@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;
}
@Override
public List<SampleDraft> getAllbetaGTMspISampleDraftsFromJobDraftId(Integer id) {
JobDraft jobDraft = jobDraftService.getJobDraftById(id);
List<SampleDraft> sampleDrafts = jobDraft.getSampleDraft();
List<SampleDraft> betaGTMspSampleDrafts = new ArrayList<SampleDraft>();
String enzymeString;
for (SampleDraft sd : sampleDrafts) {
try {
if (sd.getSampleType().getIName().equalsIgnoreCase("library")) {
enzymeString =
(String)
MetaHelper.getMetaValue(
HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, sd.getSampleDraftMeta());
} else { // genomic DNA; 1-8-15; dubin
enzymeString =
(String)
MetaHelper.getMetaValue(
HELPTAG_DNA_AREA,
TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY,
sd.getSampleDraftMeta());
}
if (enzymeString.equals("beta-GT-MspI")) betaGTMspSampleDrafts.add(sd);
} catch (MetadataException e) {
// not found
logger.debug(
"Restriction Enzyme Meta (and libraryToCreate meta) is not found for Sample Draft id = "
+ id);
}
}
return betaGTMspSampleDrafts;
}
@Override
public String getTypeOfHelpLibrary(Sample sample) {
try {
return (String)
MetaHelper.getMetaValue(
HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, sample.getSampleMeta());
} catch (MetadataException e) {
}
// not found
return null;
}
@Override
public String getTypeOfHelpLibraryRequestedForMacromolecule(Sample sample) {
try {
return (String)
MetaHelper.getMetaValue(
HELPTAG_DNA_AREA, TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY, sample.getSampleMeta());
} catch (MetadataException e) {
}
// not found
return null;
}
