@Override
public List<SampleDraft> createNewHelpDNASampleDrafts(
SampleDraft sampleDraft, List<String> librariesToCreateList) {
List<SampleDraft> newSampleDrafts = new ArrayList<SampleDraft>();
for (String libraryTypeToCreate : librariesToCreateList) {
SampleDraft clone = sampleService.cloneSampleDraft(sampleDraft);
List<SampleDraftMeta> sampleDraftMetaList = clone.getSampleDraftMeta();
clone.setName(clone.getName() + "_" + libraryTypeToCreate);
SampleDraft cloneDB = sampleService.getSampleDraftDao().save(clone);
cloneDB.setSampleDraftMeta(sampleDraftMetaList);
this.resetLibraryToCreateMetaData(cloneDB, libraryTypeToCreate);
newSampleDrafts.add(cloneDB);
}
return newSampleDrafts;
}
@Override
public boolean isBetaGTMspI(Sample s) {
String enzymeString;
try {
if (s.getParentId() != null) {
// if it has a parent sample, which means it's a facility library, use its parent sample to
// check for library type
s = sampleService.getSampleById(s.getParentId());
}
if (!s.getSampleType().getIName().equalsIgnoreCase("dna")) { // not dna, so must be library
enzymeString =
(String)
MetaHelper.getMetaValue(
HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, s.getSampleMeta());
} else { // genomic DNA
enzymeString =
(String)
MetaHelper.getMetaValue(
HELPTAG_DNA_AREA, TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY, s.getSampleMeta());
}
if (enzymeString.equals("beta-GT-MspI")) {
return true;
}
} catch (MetadataException e) {
// not found
logger.debug(
"Restriction Enzyme Meta (and libraryToCreate meta) not found for Sample id = "
+ s.getId());
}
return false;
}
private void resetLibraryToCreateMetaData(SampleDraft clone, String libraryTypeToCreate) {
for (SampleDraftMeta sdm : clone.getSampleDraftMeta()) {
if (sdm.getK().endsWith("typeOfHelpLibraryRequested")) {
sdm.setV(libraryTypeToCreate);
}
sdm.setSampleDraftId(clone.getId()); // must do this for every meta entry
sampleService.getSampleDraftMetaDao().save(sdm); // then must do this for every meta entry
}
}