Add GraphDefinition engine
This commit is contained in:
Grahame Grieve
parent
faf31afda1
commit
93b0d74eb5
|
|
@ -0,0 +1,276 @@
|
|||
package org.hl7.fhir.r5.utils;
|
||||
|
||||
import java.io.UnsupportedEncodingException;
|
||||
import java.net.URLDecoder;
|
||||
import java.util.ArrayList;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import org.apache.xmlbeans.xml.stream.ReferenceResolver;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.r5.context.IWorkerContext;
|
||||
import org.hl7.fhir.r5.model.Base;
|
||||
import org.hl7.fhir.r5.model.Bundle;
|
||||
import org.hl7.fhir.r5.model.Expression;
|
||||
import org.hl7.fhir.r5.model.ExpressionNode;
|
||||
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
|
||||
import org.hl7.fhir.r5.model.GraphDefinition;
|
||||
import org.hl7.fhir.r5.model.GraphDefinition.GraphDefinitionLinkComponent;
|
||||
import org.hl7.fhir.r5.model.GraphDefinition.GraphDefinitionLinkTargetComponent;
|
||||
import org.hl7.fhir.r5.model.Reference;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.model.StringType;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.graphql.Argument;
|
||||
import org.hl7.fhir.utilities.graphql.EGraphEngine;
|
||||
import org.hl7.fhir.utilities.graphql.EGraphQLException;
|
||||
import org.hl7.fhir.utilities.graphql.GraphQLResponse;
|
||||
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
|
||||
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices.ReferenceResolution;
|
||||
import org.hl7.fhir.utilities.graphql.StringValue;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
|
||||
public class GraphDefinitionEngine {
|
||||
|
||||
|
||||
private static final String TAG_NAME = "Compiled.expression";
|
||||
|
||||
private IGraphQLStorageServices services;
|
||||
private IWorkerContext context;
|
||||
/**
|
||||
* for the host to pass context into and get back on the reference resolution interface
|
||||
*/
|
||||
private Object appInfo;
|
||||
|
||||
/**
|
||||
* the focus resource - if (there instanceof one. if (there isn"t,) there instanceof no focus
|
||||
*/
|
||||
private Resource start;
|
||||
|
||||
/**
|
||||
* The package that describes the graphQL to be executed, operation name, and variables
|
||||
*/
|
||||
private GraphDefinition graphDefinition;
|
||||
|
||||
/**
|
||||
* If the graph definition is being run to validate a grph
|
||||
*/
|
||||
private boolean validating;
|
||||
|
||||
/**
|
||||
* where the output from executing the query instanceof going to go
|
||||
*/
|
||||
private Bundle bundle;
|
||||
|
||||
private String baseURL;
|
||||
private FHIRPathEngine engine;
|
||||
|
||||
public GraphDefinitionEngine(IGraphQLStorageServices services, IWorkerContext context) {
|
||||
super();
|
||||
this.services = services;
|
||||
this.context = context;
|
||||
}
|
||||
|
||||
public Object getAppInfo() {
|
||||
return appInfo;
|
||||
}
|
||||
|
||||
public void setAppInfo(Object appInfo) {
|
||||
this.appInfo = appInfo;
|
||||
}
|
||||
|
||||
public Resource getFocus() {
|
||||
return start;
|
||||
}
|
||||
|
||||
public void setFocus(Resource focus) {
|
||||
this.start = focus;
|
||||
}
|
||||
|
||||
public GraphDefinition getGraphDefinition() {
|
||||
return graphDefinition;
|
||||
}
|
||||
|
||||
public void setGraphDefinition(GraphDefinition graphDefinition) {
|
||||
this.graphDefinition = graphDefinition;
|
||||
}
|
||||
|
||||
public Bundle getOutput() {
|
||||
return bundle;
|
||||
}
|
||||
|
||||
public void setOutput(Bundle bundle) {
|
||||
this.bundle = bundle;
|
||||
}
|
||||
|
||||
public IGraphQLStorageServices getServices() {
|
||||
return services;
|
||||
}
|
||||
|
||||
public IWorkerContext getContext() {
|
||||
return context;
|
||||
}
|
||||
|
||||
public String getBaseURL() {
|
||||
return baseURL;
|
||||
}
|
||||
|
||||
public void setBaseURL(String baseURL) {
|
||||
this.baseURL = baseURL;
|
||||
}
|
||||
|
||||
public boolean isValidating() {
|
||||
return validating;
|
||||
}
|
||||
|
||||
public void setValidating(boolean validating) {
|
||||
this.validating = validating;
|
||||
}
|
||||
|
||||
public void execute() throws EGraphEngine, EGraphQLException, FHIRException {
|
||||
assert services != null;
|
||||
assert start != null;
|
||||
assert bundle != null;
|
||||
assert baseURL != null;
|
||||
assert graphDefinition != null;
|
||||
graphDefinition.checkNoModifiers("definition", "Building graph from GraphDefinition");
|
||||
|
||||
check(!start.fhirType().equals(graphDefinition.getStart()), "The Graph definition requires that the start (focus reosource) is "+graphDefinition.getStart()+", but instead found "+start.fhirType());
|
||||
|
||||
if (!isInBundle(start)) {
|
||||
addToBundle(start);
|
||||
}
|
||||
for (GraphDefinitionLinkComponent l : graphDefinition.getLink()) {
|
||||
processLink(start.fhirType(), start, l, 1);
|
||||
}
|
||||
}
|
||||
|
||||
private void check(boolean b, String msg) {
|
||||
if (!b) {
|
||||
throw new FHIRException(msg);
|
||||
}
|
||||
}
|
||||
|
||||
private boolean isInBundle(Resource resource) {
|
||||
for (BundleEntryComponent be : bundle.getEntry()) {
|
||||
if (be.hasResource() && be.getResource().fhirType().equals(resource.fhirType()) && be.getResource().getId().equals(resource.getId())) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
private void addToBundle(Resource resource) {
|
||||
BundleEntryComponent be = bundle.addEntry();
|
||||
be.setFullUrl(Utilities.pathURL(baseURL, resource.fhirType(), resource.getId()));
|
||||
be.setResource(resource);
|
||||
}
|
||||
|
||||
private void processLink(String focusPath, Resource focus, GraphDefinitionLinkComponent link, int depth) {
|
||||
if (link.hasPath()) {
|
||||
processLinkPath(focusPath, focus, link, depth);
|
||||
} else {
|
||||
processLinkTarget(focusPath, focus, link, depth);
|
||||
}
|
||||
}
|
||||
|
||||
private void processLinkPath(String focusPath, Resource focus, GraphDefinitionLinkComponent link, int depth) {
|
||||
String path = focusPath+" -> "+link.getPath();
|
||||
check(link.hasPath(), "Path is needed at "+path);
|
||||
check(!link.hasSliceName(), "SliceName is not yet supported at "+path);
|
||||
|
||||
ExpressionNode node;
|
||||
if (link.getPathElement().hasUserData(TAG_NAME)) {
|
||||
node = (ExpressionNode) link.getPathElement().getUserData(TAG_NAME);
|
||||
} else {
|
||||
node = engine.parse(link.getPath());
|
||||
link.getPathElement().setUserData(TAG_NAME, node);
|
||||
}
|
||||
List<Base> matches = engine.evaluate(null, focus, focus, focus, node);
|
||||
check(!validating || matches.size() >= (link.hasMin() ? link.getMin() : 0), "Link at path "+path+" requires at least "+link.getMin()+" matches, but only found "+matches.size());
|
||||
check(!validating || matches.size() <= (link.hasMax() ? Integer.parseInt(link.getMax()) : Integer.MAX_VALUE), "Link at path "+path+" requires at most "+link.getMax()+" matches, but found "+matches.size());
|
||||
for (Base sel : matches) {
|
||||
check(sel.fhirType().equals("Reference"), "Selected node from an expression must be a Reference"); // todo: should a URL be ok?
|
||||
ReferenceResolution res = services.lookup(appInfo, focus, (Reference) sel);
|
||||
if (res != null) {
|
||||
check(res.getTargetContext() != focus, "how to handle contained resources is not yet resolved"); // todo
|
||||
for (GraphDefinitionLinkTargetComponent tl : link.getTarget()) {
|
||||
if (tl.getType().equals(res.getTarget().fhirType())) {
|
||||
Resource r = (Resource) res.getTarget();
|
||||
if (!isInBundle(r)) {
|
||||
addToBundle(r);
|
||||
for (GraphDefinitionLinkComponent l : graphDefinition.getLink()) {
|
||||
processLink(focus.fhirType(), r, l, depth+1);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void processLinkTarget(String focusPath, Resource focus, GraphDefinitionLinkComponent link, int depth) {
|
||||
check(link.getTarget().size() == 1, "If there is no path, there must be one and only one target at "+focusPath);
|
||||
check(link.getTarget().get(0).hasType(), "If there is no path, there must be type on the target at "+focusPath);
|
||||
check(link.getTarget().get(0).getParams().contains("{ref}"), "If there is no path, the target must have parameters that include a parameter using {ref} at "+focusPath);
|
||||
String path = focusPath+" -> "+link.getTarget().get(0).getType()+"?"+link.getTarget().get(0).getParams();
|
||||
|
||||
List<IBaseResource> list = new ArrayList<>();
|
||||
List<Argument> params = new ArrayList<>();
|
||||
parseParams(params, link.getTarget().get(0).getParams(), focus);
|
||||
services.listResources(appInfo, link.getTarget().get(0).getType(), params, list);
|
||||
check(!validating || (list.size() >= (link.hasMin() ? link.getMin() : 0)), "Link at path "+path+" requires at least "+link.getMin()+" matches, but only found "+list.size());
|
||||
check(!validating || (list.size() <= (link.hasMax() && !link.getMax().equals("*") ? Integer.parseInt(link.getMax()) : Integer.MAX_VALUE)), "Link at path "+path+" requires at most "+link.getMax()+" matches, but found "+list.size());
|
||||
for (IBaseResource res : list) {
|
||||
Resource r = (Resource) res;
|
||||
if (!isInBundle(r)) {
|
||||
addToBundle(r);
|
||||
// Grahame Grieve 17-06-2020: this seems wrong to me - why restart?
|
||||
for (GraphDefinitionLinkComponent l : graphDefinition.getLink()) {
|
||||
processLink(start.fhirType(), start, l, depth+1);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void parseParams(List<Argument> params, String value, Resource res) {
|
||||
boolean refed = false;
|
||||
Map<String, List<String>> p = splitQuery(value);
|
||||
for (String n : p.keySet()) {
|
||||
for (String v : p.get(n)) {
|
||||
if (v.equals("{ref}")) {
|
||||
refed = true;
|
||||
v = res.fhirType()+'/'+res.getId();
|
||||
}
|
||||
params.add(new Argument(n, new StringValue(v)));
|
||||
}
|
||||
}
|
||||
check(refed, "no use of {ref} found");
|
||||
}
|
||||
|
||||
public Map<String, List<String>> splitQuery(String string) {
|
||||
final Map<String, List<String>> query_pairs = new LinkedHashMap<String, List<String>>();
|
||||
final String[] pairs = string.split("&");
|
||||
for (String pair : pairs) {
|
||||
final int idx = pair.indexOf("=");
|
||||
final String key = idx > 0 ? decode(pair.substring(0, idx), "UTF-8") : pair;
|
||||
if (!query_pairs.containsKey(key)) {
|
||||
query_pairs.put(key, new LinkedList<String>());
|
||||
}
|
||||
final String value = idx > 0 && pair.length() > idx + 1 ? decode(pair.substring(idx + 1), "UTF-8") : null;
|
||||
query_pairs.get(key).add(value);
|
||||
}
|
||||
return query_pairs;
|
||||
}
|
||||
|
||||
private String decode(String s, String enc) {
|
||||
try {
|
||||
return URLDecoder.decode(s, enc);
|
||||
} catch (UnsupportedEncodingException e) {
|
||||
return s;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
package org.hl7.fhir.r5.utils;
|
||||
|
||||
/*
|
||||
Copyright (c) 2011+, HL7, Inc.
|
||||
All rights reserved.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without modification,
|
||||
are permitted provided that the following conditions are met:
|
||||
|
||||
* Redistributions of source code must retain the above copyright notice, this
|
||||
list of conditions and the following disclaimer.
|
||||
* Redistributions in binary form must reproduce the above copyright notice,
|
||||
this list of conditions and the following disclaimer in the documentation
|
||||
and/or other materials provided with the distribution.
|
||||
* Neither the name of HL7 nor the names of its contributors may be used to
|
||||
endorse or promote products derived from this software without specific
|
||||
prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
|
||||
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
|
||||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
|
||||
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
|
||||
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
|
||||
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
||||
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
|
||||
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
|
||||
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
*/
|
||||
|
||||
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r5.model.Bundle;
|
||||
import org.hl7.fhir.r5.model.GraphDefinition;
|
||||
import org.hl7.fhir.utilities.graphql.EGraphEngine;
|
||||
import org.hl7.fhir.utilities.graphql.EGraphQLException;
|
||||
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
|
||||
|
||||
public interface IGraphDefinitionEngine {
|
||||
|
||||
void execute() throws EGraphEngine, EGraphQLException, FHIRException;
|
||||
|
||||
Bundle getOutput();
|
||||
|
||||
void setAppInfo(Object appInfo);
|
||||
|
||||
void setFocus(IBaseResource focus);
|
||||
|
||||
void setGraphDefinition(GraphDefinition graphDefinition);
|
||||
|
||||
void setServices(IGraphQLStorageServices services);
|
||||
}
|
||||
Loading…
Reference in New Issue