honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

breaking up package installer and package config (#4319) 

* breaking up package installer and package config

* breaking out parsing of resources

* wrong nullable

* added an integration test

* adding a changelog

* added a few minor tests

* review fixes

* unit test fixes

* fixing code checkstyle

* moving fetching local package data to package loader svc

* updating the method name

* splitting the fhirversion parsing

* updating table creation task for pretty printing and use in RTE

* adding foreign keys

* Adding mroe info

* minor prettiness changes

* fixing fk generation

* minor changes

* update version

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
This commit is contained in:
TipzCM 2023-01-16 20:58:14 -05:00 committed by GitHub
parent 04c28b6c08
commit 23b593aa17
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
94 changed files with 923 additions and 217 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
.gitignore vendored
View File

@ -168,4 +168,5 @@ Snap.*
/database/
/activemq-data/
/.run/

2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-bom/pom.xml
View File

@ -4,14 +4,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

10
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java
View File

@ -579,20 +579,24 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
return value;
}
protected void parseFhirContext(CommandLine theCommandLine) throws ParseException {
protected FhirVersionEnum parseFhirVersion(CommandLine theCommandLine) throws ParseException {
String version = theCommandLine.getOptionValue(FHIR_VERSION_PARAM);
if (isBlank(version)) {
throw new ParseException(Msg.code(1581) + "Missing required option: -" + FHIR_VERSION_PARAM);
}
try {
FhirVersionEnum versionEnum = FhirVersionEnum.valueOf(version.toUpperCase());
myFhirCtx = versionEnum.newContext();
return versionEnum;
} catch (Exception e) {
throw new ParseException(Msg.code(1582) + "Invalid FHIR version string: " + version);
}
}
protected void parseFhirContext(CommandLine theCommandLine) throws ParseException {
FhirVersionEnum versionEnum = parseFhirVersion(theCommandLine);
myFhirCtx = versionEnum.newContext();
}
public abstract void run(CommandLine theCommandLine) throws ParseException, ExecutionException;

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4309-breakout-package-loader-and-resource-parser.yaml Normal file
View File

@ -0,0 +1,8 @@
---
type: fix
issue: 4309
title: "
Broke out services for loading npm packages
and parsing npm package resources that will
not be dependent on any the DAO layer.
"

2
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -63,6 +63,7 @@ import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.packages.JpaPackageCache;
import ca.uhn.fhir.jpa.packages.NpmJpaValidationSupport;
import ca.uhn.fhir.jpa.packages.PackageInstallerSvcImpl;
import ca.uhn.fhir.jpa.packages.util.PackageUtils;
import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl;
@ -148,7 +149,6 @@ import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.npm.PackageClient;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -195,7 +195,8 @@ import java.util.Date;
ValidationSupportConfig.class,
Batch2SupportConfig.class,
JpaBulkExportConfig.class,
SearchConfig.class
SearchConfig.class,
PackageLoaderConfig.class
})
public class JpaConfig {
public static final String JPA_VALIDATION_SUPPORT_CHAIN = "myJpaValidationSupportChain";
@ -305,13 +306,9 @@ public class JpaConfig {
return new DaoResourceLinkResolver<JpaPid>();
}
@Bean
@Bean(name = PackageUtils.LOADER_WITH_CACHE)
public IHapiPackageCacheManager packageCacheManager() {
JpaPackageCache retVal = new JpaPackageCache();
retVal.getPackageServers().clear();
retVal.getPackageServers().add(PackageClient.PRIMARY_SERVER);
retVal.getPackageServers().add(PackageClient.SECONDARY_SERVER);
return retVal;
return new JpaPackageCache();
}
@Bean

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/PackageLoaderConfig.java Normal file
View File

@ -0,0 +1,26 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.packages.loader.PackageLoaderSvc;
import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc;
import org.hl7.fhir.utilities.npm.PackageClient;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class PackageLoaderConfig {
@Bean
public PackageLoaderSvc packageLoaderSvc() {
PackageLoaderSvc svc = new PackageLoaderSvc();
svc.getPackageServers().clear();
svc.getPackageServers().add(PackageClient.PRIMARY_SERVER);
svc.getPackageServers().add(PackageClient.SECONDARY_SERVER);
return svc;
}
@Bean
public PackageResourceParsingSvc resourceParsingSvc(FhirContext theContext) {
return new PackageResourceParsingSvc(theContext);
}
}

143
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
View File

@ -41,23 +41,18 @@ import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionResourceEntity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.jpa.packages.loader.NpmPackageData;
import ca.uhn.fhir.jpa.packages.loader.PackageLoaderSvc;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.BinaryUtil;
import ca.uhn.fhir.util.ClasspathUtil;
import ca.uhn.fhir.util.ResourceUtil;
import ca.uhn.fhir.util.StringUtil;
import org.apache.commons.collections4.comparators.ReverseComparator;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.conn.HttpClientConnectionManager;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.BasicHttpClientConnectionManager;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -89,11 +84,7 @@ import javax.persistence.criteria.Root;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@ -131,9 +122,43 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
@Autowired
private PartitionSettings myPartitionSettings;
@Autowired
private PackageLoaderSvc myPackageLoaderSvc;
@Autowired(required = false)//It is possible that some implementers will not create such a bean.
private IBinaryStorageSvc myBinaryStorageSvc;
@Override
public void addPackageServer(@Nonnull String theUrl) {
assert myPackageLoaderSvc != null;
myPackageLoaderSvc.addPackageServer(theUrl);
}
@Override
public String getPackageId(String theS) throws IOException {
return myPackageLoaderSvc.getPackageId(theS);
}
@Override
public void setSilent(boolean silent) {
myPackageLoaderSvc.setSilent(silent);
}
@Override
public String getPackageUrl(String theS) throws IOException {
return myPackageLoaderSvc.getPackageUrl(theS);
}
@Override
public List<String> getPackageServers() {
return myPackageLoaderSvc.getPackageServers();
}
@Override
protected BasePackageCacheManager.InputStreamWithSrc loadFromPackageServer(String id, String version) {
throw new UnsupportedOperationException(Msg.code(2220) + "Use PackageLoaderSvc for loading packages.");
}
@Override
@Transactional
public NpmPackage loadPackageFromCacheOnly(String theId, @Nullable String theVersion) {
@ -221,22 +246,19 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
return myDaoRegistry.getResourceDao("Binary");
}
@Override
public NpmPackage addPackageToCache(String thePackageId, String thePackageVersionId, InputStream thePackageTgzInputStream, String theSourceDesc) throws IOException {
Validate.notBlank(thePackageId, "thePackageId must not be null");
Validate.notBlank(thePackageVersionId, "thePackageVersionId must not be null");
Validate.notNull(thePackageTgzInputStream, "thePackageTgzInputStream must not be null");
private NpmPackage addPackageToCacheInternal(
NpmPackageData thePackageData
) {
NpmPackage npmPackage = thePackageData.getPackage();
String packageId = thePackageData.getPackageId();
String initialPackageVersionId = thePackageData.getPackageVersionId();
byte[] bytes = thePackageData.getBytes();
byte[] bytes = IOUtils.toByteArray(thePackageTgzInputStream);
ourLog.info("Parsing package .tar.gz ({} bytes) from {}", bytes.length, theSourceDesc);
NpmPackage npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(bytes));
if (!npmPackage.id().equalsIgnoreCase(thePackageId)) {
throw new InvalidRequestException(Msg.code(1297) + "Package ID " + npmPackage.id() + " doesn't match expected: " + thePackageId);
if (!npmPackage.id().equalsIgnoreCase(packageId)) {
throw new InvalidRequestException(Msg.code(1297) + "Package ID " + npmPackage.id() + " doesn't match expected: " + packageId);
}
if (!PackageVersionComparator.isEquivalent(thePackageVersionId, npmPackage.version())) {
throw new InvalidRequestException(Msg.code(1298) + "Package ID " + npmPackage.version() + " doesn't match expected: " + thePackageVersionId);
if (!PackageVersionComparator.isEquivalent(initialPackageVersionId, npmPackage.version())) {
throw new InvalidRequestException(Msg.code(1298) + "Package ID " + npmPackage.version() + " doesn't match expected: " + initialPackageVersionId);
}
String packageVersionId = npmPackage.version();
@ -249,19 +271,18 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
IBaseBinary binary = createPackageBinary(bytes);
return newTxTemplate().execute(tx -> {
ResourceTable persistedPackage = createResourceBinary(binary);
NpmPackageEntity pkg = myPackageDao.findByPackageId(thePackageId).orElseGet(() -> createPackage(npmPackage));
NpmPackageVersionEntity packageVersion = myPackageVersionDao.findByPackageIdAndVersion(thePackageId, packageVersionId).orElse(null);
NpmPackageEntity pkg = myPackageDao.findByPackageId(packageId).orElseGet(() -> createPackage(npmPackage));
NpmPackageVersionEntity packageVersion = myPackageVersionDao.findByPackageIdAndVersion(packageId, packageVersionId).orElse(null);
if (packageVersion != null) {
NpmPackage existingPackage = loadPackageFromCacheOnly(packageVersion.getPackageId(), packageVersion.getVersionId());
String msg = "Package version already exists in local storage, no action taken: " + thePackageId + "#" + packageVersionId;
String msg = "Package version already exists in local storage, no action taken: " + packageId + "#" + packageVersionId;
getProcessingMessages(existingPackage).add(msg);
ourLog.info(msg);
return existingPackage;
}
boolean currentVersion = updateCurrentVersionFlagForAllPackagesBasedOnNewIncomingVersion(thePackageId, packageVersionId);
boolean currentVersion = updateCurrentVersionFlagForAllPackagesBasedOnNewIncomingVersion(packageId, packageVersionId);
String packageDesc = null;
if (npmPackage.description() != null) {
if (npmPackage.description().length() > NpmPackageVersionEntity.PACKAGE_DESC_LENGTH) {
@ -271,16 +292,16 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
}
}
if (currentVersion) {
getProcessingMessages(npmPackage).add("Marking package " + thePackageId + "#" + thePackageVersionId + " as current version");
getProcessingMessages(npmPackage).add("Marking package " + packageId + "#" + initialPackageVersionId + " as current version");
pkg.setCurrentVersionId(packageVersionId);
pkg.setDescription(packageDesc);
myPackageDao.save(pkg);
} else {
getProcessingMessages(npmPackage).add("Package " + thePackageId + "#" + thePackageVersionId + " is not the newest version");
getProcessingMessages(npmPackage).add("Package " + packageId + "#" + initialPackageVersionId + " is not the newest version");
}
packageVersion = new NpmPackageVersionEntity();
packageVersion.setPackageId(thePackageId);
packageVersion.setPackageId(packageId);
packageVersion.setVersionId(packageVersionId);
packageVersion.setPackage(pkg);
packageVersion.setPackageBinary(persistedPackage);
@ -353,7 +374,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
String resType = packageContext.getResourceType(resource);
String msg = "Indexing " + resType + " Resource[" + dirName + '/' + nextFile + "] with URL: " + defaultString(url) + "|" + defaultString(version);
getProcessingMessages(npmPackage).add(msg);
ourLog.info("Package[{}#{}] " + msg, thePackageId, packageVersionId);
ourLog.info("Package[{}#{}] " + msg, packageId, packageVersionId);
}
}
@ -361,7 +382,13 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
return npmPackage;
});
}
@Override
public NpmPackage addPackageToCache(String thePackageId, String thePackageVersionId, InputStream thePackageTgzInputStream, String theSourceDesc) throws IOException {
NpmPackageData npmData = myPackageLoaderSvc.createNpmPackageDataFromData(thePackageId, thePackageVersionId, theSourceDesc, thePackageTgzInputStream);
return addPackageToCacheInternal(npmData);
}
private ResourceTable createResourceBinary(IBaseBinary theResourceBinary) {
@ -426,24 +453,29 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
@Override
@Transactional
public NpmPackage loadPackage(String thePackageId, String thePackageVersion) throws FHIRException, IOException {
// check package cache
NpmPackage cachedPackage = loadPackageFromCacheOnly(thePackageId, thePackageVersion);
if (cachedPackage != null) {
return cachedPackage;
}
InputStreamWithSrc pkg = super.loadFromPackageServer(thePackageId, thePackageVersion);
if (pkg == null) {
throw new ResourceNotFoundException(Msg.code(1301) + "Unable to locate package " + thePackageId + "#" + thePackageVersion);
}
// otherwise we have to load it from packageloader
NpmPackageData pkgData = myPackageLoaderSvc.fetchPackageFromPackageSpec(thePackageId, thePackageVersion);
try {
NpmPackage retVal = addPackageToCache(thePackageId, thePackageVersion == null ? pkg.version : thePackageVersion, pkg.stream, pkg.url);
getProcessingMessages(retVal).add(0, "Package fetched from server at: " + pkg.url);
// and add it to the cache
NpmPackage retVal = addPackageToCacheInternal(pkgData);
getProcessingMessages(retVal)
.add(0, "Package fetched from server at: " + pkgData.getPackage().url());
return retVal;
} finally {
pkg.stream.close();
pkgData.getInputStream().close();
}
}
@Override
public NpmPackage loadPackage(String theS) throws FHIRException, IOException {
return loadPackage(theS, null);
}
private TransactionTemplate newTxTemplate() {
@ -458,7 +490,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
String sourceDescription = "Embedded content";
if (isNotBlank(theInstallationSpec.getPackageUrl())) {
byte[] contents = loadPackageUrlContents(theInstallationSpec.getPackageUrl());
byte[] contents = myPackageLoaderSvc.loadPackageUrlContents(theInstallationSpec.getPackageUrl());
theInstallationSpec.setPackageContents(contents);
sourceDescription = theInstallationSpec.getPackageUrl();
}
@ -476,33 +508,6 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
});
}
protected byte[] loadPackageUrlContents(String thePackageUrl) {
if (thePackageUrl.startsWith("classpath:")) {
return ClasspathUtil.loadResourceAsByteArray(thePackageUrl.substring("classpath:" .length()));
} else if (thePackageUrl.startsWith("file:")) {
try {
byte[] bytes = Files.readAllBytes(Paths.get(new URI(thePackageUrl)));
return bytes;
} catch (IOException | URISyntaxException e) {
throw new InternalErrorException(Msg.code(2031) + "Error loading \"" + thePackageUrl + "\": " + e.getMessage());
}
} else {
HttpClientConnectionManager connManager = new BasicHttpClientConnectionManager();
try (CloseableHttpResponse request = HttpClientBuilder
.create()
.setConnectionManager(connManager)
.build()
.execute(new HttpGet(thePackageUrl))) {
if (request.getStatusLine().getStatusCode() != 200) {
throw new ResourceNotFoundException(Msg.code(1303) + "Received HTTP " + request.getStatusLine().getStatusCode() + " from URL: " + thePackageUrl);
}
return IOUtils.toByteArray(request.getEntity().getContent());
} catch (IOException e) {
throw new InternalErrorException(Msg.code(1304) + "Error loading \"" + thePackageUrl + "\": " + e.getMessage());
}
}
}
@Override
@Transactional
public IBaseResource loadPackageAssetByUrl(FhirVersionEnum theFhirVersion, String theCanonicalUrl) {

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java
View File

@ -36,6 +36,7 @@ import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistryController;
import ca.uhn.fhir.jpa.searchparam.util.SearchParameterHelper;
@ -43,7 +44,6 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.SearchParameterUtil;
@ -67,12 +67,12 @@ import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.annotation.PostConstruct;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static ca.uhn.fhir.jpa.packages.util.PackageUtils.DEFAULT_INSTALL_TYPES;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -82,15 +82,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
private static final Logger ourLog = LoggerFactory.getLogger(PackageInstallerSvcImpl.class);
public static List<String> DEFAULT_INSTALL_TYPES = Collections.unmodifiableList(Lists.newArrayList(
"NamingSystem",
"CodeSystem",
"ValueSet",
"StructureDefinition",
"ConceptMap",
"SearchParameter",
"Subscription"
));
boolean enabled = true;
@Autowired
@ -113,6 +105,8 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
private PartitionSettings myPartitionSettings;
@Autowired
private SearchParameterHelper mySearchParameterHelper;
@Autowired
private PackageResourceParsingSvc myPackageResourceParsingSvc;
/**
* Constructor
@ -220,11 +214,12 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
int[] count = new int[installTypes.size()];
for (int i = 0; i < installTypes.size(); i++) {
Collection<IBaseResource> resources = parseResourcesOfType(installTypes.get(i), npmPackage);
String type = installTypes.get(i);
Collection<IBaseResource> resources = myPackageResourceParsingSvc.parseResourcesOfType(type, npmPackage);
count[i] = resources.size();
for (IBaseResource next : resources) {
try {
next = isStructureDefinitionWithoutSnapshot(next) ? generateSnapshot(next) : next;
create(next, theInstallationSpec, theOutcome);
@ -307,24 +302,6 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
* ============================= Utility methods ===============================
*/
private List<IBaseResource> parseResourcesOfType(String type, NpmPackage pkg) {
if (!pkg.getFolders().containsKey("package")) {
return Collections.emptyList();
}
ArrayList<IBaseResource> resources = new ArrayList<>();
List<String> filesForType = pkg.getFolders().get("package").getTypes().get(type);
if (filesForType != null) {
for (String file : filesForType) {
try {
byte[] content = pkg.getFolders().get("package").fetchFile(file);
resources.add(myFhirContext.newJsonParser().parseResource(new String(content)));
} catch (IOException e) {
throw new InternalErrorException(Msg.code(1289) + "Cannot install resource of type " + type + ": Could not fetch file " + file, e);
}
}
}
return resources;
}
private void create(IBaseResource theResource, PackageInstallationSpec theInstallationSpec, PackageInstallOutcomeJson theOutcome) {
IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());

78
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/loader/NpmPackageData.java Normal file
View File

@ -0,0 +1,78 @@
package ca.uhn.fhir.jpa.packages.loader;
import org.hl7.fhir.utilities.npm.NpmPackage;
import java.io.InputStream;
public class NpmPackageData {
/**
* package id (npm id)
*/
private final String myPackageId;
/**
* package version id (npm version)
*/
private final String myPackageVersionId;
/**
* package description (url to find package, often)
*/
private final String mySourceDesc;
/**
* The raw bytes of the entire package
*/
private final byte[] myBytes;
/**
* The actual NpmPackage.
*/
private final NpmPackage myPackage;
/**
* The raw stream of the entire npm package contents
*/
private final InputStream myInputStream;
public NpmPackageData(
String thePackageId,
String thePackageVersionId,
String theSourceDesc,
byte[] theBytes,
NpmPackage thePackage,
InputStream theStream
) {
myPackageId = thePackageId;
myPackageVersionId = thePackageVersionId;
mySourceDesc = theSourceDesc;
myBytes = theBytes;
myPackage = thePackage;
myInputStream = theStream;
}
public byte[] getBytes() {
return myBytes;
}
public NpmPackage getPackage() {
return myPackage;
}
public InputStream getInputStream() {
return myInputStream;
}
public String getPackageId() {
return myPackageId;
}
public String getPackageVersionId() {
return myPackageVersionId;
}
public String getSourceDesc() {
return mySourceDesc;
}
}

183
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/loader/PackageLoaderSvc.java Normal file
View File

@ -0,0 +1,183 @@
package ca.uhn.fhir.jpa.packages.loader;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.ClasspathUtil;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.conn.HttpClientConnectionManager;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.BasicHttpClientConnectionManager;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nullable;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.nio.file.Paths;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class PackageLoaderSvc extends BasePackageCacheManager {
private static final Logger ourLog = LoggerFactory.getLogger(PackageLoaderSvc.class);
public NpmPackageData fetchPackageFromPackageSpec(PackageInstallationSpec theSpec) throws IOException {
if (isNotBlank(theSpec.getPackageUrl())) {
byte[] contents = loadPackageUrlContents(theSpec.getPackageUrl());
return createNpmPackageDataFromData(
theSpec.getName(),
theSpec.getVersion(),
theSpec.getPackageUrl(),
new ByteArrayInputStream(contents)
);
}
return fetchPackageFromServerInternal(theSpec.getName(), theSpec.getVersion());
}
/**
* Loads the package, but won't save it anywhere.
* Returns the data to the caller
*
* @return - a POJO containing information about the NpmPackage, as well as it's contents
* as fetched from the server
* @throws IOException
*/
public NpmPackageData fetchPackageFromPackageSpec(
String thePackageId,
String thePackageVersion
) throws FHIRException, IOException {
return fetchPackageFromServerInternal(thePackageId, thePackageVersion);
}
private NpmPackageData fetchPackageFromServerInternal(
String thePackageId,
String thePackageVersion
) throws IOException {
BasePackageCacheManager.InputStreamWithSrc pkg = this.loadFromPackageServer(thePackageId, thePackageVersion);
if (pkg == null) {
throw new ResourceNotFoundException(Msg.code(1301) + "Unable to locate package " + thePackageId + "#" + thePackageVersion);
}
NpmPackageData npmPackage = createNpmPackageDataFromData(
thePackageId,
thePackageVersion == null ? pkg.version : thePackageVersion,
pkg.url,
pkg.stream
);
return npmPackage;
}
/**
* Creates an NpmPackage data object.
*
* @param thePackageId - the id of the npm package
* @param thePackageVersionId - the version id of the npm package
* @param theSourceDesc - the installation spec description or package url
* @param thePackageTgzInputStream - the package contents.
* Typically fetched from a server, but can be added directly to the package spec
* @return
* @throws IOException
*/
public NpmPackageData createNpmPackageDataFromData(
String thePackageId,
String thePackageVersionId,
String theSourceDesc,
InputStream thePackageTgzInputStream
) throws IOException {
Validate.notBlank(thePackageId, "thePackageId must not be null");
Validate.notBlank(thePackageVersionId, "thePackageVersionId must not be null");
Validate.notNull(thePackageTgzInputStream, "thePackageTgzInputStream must not be null");
byte[] bytes = IOUtils.toByteArray(thePackageTgzInputStream);
ourLog.info("Parsing package .tar.gz ({} bytes) from {}", bytes.length, theSourceDesc);
NpmPackage npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(bytes));
return new NpmPackageData(
thePackageId,
thePackageVersionId,
theSourceDesc,
bytes,
npmPackage,
thePackageTgzInputStream
);
}
@Override
public NpmPackage loadPackageFromCacheOnly(String theS, @Nullable String theS1) {
throw new UnsupportedOperationException(
Msg.code(2215)
+ "Cannot load from cache. "
+ "Caching not supported in PackageLoaderSvc. Use JpaPackageCache instead."
);
}
@Override
public NpmPackage addPackageToCache(String theS, String theS1, InputStream theInputStream, String theS2) throws IOException {
throw new UnsupportedOperationException(
Msg.code(2216)
+ "Cannot add to cache. "
+ "Caching not supported in PackageLoaderSvc. Use JpaPackageCache instead."
);
}
@Override
public NpmPackage loadPackage(String theS, String theS1) throws FHIRException {
/*
* We throw an exception because while we could pipe this call through
* to loadPackageOnly ourselves, returning NpmPackage details
* on their own provides no value if nothing is cached/loaded onto hard disk somewhere
*
*/
throw new UnsupportedOperationException(
Msg.code(2217)
+ "No packages are cached; "
+ " this service only loads from the server directly. "
+ "Call fetchPackageFromServer to fetch the npm package from the server. "
+ "Or use JpaPackageCache for a cache implementation."
);
}
public byte[] loadPackageUrlContents(String thePackageUrl) {
if (thePackageUrl.startsWith("classpath:")) {
return ClasspathUtil.loadResourceAsByteArray(thePackageUrl.substring("classpath:" .length()));
} else if (thePackageUrl.startsWith("file:")) {
try {
byte[] bytes = Files.readAllBytes(Paths.get(new URI(thePackageUrl)));
return bytes;
} catch (IOException | URISyntaxException e) {
throw new InternalErrorException(Msg.code(2031) + "Error loading \"" + thePackageUrl + "\": " + e.getMessage());
}
} else {
HttpClientConnectionManager connManager = new BasicHttpClientConnectionManager();
try (CloseableHttpResponse request = HttpClientBuilder
.create()
.setConnectionManager(connManager)
.build()
.execute(new HttpGet(thePackageUrl))) {
if (request.getStatusLine().getStatusCode() != 200) {
throw new ResourceNotFoundException(Msg.code(1303) + "Received HTTP " + request.getStatusLine().getStatusCode() + " from URL: " + thePackageUrl);
}
return IOUtils.toByteArray(request.getEntity().getContent());
} catch (IOException e) {
throw new InternalErrorException(Msg.code(1304) + "Error loading \"" + thePackageUrl + "\": " + e.getMessage());
}
}
}
}

46
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/loader/PackageResourceParsingSvc.java Normal file
View File

@ -0,0 +1,46 @@
package ca.uhn.fhir.jpa.packages.loader;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.npm.NpmPackage;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class PackageResourceParsingSvc {
private final FhirContext myFhirContext;
public PackageResourceParsingSvc(FhirContext theContext) {
myFhirContext = theContext;
}
/**
* Parses out resource of theType from provided package
* @param theType - the resource type
* @param thePkg - the npm package
* @return - a list of all resources that match type theType in package thePkg
*/
public List<IBaseResource> parseResourcesOfType(String theType, NpmPackage thePkg) {
if (!thePkg.getFolders().containsKey("package")) {
return Collections.emptyList();
}
ArrayList<IBaseResource> resources = new ArrayList<>();
List<String> filesForType = thePkg.getFolders().get("package").getTypes().get(theType);
if (filesForType != null) {
for (String file : filesForType) {
try {
byte[] content = thePkg.getFolders().get("package").fetchFile(file);
resources.add(myFhirContext.newJsonParser().parseResource(new String(content)));
} catch (IOException e) {
throw new InternalErrorException(Msg.code(1289) + "Cannot install resource of type " + theType + ": Could not fetch file " + file, e);
}
}
}
return resources;
}
}

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/util/PackageUtils.java Normal file
View File

@ -0,0 +1,24 @@
package ca.uhn.fhir.jpa.packages.util;
import com.google.common.collect.Lists;
import java.util.Collections;
import java.util.List;
public class PackageUtils {
public static final String LOADER_WITH_CACHE = "loaderWithCache";
/**
* Default install types
*/
public static List<String> DEFAULT_INSTALL_TYPES = Collections.unmodifiableList(Lists.newArrayList(
"NamingSystem",
"CodeSystem",
"ValueSet",
"StructureDefinition",
"ConceptMap",
"SearchParameter",
"Subscription"
));
}

2
hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-model/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-searchparam/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu2/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu3/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

5
hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/packages/IgInstallerDstu3Test.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.packages.util.PackageUtils;
import ca.uhn.fhir.jpa.test.BaseJpaDstu3Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -25,6 +26,7 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Date;
import java.util.Optional;
@ -51,7 +53,8 @@ public class IgInstallerDstu3Test extends BaseJpaDstu3Test {
@Autowired
private PackageInstallerSvcImpl igInstaller;
@Autowired
private IPackageCacheManager myPackageCacheManager;
@Qualifier(PackageUtils.LOADER_WITH_CACHE)
private IHapiPackageCacheManager myPackageCacheManager;
private Server myServer;
private FakeNpmServlet myFakeNpmServlet;
@Autowired

2
hapi-fhir-jpaserver-test-r4/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

24
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
View File

@ -204,7 +204,10 @@ public class NpmR4Test extends BaseJpaR4Test {
byte[] bytes = ClasspathUtil.loadResourceAsByteArray("/packages/hl7.fhir.uv.shorthand-0.12.0.tgz");
myFakeNpmServlet.responses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallationSpec spec = new PackageInstallationSpec()
.setName("hl7.fhir.uv.shorthand")
.setVersion("0.12.0")
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
@ -409,7 +412,10 @@ public class NpmR4Test extends BaseJpaR4Test {
List<String> resourceList = new ArrayList<>();
resourceList.add("Organization");
PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-organizations").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallationSpec spec = new PackageInstallationSpec()
.setName("test-organizations")
.setVersion("1.0.0")
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
spec.setInstallResourceTypes(resourceList);
PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
assertEquals(3, outcome.getResourcesInstalled().get("Organization"));
@ -448,7 +454,10 @@ public class NpmR4Test extends BaseJpaR4Test {
List<String> resourceList = new ArrayList<>();
resourceList.add("Organization");
PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-missing-identifier-package").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallationSpec spec = new PackageInstallationSpec()
.setName("test-missing-identifier-package")
.setVersion("1.0.0")
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
spec.setInstallResourceTypes(resourceList);
try {
PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
@ -471,7 +480,10 @@ public class NpmR4Test extends BaseJpaR4Test {
List<String> resourceList = new ArrayList<>();
resourceList.add("ImplementationGuide");
PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-ig").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallationSpec spec = new PackageInstallationSpec()
.setName("test-ig")
.setVersion("1.0.0")
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
spec.setInstallResourceTypes(resourceList);
PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
ourLog.info("Outcome: {}", outcome);
@ -499,7 +511,6 @@ public class NpmR4Test extends BaseJpaR4Test {
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.onlydrafts").setVersion("0.11.1").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
assertEquals(0, outcome.getResourcesInstalled().size(), outcome.getResourcesInstalled().toString());
}
@Test
@ -547,10 +558,8 @@ public class NpmR4Test extends BaseJpaR4Test {
// Ensure that we loaded the contents
IBundleProvider searchResult = myCodeSystemDao.search(SearchParameterMap.newSynchronous("url", new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@Test
public void testInstallR4PackageWithNoDescription() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
@ -597,7 +606,6 @@ public class NpmR4Test extends BaseJpaR4Test {
}
@Test
public void testLoadPackageUsingImpreciseId() throws Exception {
myDaoConfig.setAllowExternalReferences(true);

138
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/packages/loader/PackageLoaderSvcIT.java Normal file
View File

@ -0,0 +1,138 @@
package ca.uhn.fhir.jpa.packages.loader;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.packages.FakeNpmServlet;
import ca.uhn.fhir.jpa.packages.util.PackageUtils;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.ClasspathUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.mockito.Mockito;
import org.mockito.Spy;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
public class PackageLoaderSvcIT {
@Spy
private FhirContext myFhirContext = FhirContext.forR4Cached();
private Server myServer;
private FakeNpmServlet myFakeNpmServlet;
private PackageLoaderSvc myPackageLoaderSvc;
private PackageResourceParsingSvc myResourceParsingSvc;
@BeforeEach
public void before() throws Exception {
myPackageLoaderSvc = new PackageLoaderSvc();
myResourceParsingSvc = new PackageResourceParsingSvc(myFhirContext);
myServer = new Server(0);
ServletHandler proxyHandler = new ServletHandler();
myFakeNpmServlet = new FakeNpmServlet();
ServletHolder servletHolder = new ServletHolder(myFakeNpmServlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
myServer.setHandler(proxyHandler);
myServer.start();
int port = JettyUtil.getPortForStartedServer(myServer);
myPackageLoaderSvc.getPackageServers().clear();
myPackageLoaderSvc.addPackageServer("http://localhost:" + port);
myFakeNpmServlet.getResponses().clear();
}
@AfterEach
public void after() throws Exception {
JettyUtil.closeServer(myServer);
}
@Test
public void fetchPackageFromServer_thenParseoutResources_inMemory() throws IOException {
// setup
String id = "test-exchange.fhir.us.com/2.1.1";
String versionId = "2.1.";
// this package has SearchParameters in it
byte[] bytes = ClasspathUtil.loadResourceAsByteArray("/packages/test-exchange-sample.tgz");
myFakeNpmServlet.getResponses().put(String.format("/%s/%s", id, versionId), bytes);
// test fetch from server by id and version
NpmPackageData result = myPackageLoaderSvc.fetchPackageFromPackageSpec(id, versionId);
// verify fetched data
assertNotNull(result);
assertNotNull(result.getPackage());
NpmPackage npmPackage = result.getPackage();
// test parse resources
List<IBaseResource> resources = new ArrayList<>();
List<String> resourcesToParse = PackageUtils.DEFAULT_INSTALL_TYPES;
for (String resourceType : resourcesToParse) {
resources.addAll(
myResourceParsingSvc.parseResourcesOfType(resourceType, npmPackage)
);
}
// verify fetched resources
assertFalse(resources.isEmpty());
assertEquals(1, resources.size());
assertEquals("SearchParameter", resources.get(0).fhirType());
}
/**
* PackageLoaderSvc extends BasePackageCacheManger.
* However, we do not want this service to have any
* DAO dependence (ie, no cache).
*
* But since BasePackageCacheManger is in a different
* codebase, we cannot remove some methods and must just
* not support them.
*
* We'll test to make sure these stay unsupported
* (barring a breakup of BasePackageCacheManager itself)
*/
@Test
public void anyCacheUtilizingMethod_throwsUnsupported() throws IOException {
// loadPackageFromCacheOnly
try {
myPackageLoaderSvc.loadPackageFromCacheOnly("id", "versionId");
fail();
} catch (UnsupportedOperationException ex) {
assertTrue(ex.getMessage().contains("Cannot load from cache."));
}
// addPackageToCache
try {
myPackageLoaderSvc.addPackageToCache("id", "version", Mockito.mock(InputStream.class), "description or url");
fail();
} catch (UnsupportedOperationException ex) {
assertTrue(ex.getMessage().contains("Cannot add to cache."));
}
// loadPackage
try {
myPackageLoaderSvc.loadPackage("id", "version");
fail();
} catch (UnsupportedOperationException ex) {
assertTrue(ex.getMessage().contains("No packages are cached;"));
}
}
}

2
hapi-fhir-jpaserver-test-r4b/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-r5/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/packages/FakeNpmServlet.java
View File

@ -32,7 +32,7 @@ import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
class FakeNpmServlet extends HttpServlet {
public class FakeNpmServlet extends HttpServlet {
private static final Logger ourLog = LoggerFactory.getLogger(FakeNpmServlet.class);
final Map<String, byte[]> responses = new HashMap<>();

2
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestDstu3Config.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.PackageLoaderConfig;
import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
@ -60,6 +61,7 @@ import static org.junit.jupiter.api.Assertions.fail;
@Configuration
@Import({
JpaDstu3Config.class,
PackageLoaderConfig.class,
HapiJpaConfig.class,
TestJPAConfig.class,
JpaBatch2Config.class,

2
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestR4Config.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
import ca.uhn.fhir.jpa.binary.api.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.PackageLoaderConfig;
import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
@ -63,6 +64,7 @@ import static org.junit.jupiter.api.Assertions.fail;
@Configuration
@Import({
JpaR4Config.class,
PackageLoaderConfig.class,
HapiJpaConfig.class,
TestJPAConfig.class,
TestHSearchAddInConfig.DefaultLuceneHeap.class,

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-server-mdm/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server-openapi/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-api/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

4
hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -20,7 +20,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-guava/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-testing/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
hapi-fhir-serviceloaders/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<artifactId>hapi-fhir</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

22
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddColumnTask.java
View File

@ -32,6 +32,12 @@ public class AddColumnTask extends BaseTableColumnTypeTask {
private static final Logger ourLog = LoggerFactory.getLogger(AddColumnTask.class);
public AddColumnTask() {
this(null, null);
setDryRun(true);
myCheckForExistingTables = false;
}
public AddColumnTask(String theProductVersion, String theSchemaVersion) {
super(theProductVersion, theSchemaVersion);
}
@ -44,10 +50,12 @@ public class AddColumnTask extends BaseTableColumnTypeTask {
@Override
public void doExecute() throws SQLException {
Set<String> columnNames = JdbcUtils.getColumnNames(getConnectionProperties(), getTableName());
if (columnNames.contains(getColumnName())) {
logInfo(ourLog, "Column {} already exists on table {} - No action performed", getColumnName(), getTableName());
return;
if (myCheckForExistingTables) {
Set<String> columnNames = JdbcUtils.getColumnNames(getConnectionProperties(), getTableName());
if (columnNames.contains(getColumnName())) {
logInfo(ourLog, "Column {} already exists on table {} - No action performed", getColumnName(), getTableName());
return;
}
}
String typeStatement = getTypeStatement();
@ -82,7 +90,11 @@ public class AddColumnTask extends BaseTableColumnTypeTask {
if (isNullable()) {
nullable = "";
}
return type + " " + nullable;
if (myPrettyPrint) {
nullable = nullable.trim();
}
String space = isNullable() ? "" : " ";
return type + space + nullable;
}
}

101
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddTableByColumnTask.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
* #L%
*/
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
@ -35,8 +36,15 @@ public class AddTableByColumnTask extends BaseTableTask {
private static final Logger ourLog = LoggerFactory.getLogger(AddTableByColumnTask.class);
private List<AddColumnTask> myAddColumnTasks = new ArrayList<>();
private final List<AddColumnTask> myAddColumnTasks = new ArrayList<>();
private List<String> myPkColumns;
private final List<ForeignKeyContainer> myFKColumns = new ArrayList<>();
public AddTableByColumnTask() {
this(null, null);
setDryRun(true);
myCheckForExistingTables = false;
}
public AddTableByColumnTask(String theProductVersion, String theSchemaVersion) {
super(theProductVersion, theSchemaVersion);
@ -57,45 +65,98 @@ public class AddTableByColumnTask extends BaseTableTask {
myPkColumns = thePkColumns;
}
@Override
public void doExecute() throws SQLException {
public void addForeignKey(ForeignKeyContainer theForeignKeyContainer) {
myFKColumns.add(theForeignKeyContainer);
}
if (JdbcUtils.getTableNames(getConnectionProperties()).contains(getTableName())) {
logInfo(ourLog, "Already have table named {} - No action performed", getTableName());
return;
}
public List<String> getPkColumns() {
return myPkColumns;
}
public String generateSQLCreateScript() {
StringBuilder sb = new StringBuilder();
sb.append("CREATE TABLE ");
sb.append(getTableName());
sb.append(" ( ");
sb.append(" (");
if (myPrettyPrint) {
sb.append("\n");
} else {
sb.append(" ");
}
for (AddColumnTask next : myAddColumnTasks) {
next.setDriverType(getDriverType());
next.setTableName(getTableName());
next.validate();
if (myPrettyPrint) {
sb.append("\t");
}
sb.append(next.getColumnName());
sb.append(" ");
sb.append(next.getTypeStatement());
sb.append(", ");
sb.append(",");
if (myPrettyPrint) {
sb.append("\n");
} else {
sb.append(" ");
}
}
sb.append(" PRIMARY KEY (");
// primary keys
if (myPrettyPrint) {
sb.append("\t");
} else {
sb.append(" ");
}
sb.append("PRIMARY KEY (");
for (int i = 0; i < myPkColumns.size(); i++) {
if (i > 0) {
sb.append(", ");
}
sb.append(myPkColumns.get(i));
}
boolean hasForeignKeys = !myFKColumns.isEmpty();
sb.append(")");
if (hasForeignKeys) {
sb.append(",");
}
if (myPrettyPrint) {
sb.append("\n");
} else {
sb.append(" ");
}
DriverTypeEnum sqlEngine = getDriverType();
// foreign keys
if (!myFKColumns.isEmpty()) {
for (int i =0; i < myFKColumns.size(); i++) {
if (i > 0) {
sb.append(", ");
}
ForeignKeyContainer fk = myFKColumns.get(i);
if (myPrettyPrint) {
sb.append("\t");
}
sb.append(fk.generateSQL(sqlEngine, myPrettyPrint));
if (myPrettyPrint) {
sb.append("\n");
} else {
sb.append(" ");
}
}
}
sb.append(")");
sb.append(" ) ");
switch (getDriverType()) {
switch (sqlEngine) {
case MARIADB_10_1:
case MYSQL_5_7:
sb.append("engine=InnoDB");
sb.append(" engine=InnoDB");
break;
case DERBY_EMBEDDED:
case POSTGRES_9_4:
@ -106,7 +167,17 @@ public class AddTableByColumnTask extends BaseTableTask {
break;
}
executeSql(getTableName(), sb.toString());
return sb.toString();
}
@Override
public void doExecute() throws SQLException {
if (myCheckForExistingTables && JdbcUtils.getTableNames(getConnectionProperties()).contains(getTableName())) {
logInfo(ourLog, "Already have table named {} - No action performed", getTableName());
return;
}
executeSql(getTableName(), generateSQLCreateScript());
}

14
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTask.java
View File

@ -73,6 +73,16 @@ public abstract class BaseTask {
private boolean myNoColumnShrink;
private boolean myFailureAllowed;
private boolean myRunDuringSchemaInitialization;
/**
* Whether or not to check for existing tables
* before generating SQL
*/
protected boolean myCheckForExistingTables = true;
/**
* Whether or not to generate the SQL in a 'readable format'
*/
protected boolean myPrettyPrint = false;
protected BaseTask(String theProductVersion, String theSchemaVersion) {
myProductVersion = theProductVersion;
@ -83,6 +93,10 @@ public abstract class BaseTask {
return myRunDuringSchemaInitialization;
}
public void setPrettyPrint(boolean thePrettyPrint) {
myPrettyPrint = thePrettyPrint;
}
/**
* Should this task run even if we're doing the very first initialization of an empty schema. By
* default we skip most tasks during that pass, since they just take up time and the

107
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ForeignKeyContainer.java Normal file
View File

@ -0,0 +1,107 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import javax.annotation.Nonnull;
public class ForeignKeyContainer {
/**
* The parent table name
*/
private String myParentTableName;
/**
* The name of the column in this table that holds the foreign key
*/
private String myColumnName;
/**
* The column data type
*/
private ColumnTypeEnum myColumnTypeEnum;
/**
* The name of the column in the parent table (that is the foreign key)
*/
private String myParentTableColumnName;
public ForeignKeyContainer(
String theColumnName,
ColumnTypeEnum theColumnTypeEnum,
String theParentTableName,
String theParentTableColumnName
) {
myColumnName = theColumnName;
myColumnTypeEnum = theColumnTypeEnum;
myParentTableName = theParentTableName;
myParentTableColumnName = theParentTableColumnName;
}
public String getParentTableName() {
return myParentTableName;
}
public void setParentTableName(String theParentTableName) {
myParentTableName = theParentTableName;
}
public String getColumnName() {
return myColumnName;
}
public void setColumnName(String theColumnName) {
myColumnName = theColumnName;
}
public String getParentTableColumnName() {
return myParentTableColumnName;
}
public void setParentTableColumnName(String theParentTableColumnName) {
myParentTableColumnName = theParentTableColumnName;
}
public ColumnTypeEnum getColumnTypeEnum() {
return myColumnTypeEnum;
}
public void setColumnTypeEnum(ColumnTypeEnum theColumnTypeEnum) {
myColumnTypeEnum = theColumnTypeEnum;
}
public String generateSQL(
@Nonnull DriverTypeEnum theDriverTypeEnum,
boolean thePrettyPrint
) {
switch (theDriverTypeEnum) {
case MYSQL_5_7:
return String.format(
"FOREIGN KEY (%s) REFERENCES %s(%s)",
myColumnName,
myParentTableName,
myParentTableColumnName
);
case MSSQL_2012:
case ORACLE_12C:
return String.format(
"%s %s FOREIGN KEY REFERENCES %s(%s)",
myColumnName,
myColumnTypeEnum.name(),
myParentTableName,
myParentTableColumnName
);
case POSTGRES_9_4:
return String.format(
"FOREIGN KEY(%s) REFERENCES %s(%s)",
myColumnName,
myParentTableName,
myParentTableColumnName
);
default:
throw new UnsupportedOperationException(
Msg.code(2232) + " SQL Engine " + theDriverTypeEnum.name() + " not supported for foreign key!");
}
}
}

2
hapi-fhir-storage-batch2-jobs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage-batch2/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage-cr/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage-mdm/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4b/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-testpage-overlay/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2.1/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu3/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r4/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r5/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-tinder-plugin/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-tinder-test/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

4
pom.xml
View File

@ -6,7 +6,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<name>HAPI-FHIR</name>
<description>An open-source implementation of the FHIR specification in Java.</description>
<url>https://hapifhir.io</url>
@ -2117,7 +2117,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-checkstyle</artifactId>
<!-- Remember to bump this when you upgrade the version -->
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
</dependency>
</dependencies>
</plugin>

2
tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.8-SNAPSHOT</version>
<version>6.3.9-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>