Cleanup of package installer
This commit is contained in:
parent
c44c1ff11f
commit
5f1078ac13
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@ -26,7 +26,9 @@ import com.fasterxml.jackson.annotation.JsonProperty;
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import io.swagger.annotations.ApiModel;
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import io.swagger.annotations.ApiModel;
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import java.util.ArrayList;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.List;
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import java.util.Map;
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@ApiModel("Represents an NPM package installation response")
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@ApiModel("Represents an NPM package installation response")
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@JsonInclude(JsonInclude.Include.NON_NULL)
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@JsonInclude(JsonInclude.Include.NON_NULL)
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@ -36,6 +38,9 @@ public class PackageInstallOutcomeJson {
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@JsonProperty("messages")
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@JsonProperty("messages")
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private List<String> myMessage;
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private List<String> myMessage;
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@JsonProperty("resourcesInstalled")
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private Map<String, Integer> myResourcesInstalled;
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public List<String> getMessage() {
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public List<String> getMessage() {
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if (myMessage == null) {
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if (myMessage == null) {
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myMessage = new ArrayList<>();
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myMessage = new ArrayList<>();
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@ -43,4 +48,19 @@ public class PackageInstallOutcomeJson {
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return myMessage;
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return myMessage;
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}
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}
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public Map<String, Integer> getResourcesInstalled() {
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if (myResourcesInstalled == null) {
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myResourcesInstalled = new HashMap<>();
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}
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return myResourcesInstalled;
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}
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public void incrementResourcesInstalled(String theResourceType) {
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Integer existing = getResourcesInstalled().get(theResourceType);
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if (existing == null) {
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getResourcesInstalled().put(theResourceType, 1);
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} else {
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getResourcesInstalled().put(theResourceType, existing + 1);
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}
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}
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}
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}
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@ -26,12 +26,13 @@ import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
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import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.UriParam;
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import ca.uhn.fhir.rest.param.UriParam;
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import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.util.FhirTerser;
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import ca.uhn.fhir.util.FhirTerser;
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import ca.uhn.fhir.util.SearchParameterUtil;
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import ca.uhn.fhir.util.SearchParameterUtil;
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@ -48,6 +49,8 @@ import org.hl7.fhir.utilities.cache.NpmPackage;
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import org.slf4j.Logger;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.support.TransactionTemplate;
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import javax.annotation.PostConstruct;
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import javax.annotation.PostConstruct;
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import java.io.IOException;
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import java.io.IOException;
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@ -57,6 +60,7 @@ import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashMap;
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import java.util.List;
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import java.util.List;
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import java.util.Map;
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import java.util.Map;
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import java.util.Optional;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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@ -85,7 +89,11 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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@Autowired
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@Autowired
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private IValidationSupport validationSupport;
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private IValidationSupport validationSupport;
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@Autowired
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@Autowired
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private IHapiPackageCacheManager packageCacheManager;
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private IHapiPackageCacheManager myPackageCacheManager;
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@Autowired
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private PlatformTransactionManager myTxManager;
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@Autowired
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private INpmPackageVersionDao myPackageVersionDao;
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/**
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/**
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* Constructor
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* Constructor
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@ -125,12 +133,22 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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*
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*
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* @param theInstallationSpec The details about what should be installed
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* @param theInstallationSpec The details about what should be installed
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*/
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*/
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@SuppressWarnings("ConstantConditions")
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@Override
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@Override
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public PackageInstallOutcomeJson install(PackageInstallationSpec theInstallationSpec) throws ImplementationGuideInstallationException {
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public PackageInstallOutcomeJson install(PackageInstallationSpec theInstallationSpec) throws ImplementationGuideInstallationException {
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PackageInstallOutcomeJson retVal = new PackageInstallOutcomeJson();
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PackageInstallOutcomeJson retVal = new PackageInstallOutcomeJson();
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if (enabled) {
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if (enabled) {
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try {
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try {
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NpmPackage npmPackage = packageCacheManager.installPackage(theInstallationSpec);
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boolean exists = new TransactionTemplate(myTxManager).execute(tx -> {
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Optional<NpmPackageVersionEntity> existing = myPackageVersionDao.findByPackageIdAndVersion(theInstallationSpec.getName(), theInstallationSpec.getVersion());
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return existing.isPresent();
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});
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if (exists) {
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ourLog.info("Package {}#{} is already installed", theInstallationSpec.getName(), theInstallationSpec.getVersion());
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}
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NpmPackage npmPackage = myPackageCacheManager.installPackage(theInstallationSpec);
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if (npmPackage == null) {
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if (npmPackage == null) {
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throw new IOException("Package not found");
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throw new IOException("Package not found");
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}
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}
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@ -142,7 +160,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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}
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}
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if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
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if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
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install(npmPackage, theInstallationSpec);
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install(npmPackage, theInstallationSpec, retVal);
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}
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}
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} catch (IOException e) {
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} catch (IOException e) {
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@ -160,7 +178,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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*
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*
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* @throws ImplementationGuideInstallationException if installation fails
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* @throws ImplementationGuideInstallationException if installation fails
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*/
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*/
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private void install(NpmPackage npmPackage, PackageInstallationSpec theInstallationSpec) throws ImplementationGuideInstallationException {
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private void install(NpmPackage npmPackage, PackageInstallationSpec theInstallationSpec, PackageInstallOutcomeJson theOutcome) throws ImplementationGuideInstallationException {
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String name = npmPackage.getNpm().get("name").getAsString();
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String name = npmPackage.getNpm().get("name").getAsString();
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String version = npmPackage.getNpm().get("version").getAsString();
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String version = npmPackage.getNpm().get("version").getAsString();
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@ -182,13 +200,16 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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Collection<IBaseResource> resources = parseResourcesOfType(installTypes.get(i), npmPackage);
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Collection<IBaseResource> resources = parseResourcesOfType(installTypes.get(i), npmPackage);
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count[i] = resources.size();
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count[i] = resources.size();
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try {
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for (IBaseResource next : resources) {
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resources.stream()
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try {
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.map(r -> isStructureDefinitionWithoutSnapshot(r) ? generateSnapshot(r) : r)
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next = isStructureDefinitionWithoutSnapshot(next) ? generateSnapshot(next) : next;
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.forEach(r -> createOrUpdate(r));
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create(next, theOutcome);
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} catch (Exception e) {
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} catch (Exception e) {
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throw new ImplementationGuideInstallationException(String.format("Error installing IG %s#%s: %s", name, version, e.toString()), e);
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ourLog.warn("Failed to upload resource of type {} with ID {} - Error: {}", myFhirContext.getResourceType(next), next.getIdElement().getValue(), e.toString());
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throw new ImplementationGuideInstallationException(String.format("Error installing IG %s#%s: %s", name, version, e.toString()), e);
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}
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}
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}
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}
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}
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ourLog.info(String.format("Finished installation of package %s#%s:", name, version));
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ourLog.info(String.format("Finished installation of package %s#%s:", name, version));
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@ -220,13 +241,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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}
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}
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// resolve in local cache or on packages.fhir.org
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// resolve in local cache or on packages.fhir.org
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NpmPackage dependency = packageCacheManager.loadPackage(id, ver);
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NpmPackage dependency = myPackageCacheManager.loadPackage(id, ver);
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// recursive call to install dependencies of a package before
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// recursive call to install dependencies of a package before
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// installing the package
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// installing the package
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fetchAndInstallDependencies(dependency, theInstallationSpec, theOutcome);
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fetchAndInstallDependencies(dependency, theInstallationSpec, theOutcome);
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if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
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if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
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install(dependency, theInstallationSpec);
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install(dependency, theInstallationSpec, theOutcome);
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}
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}
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} catch (IOException e) {
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} catch (IOException e) {
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@ -260,9 +281,9 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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* ============================= Utility methods ===============================
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* ============================= Utility methods ===============================
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*/
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*/
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private Collection<IBaseResource> parseResourcesOfType(String type, NpmPackage pkg) {
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private List<IBaseResource> parseResourcesOfType(String type, NpmPackage pkg) {
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if (!pkg.getFolders().containsKey("package")) {
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if (!pkg.getFolders().containsKey("package")) {
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return Collections.EMPTY_LIST;
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return Collections.emptyList();
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}
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}
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ArrayList<IBaseResource> resources = new ArrayList<>();
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ArrayList<IBaseResource> resources = new ArrayList<>();
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List<String> filesForType = pkg.getFolders().get("package").getTypes().get(type);
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List<String> filesForType = pkg.getFolders().get("package").getTypes().get(type);
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@ -279,28 +300,17 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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return resources;
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return resources;
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}
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}
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/**
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private void create(IBaseResource theResource, PackageInstallOutcomeJson theOutcome) {
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* Create a resource or update it, if its already existing.
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IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
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*/
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SearchParameterMap map = createSearchParameterMapFor(theResource);
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private void createOrUpdate(IBaseResource resource) {
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IBundleProvider searchResult = dao.search(map);
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try {
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if (searchResult.isEmpty()) {
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IFhirResourceDao dao = myDaoRegistry.getResourceDao(resource.getClass());
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IBundleProvider searchResult = dao.search(createSearchParameterMapFor(resource));
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if (searchResult.isEmpty()) {
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if (validForUpload(resource)) {
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if (validForUpload(theResource)) {
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dao.create(resource);
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theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
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}
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dao.create(theResource);
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} else {
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IBaseResource existingResource = verifySearchResultFor(resource, searchResult);
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if (existingResource != null) {
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resource.setId(existingResource.getIdElement().getValue());
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dao.update(resource);
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}
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}
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}
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} catch (BaseServerResponseException e) {
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ourLog.warn("Failed to upload resource of type {} with ID {} - Error: {}", myFhirContext.getResourceType(resource), resource.getIdElement().getValue(), e.toString());
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}
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}
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}
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}
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@ -344,40 +354,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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private SearchParameterMap createSearchParameterMapFor(IBaseResource resource) {
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private SearchParameterMap createSearchParameterMapFor(IBaseResource resource) {
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if (resource.getClass().getSimpleName().equals("NamingSystem")) {
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if (resource.getClass().getSimpleName().equals("NamingSystem")) {
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String uniqueId = extractUniqeIdFromNamingSystem(resource);
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String uniqueId = extractUniqeIdFromNamingSystem(resource);
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return new SearchParameterMap().add("value", new StringParam(uniqueId).setExact(true));
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return SearchParameterMap.newSynchronous().add("value", new StringParam(uniqueId).setExact(true));
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} else if (resource.getClass().getSimpleName().equals("Subscription")) {
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} else if (resource.getClass().getSimpleName().equals("Subscription")) {
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String id = extractIdFromSubscription(resource);
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String id = extractIdFromSubscription(resource);
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return new SearchParameterMap().add("_id", new TokenParam(id));
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return SearchParameterMap.newSynchronous().add("_id", new TokenParam(id));
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} else {
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} else {
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String url = extractUniqueUrlFromMetadataResouce(resource);
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String url = extractUniqueUrlFromMetadataResource(resource);
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return new SearchParameterMap().add("url", new UriParam(url));
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return SearchParameterMap.newSynchronous().add("url", new UriParam(url));
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}
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}
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private IBaseResource verifySearchResultFor(IBaseResource resource, IBundleProvider searchResult) {
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FhirTerser terser = myFhirContext.newTerser();
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if (resource.getClass().getSimpleName().equals("NamingSystem")) {
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if (searchResult.size() > 1) {
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ourLog.warn("Expected 1 NamingSystem with unique ID {}, found {}. Will not attempt to update resource.",
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extractUniqeIdFromNamingSystem(resource), searchResult.size());
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return null;
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}
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return getFirstResourceFrom(searchResult);
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} else if (resource.getClass().getSimpleName().equals("Subscription")) {
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if (searchResult.size() > 1) {
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ourLog.warn("Expected 1 Subscription with ID {}, found {}. Will not attempt to update resource.",
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extractIdFromSubscription(resource), searchResult.size());
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return null;
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}
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return getFirstResourceFrom(searchResult);
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} else {
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// Resource is of type CodeSystem, ValueSet, StructureDefinition, ConceptMap or SearchParameter
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if (searchResult.size() > 1) {
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ourLog.warn("Expected 1 MetadataResource with globally unique URL {}, found {}. " +
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"Will not attempt to update resource.", extractUniqueUrlFromMetadataResouce(resource), searchResult.size());
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return null;
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}
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return getFirstResourceFrom(searchResult);
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}
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}
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}
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}
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@ -387,19 +370,19 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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if (uniqueIdComponent == null) {
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if (uniqueIdComponent == null) {
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throw new ImplementationGuideInstallationException("NamingSystem does not have uniqueId component.");
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throw new ImplementationGuideInstallationException("NamingSystem does not have uniqueId component.");
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}
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}
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IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(uniqueIdComponent, "value");
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IPrimitiveType<?> asPrimitiveType = (IPrimitiveType<?>) terser.getSingleValueOrNull(uniqueIdComponent, "value");
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return (String) asPrimitiveType.getValue();
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return (String) asPrimitiveType.getValue();
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}
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}
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private String extractIdFromSubscription(IBaseResource resource) {
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private String extractIdFromSubscription(IBaseResource resource) {
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FhirTerser terser = myFhirContext.newTerser();
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FhirTerser terser = myFhirContext.newTerser();
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IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(resource, "id");
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IPrimitiveType<?> asPrimitiveType = (IPrimitiveType<?>) terser.getSingleValueOrNull(resource, "id");
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return (String) asPrimitiveType.getValue();
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return (String) asPrimitiveType.getValue();
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}
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}
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private String extractUniqueUrlFromMetadataResouce(IBaseResource resource) {
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private String extractUniqueUrlFromMetadataResource(IBaseResource resource) {
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FhirTerser terser = myFhirContext.newTerser();
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FhirTerser terser = myFhirContext.newTerser();
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IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(resource, "url");
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IPrimitiveType<?> asPrimitiveType = (IPrimitiveType<?>) terser.getSingleValueOrNull(resource, "url");
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return (String) asPrimitiveType.getValue();
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return (String) asPrimitiveType.getValue();
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}
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}
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@ -408,13 +391,4 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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myFhirContext = theCtx;
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myFhirContext = theCtx;
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}
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}
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private static IBaseResource getFirstResourceFrom(IBundleProvider searchResult) {
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try {
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return searchResult.getResources(0, 0).get(0);
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} catch (IndexOutOfBoundsException e) {
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ourLog.warn("Error when extracting resource from search result " +
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"(search result should have been non-empty))", e);
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return null;
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}
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}
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}
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}
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@ -211,6 +211,25 @@ public class NpmTestR4 extends BaseJpaR4Test {
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});
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});
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}
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}
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@Test
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|
public void testInstallR4Package_Twice() throws Exception {
|
||||||
|
myDaoConfig.setAllowExternalReferences(true);
|
||||||
|
|
||||||
|
byte[] bytes = loadClasspathBytes("/packages/hl7.fhir.uv.shorthand-0.12.0.tgz");
|
||||||
|
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
|
||||||
|
|
||||||
|
PackageInstallOutcomeJson outcome;
|
||||||
|
|
||||||
|
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
|
||||||
|
outcome = igInstaller.install(spec);
|
||||||
|
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
|
||||||
|
|
||||||
|
igInstaller.install(spec);
|
||||||
|
outcome = igInstaller.install(spec);
|
||||||
|
assertEquals(null, outcome.getResourcesInstalled().get("CodeSystem"));
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
public void testInstallR4PackageWithNoDescription() throws Exception {
|
public void testInstallR4PackageWithNoDescription() throws Exception {
|
||||||
|
|
|
@ -6,10 +6,10 @@ import org.hl7.fhir.dstu3.model.CodeType;
|
||||||
import org.hl7.fhir.dstu3.model.Patient;
|
import org.hl7.fhir.dstu3.model.Patient;
|
||||||
import org.hl7.fhir.dstu3.model.Reference;
|
import org.hl7.fhir.dstu3.model.Reference;
|
||||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||||
import org.junit.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import static org.junit.Assert.assertNotNull;
|
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||||
import static org.junit.Assert.assertSame;
|
import static org.junit.jupiter.api.Assertions.assertSame;
|
||||||
|
|
||||||
public class ExtendedPatientTest {
|
public class ExtendedPatientTest {
|
||||||
|
|
||||||
|
|
|
@ -1,15 +1,15 @@
|
||||||
package ca.uhn.fhir.parser;
|
package ca.uhn.fhir.parser;
|
||||||
|
|
||||||
import ca.uhn.fhir.context.FhirContext;
|
import ca.uhn.fhir.context.FhirContext;
|
||||||
|
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||||
import org.hl7.fhir.r4.model.Bundle;
|
import org.hl7.fhir.r4.model.Bundle;
|
||||||
import org.hl7.fhir.r4.model.CodeType;
|
import org.hl7.fhir.r4.model.CodeType;
|
||||||
import org.hl7.fhir.r4.model.Patient;
|
import org.hl7.fhir.r4.model.Patient;
|
||||||
import org.hl7.fhir.r4.model.Reference;
|
import org.hl7.fhir.r4.model.Reference;
|
||||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
import org.junit.jupiter.api.Test;
|
||||||
import org.junit.Test;
|
|
||||||
|
|
||||||
import static org.junit.Assert.assertNotNull;
|
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||||
import static org.junit.Assert.assertSame;
|
import static org.junit.jupiter.api.Assertions.assertSame;
|
||||||
|
|
||||||
public class ExtendedPatientTest {
|
public class ExtendedPatientTest {
|
||||||
|
|
||||||
|
@ -45,8 +45,8 @@ public class ExtendedPatientTest {
|
||||||
|
|
||||||
Bundle parsedBundle = p.parseResource(Bundle.class, encoded);
|
Bundle parsedBundle = p.parseResource(Bundle.class, encoded);
|
||||||
|
|
||||||
ExtendedPatient parsedHomer = (ExtendedPatient)parsedBundle.getEntry().get(0).getResource();
|
ExtendedPatient parsedHomer = (ExtendedPatient) parsedBundle.getEntry().get(0).getResource();
|
||||||
ExtendedPatient parsedMarge = (ExtendedPatient)parsedBundle.getEntry().get(1).getResource();
|
ExtendedPatient parsedMarge = (ExtendedPatient) parsedBundle.getEntry().get(1).getResource();
|
||||||
|
|
||||||
IBaseResource referencedHomer = parsedMarge.getLinkFirstRep().getOther().getResource();
|
IBaseResource referencedHomer = parsedMarge.getLinkFirstRep().getOther().getResource();
|
||||||
assertNotNull(referencedHomer);
|
assertNotNull(referencedHomer);
|
||||||
|
|
Loading…
Reference in New Issue