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Incorporated the directory-sync library into the code
Took the code from https://github.com/samply/directory-sync and added it to this repository. This means that there is no dependency with the directory-sync repository any more. The original rational behind the separation was that the library might be used elsewhere, not just in a standalone service. This never actually happened, hence the decision to combine service and library, which makes the code easier to maintain.
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,40 @@ | ||
| package de.samply.directory_sync_service; | ||
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| import java.io.PrintWriter; | ||
| import java.io.StringWriter; | ||
| import java.util.HashMap; | ||
| import java.util.Map; | ||
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| import com.google.gson.Gson; | ||
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| public class Util { | ||
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| public static <K, V> Map<K, V> mapOf() { | ||
| return new HashMap<>(); | ||
| } | ||
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| /** | ||
| * Creates a new map with a single entry consisting of the specified key and value. | ||
| * | ||
| * @param key the key for the entry | ||
| * @param value the value associated with the key | ||
| * @return a new map containing the specified key-value pair | ||
| */ | ||
| public static <K, V> Map<K, V> mapOf(K key, V value) { | ||
| HashMap<K, V> map = new HashMap<>(); | ||
| map.put(key, value); | ||
| return map; | ||
| } | ||
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| /** | ||
| * Get a printable stack trace from an Exception object. | ||
| * @param e | ||
| * @return | ||
| */ | ||
| public static String traceFromException(Exception e) { | ||
| StringWriter sw = new StringWriter(); | ||
| PrintWriter pw = new PrintWriter(sw); | ||
| e.printStackTrace(pw); | ||
| return sw.toString(); | ||
| } | ||
| } |
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155 changes: 155 additions & 0 deletions
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...ply/directory_sync_service/converter/FhirCollectionToDirectoryCollectionPutConverter.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,155 @@ | ||
| package de.samply.directory_sync_service.converter; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
| import java.util.Objects; | ||
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| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import de.samply.directory_sync_service.Util; | ||
| import de.samply.directory_sync_service.directory.model.DirectoryCollectionPut; | ||
| import de.samply.directory_sync_service.fhir.model.FhirCollection; | ||
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| /** | ||
| * Takes a list of FhirCollection objects and converts them into a | ||
| * DirectoryCollectionPut object. | ||
| * | ||
| * This is a kind of FHIR to Directory conversion, so there are differences | ||
| * in vocabularies, and it is the job of this converter to impedence match them. | ||
| */ | ||
| public class FhirCollectionToDirectoryCollectionPutConverter { | ||
| private static final Logger logger = LoggerFactory.getLogger(FhirCollectionToDirectoryCollectionPutConverter.class); | ||
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| public static DirectoryCollectionPut convert(List<FhirCollection> fhirCollections) { | ||
| DirectoryCollectionPut directoryCollectionPut = new DirectoryCollectionPut(); | ||
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| for (FhirCollection fhirCollection: fhirCollections) | ||
| if (convert(directoryCollectionPut, fhirCollection) == null) { | ||
| directoryCollectionPut = null; | ||
| break; | ||
| } | ||
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| return directoryCollectionPut; | ||
| } | ||
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| private static DirectoryCollectionPut convert(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| try { | ||
| convertSize(directoryCollectionPut, fhirCollection); | ||
| convertNumberOfDonors(directoryCollectionPut, fhirCollection); | ||
| convertSex(directoryCollectionPut, fhirCollection); | ||
| convertAgeLow(directoryCollectionPut, fhirCollection); | ||
| convertAgeHigh(directoryCollectionPut, fhirCollection); | ||
| convertMaterials(directoryCollectionPut, fhirCollection); | ||
| convertStorageTemperatures(directoryCollectionPut, fhirCollection); | ||
| // convertDiagnosisAvailableEmpty(directoryCollectionPut, fhirCollection); | ||
| convertDiagnosisAvailable(directoryCollectionPut, fhirCollection); | ||
| } catch(Exception e) { | ||
| logger.error("Problem converting FHIR attributes to Directory attributes. " + Util.traceFromException(e)); | ||
| return null; | ||
| } | ||
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| return directoryCollectionPut; | ||
| } | ||
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| private static void convertSize(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| Integer size = fhirCollection.getSize(); | ||
| directoryCollectionPut.setSize(id, size); | ||
| // Order of magnitude is mandatory in the Directory and can be derived from size | ||
| directoryCollectionPut.setOrderOfMagnitude(id, (int) Math.floor(Math.log10(size))); | ||
| } | ||
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| public static void convertNumberOfDonors(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| Integer size = fhirCollection.getNumberOfDonors(); | ||
| directoryCollectionPut.setNumberOfDonors(id, size); | ||
| // Order of magnitude is mandatory in the Directory and can be derived from size | ||
| directoryCollectionPut.setOrderOfMagnitudeDonors(id, (int) Math.floor(Math.log10(size))); | ||
| } | ||
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| public static void convertSex(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| List<String> sex = fhirCollection.getSex(); | ||
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| List<String> ucSex = sex.stream() | ||
| .map(s -> FhirToDirectoryAttributeConverter.convertSex(s)) | ||
| .filter(Objects::nonNull) // Use a method reference to check for non-null values | ||
| .distinct() // Remove duplicate elements | ||
| .collect(Collectors.toList()); | ||
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| directoryCollectionPut.setSex(id, ucSex); | ||
| } | ||
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| public static void convertAgeLow(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| Integer ageLow = fhirCollection.getAgeLow(); | ||
| // No conversion needed | ||
| directoryCollectionPut.setAgeLow(id, ageLow); | ||
| } | ||
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| public static void convertAgeHigh(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| Integer ageHigh = fhirCollection.getAgeHigh(); | ||
| // No conversion needed | ||
| directoryCollectionPut.setAgeHigh(id, ageHigh); | ||
| } | ||
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| public static void convertMaterials(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| List<String> materials = fhirCollection.getMaterials(); | ||
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| if (materials == null) | ||
| materials = new ArrayList<String>(); | ||
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| List<String> directoryMaterials = materials.stream() | ||
| .map(s -> FhirToDirectoryAttributeConverter.convertMaterial(s)) | ||
| .filter(Objects::nonNull) // Use a method reference to check for non-null values | ||
| .distinct() // Remove duplicate elements | ||
| .collect(Collectors.toList()); | ||
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| directoryCollectionPut.setMaterials(id, directoryMaterials); | ||
| } | ||
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| public static void convertStorageTemperatures(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| List<String> storageTemperatures = fhirCollection.getStorageTemperatures(); | ||
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| if (storageTemperatures == null) | ||
| storageTemperatures = new ArrayList<String>(); | ||
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| List<String> directoryStorageTemperatures = storageTemperatures.stream() | ||
| .map(s -> FhirToDirectoryAttributeConverter.convertStorageTemperature(s)) | ||
| .filter(Objects::nonNull) // Use a method reference to check for non-null values | ||
| .distinct() // Remove duplicate elements | ||
| .collect(Collectors.toList()); | ||
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| directoryCollectionPut.setStorageTemperatures(id, directoryStorageTemperatures); | ||
| } | ||
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| public static void convertDiagnosisAvailableEmpty(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| // The Directory is very picky about which ICD10 codes it will accept, and some | ||
| // of the codes that are in our test data are not known to the Directory and | ||
| // give rise to errors, which lead to the entire PUT to the Directory being | ||
| // rejected. So, for the time being, I am turning off the diagnosis conversion. | ||
| directoryCollectionPut.setDiagnosisAvailable(id, new ArrayList<String>()); | ||
| } | ||
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| public static void convertDiagnosisAvailable(DirectoryCollectionPut directoryCollectionPut, FhirCollection fhirCollection) { | ||
| String id = fhirCollection.getId(); | ||
| List<String> diagnoses = fhirCollection.getDiagnosisAvailable(); | ||
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| if (diagnoses == null) | ||
| diagnoses = new ArrayList<String>(); | ||
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| List<String> miriamDiagnoses = diagnoses.stream() | ||
| .map(icd -> FhirToDirectoryAttributeConverter.convertDiagnosis(icd)) | ||
| .filter(Objects::nonNull) // Use a method reference to check for non-null values | ||
| .distinct() // Remove duplicate diagnoses | ||
| .collect(Collectors.toList()); | ||
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| directoryCollectionPut.setDiagnosisAvailable(id, miriamDiagnoses); | ||
| } | ||
| } |
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