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Merge pull request #1550 from hapifhir/do-20230119-fix-filetype-detect-in-service 

Fix file type inference in ValidationService
This commit is contained in:
Grahame Grieve 2024-01-28 23:12:08 +11:00 committed by GitHub
parent 42bddb9fdb fa88082c14
commit c34f439da5
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GPG Key ID: B5690EEEBB952194
1 changed files with 56 additions and 27 deletions
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83
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
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@ -110,39 +110,29 @@ public class ValidationService {
fileToValidate.getFileContent().getBytes(), fileToValidate.getFileContent().getBytes(),
fileToValidate.getFileName(), fileToValidate.getFileName(),
false); false);
fileToValidate.setFileType(format.getExtension()); if (format != null) {
fileToValidate.setFileType(format.getExtension());
}
} }
List<ValidationMessage> messages = new ArrayList<>(); List<ValidationMessage> messages = new ArrayList<>();
ValidatedFragments validatedFragments = validator.validateAsFragments(fileToValidate.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fileToValidate.getFileType()), if (fileToValidate.getFileType() == null) {
request.getCliContext().getProfiles(), messages); ValidationOutcome outcome = getValidationOutcomeForUnknownFileFormat(
new FileInfo(fileToValidate.getFileName(), fileToValidate.getFileContent(), null));
if (validatedFragments.getValidatedFragments().size() == 1 && !validatedFragments.getValidatedFragments().get(0).isDerivedContent()) {
ValidatedFragment validatedFragment = validatedFragments.getValidatedFragments().get(0);
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
fileToValidate.getFileName(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
response.addOutcome(outcome);
} else {
for (ValidatedFragment validatedFragment : validatedFragments.getValidatedFragments()) {
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
validatedFragment.getFilename(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
response.addOutcome(outcome); response.addOutcome(outcome);
} } else {
} ValidatedFragments validatedFragments = validator.validateAsFragments(fileToValidate.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fileToValidate.getFileType()),
request.getCliContext().getProfiles(), messages);
if (request.getCliContext().isShowTimes()) { List<ValidationOutcome> validationOutcomes = getValidationOutcomesFromValidatedFragments(fileToValidate, validatedFragments);
response.getValidationTimes().put(fileToValidate.getFileName(), validatedFragments.getValidationTime()); for (ValidationOutcome validationOutcome : validationOutcomes) {
response.addOutcome(validationOutcome);
}
if (request.getCliContext().isShowTimes()) {
response.getValidationTimes().put(fileToValidate.getFileName(), validatedFragments.getValidationTime());
}
} }
} }
@ -150,6 +140,45 @@ public class ValidationService {
return response; return response;
} }
private List<ValidationOutcome> getValidationOutcomesFromValidatedFragments(FileInfo fileToValidate, ValidatedFragments validatedFragments) {
List<ValidationOutcome> outcomes = new LinkedList<>();
if (validatedFragments.getValidatedFragments().size() == 1 && !validatedFragments.getValidatedFragments().get(0).isDerivedContent()) {
ValidatedFragment validatedFragment = validatedFragments.getValidatedFragments().get(0);
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
fileToValidate.getFileName(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
outcomes.add(outcome);
} else {
for (ValidatedFragment validatedFragment : validatedFragments.getValidatedFragments()) {
ValidationOutcome outcome = new ValidationOutcome();
FileInfo fileInfo = new FileInfo(
validatedFragment.getFilename(),
new String(validatedFragment.getContent()),
validatedFragment.getExtension());
outcome.setMessages(validatedFragment.getErrors());
outcome.setFileInfo(fileInfo);
outcomes.add(outcome);
}
}
return outcomes;
}
private ValidationOutcome getValidationOutcomeForUnknownFileFormat(FileInfo fileInfo) {
ValidationOutcome outcome = new ValidationOutcome();
List<ValidationMessage> errorList = new ArrayList<>() {{
add(new ValidationMessage().setType(ValidationMessage.IssueType.EXCEPTION).setLevel(ValidationMessage.IssueSeverity.FATAL).setMessage("Unable to infer format from file. Please check that your file is in a valid FHIR format."));
} };
outcome.setMessages(errorList);
outcome.setFileInfo(fileInfo);
return outcome;
}
public VersionSourceInformation scanForVersions(CliContext cliContext) throws Exception { public VersionSourceInformation scanForVersions(CliContext cliContext) throws Exception {
VersionSourceInformation versions = new VersionSourceInformation(); VersionSourceInformation versions = new VersionSourceInformation();
IgLoader igLoader = new IgLoader( IgLoader igLoader = new IgLoader(