Examples with FeederAuditEncoding org.ehrbase.serialisation.dbencoding.rmobject.FeederAuditEncoding used on opensource projects

Example 1 with FeederAuditEncoding

use of org.ehrbase.serialisation.dbencoding.rmobject.FeederAuditEncoding in project ehrbase by ehrbase.

the class EntryAccess method retrieveInstanceInCompositionVersion.

public static List<I_EntryAccess> retrieveInstanceInCompositionVersion(I_DomainAccess domainAccess, I_CompositionAccess compositionHistoryAccess, int version) {
    Result<EntryHistoryRecord> entryHistoryRecords = domainAccess.getContext().selectFrom(ENTRY_HISTORY).where(ENTRY_HISTORY.COMPOSITION_ID.eq(compositionHistoryAccess.getId())).and(ENTRY_HISTORY.SYS_TRANSACTION.eq(compositionHistoryAccess.getSysTransaction())).fetch();
    // build the list of parameters to recreate the composition
    Map<SystemValue, Object> values = new HashMap<>();
    values.put(SystemValue.COMPOSER, new PersistedPartyProxy(domainAccess).retrieve(compositionHistoryAccess.getComposerId()));
    EventContext context = I_ContextAccess.retrieveHistoricalEventContext(domainAccess, compositionHistoryAccess.getId(), compositionHistoryAccess.getSysTransaction());
    if (context == null) {
        // unchanged context use the current one!
        // also optional handling of context, because persistent compositions don't have a context
        compositionHistoryAccess.getContextId().ifPresent(uuid -> I_ContextAccess.retrieveInstance(domainAccess, uuid).mapRmEventContext());
    }
    values.put(SystemValue.CONTEXT, context);
    values.put(SystemValue.LANGUAGE, new CodePhrase(new TerminologyId("ISO_639-1"), compositionHistoryAccess.getLanguageCode()));
    String territory2letters = domainAccess.getContext().fetchOne(TERRITORY, TERRITORY.CODE.eq(compositionHistoryAccess.getTerritoryCode())).getTwoletter();
    values.put(SystemValue.TERRITORY, new CodePhrase(new TerminologyId("ISO_3166-1"), territory2letters));
    values.put(SystemValue.FEEDER_AUDIT, new FeederAuditEncoding().fromDB(compositionHistoryAccess.getFeederAudit()));
    List<I_EntryAccess> content = new ArrayList<>();
    try {
        EntryAccess entryAccess = new EntryAccess(domainAccess);
        for (EntryHistoryRecord record : entryHistoryRecords) {
            // set the record UID in the composition
            UUID compositionId = compositionHistoryAccess.getId();
            values.put(SystemValue.UID, new ObjectVersionId(compositionId.toString() + "::" + domainAccess.getServerConfig().getNodename() + "::" + version));
            entryAccess.entryRecord = domainAccess.getContext().newRecord(ENTRY);
            entryAccess.entryRecord.from(record);
            entryAccess.composition = new RawJson().unmarshal(record.getEntry().data(), Composition.class);
            setCompositionAttributes(entryAccess.composition, values);
            buildArchetypeDetails(entryAccess);
            content.add(entryAccess);
        }
    } catch (Exception e) {
        throw new IllegalArgumentException(DB_INCONSISTENCY + e);
    }
    return content;
}

Example 2 with FeederAuditEncoding

use of org.ehrbase.serialisation.dbencoding.rmobject.FeederAuditEncoding in project openEHR_SDK by ehrbase.

the class DBEncodeTest method testEncodeDecodeFeederAudit.

@Test
public void testEncodeDecodeFeederAudit() {
    String jsonFeederAudit = "{\n" + "              \"originating_system_item_ids\": [\n" + "                {\n" + "                  \"issuer\": \"EMIS\",\n" + "                  \"assigner\": \"EMIS\",\n" + "                  \"id\": \"123456\",\n" + "                  \"type\": \"FHIR\"\n" + "                }\n" + "              ],\n" + "              \"feeder_system_item_ids\": [],\n" + "              \"originating_system_audit\": {\n" + "                \"system_id\": \"EMIS\",\n" + "                \"time\": {\n" + "                  \"value\": \"2016-12-20T00:11:02.518+02:00\",\n" + "                  \"epoch_offset\": 1.482185462E9\n" + "                }\n" + "              }\n" + "            }";
    CanonicalJson cut = new CanonicalJson();
    FeederAudit feederAudit = cut.unmarshal(jsonFeederAudit, FeederAudit.class);
    String encodedToDB = new FeederAuditEncoding().toDB(feederAudit);
    FeederAudit decodedFromDB = new FeederAuditEncoding().fromDB(encodedToDB);
    assertEquals(feederAudit.getOriginatingSystemAudit().getSystemId(), decodedFromDB.getOriginatingSystemAudit().getSystemId());
}

Example 3 with FeederAuditEncoding

use of org.ehrbase.serialisation.dbencoding.rmobject.FeederAuditEncoding in project openEHR_SDK by ehrbase.

the class DBEncodeTest method testEncodeDecodeFeederAuditWithOriginalContent.

@Test
public void testEncodeDecodeFeederAuditWithOriginalContent() {
    String jsonFeederAudit = " {\n" + "    \"_type\" : \"FEEDER_AUDIT\",\n" + "    \"original_content\" : {\n" + "      \"_type\" : \"DV_PARSABLE\",\n" + "      \"value\" : \"{\\\"resourceType\\\":\\\"Observation\\\",\\\"meta\\\":{\\\"profile\\\":[\\\"https://www.medizininformatik-initiative.de/fhir/core/StructureDefinition/ObservationLab\\\"]},\\\"identifier\\\":[{\\\"type\\\":{\\\"coding\\\":[{\\\"system\\\":\\\"http://terminology.hl7.org/CodeSystem/v2-0203\\\",\\\"code\\\":\\\"OBI\\\"}]},\\\"system\\\":\\\"https://diz.mii.de/fhir/core/NamingSystem/test-lab-results\\\",\\\"value\\\":\\\"59826-8_1234567890\\\",\\\"assigner\\\":{\\\"identifier\\\":{\\\"system\\\":\\\"https://www.medizininformatik-initiative.de/fhir/core/NamingSystem/org-identifier\\\",\\\"value\\\":\\\"DIZ-ID\\\"}}}],\\\"status\\\":\\\"final\\\",\\\"category\\\":[{\\\"coding\\\":[{\\\"system\\\":\\\"http://loinc.org\\\",\\\"code\\\":\\\"26436-6\\\"},{\\\"system\\\":\\\"http://terminology.hl7.org/CodeSystem/observation-category\\\",\\\"code\\\":\\\"laboratory\\\"}]}],\\\"code\\\":{\\\"coding\\\":[{\\\"system\\\":\\\"http://loinc.org\\\",\\\"code\\\":\\\"59826-8\\\",\\\"display\\\":\\\"Creatinine [Moles/volume] in Blood\\\"}],\\\"text\\\":\\\"Kreatinin\\\"},\\\"subject\\\":{\\\"reference\\\":\\\"Patient/679e3fc3-cc9a-4e04-bc81-cb4d4a7e8e1c\\\"},\\\"encounter\\\":{\\\"reference\\\":\\\"Encounter/555\\\"},\\\"effectiveDateTime\\\":\\\"2018-11-20T12:05:00+01:00\\\",\\\"issued\\\":\\\"2018-03-11T10:28:00+01:00\\\",\\\"performer\\\":[{\\\"reference\\\":\\\"Organization/7772\\\",\\\"display\\\":\\\"Zentrallabor des IKCL\\\"}],\\\"valueQuantity\\\":{\\\"value\\\":72,\\\"unit\\\":\\\"..mol/l\\\",\\\"system\\\":\\\"http://unitsofmeasure.org\\\",\\\"code\\\":\\\"umol/L\\\"},\\\"interpretation\\\":[{\\\"coding\\\":[{\\\"system\\\":\\\"http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation\\\",\\\"code\\\":\\\"N\\\"}]}],\\\"referenceRange\\\":[{\\\"low\\\":{\\\"value\\\":72},\\\"high\\\":{\\\"value\\\":127},\\\"type\\\":{\\\"coding\\\":[{\\\"system\\\":\\\"http://terminology.hl7.org/CodeSystem/referencerange-meaning\\\",\\\"code\\\":\\\"normal\\\",\\\"display\\\":\\\"Normal Range\\\"}]}}]}\",\n" + "      \"formalism\" : \"application/json\"\n" + "    },\n" + "    \"originating_system_audit\" : {\n" + "      \"_type\" : \"FEEDER_AUDIT_DETAILS\",\n" + "      \"system_id\" : \"FHIR-bridge\"\n" + "    }\n" + "  }";
    CanonicalJson cut = new CanonicalJson();
    FeederAudit feederAudit = cut.unmarshal(jsonFeederAudit, FeederAudit.class);
    String encodedToDB = new FeederAuditEncoding().toDB(feederAudit);
    FeederAudit decodedFromDB = new FeederAuditEncoding().fromDB(encodedToDB);
    assertEquals(feederAudit.getOriginatingSystemAudit().getSystemId(), decodedFromDB.getOriginatingSystemAudit().getSystemId());
}

Example 4 with FeederAuditEncoding

use of org.ehrbase.serialisation.dbencoding.rmobject.FeederAuditEncoding in project ehrbase by ehrbase.

the class EntryAccess method retrieveInstanceInComposition.

/**
 * @throws IllegalArgumentException if DB is inconsistent or operation fails
 */
public static List<I_EntryAccess> retrieveInstanceInComposition(I_DomainAccess domainAccess, I_CompositionAccess compositionAccess) {
    Result<EntryRecord> entryRecords = domainAccess.getContext().selectFrom(ENTRY).where(ENTRY.COMPOSITION_ID.eq(compositionAccess.getId())).fetch();
    // build the list of parameters to recreate the composition
    Map<SystemValue, Object> values = new HashMap<>();
    values.put(SystemValue.COMPOSER, new PersistedPartyProxy(domainAccess).retrieve(compositionAccess.getComposerId()));
    // optional handling for persistent compositions that do not have a context
    Optional<I_ContextAccess> opContextAccess = compositionAccess.getContextId().map(id -> I_ContextAccess.retrieveInstance(domainAccess, id));
    opContextAccess.ifPresent(context -> values.put(SystemValue.CONTEXT, context.mapRmEventContext()));
    values.put(SystemValue.LANGUAGE, new CodePhrase(new TerminologyId("ISO_639-1"), compositionAccess.getLanguageCode()));
    String territory2letters = domainAccess.getContext().fetchOne(TERRITORY, TERRITORY.CODE.eq(compositionAccess.getTerritoryCode())).getTwoletter();
    values.put(SystemValue.TERRITORY, new CodePhrase(new TerminologyId("ISO_3166-1"), territory2letters));
    if (compositionAccess.getFeederAudit() != null) {
        values.put(SystemValue.FEEDER_AUDIT, new FeederAuditEncoding().fromDB(compositionAccess.getFeederAudit()));
    }
    if (compositionAccess.getLinks() != null) {
        values.put(SystemValue.LINKS, new LinksEncoding().fromDB(compositionAccess.getLinks()));
    }
    List<I_EntryAccess> content = new ArrayList<>();
    try {
        EntryAccess entryAccess = new EntryAccess(domainAccess);
        for (EntryRecord record : entryRecords) {
            // set the record UID in the composition with matching version number
            Integer version = I_CompositionAccess.getLastVersionNumber(domainAccess, compositionAccess.getId());
            values.put(SystemValue.UID, new ObjectVersionId(compositionAccess.getId().toString() + "::" + domainAccess.getServerConfig().getNodename() + "::" + version));
            entryAccess.entryRecord = record;
            String value = record.getEntry().data();
            entryAccess.composition = new RawJson().unmarshal(value, Composition.class);
            // continuing optional handling for persistent compositions
            opContextAccess.map(I_ContextAccess::mapRmEventContext).ifPresent(ec -> values.put(SystemValue.CONTEXT, ec));
            values.put(SystemValue.CATEGORY, new RecordedDvCodedText().fromDB(record, ENTRY.CATEGORY));
            setCompositionAttributes(entryAccess.composition, values);
            buildArchetypeDetails(entryAccess);
            content.add(entryAccess);
        }
    } catch (Exception e) {
        throw new IllegalArgumentException(DB_INCONSISTENCY + e);
    }
    return content;
}