Examples with MetadataEntry ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry used on opensource projects

Example 11 with MetadataEntry

use of ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry in project irida by phac-nml.

the class AnalysisController method getMetadataForAnalysisSamples.

/**
 * Get the metadata associated with a template for an analysis.
 *
 * @param submissionId {@link Long} identifier for the {@link AnalysisSubmission}
 * @return {@link Map}
 */
@RequestMapping("/ajax/{submissionId}/metadata")
@ResponseBody
public Map<String, Object> getMetadataForAnalysisSamples(@PathVariable Long submissionId) {
    AnalysisSubmission submission = analysisSubmissionService.read(submissionId);
    Collection<Sample> samples = sampleService.getSamplesForAnalysisSubmission(submission);
    // Let's get a list of all the metadata available that is unique.
    Set<String> terms = new HashSet<>();
    for (Sample sample : samples) {
        if (!sample.getMetadata().isEmpty()) {
            Map<MetadataTemplateField, MetadataEntry> metadata = sample.getMetadata();
            terms.addAll(metadata.keySet().stream().map(MetadataTemplateField::getLabel).collect(Collectors.toSet()));
        }
    }
    // Get the metadata for the samples;
    Map<String, Object> metadata = new HashMap<>();
    for (Sample sample : samples) {
        Map<MetadataTemplateField, MetadataEntry> sampleMetadata = sample.getMetadata();
        Map<String, MetadataEntry> stringMetadata = new HashMap<>();
        sampleMetadata.entrySet().forEach(e -> {
            stringMetadata.put(e.getKey().getLabel(), e.getValue());
        });
        Map<String, MetadataEntry> valuesMap = new HashMap<>();
        for (String term : terms) {
            MetadataEntry value = stringMetadata.get(term);
            if (value == null) {
                // Not all samples will have the same metadata associated with it.  If a sample
                // is missing one of the terms, just give it an empty string.
                value = new MetadataEntry("", "text");
            }
            valuesMap.put(term, value);
        }
        metadata.put(sample.getLabel(), valuesMap);
    }
    return ImmutableMap.of("terms", terms, "metadata", metadata);
}