public static Integer intValue(String value) {
for (BioSafetyOption option : BioSafetyOption.values()) {
if (option.displayName.equalsIgnoreCase(value) || option.getValue().equals(value)) {
return Integer.valueOf(option.getValue());
}
}
return null;
}
public static boolean isValidOption(Integer integer) {
if (integer == null) return false;
for (BioSafetyOption option : BioSafetyOption.values()) {
Integer intValue = intValue(option.toString());
if (intValue != null && integer.intValue() == intValue) return true;
}
return false;
}
/**
* 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};
}