Skip to content

Commit

Permalink
Csv export prototype complete
Browse files Browse the repository at this point in the history
  • Loading branch information
@cerbeor
cerbeor committed Dec 12, 2023
1 parent e6f0eb5 commit 174ee47
Show file tree
Hide file tree
Showing 14 changed files with 323 additions and 84 deletions.
15 changes: 10 additions & 5 deletions src/main/java/org/immregistries/iis/kernal/InternalClient/RepositoryClientFactory.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,8 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.env.Environment;
import org.springframework.security.core.Authentication;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.stereotype.Component;
Expand All @@ -27,6 +29,9 @@

import javax.servlet.http.HttpServletRequest;

import java.net.InetAddress;
import java.net.UnknownHostException;

import static org.immregistries.iis.kernal.fhir.interceptors.SessionAuthorizationInterceptor.CONNECTATHON_USER;
import static org.immregistries.iis.kernal.fhir.security.ServletHelper.GITHUB_PREFIX;
import static org.immregistries.iis.kernal.fhir.security.ServletHelper.SESSION_TENANT;
Expand All @@ -41,7 +46,9 @@ public class RepositoryClientFactory extends ApacheRestfulClientFactory implemen
private IFhirSystemDao fhirSystemDao;
private final Logger logger = LoggerFactory.getLogger(RepositoryClientFactory.class);
private LoggingInterceptor loggingInterceptor;
private static String serverBase = "";

@Autowired
Environment environment;

@Autowired
public RepositoryClientFactory(){
Expand All @@ -55,14 +62,12 @@ private void asynchInit() {
loggingInterceptor = new LoggingInterceptor();
loggingInterceptor.setLogger(logger);
}
if (serverBase.equals("")) {
serverBase = ServletUriComponentsBuilder.fromCurrentContextPath().build().toUriString() + "/fhir";
}
}

public IGenericClient newGenericClient(Tenant tenant) {
asynchInit();
IGenericClient client = newGenericClient(serverBase + "/" + tenant.getOrganizationName());
IGenericClient client;
client = newGenericClient( "http://" + InetAddress.getLoopbackAddress().getHostAddress() + ":" + environment.getProperty("server.port") + "/iis/fhir/" + tenant.getOrganizationName());
IClientInterceptor authInterceptor;
if (tenant.getOrganizationName().equals(CONNECTATHON_USER) && tenant.getUserAccess().getAccessName() == null) {
/**
Expand Down
55 changes: 31 additions & 24 deletions src/main/java/org/immregistries/iis/kernal/mapping/MappingHelper.java
View file
Original file line number Diff line number Diff line change
@@ -1,9 +1,7 @@
package org.immregistries.iis.kernal.mapping;


import ca.uhn.fhir.util.CanonicalIdentifier;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.r5.model.*;

import java.text.SimpleDateFormat;
Expand All @@ -23,25 +21,31 @@ public class MappingHelper {
public static final SimpleDateFormat sdf = new SimpleDateFormat("E MMM dd HH:mm:ss yyyy");

//TODO choose system id or not
public static Reference getFhirReference(String fhirType, String dbType, String identifier) {
public static Reference getFhirReferenceR5(String fhirType, String dbType, String identifier) {
if (StringUtils.isBlank(identifier)) {
return null;
} else {
return new Reference()
.setType(fhirType)
.setIdentifier(getFhirIdentifier(dbType, identifier));
.setIdentifier(getFhirIdentifierR5(dbType, identifier));
}
}

public static CodeableReference getFhirCodeableReference(String fhirType, String dbType, String identifier) {
public static Reference getFhirReferenceR5(String fhirType, String dbType, String identifier, String fhirId) {
return new Reference(fhirType + "/" + fhirId)
.setType(fhirType)
.setIdentifier(getFhirIdentifierR5(dbType, identifier));
}

public static CodeableReference getFhirCodeableReferenceR5(String fhirType, String dbType, String identifier) {
if (StringUtils.isBlank(identifier)) {
return null;
} else {
return new CodeableReference(getFhirReference(fhirType, dbType, identifier));
return new CodeableReference(getFhirReferenceR5(fhirType, dbType, identifier));
}
}

public static org.hl7.fhir.r4.model.Reference getFhirR4Reference(String fhirType, String dbType, String identifier) {
public static org.hl7.fhir.r4.model.Reference getFhirReferenceR4(String fhirType, String dbType, String identifier) {
if (StringUtils.isBlank(identifier)) {
return null;
} else {
Expand All @@ -52,25 +56,20 @@ public static org.hl7.fhir.r4.model.Reference getFhirR4Reference(String fhirType
.setValue(identifier));
}
}
public static Reference getFhirReference(String fhirType, String dbType, String identifier, String fhirId) {
return new Reference(fhirType + "/" + fhirId)
.setType(fhirType)
.setIdentifier(getFhirIdentifier(dbType,identifier));
}

public static Identifier getFhirIdentifier(String dbType, String identifier) {
public static Identifier getFhirIdentifierR5(String dbType, String identifier) {
return new Identifier()
.setSystem(dbType)
.setValue(identifier);
.setSystem(dbType)
.setValue(identifier);
}

public static org.hl7.fhir.r4.model.Identifier getFhirR4Identifier(String dbType, String identifier) {
public static org.hl7.fhir.r4.model.Identifier getFhirIdentifierR4(String dbType, String identifier) {
return new org.hl7.fhir.r4.model.Identifier()
.setSystem(dbType)
.setValue(identifier);
.setSystem(dbType)
.setValue(identifier);
}

public static String identifierToString(List<Identifier> identifiers) {
public static String identifierToString(List<Identifier> identifiers) {
if (identifiers.size() > 0) {
return identifiers.get(0).getSystem() + "|" + identifiers.get(0).getValue();
} else {
Expand All @@ -82,19 +81,27 @@ public static String identifierToString(List<Identifier> identifiers) {
// return identifiers.stream().filter(identifier -> identifier.getSystemElement().getValue() != null && identifier.getSystemElement().getValue().equals(system)).findFirst().orElse(identifiers.get(0));
// }

public static Identifier filterIdentifier(List<Identifier> identifiers, String system) {
public static Identifier filterIdentifierR5(List<Identifier> identifiers, String system) {
return identifiers.stream().filter(identifier -> identifier.getSystem() != null && identifier.getSystem().equals(system)).findFirst().orElse(null);
}

public static org.hl7.fhir.r4.model.Identifier filterR4Identifier(List<org.hl7.fhir.r4.model.Identifier> identifiers, String system) {
public static org.hl7.fhir.r4.model.Identifier filterIdentifierR4(List<org.hl7.fhir.r4.model.Identifier> identifiers, String system) {
return identifiers.stream().filter(identifier -> identifier.getSystem() != null && identifier.getSystem().equals(system)).findFirst().orElse(null);
}

public static Coding filterCodeableConcept(CodeableConcept concept, String system) {
return filterCodingList(concept.getCoding(), system);
public static Identifier filterIdentifierTypeR5(List<Identifier> identifiers, String type) {
return identifiers.stream().filter(identifier -> identifier.hasType() && identifier.getType().hasCoding() && identifier.getType().getCodingFirstRep().getCode().equals(type)).findFirst().orElse(null);
}

public static org.hl7.fhir.r4.model.Identifier filterIdentifierTypeR4(List<org.hl7.fhir.r4.model.Identifier> identifiers, String type) {
return identifiers.stream().filter(identifier -> identifier.hasType() && identifier.getType().hasCoding() && identifier.getType().getCodingFirstRep().getCode().equals(type)).findFirst().orElse(null);
}

public static Coding filterCodeableConceptR5(CodeableConcept concept, String system) {
return filterCodingListR5(concept.getCoding(), system);
}

public static Coding filterCodingList(List<Coding> codings, String system) {
public static Coding filterCodingListR5(List<Coding> codings, String system) {
return codings.stream().filter(coding -> coding.getSystem().equals(system)).findFirst().get();
}

Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/immregistries/iis/kernal/mapping/forR4/LocationMapperR4.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ public org.hl7.fhir.r4.model.Location getFhirResource(OrgLocation ol) {
if (ol != null) {
org.hl7.fhir.r4.model.Location location = new org.hl7.fhir.r4.model.Location();
location.setId(ol.getOrgLocationId());
location.addIdentifier(MappingHelper.getFhirR4Identifier("", ol.getOrgFacilityCode()));
location.addIdentifier(MappingHelper.getFhirIdentifierR4("", ol.getOrgFacilityCode()));
location.setName(ol.getOrgFacilityName());
if (!ol.getVfcProviderPin().isBlank()) {
location.addExtension().setUrl(VFC_PROVIDER_PIN).setValue(new StringType(ol.getVfcProviderPin()));
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/immregistries/iis/kernal/mapping/forR4/ObservationMapperR4.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ public Observation getFhirResource(ObservationReported observationReported) {
.setCode(observationReported.getMethodCode())
.setSystem(observationReported.getMethodTable())
.setDisplay(observationReported.getMethodLabel());
o.addIdentifier(MappingHelper.getFhirR4Identifier(
o.addIdentifier(MappingHelper.getFhirIdentifierR4(
observationReported.getIdentifierTable(),observationReported.getIdentifierCode())); //TODO label
o.addComponent().setValue(new org.hl7.fhir.r4.model.DateTimeType(observationReported.getObservationDate()))
.setCode(new org.hl7.fhir.r4.model.CodeableConcept().setText(OBSERVATION_DATE));
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/immregistries/iis/kernal/mapping/forR4/OrganizationMapperR4.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,15 @@ public class OrganizationMapperR4 implements OrganizationMapper<Organization> {

public Organization getFhirResource(Tenant tenant) {
Organization o = new Organization();
o.addIdentifier(MappingHelper.getFhirR4Identifier("Tenant", Integer.toString(tenant.getOrgId())));
o.addIdentifier(MappingHelper.getFhirIdentifierR4("Tenant", Integer.toString(tenant.getOrgId())));
o.setName(tenant.getOrganizationName());
return o;
}

public Tenant getTenant(Organization organization) {
Tenant tenant = new Tenant();
tenant.setOrganizationName(organization.getName());
tenant.setOrgId(Integer.parseInt(MappingHelper.filterR4Identifier(organization.getIdentifier(),"Tenant").getValue()));
tenant.setOrgId(Integer.parseInt(MappingHelper.filterIdentifierR4(organization.getIdentifier(),"Tenant").getValue()));
return tenant;
}
}
2 changes: 1 addition & 1 deletion src/main/java/org/immregistries/iis/kernal/mapping/forR4/PersonMapperR4.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ public Person getFhirResource(ModelPerson modelPerson) {
if ( modelPerson.getProfessionalSuffix() != null) {
name.addSuffix(modelPerson.getProfessionalSuffix());
}
p.setManagingOrganization(MappingHelper.getFhirR4Reference(MappingHelper.ORGANIZATION,ORGANIZATION_ASSIGNING_AUTHORITY, modelPerson.getAssigningAuthority()));
p.setManagingOrganization(MappingHelper.getFhirReferenceR4(MappingHelper.ORGANIZATION,ORGANIZATION_ASSIGNING_AUTHORITY, modelPerson.getAssigningAuthority()));
return p;
}

Expand Down
6 changes: 3 additions & 3 deletions src/main/java/org/immregistries/iis/kernal/mapping/forR5/ImmunizationMapperR5.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ public VaccinationMaster getMaster(Immunization i){
*/
public Immunization getFhirResource(VaccinationMaster vr) {
Immunization i = new Immunization();
i.addIdentifier(MappingHelper.getFhirIdentifier(vr.getExternalLinkSystem(), vr.getExternalLink())); // TODO if system empty ?
i.addIdentifier(MappingHelper.getFhirIdentifierR5(vr.getExternalLinkSystem(), vr.getExternalLink())); // TODO if system empty ?
Reference patientReference = new Reference()
.setReference("Patient/" + vr.getPatientReported().getPatientId())
// .setIdentifier(new Identifier()
Expand All @@ -186,7 +186,7 @@ public Immunization getFhirResource(VaccinationMaster vr) {
if (StringUtils.isNotBlank(vr.getVaccineNdcCode())) {
i.getVaccineCode().addCoding().setCode(vr.getVaccineNdcCode()).setSystem(NDC);
}
i.setManufacturer(MappingHelper.getFhirCodeableReference(MappingHelper.ORGANIZATION, MVX, vr.getVaccineMvxCode()));
i.setManufacturer(MappingHelper.getFhirCodeableReferenceR5(MappingHelper.ORGANIZATION, MVX, vr.getVaccineMvxCode()));

i.setDoseQuantity(new Quantity().setValue(new BigDecimal(vr.getAdministeredAmount())));

Expand Down Expand Up @@ -255,7 +255,7 @@ private Immunization.ImmunizationPerformerComponent performer(ModelPerson person
break;
}
default:{
actor = MappingHelper.getFhirReference(MappingHelper.PRACTITIONER, person.getIdentifierTypeCode(), person.getPersonExternalLink(), person.getPersonId());
actor = MappingHelper.getFhirReferenceR5(MappingHelper.PRACTITIONER, person.getIdentifierTypeCode(), person.getPersonExternalLink(), person.getPersonId());
}
}
performer.setActor(actor);
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/immregistries/iis/kernal/mapping/forR5/ObservationMapperR5.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ public Observation getFhirResource(ObservationReported observationReported) {
.setCode(observationReported.getMethodCode())
.setSystem(observationReported.getMethodTable())
.setDisplay(observationReported.getMethodLabel());
o.addIdentifier(MappingHelper.getFhirIdentifier(
o.addIdentifier(MappingHelper.getFhirIdentifierR5(
observationReported.getIdentifierTable(),observationReported.getIdentifierCode())); //TODO label
o.addComponent().setValue(new DateTimeType(observationReported.getObservationDate()))
.setCode(new CodeableConcept().setText(OBSERVATION_DATE));
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/immregistries/iis/kernal/mapping/forR5/OrganizationMapperR5.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,15 @@ public class OrganizationMapperR5 implements OrganizationMapper<Organization> {

public Organization getFhirResource(Tenant tenant) {
Organization o = new Organization();
o.addIdentifier(MappingHelper.getFhirIdentifier("Tenant", Integer.toString(tenant.getOrgId())));
o.addIdentifier(MappingHelper.getFhirIdentifierR5("Tenant", Integer.toString(tenant.getOrgId())));
o.setName(tenant.getOrganizationName());
return o;
}

public Tenant getTenant(Organization organization) {
Tenant tenant = new Tenant();
tenant.setOrganizationName(organization.getName());
tenant.setOrgId(Integer.parseInt(MappingHelper.filterIdentifier(organization.getIdentifier(),"Tenant").getValue()));
tenant.setOrgId(Integer.parseInt(MappingHelper.filterIdentifierR5(organization.getIdentifier(),"Tenant").getValue()));
return tenant;
}
}
4 changes: 2 additions & 2 deletions src/main/java/org/immregistries/iis/kernal/mapping/forR5/PersonMapperR5.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,15 +33,15 @@ public ModelPerson getModelPerson(org.hl7.fhir.r5.model.Person p) {
public Person getFhirResource(ModelPerson modelPerson) {
org.hl7.fhir.r5.model.Person p = new org.hl7.fhir.r5.model.Person();
p.setId(modelPerson.getPersonId());
p.addIdentifier(MappingHelper.getFhirIdentifier(MappingHelper.PERSON, modelPerson.getPersonExternalLink()));
p.addIdentifier(MappingHelper.getFhirIdentifierR5(MappingHelper.PERSON, modelPerson.getPersonExternalLink()));
HumanName name = p.addName();
name.setFamily(modelPerson.getNameLast());
name.addGiven(modelPerson.getNameFirst());
name.addGiven(modelPerson.getNameMiddle());
if ( modelPerson.getProfessionalSuffix() != null) {
name.addSuffix(modelPerson.getProfessionalSuffix());
}
p.setManagingOrganization(MappingHelper.getFhirReference(MappingHelper.ORGANIZATION, ORGANIZATION_ASSIGNING_AUTHORITY, modelPerson.getAssigningAuthority()));
p.setManagingOrganization(MappingHelper.getFhirReferenceR5(MappingHelper.ORGANIZATION, ORGANIZATION_ASSIGNING_AUTHORITY, modelPerson.getAssigningAuthority()));
return p;
}

Expand Down
8 changes: 4 additions & 4 deletions src/main/java/org/immregistries/iis/kernal/mapping/forR5/PractitionerMapperR5.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,19 +39,19 @@ public Practitioner getFhirResource(ModelPerson modelPerson) {
try {
switch (new Reference(modelPerson.getIdentifierTypeCode()).getType()) {
case "Organization": {
practitioner.addIdentifier(MappingHelper.getFhirIdentifier(PRACTITIONER,modelPerson.getPersonExternalLink()).setAssigner(new Reference(modelPerson.getAssigningAuthority())));
practitioner.addIdentifier(MappingHelper.getFhirIdentifierR5(PRACTITIONER,modelPerson.getPersonExternalLink()).setAssigner(new Reference(modelPerson.getAssigningAuthority())));
break;
}
case "System" : {
practitioner.addIdentifier(MappingHelper.getFhirIdentifier(modelPerson.getIdentifierTypeCode(),modelPerson.getPersonExternalLink()));
practitioner.addIdentifier(MappingHelper.getFhirIdentifierR5(modelPerson.getIdentifierTypeCode(),modelPerson.getPersonExternalLink()));
break;
} default: {
practitioner.addIdentifier(MappingHelper.getFhirIdentifier(PRACTITIONER,modelPerson.getPersonExternalLink()));
practitioner.addIdentifier(MappingHelper.getFhirIdentifierR5(PRACTITIONER,modelPerson.getPersonExternalLink()));
break;
}
}
} catch (NullPointerException e) { // If typecode is not reference
practitioner.addIdentifier(MappingHelper.getFhirIdentifier(modelPerson.getIdentifierTypeCode(),modelPerson.getPersonExternalLink()));
practitioner.addIdentifier(MappingHelper.getFhirIdentifierR5(modelPerson.getIdentifierTypeCode(),modelPerson.getPersonExternalLink()));
}


Expand Down
2 changes: 2 additions & 0 deletions src/main/java/org/immregistries/iis/kernal/servlet/LoginServlet.java
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
package org.immregistries.iis.kernal.servlet;

import org.apache.commons.codec.binary.Base64;
import org.hibernate.Session;
import org.immregistries.iis.kernal.fhir.security.ServletHelper;
import org.immregistries.iis.kernal.model.Tenant;
import org.springframework.security.authentication.AnonymousAuthenticationToken;
import org.springframework.security.core.Authentication;
Expand Down
Loading

0 comments on commit 174ee47

Please sign in to comment.