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Merge pull request #349 from ncats/ep_validation_msg_fix
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Normalize the ValidationMassages texts
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@blueSwordfish
blueSwordfish authored Jul 9, 2024
2 parents 8c59bfc + b2374e6 commit 8a8041a
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Showing 16 changed files with 39 additions and 45 deletions.
6 changes: 3 additions & 3 deletions ...nce-extension/src/main/java/fda/gsrs/substance/validators/BdNumModificationValidator.java
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Expand Up @@ -61,10 +61,10 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
if(!allCurrentBdNums.contains(bd)){
if(! ("SUPERSEDED".equalsIgnoreCase(bdnumType) || "SUPERCEDED".equalsIgnoreCase(bdnumType))){
//1. If the BDNUM literal that existed in the old record (e.g. XXXXXX) no longer exists in the current record, throw an error unless that BDNUM was marked as type "superseded".
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE(bdnumType + " BDNUM " + bd + " has been removed, but only SUPERSEDED BDNUM codes may be removed"));
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("%s BDNUM %s has been removed, but only SUPERSEDED BDNUM codes may be removed", bdnumType, bd));

}else {
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE(bdnumType + " BDNUM " + bd + " has been removed"));
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("%s BDNUM %s has been removed", bdnumType, bd));
}
}
}
Expand All @@ -75,7 +75,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
//or if it has been removed (in which case we alrady added an error above for that)
if(primaries !=null && primaries.size() > 1){
//2. If there are 2 or more BDNUMs where both are type "PRIMARY", throw an error.
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("can not have more than 1 PRIMARY BDNUM but have : " + primaries));
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Cannot have more than 1 PRIMARY BDNUM but have : %s", primaries));
}

}
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4 changes: 2 additions & 2 deletions gsrs-module-substances-core/src/main/java/ix/core/models/Structure.java
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Expand Up @@ -509,15 +509,15 @@ public Chemical toChemical(List<GinasProcessingMessage> messages, boolean comput
}
}catch(Exception e){
e.printStackTrace();
messages.add(GinasProcessingMessage.ERROR_MESSAGE(e.getMessage()));
messages.add(GinasProcessingMessage.ERROR_MESSAGE("SMILES parsing error: %s", e.getMessage()));
}

}else{
try {
c = Chemical.parseMol(molfile);
}catch(Exception e){
e.printStackTrace();
messages.add(GinasProcessingMessage.ERROR_MESSAGE(e.getMessage()));
messages.add(GinasProcessingMessage.ERROR_MESSAGE("Molfile parsing error: %s", e.getMessage()));
}
}

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4 changes: 2 additions & 2 deletions gsrs-module-substances-core/src/main/java/ix/ginas/utils/ChemUtils.java
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Expand Up @@ -58,7 +58,7 @@ public static void checkValance(Structure newstr, List<GinasProcessingMessage> g
for (Atom atom : c.getAtoms()) {
if (atom.hasValenceError()) {
GinasProcessingMessage mes = GinasProcessingMessage
.WARNING_MESSAGE("Valence Error on " + atom.getSymbol() + " atom (" + (atom.getAtomIndexInParent() + 1) + ") ");
.WARNING_MESSAGE("Valence Error on %s atom (%s)", atom.getSymbol(), (atom.getAtomIndexInParent() + 1));
gpm.add(mes);
}
}
Expand All @@ -73,7 +73,7 @@ public static void checkValance(Structure newstr, List<GinasProcessingMessage> g
public static void checkChargeBalance(Structure newstr, List<GinasProcessingMessage> gpm) {
if (newstr.charge != 0) {
GinasProcessingMessage mes = GinasProcessingMessage
.WARNING_MESSAGE("Structure is not charge-balanced, net charge of: " + newstr.charge);
.WARNING_MESSAGE("Structure is not charge-balanced, net charge of: %s", newstr.charge);
gpm.add(mes);
}
}
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7 changes: 2 additions & 5 deletions gsrs-module-substances-core/src/main/java/ix/ginas/utils/GinasV1ProblemHandler.java
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Expand Up @@ -62,10 +62,7 @@ else if ("count".equals(property)) {
}

if (!parsed) {
messages.add(GinasProcessingMessage.WARNING_MESSAGE("Unknown property \""
+property+"\" while parsing "
+bean+"; skipping it.."));

messages.add(GinasProcessingMessage.WARNING_MESSAGE("Unknown property \"%s\" while parsing %s; skipping it..", property, bean));
log.debug("Unknown property \""
+property+"\" while parsing "
+bean+"; skipping it..");
Expand All @@ -74,7 +71,7 @@ else if ("count".equals(property)) {
}
}
catch (Exception ex) {
messages.add(GinasProcessingMessage.ERROR_MESSAGE("Error parsing substance JSON:" + ex.getMessage()));
messages.add(GinasProcessingMessage.ERROR_MESSAGE("Error parsing substance JSON:%s", ex.getMessage()));
ex.printStackTrace();
}
return true;
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19 changes: 8 additions & 11 deletions gsrs-module-substances-core/src/main/java/ix/ginas/utils/ProteinUtils.java
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Expand Up @@ -350,9 +350,8 @@ public static MolecularWeightAndFormulaContribution generateProteinWeightAndForm
//There is no computable fragment to use
log.info("No usable molecular weight contribution from structural modification fragment: " + mod.molecularFragment.refuuid);
messages.add(
GinasProcessingMessage.WARNING_MESSAGE(
String.format("Structural modification will not affect the molecular weight because %s has no associated molecular weight",
mod.molecularFragment.refPname)));
GinasProcessingMessage.WARNING_MESSAGE("Structural modification will not affect the molecular weight because %s has no associated molecular weight",
mod.molecularFragment.refPname));
}
else if (contribution.getMw() > 0 || (contribution.getMwHigh() > 0 && contribution.getMwLow() > 0)) {
//removeWater(contribution.getFormulaMap()); 1 December 2020 MAM no need for this
Expand Down Expand Up @@ -405,9 +404,8 @@ else if (contribution.getMw() > 0 || (contribution.getMwHigh() > 0 && contributi
}
else {
log.trace("extent other than complete: " + mod.extent);
messages.add(GinasProcessingMessage.WARNING_MESSAGE(
String.format("Note: structural modification with extent '%s' will not be counted toward the molecular weight",
mod.extent != null ? mod.extent : "[missing]")));
messages.add(GinasProcessingMessage.WARNING_MESSAGE("Note: structural modification with extent '%s' will not be counted toward the molecular weight",
mod.extent != null ? mod.extent : "[missing]"));
}
}
}
Expand Down Expand Up @@ -680,15 +678,14 @@ private static MolecularWeightAndFormulaContribution getContributionForID(Substa
log.trace("contribution: " + ((contribution == null) ? "null" : "not null"));
if ((mwHigh != null && mwHigh > 0) || (mwHighLimit != null && mwHighLimit > 0)
|| (mwLow != null && mwLow > 0) || (mwLowLimit != null && mwLowLimit > 0)) {
contribution.getMessages().add(GinasProcessingMessage.WARNING_MESSAGE(
String.format("Using range of molecular weights for substance %s in structural modification",
referencedSubstance.getName())));
contribution.getMessages().add(GinasProcessingMessage.WARNING_MESSAGE("Using range of molecular weights for substance %s in structural modification",
referencedSubstance.getName()));
}
}
else {
GinasProcessingMessage warning = GinasProcessingMessage.WARNING_MESSAGE(
String.format("Structural modification molecular fragment %s has no average molecular weight and will not be used in the molecular weight calculation",
referencedSubstance.getApprovalIDDisplay()));
"Structural modification molecular fragment %s has no average molecular weight and will not be used in the molecular weight calculation",
referencedSubstance.getApprovalIDDisplay());
contribution = new MolecularWeightAndFormulaContribution(referencedSubstance.substanceClass.name(), warning);
}
log.trace("containsStarAtom: " + containsStarAtom);
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2 changes: 1 addition & 1 deletion gsrs-module-substances-core/src/main/java/ix/ginas/utils/validation/ValidationUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,7 @@ public static boolean validateReference(Substance s,
Reference dbReference = referenceRepository.getOne(UUID.fromString(ref.getValue()));
if(dbReference !=null) {
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE(
"Reference type: \"%s\" citation: \"%s\" uuid \"%s\" not found on substance.",
"Reference type: \"%s\" citation: \"%s\" uuid \"%s\" not found on substance.",
dbReference.docType, dbReference.citation, ref.getValue()));
}else{
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Reference \"%s\" not found on substance.",
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2 changes: 1 addition & 1 deletion ...substances-core/src/main/java/ix/ginas/utils/validation/validators/ChemicalValidator.java
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Expand Up @@ -124,7 +124,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
//not a mol convert it
//struc is already standardized
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE(
"structure should always be specified as mol file converting to format to mol automatically").appliableChange(true),
"Structure should always be specified as mol file converting to format to mol automatically").appliableChange(true),
() -> {
try {
cs.setStructure(cs.getStructure().copy());
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2 changes: 1 addition & 1 deletion ...bstances-core/src/main/java/ix/ginas/utils/validation/validators/CodeFormatValidator.java
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Expand Up @@ -66,7 +66,7 @@ public void validate(Substance s, Substance oldSubstance, ValidatorCallback call
}
}
} catch (IOException e) {
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("could not validate CV"));
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("Could not validate CV"));
}
}

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4 changes: 2 additions & 2 deletions ...es-core/src/main/java/ix/ginas/utils/validation/validators/DefinitionalHashValidator.java
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Expand Up @@ -140,10 +140,10 @@ private GinasProcessingMessage createDiffMessage(List<DefinitionalElements.Defin
}
}
if(messageParts.size() == 1) {
return GinasProcessingMessage.WARNING_MESSAGE("A definitional change has been made: %s please reaffirm. ",
return GinasProcessingMessage.WARNING_MESSAGE("A definitional change has been made: %s please reaffirm.",
messageParts.get(0));
}
return GinasProcessingMessage.WARNING_MESSAGE("Definitional changes have been made: %s; please reaffirm. ",
return GinasProcessingMessage.WARNING_MESSAGE("Definitional changes have been made: %s; please reaffirm.",
String.join("; ", messageParts));
}
}
4 changes: 2 additions & 2 deletions ...le-substances-core/src/main/java/ix/ginas/utils/validation/validators/NamesValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)

}
if (n.getName() == null) {
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("name can not be null"));
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Name can not be null"));
continue;
}
if (n.preferred) {
Expand Down Expand Up @@ -188,7 +188,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
if (name != null && r.matches(name)) {
GinasProcessingMessage mes = GinasProcessingMessage
.WARNING_MESSAGE(
r.getMessage(name))
r.getMessage("%s"), name)
.appliableChange(true);
callback.addMessage(mes, () -> n.setName(r.fix(name)));

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8 changes: 4 additions & 4 deletions ...stances-core/src/main/java/ix/ginas/utils/validation/validators/NucleicAcidValidator.java
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Expand Up @@ -99,9 +99,9 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
//for now just null/blank need to confer with stakeholders if validation is needed or not
if(su.sequence == null || su.sequence.trim().isEmpty()){
if(Substance.SubstanceDefinitionLevel.INCOMPLETE.equals(cs.definitionLevel)){
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("subunit at position %s is blank. This is allowed but discouraged for incomplete nucleic acid records.", (i +1)));
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("Subunit at position %s is blank. This is allowed but discouraged for incomplete nucleic acid records.", (i +1)));
}else {
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("subunit at position %s is blank", (i +1)));
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Subunit at position %s is blank", (i +1)));
}
}
}
Expand Down Expand Up @@ -190,7 +190,7 @@ private void validateSequence(NucleicAcidSubstance s, ValidatorCallback callback
}catch(Exception e){
//invalid bases
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE(
"invalid nucleic acid sequence base in subunit %s %s", subunit.subunitIndex, e.getMessage()));
"Invalid nucleic acid sequence base in subunit %s %s", subunit.subunitIndex, e.getMessage()));

}
}
Expand Down Expand Up @@ -351,7 +351,7 @@ private void validateSequenceDuplicates(
} catch (Exception e) {
log.error("Problem executing duplicate search function", e);
callback.addMessage(GinasProcessingMessage
.ERROR_MESSAGE("Error performing seqeunce search on Nucleic Acid:",
.ERROR_MESSAGE("Error performing seqeunce search on Nucleic Acid:%s",
e.getMessage()));
}
}
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4 changes: 2 additions & 2 deletions ...-substances-core/src/main/java/ix/ginas/utils/validation/validators/PolymerValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
if (mentioned != null) {
if (!contained.containsAll(mentioned)) {
callback.addMessage(GinasProcessingMessage
.ERROR_MESSAGE("Mentioned attachment points '%s' in unit '%s' are not all found in actual connecitons '%s'. ",
.ERROR_MESSAGE("Mentioned attachment points '%s' in unit '%s' are not all found in actual connecitons '%s'.",
mentioned.toString(), u.label, contained.toString()));
}
}
Expand All @@ -121,7 +121,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
Set<String> leftovers = new HashSet<String>(rgroupMentions);
leftovers.removeAll(rgroupsWithMappings);
callback.addMessage(GinasProcessingMessage
.ERROR_MESSAGE("Mentioned attachment point(s) '%s' cannot be found ",
.ERROR_MESSAGE("Mentioned attachment point(s) '%s' cannot be found",
leftovers.toString()));
}

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2 changes: 1 addition & 1 deletion ...s-core/src/main/java/ix/ginas/utils/validation/validators/PrimaryDefinitionValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ public void validate(Substance s, Substance objold, ValidatorCallback callback)
Substance subAlternative = substanceRepository.findBySubstanceReference(relsub);
if(subAlternative ==null){
//does not exist
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("alternative definition not found %s", relsub.refPname));
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("Alternative definition not found %s", relsub.refPname));
}else if (subAlternative.isPrimaryDefinition()) {
callback.addMessage(GinasProcessingMessage
.ERROR_MESSAGE("Primary definitions cannot be alternative definitions for other Primary definitions"));
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8 changes: 4 additions & 4 deletions ...-substances-core/src/main/java/ix/ginas/utils/validation/validators/ProteinValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -97,10 +97,10 @@ public void validate(Substance objnew, Substance objold, ValidatorCallback callb
//for now just null/blank need to confer with stakeholders if amino acid validation is needed or not
if (su.sequence == null || su.sequence.trim().isEmpty()) {
if (Substance.SubstanceDefinitionLevel.INCOMPLETE.equals(cs.definitionLevel)) {
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("subunit at position %s is blank. This is allowed but discouraged for incomplete protein records.", (i + 1)));
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("Subunit at position %s is blank. This is allowed but discouraged for incomplete protein records.", (i + 1)));
}
else {
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("subunit at position %s is blank", (i + 1)));
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Subunit at position %s is blank", (i + 1)));
}
}
}
Expand Down Expand Up @@ -398,8 +398,8 @@ private void validateSequenceDuplicates(
} catch (Exception e) {
log.error("Problem executing duplicate search function", e);
callback.addMessage(GinasProcessingMessage
.ERROR_MESSAGE("Error performing seqeunce search on protein:"
+ e.getMessage()));
.ERROR_MESSAGE("Error performing seqeunce search on protein:%s",
e.getMessage()));
}
}

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4 changes: 2 additions & 2 deletions ...tances-core/src/main/java/ix/ginas/utils/validation/validators/StandardNameValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -161,10 +161,10 @@ public void validateFull(Substance objnew, Substance objold, ValidatorCallback c
if (!stdNameStandardizer.isStandardized(name.stdName)) {
warnedAboutThisNameStandardization =true;
if( invalidStdNameBehavior== InvalidStdNameBehavior.error) {
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Standardized name does not meet standards. This name may contain one or more non-allowed character: '%s'",
callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Standardized name does not meet standards. This name may contain one or more non-allowed character: '%s'",
name.stdName));
}else {
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("Standardized name does not meet standards. This name may contain one or more non-allowed character: '%s'",
callback.addMessage(GinasProcessingMessage.WARNING_MESSAGE("Standardized name does not meet standards. This name may contain one or more non-allowed character: '%s'",
name.stdName));
}
}
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4 changes: 2 additions & 2 deletions ...core/src/main/java/ix/ginas/utils/validation/validators/SubstanceUniquenessValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ public void validate(Substance testSubstance, Substance oldSubstance, ValidatorC
if (fullMatches.size() > 0) {
for (int i = 0; i < fullMatches.size(); i++) {
Substance possibleMatch = fullMatches.get(i);
GinasProcessingMessage mes = GinasProcessingMessage.ERROR_MESSAGE("Substance %s (ID: %s) appears to be a full duplicate\n",
GinasProcessingMessage mes = GinasProcessingMessage.ERROR_MESSAGE("Substance %s (ID: %s) appears to be a full duplicate",
possibleMatch.getName(), possibleMatch.uuid);
mes.addLink(ValidationUtils.createSubstanceLink(possibleMatch.asSubstanceReference()));
//.createSubstanceLink((possibleMatch));
Expand All @@ -73,7 +73,7 @@ public void validate(Substance testSubstance, Substance oldSubstance, ValidatorC
for (int i = 0; i < matches.size(); i++) {
Substance possibleMatch = matches.get(i);
log.debug("in SubstanceUniquenessValidator before message creation");
GinasProcessingMessage mes = GinasProcessingMessage.WARNING_MESSAGE("Substance %s (ID: %s) is a possible duplicate\n",
GinasProcessingMessage mes = GinasProcessingMessage.WARNING_MESSAGE("Substance %s (ID: %s) is a possible duplicate",
possibleMatch.getName(), possibleMatch.uuid);
log.debug("in SubstanceUniquenessValidator, created warning with message " + mes.getMessage());
mes.addLink(ValidationUtils.createSubstanceLink(possibleMatch.asSubstanceReference()));
Expand Down

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