Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix release pipeline Originally Issue 4106 process map to properties when uploading loinc terminology #4246

Merged
merged 13 commits into from
Nov 4, 2022
Merged

Fix release pipeline Originally Issue 4106 process map to properties when uploading loinc terminology #4246

Changes from 1 commit
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
6a29bbf
Add loinc upload handler to process MAP_TO properties.
Oct 5, 2022
071a890
Move test to test folder
Oct 6, 2022
3d094bb
Fix mapto file location property name
Oct 6, 2022
c19ce09
Allow override as full loinc upload tests take (much) longer than def…
Oct 6, 2022
c6644f8
merge master in
Oct 31, 2022
c90fc74
Move handler later to make sure all concepts were added to map
Oct 31, 2022
b16a44e
Update test to check all project enhancements
Nov 2, 2022
b65def5
Restore project unrelated changes
Nov 2, 2022
b54ea2d
Rename base test class properly and move to right package
Nov 2, 2022
fe1059e
Condition MapTo.csv file processing to file presence for backwards as…
Nov 2, 2022
80bb839
Document and annotate test-only usage for disabling deferred tasks ti…
Nov 2, 2022
8f8ced4
Merge branch 'master' into issue-4106-process-map-to-properties-when-…
Nov 4, 2022
4564369
Fix alignments to try to make release pipeline work
Nov 4, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Restore project unrelated changes
  • Loading branch information
juan.marchionatto committed Nov 2, 2022
commit b65def5a4097010f3c73719ad7f6c36b7af41930
13 changes: 11 additions & 2 deletions hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,7 @@ public UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetail

ourLog.info("Beginning IMGTHLA processing");

return processImgthlaFiles(descriptors);
return processImgthlaFiles(descriptors, theRequestDetails);
}
}

Expand Down Expand Up @@ -492,9 +492,18 @@ private Optional<String> loadFile(LoadedFileDescriptors theDescriptors, String..
return Optional.empty();
}

private UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors) {
private UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final List<ValueSet> valueSets = new ArrayList<>();
final List<ConceptMap> conceptMaps = new ArrayList<>();

CodeSystem imgthlaCs;
try {
String imgthlaCsString = IOUtils.toString(TermReadSvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml"), Charsets.UTF_8);
imgthlaCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, imgthlaCsString);
} catch (IOException e) {
throw new InternalErrorException(Msg.code(869) + "Failed to load imgthla.xml", e);
}

boolean foundHlaNom = false;
boolean foundHlaXml = false;
Expand Down