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add automatic loading of package dependencies by the context

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This commit is contained in:
Grahame Grieve 2020-07-25 08:38:13 +10:00
parent 90dc97b150
commit 115fa8a497
6 changed files with 127 additions and 3 deletions
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8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -1603,4 +1603,12 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
return this;
}
public String getTxCache() {
return txCache.getFolder();
}
public TerminologyClient getTxClient() {
return txClient;
}
}

56
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
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@ -64,10 +64,13 @@ import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorCla
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.cache.BasePackageCacheManager;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import com.google.gson.JsonSyntaxException;
/**
* This is the standard interface used for access to underlying FHIR
@ -150,7 +153,18 @@ public interface IWorkerContext {
* @param resource
* @return null if not tracking paths
*/
String getResourcePath(Resource resource);
String getResourcePath(Resource resource);
/**
* called when a mew package is being loaded
*
* this is called by loadPacakgeAndDependencies when a new package is loaded
* @param npm
* @return
* @throws IOException
* @throws JsonSyntaxException
*/
IContextResourceLoader getNewLoader(NpmPackage npm) throws JsonSyntaxException, IOException;
}
@ -660,7 +674,45 @@ public interface IWorkerContext {
public String getLinkForUrl(String corePath, String s);
public Map<String, byte[]> getBinaries();
void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String[] types) throws FileNotFoundException, IOException, FHIRException;
/**
* Load relevant resources of the appropriate types (as specified by the loader) from the nominated package
*
* note that the package system uses lazy loading; the loader will be called later when the classes that use the context need the relevant resource
*
* @param pi - the package to load
* @param loader - an implemenation of IContextResourceLoader that knows how to read the resources in the package (e.g. for the appropriate version).
* @return the number of resources loaded
*/
int loadFromPackage(NpmPackage pi, IContextResourceLoader loader) throws FileNotFoundException, IOException, FHIRException;
/**
* Load relevant resources of the appropriate types (as specified by the loader) from the nominated package
*
* note that the package system uses lazy loading; the loader will be called later when the classes that use the context need the relevant resource
*
* Deprecated - use the simpler method where the types come from the loader.
*
* @param pi - the package to load
* @param loader - an implemenation of IContextResourceLoader that knows how to read the resources in the package (e.g. for the appropriate version).
* @param types - which types of resources to load
* @return the number of resources loaded
*/
@Deprecated
int loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String[] types) throws FileNotFoundException, IOException, FHIRException;
/**
* Load relevant resources of the appropriate types (as specified by the loader) from the nominated package
*
* note that the package system uses lazy loading; the loader will be called later when the classes that use the context need the relevant resource
*
* This method also loads all the packages that the package depends on (recursively)
*
* @param pi - the package to load
* @param loader - an implemenation of IContextResourceLoader that knows how to read the resources in the package (e.g. for the appropriate version).
* @param pcm - used to find and load additional dependencies
* @return the number of resources loaded
*/
int loadFromPackageAndDependencies(NpmPackage pi, IContextResourceLoader loader, BasePackageCacheManager pcm) throws FileNotFoundException, IOException, FHIRException;
public boolean hasPackage(String id, String ver);

48
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
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@ -88,6 +88,8 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import com.google.gson.JsonObject;
import ca.uhn.fhir.parser.DataFormatException;
/*
@ -370,7 +372,46 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
@Override
public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
public int loadFromPackage(NpmPackage pi, IContextResourceLoader loader) throws FileNotFoundException, IOException, FHIRException {
return loadFromPackageInt(pi, loader, loader == null ? defaultTypesToLoad() : loader.getTypes());
}
public static String[] defaultTypesToLoad() {
// there's no penalty for listing resources that don't exist, so we just all the relevant possibilities for all versions
return new String[] {"CodeSystem", "ValueSet", "ConceptMap", "NamingSystem",
"StructureDefinition", "StructureMap",
"SearchParameter", "OperationDefinition", "CapabilityStatement", "Conformance",
"Questionnaire", "ImplementationGuide" };
}
@Override
public int loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String[] types) throws FileNotFoundException, IOException, FHIRException {
return loadFromPackageInt(pi, loader, types);
}
@Override
public int loadFromPackageAndDependencies(NpmPackage pi, IContextResourceLoader loader, BasePackageCacheManager pcm) throws FileNotFoundException, IOException, FHIRException {
return loadFromPackageAndDependenciesInt(pi, loader, pcm, pi.name()+"#"+pi.version());
}
public int loadFromPackageAndDependenciesInt(NpmPackage pi, IContextResourceLoader loader, BasePackageCacheManager pcm, String path) throws FileNotFoundException, IOException, FHIRException {
int t = 0;
for (String e : pi.dependencies()) {
if (!loadedPackages.contains(e) && !VersionUtilities.isCorePackage(e)) {
NpmPackage npm = pcm.loadPackage(e);
if (!version.equals(npm.fhirVersion())) {
System.out.println(formatMessage(I18nConstants.PACKAGE_VERSION_MISMATCH, e, version, npm.fhirVersion(), path));
}
t = t + loadFromPackageAndDependenciesInt(npm, loader.getNewLoader(npm), pcm, path+" -> "+npm.name()+"#"+npm.version());
}
}
t = t + loadFromPackageInt(pi, loader, loader.getTypes());
return t;
}
public int loadFromPackageInt(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
int t = 0;
if (progress) {
System.out.println("Load Package "+pi.name()+"#"+pi.version());
}
@ -388,6 +429,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
for (String s : pi.listResources(loader.getTypes())) {
try {
loadDefinitionItem(s, pi.load("package", s), loader, null, new PackageVersion(pi.id(), pi.version()));
t++;
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, s, pi.name(), pi.version(), e.getMessage()), e);
}
@ -399,6 +441,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
try {
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version()));
t++;
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
}
@ -410,6 +453,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
if (version == null) {
version = pi.version();
}
return t;
}
public void loadFromFile(String file, IContextResourceLoader loader) throws IOException, FHIRException {
@ -757,5 +801,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/TerminologyCache.java
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@ -469,6 +469,10 @@ public class TerminologyCache {
}
}
}
public String getFolder() {
return folder;
}
}

5
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/BasePackageCacheManager.java vendored
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@ -1,6 +1,7 @@
package org.hl7.fhir.utilities.cache;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -155,4 +156,8 @@ public abstract class BasePackageCacheManager implements IPackageCacheManager {
}
}
public NpmPackage loadPackage(String idAndVer) throws FHIRException, IOException {
return loadPackage(idAndVer, null);
}
}

9
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/IPackageCacheManager.java vendored
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@ -14,4 +14,13 @@ public interface IPackageCacheManager {
String getPackageUrl(String packageId) throws IOException;
NpmPackage loadPackage(String id, String version) throws FHIRException, IOException;
/**
*
* @param idAndVer - use id#ver
* @return
* @throws FHIRException
* @throws IOException
*/
NpmPackage loadPackage(String idAndVer) throws FHIRException, IOException;
}