@Override
public Collection<ValidatorMessage> check(InteractionEvidence interaction)
throws ValidatorException {
if (interaction.isNegative()) {
MiContext context = RuleUtils.buildContext(interaction, "interaction");
return Collections.singletonList(
new ValidatorMessage(
"Negative interactions are currently outside of the remit of IMEx and "
+ "should be removed from the record.",
MessageLevel.WARN,
context,
this));
}
return Collections.EMPTY_LIST;
}
@Override
public Collection<ValidatorMessage> check(Confidence confidence) throws ValidatorException {
if (confidence != null) {
// list of messages to return
List<ValidatorMessage> messages = Collections.EMPTY_LIST;
final OntologyAccess access = ontologyManager.getOntologyAccess("MI");
CvTerm type = confidence.getType();
if (type == null
|| PsiXmlUtils.UNSPECIFIED.equals(type.getShortName())
|| MitabUtils.UNKNOWN_TYPE.equals(type.getShortName())) {
MiContext xrefContext = RuleUtils.buildContext(confidence, "confidence");
messages = new ArrayList<ValidatorMessage>();
messages.add(
new ValidatorMessage(
"Confidences must have a valid confidence type.'",
MessageLevel.ERROR,
xrefContext,
this));
} else if (type != null && type.getMIIdentifier() != null) {
final OntologyTermI dbTerm = access.getTermForAccession(type.getMIIdentifier());
if (dbTerm == null) {
MiContext context = RuleUtils.buildContext(confidence, "confidence");
if (messages.isEmpty()) {
messages = new ArrayList<ValidatorMessage>();
}
messages.add(
new ValidatorMessage(
"The confidence type MI identifier "
+ type.getMIIdentifier()
+ " does not exist in the PSI-MI ontology. The valid MI terms for confidence types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A1064&termName=interaction%20confidence",
MessageLevel.ERROR,
context,
this));
} else {
Collection<OntologyTermI> parents = access.getAllParents(dbTerm);
boolean foundParent = false;
for (OntologyTermI p : parents) {
if ("MI:1064".equals(p.getTermAccession())) {
foundParent = true;
break;
}
}
if (!foundParent) {
MiContext context = RuleUtils.buildContext(confidence, "confidence");
if (messages.isEmpty()) {
messages = new ArrayList<ValidatorMessage>();
}
messages.add(
new ValidatorMessage(
"The MI identifier "
+ type.getMIIdentifier()
+ " is not a valid MI identifier for confidence types. The valid MI terms for confidence types are available here: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A1064&termName=interaction%20confidence",
MessageLevel.ERROR,
context,
this));
}
}
}
if (confidence.getValue() == null
|| confidence.getValue().trim().length() == 0
|| PsiXmlUtils.UNSPECIFIED.equals(confidence.getValue())
|| MitabUtils.UNKNOWN_ID.equals(confidence.getValue())) {
MiContext xrefContext = RuleUtils.buildContext(confidence, "confidence");
if (messages.isEmpty()) {
messages = new ArrayList<ValidatorMessage>();
}
messages.add(
new ValidatorMessage(
"Confidences must have a valid and non empty confidence value.'",
MessageLevel.ERROR,
xrefContext,
this));
}
return messages;
}
return Collections.EMPTY_LIST;
}