Examples with DashboardDao gov.nih.nci.ctd2.dashboard.dao.DashboardDao used on opensource projects

Example 1 with DashboardDao

use of gov.nih.nci.ctd2.dashboard.dao.DashboardDao in project nci-ctd2-dashboard by CBIIT.

the class BrowseAPI method getSubmission.

@Transactional
@RequestMapping(value = "{subjectClass}/{subjectName}", method = { RequestMethod.GET }, headers = "Accept=application/json")
public ResponseEntity<String> getSubmission(@PathVariable String subjectClass, @PathVariable String subjectName, @RequestParam(value = "center", required = false, defaultValue = "") String center, @RequestParam(value = "role", required = false, defaultValue = "") String role, @RequestParam(value = "tier", required = false, defaultValue = "") String tiers, @RequestParam(value = "maximum", required = false, defaultValue = "") String maximum) {
    HttpHeaders headers = new HttpHeaders();
    headers.add("Content-Type", "application/json; charset=utf-8");
    SubjectResponse.Filter filter = SubjectResponse.createFilter(center, role, tiers, maximum);
    DashboardEntity subject = null;
    if (subjectClass.equalsIgnoreCase("evidence") || subjectClass.equalsIgnoreCase("eco")) {
        /* API spec asks for Evidence but stable URL uses eco */
        var obj = dashboardDao.getEntityByStableURL("eco", "eco/" + subjectName);
        if (obj instanceof ECOTerm) {
            subject = (ECOTerm) obj;
        } else {
            log.error("unexpected subject type:" + obj.getClass().getName());
        }
    } else if (subjectClass.equalsIgnoreCase("gene")) {
        List<Gene> genes = dashboardDao.findGenesBySymbol(subjectName);
        if (genes.size() > 0) {
            Gene gene = genes.get(0);
            List<Protein> p = dashboardDao.findProteinByGene(gene);
            Xref xref = new XrefImpl();
            xref.setDatabaseId(p.get(0).getUniprotId());
            xref.setDatabaseName("UniProt");
            gene.getXrefs().add(xref);
            subject = gene;
        }
    } else {
        var obj = dashboardDao.getEntityByStableURL(subjectClass, subjectClass + "/" + subjectName);
        if (obj instanceof Subject) {
            subject = (Subject) obj;
        } else {
            log.error("unexpected subject type: " + (obj == null ? null : obj.getClass().getName()));
        }
    }
    if (subject == null) {
        return new ResponseEntity<String>(headers, HttpStatus.NOT_FOUND);
    }
    SubjectResponse subjectResponse = SubjectResponse.createInstance(subject, filter, dashboardDao);
    log.debug("ready to serialize");
    JSONSerializer jsonSerializer = CTD2Serializer.createJSONSerializer();
    String json = "{}";
    try {
        json = jsonSerializer.deepSerialize(subjectResponse);
    } catch (Exception e) {
        e.printStackTrace();
        return new ResponseEntity<String>(headers, HttpStatus.NOT_FOUND);
    }
    return new ResponseEntity<String>(json, headers, HttpStatus.OK);
}

Example 2 with DashboardDao

use of gov.nih.nci.ctd2.dashboard.dao.DashboardDao in project nci-ctd2-dashboard by CBIIT.

the class SubjectResponse method createInstance.

private static SubjectResponse createInstance(final Subject subject, final Filter filter, DashboardDao dashboardDao) {
    int[] tierCount = new int[3];
    Set<Integer> set = new HashSet<Integer>();
    for (ObservedSubject observedSubject : dashboardDao.findObservedSubjectBySubject(subject)) {
        ObservedSubjectRole observedSubjectRole = observedSubject.getObservedSubjectRole();
        String subjectRole = observedSubjectRole.getSubjectRole().getDisplayName();
        if (filter.rolesIncluded.size() > 0 && !filter.rolesIncluded.contains(subjectRole))
            continue;
        ObservationTemplate observatinoTemplate = observedSubject.getObservation().getSubmission().getObservationTemplate();
        Integer observationTier = observatinoTemplate.getTier();
        String centerNameBrief = observatinoTemplate.getSubmissionCenter().getStableURL().substring(7);
        if (filter.centerIncluded.size() > 0 && !filter.centerIncluded.contains(centerNameBrief))
            continue;
        if ((Arrays.asList(filter.tiersIncluded).contains(observationTier))) {
            set.add(observedSubject.getObservation().getId());
            tierCount[observationTier.intValue() - 1]++;
            if (filter.limit > 0 && set.size() >= filter.limit) {
                break;
            }
        }
    }
    List<ObservationItem> observations = dashboardDao.findObservationInfo(new ArrayList<Integer>(set));
    Set<String> roles = new TreeSet<String>();
    for (int i = 0; i < observations.size(); i++) {
        for (SubjectItem sub : observations.get(i).subject_list) {
            if (sub.getName().equals(subject.getDisplayName())) {
                roles.add(sub.getRole());
                break;
            }
        }
    }
    String[] uris = observations.stream().map(x -> x.uri).toArray(String[]::new);
    SubjectResponse subjectResponse = new SubjectResponse(subject, uris, roles.toArray(new String[0]), tierCount);
    return subjectResponse;
}

Example 3 with DashboardDao

use of gov.nih.nci.ctd2.dashboard.dao.DashboardDao in project nci-ctd2-dashboard by CBIIT.

the class SearchAPI method getSubmission.

@Transactional
@RequestMapping(value = "{term}", method = { RequestMethod.GET }, headers = "Accept=application/json")
public ResponseEntity<String> getSubmission(@PathVariable String term, @RequestParam(value = "center", required = false, defaultValue = "") String center, @RequestParam(value = "role", required = false, defaultValue = "") String role, @RequestParam(value = "tier", required = false, defaultValue = "") String tiers, @RequestParam(value = "maximum", required = false, defaultValue = "") String maximum) {
    HttpHeaders headers = new HttpHeaders();
    headers.add("Content-Type", "application/json; charset=utf-8");
    SubjectResponse.Filter filter = SubjectResponse.createFilter(center, role, tiers, maximum);
    List<SubjectResponse> allSubjects = new ArrayList<SubjectResponse>();
    List<SubjectResult> results = dashboardDao.search(term.toLowerCase()).subject_result;
    for (SubjectResult subjectResult : results) {
        try {
            Class<? extends DashboardEntity> clazz = Class.forName("gov.nih.nci.ctd2.dashboard.model." + subjectResult.className).asSubclass(DashboardEntity.class);
            ;
            DashboardEntity result = dashboardDao.getEntityById(clazz, subjectResult.id);
            SubjectResponse subjectResponse = SubjectResponse.createInstance(result, filter, dashboardDao);
            if (subjectResponse == null) {
                continue;
            }
            allSubjects.add(subjectResponse);
        } catch (ClassNotFoundException e) {
            e.printStackTrace();
            continue;
        }
    }
    log.debug("ready to serialize");
    JSONSerializer jsonSerializer = CTD2Serializer.createJSONSerializer();
    String json = "{}";
    try {
        json = jsonSerializer.deepSerialize(allSubjects);
    } catch (Exception e) {
        e.printStackTrace();
        return new ResponseEntity<String>(headers, HttpStatus.NOT_FOUND);
    }
    return new ResponseEntity<String>(json, headers, HttpStatus.OK);
}

Example 4 with DashboardDao

use of gov.nih.nci.ctd2.dashboard.dao.DashboardDao in project nci-ctd2-dashboard by CBIIT.

the class SampleImporter method run.

@Override
public void run() {
    DashboardFactory dashboardFactory = getDashboardFactory();
    DashboardDao dashboardDao = getDashboardDao();
    Synonym synonym = dashboardFactory.create(Synonym.class);
    synonym.setDisplayName("S1");
    Synonym synonym2 = dashboardFactory.create(Synonym.class);
    synonym.setDisplayName("S2");
    Synonym synonym3 = dashboardFactory.create(Synonym.class);
    synonym3.setDisplayName("S3");
    // Save with id
    Gene gene = dashboardFactory.create(Gene.class);
    gene.setDisplayName("G1");
    gene.setEntrezGeneId("E1");
    gene.getSynonyms().add(synonym);
    gene.getSynonyms().add(synonym2);
    dashboardDao.save(gene);
    // save without id
    Gene gene2 = dashboardFactory.create(Gene.class);
    gene2.setEntrezGeneId("E2");
    gene.setDisplayName("G2");
    dashboardDao.save(gene2);
    Transcript transcript = dashboardFactory.create(Transcript.class);
    transcript.setGene(gene2);
    transcript.setRefseqId("NM_21431");
    gene.setDisplayName("T1");
    dashboardDao.save(transcript);
    Protein protein = dashboardFactory.create(Protein.class);
    protein.getTranscripts().add(transcript);
    protein.setUniprotId("1000");
    protein.setDisplayName("P1");
    dashboardDao.save(protein);
    AnimalModel animalModel = dashboardFactory.create(AnimalModel.class);
    animalModel.getSynonyms().add(synonym3);
    animalModel.setDisplayName("MM1");
    dashboardDao.save(animalModel);
    UrlEvidence urlEvidence = dashboardFactory.create(UrlEvidence.class);
    urlEvidence.setUrl("http://ctd2.nci.nih.gov/");
    LabelEvidence labelEvidence = dashboardFactory.create(LabelEvidence.class);
    labelEvidence.setDisplayName("L1");
    log.info("Imported " + dashboardDao.findEntities(DashboardEntity.class).size() + " entities.");
}

Example 5 with DashboardDao

use of gov.nih.nci.ctd2.dashboard.dao.DashboardDao in project nci-ctd2-dashboard by CBIIT.

the class DashboardAdminMain method main.

@Transactional
public static void main(String[] args) {
    final CommandLineParser parser = new GnuParser();
    Options gnuOptions = new Options();
    gnuOptions.addOption("h", "help", false, "shows this help document and quits.").addOption("am", "animal-model-data", false, "imports animal model data.").addOption("cl", "cell-line-data", false, "imports cell line data.").addOption("cp", "compound-data", false, "imports compound data.").addOption("e", "eco-term", false, "import ECO terms.").addOption("g", "gene-data", false, "imports gene data.").addOption("p", "protein-data", false, "imports protein data.").addOption("r", "rank-subjects", false, "prioritize and rank the subjects according to the observation data.").addOption("sh", "shrna-data", false, "imports shrna data.").addOption("si", "sirna-data", false, "imports sirna data.").addOption("ts", "tissue-sample-data", false, "imports tissue sample data.").addOption("cv", "controlled-vocabulary", false, "imports the dashboard controlled vocabulary.").addOption("o", "observation-data", false, "imports dashboard observation data.").addOption("s", "sample-data", false, "imports sample data.").addOption("t", "taxonomy-data", false, "imports organism data.").addOption("i", "index", false, "creates lucene index.");
    // Here goes the parsing attempt
    try {
        CommandLine commandLine = parser.parse(gnuOptions, args);
        if (commandLine.getOptions().length == 0) {
            // Here goes help message about running admin
            throw new ParseException("Nothing to do!");
        }
        if (commandLine.hasOption("h")) {
            printHelpAndExit(gnuOptions, 0);
        }
        if (commandLine.hasOption("am")) {
            launchJob("animalModelImporterJob");
        }
        if (commandLine.hasOption("cl")) {
            launchJob("cellLineDataImporterJob");
        }
        if (commandLine.hasOption("cp")) {
            launchJob("compoundDataImporterJob");
        }
        if (commandLine.hasOption("g")) {
            launchJob("geneDataImporterJob");
        }
        if (commandLine.hasOption("p")) {
            launchJob("proteinDataImporterJob");
        }
        if (commandLine.hasOption("sh")) {
            launchJob("TRCshRNADataImporterJob");
        }
        if (commandLine.hasOption("si")) {
            launchJob("siRNADataImporterJob");
        }
        if (commandLine.hasOption("ts")) {
            launchJob("tissueSampleDataImporterJob");
        }
        if (commandLine.hasOption("cv")) {
            launchJob("controlledVocabularyImporterJob");
        }
        if (commandLine.hasOption("o")) {
            launchJob("observationDataImporterJob");
            String dataURL = (String) appContext.getBean("dataURL");
            APIDataBuilder b = (APIDataBuilder) appContext.getBean("apiDataBuilder");
            b.prepareData(dataURL);
        }
        if (commandLine.hasOption("s")) {
            log.info("Running sample importer...");
            // This is just for demonstration purposes
            SampleImporter sampleImporter = (SampleImporter) appContext.getBean("sampleImporter");
            sampleImporter.run();
        }
        if (commandLine.hasOption("t")) {
            launchJob("taxonomyDataImporterJob");
        }
        if (commandLine.hasOption("e")) {
            launchJob("ecotermDataImporterJob");
        }
        if (commandLine.hasOption("r")) {
            SubjectScorer subjectScorer = (SubjectScorer) appContext.getBean("subjectScorer");
            subjectScorer.scoreAllRoles();
            OverallSummary overallSummary = (OverallSummary) appContext.getBean("overallSummary");
            overallSummary.summarize();
        }
        if (commandLine.hasOption("i")) {
            DashboardDao dashboardDao = (DashboardDao) appContext.getBean("dashboardDao");
            dashboardDao.cleanIndex((Integer) appContext.getBean("indexBatchSize"));
        }
        log.info("All done.");
        System.exit(0);
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        printHelpAndExit(gnuOptions, -1);
    }
}