public void execute() throws Exception {
int rowCount = 0;
try {
String fileLoction =
propertiesUtil.getPropertyValue(
propertiesFileLocations, COSMICFUSIONEXPORT_TSV_FILE_LOCATION);
File file = new File(fileLoction);
logger.info("[01234] Processing File " + file.getName() + " ...... ");
CSVReader reader = new CSVReader(new FileReader(file), '\t');
JsonArray jsonArr = new JsonArray();
String[] record;
while ((record = reader.readNext()) != null) {
if (rowCount != 0) {
Complete_Fusion_Export cfe = factory.createComplete_Fusion_Export(CFE + rowCount);
JsonObject jsonObject = new JsonObject();
String fusion_IdValue = record[10] == null ? EMPTY_STRING : record[10];
cfe.addFusion_Id(getFusionId(fusion_IdValue));
jsonObject.addProperty(FUSION_ID, fusion_IdValue);
String fusionTypeValue = record[12] == null ? EMPTY_STRING : record[12];
cfe.addFusion_Type(fusionTypeValue);
jsonObject.addProperty(FUSION_TYPE, fusionTypeValue);
String histology_Subtype_1Value = record[9] == null ? EMPTY_STRING : record[9];
cfe.addHistology_Subtype_1(histology_Subtype_1Value);
jsonObject.addProperty(HISTOLOGY_SUBTYPE_1, histology_Subtype_1Value);
String histology_Subtype_3Value = record[11] == null ? EMPTY_STRING : record[11];
cfe.addHistology_Subtype_3(histology_Subtype_3Value);
jsonObject.addProperty(HISTOLOGY_SUBTYPE_3, histology_Subtype_3Value);
String primarySiteValue = record[2] == null ? EMPTY_STRING : record[2];
cfe.addPrimary_Site(primarySiteValue);
jsonObject.addProperty(PRIMARY_SITE, primarySiteValue);
String pubmedPMIDValue = record[13] == null ? EMPTY_STRING : record[13];
cfe.addPubmed_PMID(pubmedPMIDValue);
jsonObject.addProperty(PUBMED_PMID, pubmedPMIDValue);
String site_Subtype_1Value = record[3];
cfe.addSite_Subtype_1(site_Subtype_1Value);
jsonObject.addProperty(SITE_SUBTYPE_1_VALUE, site_Subtype_1Value);
String site_Subtype_3Value = record[5];
cfe.addSite_Subtype_3(site_Subtype_3Value);
jsonObject.addProperty(SITE_SUBTYPE_3_VALUE, site_Subtype_3Value);
String translocationName = record[11] == null ? EMPTY_STRING : record[11];
cfe.addTranslocation_Name(translocationName);
jsonObject.addProperty(TRANSLOCATION_NAME, translocationName);
jsonArr.add(jsonObject);
// TODO Uncomment before the .jar generation
// owlOntologyManager.saveOntology(cfe.getOwlOntology(),
// new FileOutputStream(new
// File(propertiesUtil.getPropertyValue(propertiesFileLocations,
// COSMICFUSIONEXPORT_RDF_FILE_LOCATION))));
// TODO Use the code below to create samples.
// if (rowCount == 100) {
File jsonSampleFile =
new File(
propertiesUtil.getPropertyValue(
propertiesFileLocations, COSMICFUSIONEXPORT_JSON_FILE_LOCATION));
FileUtils.writeStringToFile(jsonSampleFile, jsonArr.toString());
owlOntologyManager.saveOntology(
cfe.getOwlOntology(),
new FileOutputStream(
new File(
propertiesUtil.getPropertyValue(
propertiesFileLocations, COSMICFUSIONEXPORT_RDF_FILE_LOCATION))));
// break;
// }
}
rowCount++;
}
} catch (Exception e) {
logger.error("[01234] Error! " + e.getMessage());
throw new RuntimeException(e.getMessage(), e);
} finally {
logger.info("[01234] Axioms size: " + onto.getAxioms().size());
logger.info("[01234] Records: " + rowCount);
logger.info("[01234] Process of CompleteFusionExportConverterImpl finished!");
}
}
private Fusion_Id getFusionId(String fusion_IdValue) {
return factory.createFusion_Id(fusion_IdValue);
}
