Package com.infoclinika.mssharing.model.internal.entity

Examples of com.infoclinika.mssharing.model.internal.entity.FileReference

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        return searchResults;
    }

    private SearchRunResult createSearchRunResult(SequestSearchPerFileResultResponse sResult, SearchRun searchRun) {
        return (sResult.errorMessage != null) ? new SearchRunResult(sResult.errorMessage)
                        : new SearchRunResult(searchRun, new FileReference(sResult.sqtFileRef), new FileReference(sResult.sqtDecoyFileRef),
                        new FileReference(sResult.resultsFileRef), new FileReference(sResult.isotopeGroupListFileRef),
                new FileReference(sResult.ms2FileRef), new FileReference(sResult.mzmlFileRef));
    }
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    public MsDaplChartItem readChartInfoBySearchResult(long searchResultId) {
        final SearchResult searchResult = searchResultRepository.findOne(searchResultId);
        final MS2Scan scan = searchResult.getScan();
        final SearchRun searchRun = searchResult.getSearchRun();
        final String fileName = searchRun.getFile().getFileMetaData().getName();
        final FileReference chartDataRef = scan.getChartDataRef();
        final String key = chartDataRef.getKey();
        File file = new File(key);
        if (!(file.exists() && file.isFile())) {
            file = downloadMsDaplChartRef(chartDataRef, file);
        }
        final Gson gson = new GsonBuilder().serializeSpecialFloatingPointValues().create();
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        final MS2Scan scan = scanRepository.findOne(scanId);

        final IsotopeGroupPerFile isotopeGroupPerFile = scan.getIsotopeGroupPerFile();
        final SearchRun searchRun = isotopeGroupPerFile.getSearchRun();
        final String fileName = searchRun.getFile().getFileMetaData().getName();
        final FileReference chartDataRef = scan.getChartDataRef();
        final String key = chartDataRef.getKey();
        File file = new File(key);
        if (!(file.exists() && file.isFile())) {
            file = downloadMsDaplChartRef(chartDataRef, file);
        }
        final Gson gson = new GsonBuilder().serializeSpecialFloatingPointValues().create();
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        FileOperations.cleanupFile(file);
        for (IsotopeGroupPerFileDTO ig : isotopeGroups) {
            final IsotopeGroupPerFile isotopeGroupPerFile = isotopeGroupPerFileRepository.save(
                    new IsotopeGroupPerFile(searchRun, ig.getMonoMz(), ig.getRt(), ig.getCharge(), ig.getIntensity()));//todo performance!
            for (MS2ScanDTO scan : ig.getScans()) {
                final MS2Scan ms2Scan = new MS2Scan(scan.getScanNumber(), scan.getPrecursorIntensity(), isotopeGroupPerFile, new FileReference(scan.getChartInfoRef()));
                ms2ScanRepository.save(ms2Scan);       //todo performance!
            }
        }
    }
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Related Classes of com.infoclinika.mssharing.model.internal.entity.FileReference

  • com.infoclinika.common.io.api.S3ObjectReference
  • com.infoclinika.mssharing.model.internal.read.SequestSearchReaderImpl
  • com.infoclinika.mssharing.model.internal.write.sequestsearch.SequestSearcher
  • com.infoclinika.mssharing.model.internal.write.sequestsearch.SequestSearchResultsPersistService
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