Examples with CVRSegRecord org.cbioportal.cmo.pipelines.cvr.model.staging.CVRSegRecord used on opensource projects

Example 1 with CVRSegRecord

use of org.cbioportal.cmo.pipelines.cvr.model.staging.CVRSegRecord in project cmo-pipelines by knowledgesystems.

the class CVRSegDataReader method open.

@Override
public void open(ExecutionContext ec) throws ItemStreamException {
    CVRData cvrData = new CVRData();
    // load cvr data from cvr_data.json file
    File cvrFile = new File(privateDirectory, cvrUtilities.CVR_FILE);
    try {
        cvrData = cvrUtilities.readJson(cvrFile);
    } catch (IOException e) {
        log.error("Error reading file: " + cvrFile.getName());
        throw new ItemStreamException(e);
    }
    // only read from seg file if exists
    File segFile = new File(stagingDirectory, studyId + cvrUtilities.SEG_FILE);
    if (!segFile.exists()) {
        log.error("File does not exist - skipping data loading from SEG file: " + segFile.getName());
    } else {
        log.info("Loading SEG data from: " + segFile.getName());
        DelimitedLineTokenizer tokenizer = new DelimitedLineTokenizer(DelimitedLineTokenizer.DELIMITER_TAB);
        DefaultLineMapper<CVRSegRecord> mapper = new DefaultLineMapper<>();
        mapper.setLineTokenizer(tokenizer);
        mapper.setFieldSetMapper(new CVRSegFieldSetMapper());
        FlatFileItemReader<CVRSegRecord> reader = new FlatFileItemReader<>();
        reader.setResource(new FileSystemResource(segFile));
        reader.setLineMapper(mapper);
        reader.setLinesToSkip(1);
        reader.open(ec);
        try {
            CVRSegRecord to_add;
            while ((to_add = reader.read()) != null && to_add.getID() != null) {
                if (!cvrSampleListUtil.getNewDmpSamples().contains(to_add.getID())) {
                    cvrSegRecords.add(to_add);
                }
            }
        } catch (Exception e) {
            log.error("Error loading data from SEG file: " + segFile.getName());
            throw new ItemStreamException(e);
        }
        reader.close();
    }
    // merge cvr SEG data existing SEG data and new data from CVR
    for (CVRMergedResult result : cvrData.getResults()) {
        CVRSegData cvrSegData = result.getSegData();
        if (cvrSegData.getSegData() == null) {
            continue;
        }
        HashMap<Integer, String> indexMap = new HashMap<>();
        boolean first = true;
        String id = result.getMetaData().getDmpSampleId();
        for (List<String> segData : cvrSegData.getSegData()) {
            if (first) {
                for (int i = 0; i < segData.size(); i++) {
                    indexMap.put(i, segData.get(i));
                }
                first = false;
            } else {
                CVRSegRecord cvrSegRecord = new CVRSegRecord();
                for (int i = 0; i < segData.size(); i++) {
                    cvrSegRecord.setID(id);
                    // dots in source; replaced for method
                    String field = indexMap.get(i).replace(".", "_");
                    try {
                        cvrSegRecord.getClass().getMethod("set" + field, String.class).invoke(cvrSegRecord, segData.get(i));
                    } catch (Exception e) {
                        log.warn("No such method 'set" + field + "' for CVRSegRecord");
                    }
                }
                cvrSegRecords.add(cvrSegRecord);
            }
        }
    }
}

Example 2 with CVRSegRecord

use of org.cbioportal.cmo.pipelines.cvr.model.staging.CVRSegRecord in project cmo-pipelines by knowledgesystems.

the class CVRSegFieldSetMapper method mapFieldSet.

@Override
public CVRSegRecord mapFieldSet(FieldSet fs) throws BindException {
    CVRSegRecord record = new CVRSegRecord();
    List<String> fields = CVRSegRecord.getFieldNames();
    for (int i = 0; i < fields.size(); i++) {
        String field = fields.get(i);
        try {
            record.getClass().getMethod("set" + field, String.class).invoke(record, fs.readString(i));
        } catch (Exception e) {
            if (e.getClass().equals(NoSuchMethodException.class)) {
                log.info("No set method exists for " + field);
            }
        }
    }
    return record;
}