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OpenConceptLab/ocl_issues#271 developed code system create operation …
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…and code refactoring
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Harsh Patel committed Dec 30, 2020
1 parent 69f2d01 commit 916e618
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Showing 25 changed files with 1,685 additions and 718 deletions.
11 changes: 4 additions & 7 deletions ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/OclFhirApplication.java
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import org.openconceptlab.fhir.config.Config;
import org.openconceptlab.fhir.controller.OclFhirController;
import org.openconceptlab.fhir.converter.CodeSystemConverter;
import org.openconceptlab.fhir.util.OclFhirUtil;
import org.openconceptlab.fhir.interceptor.OclFhirLoggingInterceptor;
import org.openconceptlab.fhir.model.BaseOclEntity;
import org.openconceptlab.fhir.model.UserProfile;
import org.openconceptlab.fhir.provider.CodeSystemResourceProvider;
import org.openconceptlab.fhir.repository.BaseOclRepository;
import org.openconceptlab.fhir.repository.ConceptRepository;
import org.openconceptlab.fhir.repository.UserRepository;
import org.openconceptlab.fhir.util.OclFhirUtil;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
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import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.PropertySource;
import org.springframework.context.annotation.PropertySources;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;

import javax.annotation.PostConstruct;
import java.util.List;

@ServletComponentScan
@SpringBootApplication(exclude = {ErrorMvcAutoConfiguration.class})
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@PostConstruct
public void init() {
List<UserProfile> users = userRepository.findByUsernameIs("ocladmin");
if (!users.isEmpty()) {
oclUser = users.get(0);
UserProfile user = userRepository.findByUsername("ocladmin");
if (user != null) {
oclUser = user;
} else {
throw new InternalError("Can not find ocladmin user.");
}
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191 changes: 191 additions & 0 deletions ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/controller/BaseOclFhirController.java
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package org.openconceptlab.fhir.controller;

import ca.uhn.fhir.rest.gclient.IQuery;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import org.hl7.fhir.r4.model.*;
import org.openconceptlab.fhir.util.OclFhirUtil;
import org.openconceptlab.fhir.provider.CodeSystemResourceProvider;
import org.openconceptlab.fhir.provider.ValueSetResourceProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Component;

import java.util.List;
import java.util.Optional;

import static org.openconceptlab.fhir.util.OclFhirUtil.*;
import static org.openconceptlab.fhir.util.OclFhirUtil.getIdentifier;
import static org.openconceptlab.fhir.util.OclFhirConstants.*;
import static org.openconceptlab.fhir.util.OclFhirConstants.FW_SLASH;

@Component
public class BaseOclFhirController {

CodeSystemResourceProvider codeSystemResourceProvider;
ValueSetResourceProvider valueSetResourceProvider;
OclFhirUtil oclFhirUtil;

@Autowired
public BaseOclFhirController(CodeSystemResourceProvider codeSystemResourceProvider,
ValueSetResourceProvider valueSetResourceProvider,
OclFhirUtil oclFhirUtil) {
this.codeSystemResourceProvider = codeSystemResourceProvider;
this.valueSetResourceProvider = valueSetResourceProvider;
this.oclFhirUtil = oclFhirUtil;
}

protected ResponseEntity<String> handleSearchResource(final Class<? extends MetadataResource> resourceClass, final String... args) {
try {
String resource = searchResource(resourceClass, args);
return ResponseEntity.ok(resource);
} catch (BaseServerResponseException e) {
return ResponseEntity.status(e.getStatusCode()).body(e.getResponseBody());
} catch (Exception e) {
return badRequest();
}
}

protected ResponseEntity<String> handleFhirOperation(Parameters parameters, Class<? extends Resource> type, String operation) {
try {
return ResponseEntity.ok(oclFhirUtil.getResourceAsString(performFhirOperation(parameters, type, operation)));
} catch (BaseServerResponseException e) {
return ResponseEntity.status(e.getStatusCode()).body(e.getResponseBody());
} catch (Exception e) {
return badRequest();
}
}

protected String searchResource(final Class<? extends MetadataResource> resourceClass, final String... filters) {
IQuery q = oclFhirUtil.getClient().search().forResource(resourceClass);
if (filters.length % 2 == 0) {
for (int i = 0; i < filters.length; i += 2) {
if (i == 0) {
q = q.where(new StringClientParam(filters[i]).matches().value(filters[i + 1]));
} else {
q = q.and(new StringClientParam(filters[i]).matches().value(filters[i + 1]));
}
}
}
Bundle bundle = (Bundle) q.execute();
return oclFhirUtil.getResourceAsString(bundle);
}

protected Parameters performFhirOperation(Parameters parameters, Class<? extends Resource> type, String operation) {
return oclFhirUtil.getClient()
.operation()
.onType(type)
.named(operation)
.withParameters(parameters)
.execute();
}

protected void performCreate(CodeSystem resource, String auth) {
oclFhirUtil.getClient()
.create()
.resource(resource).withAdditionalHeader(AUTHORIZATION, auth)
.execute();
}

protected Parameters generateParameters(String code, String displayLanguage, String owner) {
Parameters parameters = new Parameters();
parameters.addParameter().setName(CODE).setValue(new CodeType(code));
if (isValid(displayLanguage))
parameters.addParameter().setName(DISP_LANG).setValue(new CodeType(displayLanguage));
parameters.addParameter().setName(OWNER).setValue(newStringType(owner));
return parameters;
}

protected Parameters lookupParameters(String system, String code, String version, String displayLanguage, String owner) {
Parameters parameters = generateParameters(code, displayLanguage, owner);
parameters.addParameter().setName(SYSTEM).setValue(new UriType(system));
if (isValid(version))
parameters.addParameter().setName(VERSION).setValue(newStringType(version));
return parameters;
}

protected Parameters codeSystemVCParameters(String url, String code, String version, String display, String displayLanguage,
String owner) {
Parameters parameters = generateParameters(code, displayLanguage, owner);
parameters.addParameter().setName(URL).setValue(new UriType(url));
if (isValid(version))
parameters.addParameter().setName(VERSION).setValue(newStringType(version));
if (isValid(display))
parameters.addParameter().setName(DISPLAY).setValue(newStringType(display));
return parameters;
}

protected Parameters valueSetVCParameters(String url, String valueSetId, String valueSetVersion, String code, String system, String systemVersion,
String display, String displayLanguage, String owner) {
Parameters parameters = generateParameters(code, displayLanguage, owner);
parameters.addParameter().setName(SYSTEM).setValue(new UriType(system));
if (isValid(url))
parameters.addParameter().setName(URL).setValue(new UriType(url));
if (isValid(valueSetId))
parameters.addParameter().setName("valueSetId").setValue(newStringType(valueSetId));
if (isValid(systemVersion))
parameters.addParameter().setName(SYSTEM_VERSION).setValue(newStringType(systemVersion));
if (isValid(valueSetVersion))
parameters.addParameter().setName(VALUESET_VERSION).setValue(newStringType(valueSetVersion));
if (isValid(display))
parameters.addParameter().setName(DISPLAY).setValue(newStringType(display));
return parameters;
}

protected Parameters valueSetExpandParameters(String url, String valueSetVersion, Integer offset, Integer count, Boolean includeDesignations,
Boolean includeDefinition, Boolean activeOnly, String displayLanguage, String filter, String owner) {
Parameters parameters = new Parameters();
if (isValid(url))
parameters.addParameter().setName(URL).setValue(newUri(url));
if (isValid(valueSetVersion))
parameters.addParameter().setName(VALUESET_VERSION).setValue(newStringType(valueSetVersion));
if (isValid(displayLanguage))
parameters.addParameter().setName(DISPLAY_LANGUAGE).setValue(newStringType(displayLanguage));
if (isValid(filter))
parameters.addParameter().setName(FILTER).setValue(newStringType(filter));
parameters.addParameter().setName(OFFSET).setValue(newInteger(offset));
parameters.addParameter().setName(COUNT).setValue(newInteger(count));
parameters.addParameter().setName(INCLUDE_DESIGNATIONS).setValue(newBoolean(includeDesignations));
parameters.addParameter().setName(INCLUDE_DEFINITION).setValue(newBoolean(includeDefinition));
parameters.addParameter().setName(ACTIVE_ONLY).setValue(newBoolean(activeOnly));
parameters.addParameter().setName(OWNER).setValue(newStringType(owner));
return parameters;
}

protected static String formatOrg(String org) {
return ORG_ + org;
}

protected static String formatUser(String user) {
return USER_ + user;
}

protected ResponseEntity<String> validate(String user, CodeSystem system, Optional<Identifier> acsnOpt,
String ownerType, String ownerId) {
ResponseEntity<String> response1 = validateId(system.getId());
if (response1 != null) return response1;
return validateAccessionId(acsnOpt, ownerType, ownerId);
}

protected ResponseEntity<String> validateId(String id) {
if (!isValid(id))
return badRequest("The id can not be empty.");
return null;
}

protected ResponseEntity<String> validateAccessionId(Optional<Identifier> acsnOpt, String ownerType, String ownerId) {
if (acsnOpt.isPresent()) {
String[] values = formatExpression(acsnOpt.get().getValue()).split(FW_SLASH);
if (!(values.length >= 3 && ownerType.equals(values[1]) && ownerId.equals(values[2]))) {
return badRequest("The Accession id does not match with given request.");
}
}
return null;
}

protected void addIdentifier(List<Identifier> identifiers, String ownerType, String ownerId, String resType, String resId) {
identifiers.add(getIdentifier(FW_SLASH + ownerType + FW_SLASH + ownerId + FW_SLASH + resType + FW_SLASH + resId + FW_SLASH).get());
}

}

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