuery(ImageDTO.BIOLOGICAL_SAMPLE_GROUP + ":\"experimental\"") .addFilterQuery("(" + ImageDTO.PARAMETER_ASSOCIATION_VALUE + ":\"no expression\" OR " + ObservationDTO.PARAMETER_ASSOCIATION_VALUE + ":\"expression\"" + ")"); // only have expressed and // not expressed ingnore // ambiguous and no tissue query.setFacet(true); query.setFacetLimit(-1); query.setFacetMinCount(1); query.addFacetField(ImageDTO.ANATOMY_TERM); query.addFacetField(ImageDTO.PHENOTYPING_CENTER); query.addFacetField(ImageDTO.PROCEDURE_NAME); query.addFacetField(ImageDTO.PARAMETER_ASSOCIATION_VALUE); QueryResponse response = impcImagesCore.query(query); for (FacetField facetField : response.getFacetFields()) { Set<String> filter = new TreeSet<>(); for (Count facet : facetField.getValues()) { if (!facet.getName().equals("tissue not available") && !facet.getName().equals("ambiguous")) { filter.add(facet.getName()); } } res.put(facetField.getName(), filter); } return res; }
From source file:org.mousephenotype.cda.solr.service.ImageService.java
License:Apache License
public QueryResponse getProcedureFacetsForGeneByProcedure(String mgiAccession, String experimentOrControl) throws SolrServerException, IOException { // Map<String, ResponseWrapper<ImageDTO>> map=new HashMap<String, // ResponseWrapper<ImageDTO>>(); // String queryString = "q=gene_accession_id:\"" + mgiAccession + // "\"&fq=" + ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + // experimentOrControl+"&facet=true&facet.field=procedure_name&facet.mincount=1"; // log.debug("queryString in ImageService getFacets=" + queryString); // make a facet request first to get the procedures and then reuturn // make requests for each procedure // http://wwwdev.ebi.ac.uk/mi/impc/dev/solr/impc_images/select?q=gene_accession_id:%22MGI:2384986%22&&fq=biological_sample_group:experimental&facet=true&facet.field=procedure_name SolrQuery solrQuery = new SolrQuery(); solrQuery.setQuery(ImageDTO.GENE_ACCESSION_ID + ":\"" + mgiAccession + "\""); solrQuery.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + experimentOrControl); solrQuery.setFacetMinCount(1);/*from www . j ava 2 s . co m*/ solrQuery.setFacet(true); solrQuery.addFacetField("procedure_name"); // solrQuery.setRows(0); QueryResponse response = impcImagesCore.query(solrQuery); return response; }
From source file:org.mousephenotype.cda.solr.service.ImageService.java
License:Apache License
public List<String[]> getLaczExpressionSpreadsheet(String imageCollectionLinkBase) { SolrQuery query = new SolrQuery(); ArrayList<String[]> res = new ArrayList<>(); String[] aux = new String[0]; query.setQuery(ImageDTO.PROCEDURE_NAME + ":\"Adult LacZ\" AND " + ImageDTO.BIOLOGICAL_SAMPLE_GROUP + ":experimental"); query.setRows(1000000);//from w w w. ja v a2 s .c o m query.addField(ImageDTO.GENE_SYMBOL); query.addField(ImageDTO.GENE_ACCESSION_ID); query.addField(ImageDTO.ALLELE_SYMBOL); query.addField(ImageDTO.COLONY_ID); query.addField(ImageDTO.BIOLOGICAL_SAMPLE_ID); query.addField(ImageDTO.ZYGOSITY); query.addField(ImageDTO.SEX); query.addField(ImageDTO.PARAMETER_ASSOCIATION_NAME); query.addField(ImageDTO.PARAMETER_STABLE_ID); query.addField(ImageDTO.PARAMETER_ASSOCIATION_VALUE); query.addField(ImageDTO.GENE_ACCESSION_ID); query.addField(ImageDTO.PHENOTYPING_CENTER); query.setFacet(true); query.setFacetLimit(100); query.addFacetField(ImageDTO.PARAMETER_ASSOCIATION_NAME); query.set("group", true); query.set("group.limit", 100000); query.set("group.field", ImageDTO.BIOLOGICAL_SAMPLE_ID); try { QueryResponse solrResult = impcImagesCore.query(query); ArrayList<String> allParameters = new ArrayList<>(); List<String> header = new ArrayList<>(); header.add("Gene Symbol"); header.add("MGI Gene Id"); header.add("Allele Symbol"); header.add("Colony Id"); header.add("Biological Sample Id"); header.add("Zygosity"); header.add("Sex"); header.add("Phenotyping Centre"); logger.info(SolrUtils.getBaseURL(impcImagesCore) + "/select?" + query); // Get facets as we need to turn them into columns for (Count facet : solrResult.getFacetField(ImageDTO.PARAMETER_ASSOCIATION_NAME).getValues()) { allParameters.add(facet.getName()); header.add(facet.getName()); } header.add("image_collection_link"); res.add(header.toArray(aux)); for (Group group : solrResult.getGroupResponse().getValues().get(0).getValues()) { List<String> row = new ArrayList<>(); ArrayList<String> params = new ArrayList<>(); ArrayList<String> paramValues = new ArrayList<>(); String urlToImagePicker = imageCollectionLinkBase + "/imageComparator?acc="; for (SolrDocument doc : group.getResult()) { if (row.size() == 0) { row.add(doc.getFieldValues(ImageDTO.GENE_SYMBOL).iterator().next().toString()); row.add(doc.getFieldValues(ImageDTO.GENE_ACCESSION_ID).iterator().next().toString()); urlToImagePicker += doc.getFieldValue(ImageDTO.GENE_ACCESSION_ID) + "¶meter_stable_id="; urlToImagePicker += doc.getFieldValue(ImageDTO.PARAMETER_STABLE_ID); if (doc.getFieldValue(ImageDTO.ALLELE_SYMBOL) != null) { row.add(doc.getFieldValue(ImageDTO.ALLELE_SYMBOL).toString()); } row.add(doc.getFieldValue(ImageDTO.COLONY_ID).toString()); row.add(doc.getFieldValue(ImageDTO.BIOLOGICAL_SAMPLE_ID).toString()); if (doc.getFieldValue(ImageDTO.ZYGOSITY) != null) { row.add(doc.getFieldValue(ImageDTO.ZYGOSITY).toString()); } row.add(doc.getFieldValue(ImageDTO.SEX).toString()); row.add(doc.getFieldValue(ImageDTO.PHENOTYPING_CENTER).toString()); } if (doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_NAME) != null) { for (int i = 0; i < doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_NAME).size(); i++) { params.add(doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_NAME) .toArray(new Object[0])[i].toString()); if (doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_VALUE) != null) { paramValues.add(doc.getFieldValues(ImageDTO.PARAMETER_ASSOCIATION_VALUE) .toArray(new Object[0])[i].toString()); } else { paramValues.add(Constants.NO_INFORMATION_AVAILABLE); } } } } for (String tissue : allParameters) { if (params.contains(tissue)) { row.add(paramValues.get(params.indexOf(tissue))); } else { row.add(""); } } row.add(urlToImagePicker); res.add(row.toArray(aux)); } } catch (SolrServerException | IOException e) { e.printStackTrace(); } return res; }
From source file:org.mousephenotype.cda.solr.service.ImageService.java
License:Apache License
public QueryResponse getParameterFacetsForGeneByProcedure(String acc, String procedureName, String controlOrExperimental) throws SolrServerException, IOException { // e.g./*from w w w . ja v a2 s . co m*/ // http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/impc_images/query?q=gene_accession_id:%22MGI:2384986%22&fq=biological_sample_group:experimental&fq=procedure_name:X-ray&facet=true&facet.field=parameter_stable_id SolrQuery solrQuery = new SolrQuery(); solrQuery.setQuery("gene_accession_id:\"" + acc + "\""); solrQuery.addFilterQuery(ObservationDTO.BIOLOGICAL_SAMPLE_GROUP + ":" + controlOrExperimental); solrQuery.setFacetMinCount(1); solrQuery.setFacet(true); solrQuery.addFilterQuery(ObservationDTO.PROCEDURE_NAME + ":\"" + procedureName + "\""); solrQuery.addFacetField(ObservationDTO.PARAMETER_STABLE_ID); // solrQuery.setRows(0); QueryResponse response = impcImagesCore.query(solrQuery); return response; }
From source file:org.mousephenotype.cda.solr.service.ImageService.java
License:Apache License
/** * * @param acc// w ww .j a v a2 s . c o m * @return a map containing the mp and colony_id combinations so that if we have these then we show an image link on the phenotype table on the gene page. Each row in table could have a different colony_id as well as mp id * @throws SolrServerException, IOException */ public Map<String, Set<String>> getImagePropertiesThatHaveMp(String acc) throws SolrServerException, IOException { //http://ves-ebi-d0.ebi.ac.uk:8090/mi/impc/dev/solr/impc_images/select?q=gene_accession_id:%22MGI:1913955%22&fq=mp_id:*&facet=true&facet.mincount=1&facet.limit=-1&facet.field=colony_id&facet.field=mp_id&facet.field=mp_term&rows=0 Map<String, Set<String>> mpToColony = new HashMap<>(); SolrQuery query = new SolrQuery(); query.setQuery(ImageDTO.GENE_ACCESSION_ID + ":\"" + acc + "\"").setRows(100000000); query.addFilterQuery(ImageDTO.MP_ID_TERM + ":*"); query.setFacet(true); query.setFacetLimit(-1); query.setFacetMinCount(1); String pivotFacet = ImageDTO.MP_ID_TERM + "," + ImageDTO.COLONY_ID; query.set("facet.pivot", pivotFacet); query.addFacetField(ObservationDTO.COLONY_ID); logger.debug("solr query for images properties for mp = " + query); QueryResponse response = impcImagesCore.query(query); for (PivotField pivot : response.getFacetPivot().get(pivotFacet)) { if (pivot.getPivot() != null) { //logger.info("pivot="+pivot.getValue()); String mpIdAndName = pivot.getValue().toString(); //logger.info("mpIdAndName" +mpIdAndName); String mpId = ""; Set<String> colonIds = new TreeSet<>(); if (mpIdAndName.contains("_")) { mpId = (mpIdAndName.split("_")[0]); } for (PivotField mp : pivot.getPivot()) { //logger.info("adding mp="+pivot.getValue()+" adding value="+mp.getValue()); String colonyId = mp.getValue().toString(); colonIds.add(colonyId); } mpToColony.put(mpId, colonIds); } } return mpToColony; }
From source file:org.mousephenotype.cda.solr.service.MpService.java
License:Apache License
public Set<BasicBean> getAllTopLevelPhenotypesAsBasicBeans() throws SolrServerException, IOException { SolrQuery solrQuery = new SolrQuery(); solrQuery.addFacetField("top_level_mp_term_id"); solrQuery.setRows(0);//from w ww .j av a2 s . c om QueryResponse rsp = mpCore.query(solrQuery); HashSet<BasicBean> allTopLevelPhenotypes = new LinkedHashSet<BasicBean>(); for (FacetField ff : rsp.getFacetFields()) { for (Count count : ff.getValues()) { String mpArray[] = count.getName().split("___"); BasicBean bean = new BasicBean(); bean.setName(mpArray[1]); bean.setId(mpArray[0]); allTopLevelPhenotypes.add(bean); } } return allTopLevelPhenotypes; }
From source file:org.mousephenotype.cda.solr.service.ObservationService.java
License:Apache License
/** * Returns a collection of biological sample ids for all mice matching the PROCEDURE_STABLE_ID. * * @param procedureStableId the procedure stable id (e.g. "IMPC_CAL_*" or "IMPC_IPG_*") * * @return a collection of biological sample ids for all mice matching the PROCEDURE_STABLE_ID * * @throws SolrServerException, IOException *//*w w w . java2 s. co m*/ public Collection<String> getMetabolismReportBiologicalSampleIds(String procedureStableId) throws SolrServerException, IOException { SolrQuery query = new SolrQuery(); query.setQuery(String.format("%s:%s", ObservationDTO.PROCEDURE_STABLE_ID, procedureStableId)); query.setRows(0); query.setFacetMinCount(1); query.setFacetLimit(100000); query.addFacetField(ObservationDTO.BIOLOGICAL_SAMPLE_ID); logger.info(SolrUtils.getBaseURL(experimentCore) + "/select?" + query); return getFacets(experimentCore.query(query)).get(ObservationDTO.BIOLOGICAL_SAMPLE_ID).keySet(); }