private static Set<Link> getLinks(ArrayList<String> linkList, Entry entry) {
Set<Link> existingLinks = entry.getLinks();
Set<Link> links = new HashSet<>();
if (existingLinks == null) existingLinks = new HashSet<>();
if (linkList == null) return existingLinks;
for (int i = 0; i < linkList.size(); i++) {
String currentItem = linkList.get(i);
Link link;
if (existingLinks.size() > i) {
link = (Link) existingLinks.toArray()[i];
} else {
link = new Link();
existingLinks.add(link);
}
link.setLink(currentItem);
link.setEntry(entry);
links.add(link);
}
return links;
}
private static Entry infoToPlasmidForField(Entry entry, String value, EntryField field) {
if (!entry.getRecordType().equalsIgnoreCase(EntryType.PLASMID.toString())) return entry;
Plasmid plasmid = (Plasmid) entry;
switch (field) {
case BACKBONE:
plasmid.setBackbone(value);
return plasmid;
case PROMOTERS:
plasmid.setPromoters(value);
return plasmid;
case REPLICATES_IN:
plasmid.setReplicatesIn(value);
return plasmid;
case CIRCULAR:
plasmid.setCircular(
"yes".equalsIgnoreCase(value)
|| "true".equalsIgnoreCase(value)
|| "circular".equalsIgnoreCase(value));
return plasmid;
case ORIGIN_OF_REPLICATION:
plasmid.setOriginOfReplication(value);
return plasmid;
default:
return plasmid;
}
}
private static Set<SelectionMarker> getSelectionMarkers(
ArrayList<String> markerStr, Entry entry) {
Set<SelectionMarker> existingMarkers = entry.getSelectionMarkers();
Set<SelectionMarker> markers = new HashSet<>();
if (existingMarkers == null) existingMarkers = new HashSet<>();
if (markerStr != null) {
int itemLength = markerStr.size();
for (int i = 0; i < itemLength; i++) {
String currentItem = markerStr.get(i);
SelectionMarker marker;
if (existingMarkers.size() > i) {
marker = (SelectionMarker) existingMarkers.toArray()[i];
} else {
marker = new SelectionMarker();
existingMarkers.add(marker);
}
marker.setName(currentItem);
marker.setEntry(entry);
markers.add(marker);
}
} else return null;
return markers;
}
private static Entry infoToSeedForField(Entry entry, String value, EntryField field) {
if (!entry.getRecordType().equalsIgnoreCase(EntryType.ARABIDOPSIS.toString())) return entry;
ArabidopsisSeed seed = (ArabidopsisSeed) entry;
switch (field) {
case HOMOZYGOSITY:
seed.setHomozygosity(value);
return seed;
case ECOTYPE:
seed.setEcotype(value);
return seed;
case HARVEST_DATE:
if (value != null && !value.isEmpty()) {
try {
Date date = SimpleDateFormat.getDateInstance(DateFormat.SHORT).parse(value);
seed.setHarvestDate(date);
} catch (ParseException ia) {
Logger.error(ia);
}
}
return seed;
case GENERATION:
seed.setGeneration(Generation.fromString(value));
return seed;
case SENT_TO_ABRC:
seed.setSentToABRC("yes".equalsIgnoreCase(value) || "true".equalsIgnoreCase(value));
return seed;
case PLANT_TYPE:
seed.setPlantType(PlantType.fromString(value));
return seed;
case PARENTS:
seed.setParents(value);
return seed;
default:
return seed;
}
}
public static Entry infoToEntry(PartData info) {
EntryType type = info.getType();
Entry entry;
switch (type) {
case PLASMID:
entry = setPlasmidFields(info.getPlasmidData(), new Plasmid());
break;
case STRAIN:
entry = setStrainFields(info.getStrainData(), new Strain());
break;
case ARABIDOPSIS:
entry = setSeedFields(info.getArabidopsisSeedData(), new ArabidopsisSeed());
break;
case PART:
default:
entry = new Part();
break;
}
if (entry == null) return null;
// common fields
if (StringUtils.isEmpty(info.getRecordId())) entry.setRecordId(UUID.randomUUID().toString());
else entry.setRecordId(info.getRecordId());
entry.setVersionId(entry.getRecordId());
if (info.getCreationTime() == 0) entry.setCreationTime(new Date());
else entry.setCreationTime(new Date(info.getCreationTime()));
entry.setModificationTime(entry.getCreationTime());
entry = setCommon(entry, info);
return entry;
}
private static Entry infoToStrainForField(Entry entry, String value, EntryField field) {
if (!entry.getRecordType().equalsIgnoreCase(EntryType.STRAIN.toString())) return entry;
Strain strain = (Strain) entry;
switch (field) {
case PARENTAL_STRAIN:
strain.setHost(value);
return strain;
case GENOTYPE_OR_PHENOTYPE:
strain.setGenotypePhenotype(value);
return strain;
case PLASMIDS:
strain.setPlasmids(value);
return strain;
default:
return strain;
}
}
/**
* Updates the entry based on the field that is specified. Mainly created for use by the bulk
* import auto update
*
* @param entry entry to be updated
* @param plasmid should be set if updating strain with plasmid
* @param value value to be set
* @param field to set
* @return updated entry array containing both entry and plasmid. if plasmid is null only entry is
* returned
*/
public static Entry[] infoToEntryForField(
Entry entry, Entry plasmid, String value, EntryField field) {
switch (field) {
case PI:
{
entry.setPrincipalInvestigator(value);
if (plasmid != null) plasmid.setPrincipalInvestigator(value);
break;
}
case PI_EMAIL:
{
entry.setPrincipalInvestigatorEmail(value);
break;
}
case FUNDING_SOURCE:
{
entry.setFundingSource(value);
if (plasmid != null) plasmid.setFundingSource(value);
break;
}
case IP:
entry.setIntellectualProperty(value);
if (plasmid != null) plasmid.setIntellectualProperty(value);
break;
case BIO_SAFETY_LEVEL:
Integer level = BioSafetyOption.intValue(value);
if (level == null) {
if (value.contains("1")) level = 1;
else if (value.contains("2")) level = 2;
else break;
}
entry.setBioSafetyLevel(level);
if (plasmid != null) {
plasmid.setBioSafetyLevel(level);
}
break;
case NAME:
entry.setName(value);
break;
case ALIAS:
entry.setAlias(value);
break;
case KEYWORDS:
entry.setKeywords(value);
break;
case SUMMARY:
entry.setShortDescription(value);
break;
case NOTES:
entry.setLongDescription(value);
break;
case REFERENCES:
entry.setReferences(value);
break;
case LINKS:
HashSet<Link> links = new HashSet<>();
Link link = new Link();
link.setLink(value);
link.setEntry(entry);
links.add(link);
entry.setLinks(links);
break;
case STATUS:
entry.setStatus(value);
if (plasmid != null) plasmid.setStatus(value);
break;
case SELECTION_MARKERS:
HashSet<SelectionMarker> markers = new HashSet<>();
SelectionMarker marker = new SelectionMarker(value, entry);
markers.add(marker);
entry.setSelectionMarkers(markers);
break;
case PARENTAL_STRAIN:
case GENOTYPE_OR_PHENOTYPE:
case PLASMIDS:
entry = infoToStrainForField(entry, value, field);
break;
case BACKBONE:
case ORIGIN_OF_REPLICATION:
case CIRCULAR:
case PROMOTERS:
case REPLICATES_IN:
entry = infoToPlasmidForField(entry, value, field);
break;
case HOMOZYGOSITY:
case ECOTYPE:
case HARVEST_DATE:
case GENERATION:
case SENT_TO_ABRC:
case PLANT_TYPE:
case PARENTS:
entry = infoToSeedForField(entry, value, field);
break;
default:
break;
}
if (plasmid == null) return new Entry[] {entry};
return new Entry[] {entry, plasmid};
}
private static Entry setCommon(Entry entry, PartData info) {
if (entry == null || info == null) return null;
if (info.getName() != null) entry.setName(info.getName());
if (info.getSelectionMarkers() != null) {
Set<SelectionMarker> markers = getSelectionMarkers(info.getSelectionMarkers(), entry);
entry.setSelectionMarkers(markers);
}
if (info.getReferences() != null) entry.setReferences(info.getReferences());
if (StringUtils.isBlank(entry.getPartNumber())) entry.setPartNumber(info.getPartId());
Date currentTime = new Date();
if (entry.getCreationTime() == null) entry.setCreationTime(currentTime);
entry.setModificationTime(currentTime);
if (info.getOwnerEmail() != null) {
entry.setOwnerEmail(info.getOwnerEmail());
}
if (info.getOwner() != null) entry.setOwner(info.getOwner());
if (info.getCreatorEmail() != null) {
entry.setCreatorEmail(info.getCreatorEmail());
}
if (info.getCreator() != null) entry.setCreator(info.getCreator());
if (info.getStatus() == null) {
if (StringUtils.isBlank(entry.getStatus())) entry.setStatus("");
} else entry.setStatus(info.getStatus());
if (info.getAlias() != null) entry.setAlias(info.getAlias());
if (info.getBioSafetyLevel() == null) {
if (entry.getBioSafetyLevel() == null) entry.setBioSafetyLevel(0);
} else entry.setBioSafetyLevel(info.getBioSafetyLevel());
if (info.getShortDescription() != null) entry.setShortDescription(info.getShortDescription());
if (info.getLongDescription() != null) entry.setLongDescription(info.getLongDescription());
if (info.getIntellectualProperty() != null)
entry.setIntellectualProperty(info.getIntellectualProperty());
Set<Link> links = getLinks(info.getLinks(), entry);
entry.setLinks(links);
Visibility visibility = info.getVisibility();
if (visibility != null) entry.setVisibility(visibility.getValue());
// checking for null instead of blank since it could be cleared
if (info.getFundingSource() != null) entry.setFundingSource(info.getFundingSource());
if (info.getPrincipalInvestigator() != null)
entry.setPrincipalInvestigator(info.getPrincipalInvestigator());
if (info.getPrincipalInvestigatorEmail() != null)
entry.setPrincipalInvestigatorEmail(info.getPrincipalInvestigatorEmail());
if (info.getKeywords() != null) entry.setKeywords(info.getKeywords());
// parameters
List<Parameter> parameters = getParameters(info.getCustomFields(), entry);
entry.setParameters(parameters);
return entry;
}