private void updateFileStatus(CaArrayFileSet fileSet, FileStatus status) {
final CaArrayFileSet mageTabFileSet = new CaArrayFileSet(fileSet);
for (final CaArrayFile file : fileSet.getFiles()) {
if (!isMageTabFile(file)) {
mageTabFileSet.getFiles().remove(file);
}
}
mageTabFileSet.updateStatus(status);
}
private MageTabFileSet getInputFileSet(Project project, CaArrayFileSet fileSet) {
final CaArrayFileSet fullSet = new CaArrayFileSet(fileSet);
fullSet.addAll(
Collections2.filter(
project.getImportedFiles(),
new Predicate<CaArrayFile>() {
@Override
public boolean apply(CaArrayFile f) {
return f.getFileType().isArrayData();
}
}));
final MageTabFileSet inputFileSet = new MageTabFileSet();
for (final CaArrayFile caArrayFile : fullSet.getFiles()) {
addInputFile(inputFileSet, caArrayFile);
}
return inputFileSet;
}
private void handleSelectRefFilesResult(CaArrayFileSet fileSet, ValidationResult result) {
for (final String fileName : result.getFileNames()) {
final CaArrayFile caArrayFile = fileSet.getFile(fileName);
final FileValidationResult fileResult = result.getFileValidationResult(fileName);
if (!fileResult.isValid()) {
// check whether any of the validation errors are other than data file checks
saveErrorMessages(fileResult, caArrayFile);
}
}
}
private void handleResult(CaArrayFileSet fileSet, ValidationResult result) {
for (final String fileName : result.getFileNames()) {
final CaArrayFile caArrayFile = fileSet.getFile(fileName);
final FileValidationResult fileResult = result.getFileValidationResult(fileName);
if (!fileResult.isValid()) {
caArrayFile.setFileStatus(FileStatus.VALIDATION_ERRORS);
} else {
caArrayFile.setFileStatus(FileStatus.VALIDATED);
}
caArrayFile.setValidationResult(fileResult);
this.projectDao.save(caArrayFile);
}
}
public MageTabDocumentSet validateFiles(Project targetProject, CaArrayFileSet fileSet) {
LOG.info("Validating MAGE-TAB document set");
updateFileStatus(fileSet, FileStatus.VALIDATING);
MageTabDocumentSet documentSet = null;
final MageTabFileSet inputSet = getInputFileSet(targetProject, fileSet);
try {
updateFileStatus(fileSet, FileStatus.VALIDATED);
documentSet = MageTabParser.INSTANCE.parse(inputSet);
handleResult(fileSet, this.translator.validate(documentSet, fileSet));
} catch (final MageTabParsingException e) {
updateFileStatus(fileSet, FileStatus.VALIDATION_ERRORS);
} catch (final InvalidDataException e) {
handleResult(fileSet, e.getValidationResult());
}
this.searchDao.save(fileSet.getFiles());
return documentSet;
}
/** {@inheritDoc} */
@Override
public MageTabDocumentSet importFiles(Project targetProject, CaArrayFileSet fileSet)
throws MageTabParsingException {
LOG.info("Importing MAGE-TAB document set");
updateFileStatus(fileSet, FileStatus.IMPORTING);
final MageTabFileSet inputSet = getInputFileSet(targetProject, fileSet);
MageTabDocumentSet documentSet = null;
try {
documentSet = MageTabParser.INSTANCE.parse(inputSet);
final CaArrayTranslationResult translationResult =
this.translator.translate(documentSet, fileSet);
save(targetProject, translationResult);
updateFileStatus(fileSet, FileStatus.IMPORTED);
} catch (final InvalidDataException e) {
handleResult(fileSet, e.getValidationResult());
}
this.searchDao.save(fileSet.getFiles());
return documentSet;
}
