honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

This commit is contained in:
Grahame Grieve 2019-08-16 07:19:21 +10:00
parent fb249ea098 34b6bc7e57
commit 55259ab8dc
19 changed files with 1467 additions and 454 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

7
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/Property.java
View File

@ -82,7 +82,8 @@ public class Property {
this.definition = definition;
this.minCardinality = minCardinality;
this.maxCardinality = maxCardinality;
this.values.add(value);
if (value != null)
this.values.add(value);
}
/**
@ -156,6 +157,8 @@ public class Property {
this.structure = structure;
}
public boolean isList() {
return maxCardinality > 1;
}
}

964
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/GraphQLEngine.java Normal file
View File

@ -0,0 +1,964 @@
package org.hl7.fhir.dstu3.utils;
/*-
* #%L
* org.hl7.fhir.dstu3
* %%
* Copyright (C) 2014 - 2019 Health Level 7
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.*;
import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
import org.hl7.fhir.utilities.graphql.Package;
import org.hl7.fhir.utilities.graphql.Operation.OperationType;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static org.hl7.fhir.utilities.graphql.IGraphQLStorageServices.ReferenceResolution;
public class GraphQLEngine implements IGraphQLEngine {
public static class SearchEdge extends Base {
private BundleEntryComponent be;
private String type;
SearchEdge(String type, BundleEntryComponent be) {
this.type = type;
this.be = be;
}
@Override
public String fhirType() {
return type;
}
@Override
protected void listChildren(List<Property> result) {
throw new Error("Not Implemented");
}
@Override
public String getIdBase() {
throw new Error("Not Implemented");
}
@Override
public void setIdBase(String value) {
throw new Error("Not Implemented");
}
@Override
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
switch (_hash) {
case 3357091: /*mode*/ return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasMode() ? be.getSearch().getModeElement() : null);
case 109264530: /*score*/ return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasScore() ? be.getSearch().getScoreElement() : null);
case -341064690: /*resource*/ return new Property(_name, "resource", "n/a", 0, 1, be.hasResource() ? be.getResource() : null);
default: return super.getNamedProperty(_hash, _name, _checkValid);
}
}
}
public static class SearchWrapper extends Base {
private Bundle bnd;
private String type;
private Map<String, String> map;
SearchWrapper(String type, Bundle bnd) throws FHIRException {
this.type = type;
this.bnd = bnd;
for (BundleLinkComponent bl : bnd.getLink())
if (bl.getRelation().equals("self"))
map = parseURL(bl.getUrl());
}
@Override
public String fhirType() {
return type;
}
@Override
protected void listChildren(List<Property> result) {
throw new Error("Not Implemented");
}
@Override
public String getIdBase() {
throw new Error("Not Implemented");
}
@Override
public void setIdBase(String value) {
throw new Error("Not Implemented");
}
@Override
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
switch (_hash) {
case 97440432: /*first*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case -1273775369: /*previous*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 3377907: /*next*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 3314326: /*last*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 94851343: /*count*/ return new Property(_name, "integer", "n/a", 0, 1, bnd.getTotalElement());
case -1019779949:/*offset*/ return new Property(_name, "integer", "n/a", 0, 1, extractParam("search-offset"));
case 860381968: /*pagesize*/ return new Property(_name, "integer", "n/a", 0, 1, extractParam("_count"));
case 96356950: /*edges*/ return new Property(_name, "edge", "n/a", 0, Integer.MAX_VALUE, getEdges());
default: return super.getNamedProperty(_hash, _name, _checkValid);
}
}
private List<Base> getEdges() {
List<Base> list = new ArrayList<>();
for (BundleEntryComponent be : bnd.getEntry())
list.add(new SearchEdge(type.substring(0, type.length() - 10) + "Edge", be));
return list;
}
private Base extractParam(String name) throws FHIRException {
return map != null ? new IntegerType(map.get(name)) : null;
}
private Map<String, String> parseURL(String url) throws FHIRException {
try {
Map<String, String> map = new HashMap<String, String>();
String[] pairs = url.split("&");
for (String pair : pairs) {
int idx = pair.indexOf("=");
String key;
key = idx > 0 ? URLDecoder.decode(pair.substring(0, idx), "UTF-8") : pair;
String value = idx > 0 && pair.length() > idx + 1 ? URLDecoder.decode(pair.substring(idx + 1), "UTF-8") : null;
map.put(key, value);
}
return map;
} catch (UnsupportedEncodingException e) {
throw new FHIRException(e);
}
}
private Base extractLink(String _name) throws FHIRException {
for (BundleLinkComponent bl : bnd.getLink()) {
if (bl.getRelation().equals(_name)) {
Map<String, String> map = parseURL(bl.getUrl());
return new StringType(map.get("search-id")+':'+map.get("search-offset"));
}
}
return null;
}
}
private IWorkerContext context;
public GraphQLEngine(IWorkerContext context) {
super();
this.context = 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 focus;
/**
* The package that describes the graphQL to be executed, operation name, and variables
*/
private Package graphQL;
/**
* where the output from executing the query instanceof going to go
*/
private ObjectValue output;
/**
* Application provided reference resolution services
*/
private IGraphQLStorageServices services;
// internal stuff
private Map<String, Argument> workingVariables = new HashMap<String, Argument>();
private FHIRPathEngine fpe;
private ExpressionNode magicExpression;
public void execute() throws EGraphEngine, EGraphQLException, FHIRException {
if (graphQL == null)
throw new EGraphEngine("Unable to process graphql - graphql document missing");
fpe = new FHIRPathEngine(this.context);
magicExpression = new ExpressionNode(0);
output = new ObjectValue();
Operation op = null;
// todo: initial conditions
if (!Utilities.noString(graphQL.getOperationName())) {
op = graphQL.getDocument().operation(graphQL.getOperationName());
if (op == null)
throw new EGraphEngine("Unable to find operation \""+graphQL.getOperationName()+"\"");
} else if ((graphQL.getDocument().getOperations().size() == 1))
op = graphQL.getDocument().getOperations().get(0);
else
throw new EGraphQLException("No operation name provided, so expected to find a single operation");
if (op.getOperationType() == OperationType.qglotMutation)
throw new EGraphQLException("Mutation operations are not supported (yet)");
checkNoDirectives(op.getDirectives());
processVariables(op);
if (focus == null)
processSearch(output, op.getSelectionSet(), false, "");
else
processObject(focus, focus, output, op.getSelectionSet(), false, "");
}
private boolean checkBooleanDirective(Directive dir) throws EGraphQLException {
if (dir.getArguments().size() != 1)
throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
if (!dir.getArguments().get(0).getName().equals("if"))
throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
List<Value> vl = resolveValues(dir.getArguments().get(0), 1);
return vl.get(0).toString().equals("true");
}
private boolean checkDirectives(List<Directive> directives) throws EGraphQLException {
Directive skip = null;
Directive include = null;
for (Directive dir : directives) {
if (dir.getName().equals("skip")) {
if ((skip == null))
skip = dir;
else
throw new EGraphQLException("Duplicate @skip directives");
} else if (dir.getName().equals("include")) {
if ((include == null))
include = dir;
else
throw new EGraphQLException("Duplicate @include directives");
}
else if (!Utilities.existsInList(dir.getName(), "flatten", "first", "singleton", "slice"))
throw new EGraphQLException("Directive \""+dir.getName()+"\" instanceof not recognised");
}
if ((skip != null && include != null))
throw new EGraphQLException("Cannot mix @skip and @include directives");
if (skip != null)
return !checkBooleanDirective(skip);
else if (include != null)
return checkBooleanDirective(include);
else
return true;
}
private void checkNoDirectives(List<Directive> directives) {
}
private boolean targetTypeOk(List<Argument> arguments, IBaseResource dest) throws EGraphQLException {
List<String> list = new ArrayList<String>();
for (Argument arg : arguments) {
if ((arg.getName().equals("type"))) {
List<Value> vl = resolveValues(arg);
for (Value v : vl)
list.add(v.toString());
}
}
if (list.size() == 0)
return true;
else
return list.indexOf(dest.fhirType()) > -1;
}
private boolean hasExtensions(Base obj) {
if (obj instanceof BackboneElement)
return ((BackboneElement) obj).getExtension().size() > 0 || ((BackboneElement) obj).getModifierExtension().size() > 0;
else if (obj instanceof DomainResource)
return ((DomainResource)obj).getExtension().size() > 0 || ((DomainResource)obj).getModifierExtension().size() > 0;
else if (obj instanceof Element)
return ((Element)obj).getExtension().size() > 0;
else
return false;
}
private boolean passesExtensionMode(Base obj, boolean extensionMode) {
if (!obj.isPrimitive())
return !extensionMode;
else if (extensionMode)
return !Utilities.noString(obj.getIdBase()) || hasExtensions(obj);
else
return obj.primitiveValue() != "";
}
private List<Base> filter(Resource context, Property prop, List<Argument> arguments, List<Base> values, boolean extensionMode) throws FHIRException, EGraphQLException {
List<Base> result = new ArrayList<Base>();
if (values.size() > 0) {
int count = Integer.MAX_VALUE;
int offset = 0;
StringBuilder fp = new StringBuilder();
for (Argument arg : arguments) {
List<Value> vl = resolveValues(arg);
if ((vl.size() != 1))
throw new EGraphQLException("Incorrect number of arguments");
if (values.get(0).isPrimitive())
throw new EGraphQLException("Attempt to use a filter ("+arg.getName()+") on a primtive type ("+prop.getTypeCode()+")");
if ((arg.getName().equals("fhirpath")))
fp.append(" and "+vl.get(0).toString());
else if ((arg.getName().equals("_count")))
count = Integer.valueOf(vl.get(0).toString());
else if ((arg.getName().equals("_offset")))
offset = Integer.valueOf(vl.get(0).toString());
else {
Property p = values.get(0).getNamedProperty(arg.getName());
if (p == null)
throw new EGraphQLException("Attempt to use an unknown filter ("+arg.getName()+") on a type ("+prop.getTypeCode()+")");
fp.append(" and "+arg.getName()+" = '"+vl.get(0).toString()+"'");
}
}
int i = 0;
int t = 0;
if (fp.length() == 0)
for (Base v : values) {
if ((i >= offset) && passesExtensionMode(v, extensionMode)) {
result.add(v);
t++;
if (t >= count)
break;
}
i++;
} else {
ExpressionNode node = fpe.parse(fp.toString().substring(5));
for (Base v : values) {
if ((i >= offset) && passesExtensionMode(v, extensionMode) && fpe.evaluateToBoolean(null, context, v, node)) {
result.add(v);
t++;
if (t >= count)
break;
}
i++;
}
}
}
return result;
}
private List<Resource> filterResources(Argument fhirpath, Bundle bnd) throws EGraphQLException, FHIRException {
List<Resource> result = new ArrayList<Resource>();
if (bnd.getEntry().size() > 0) {
if ((fhirpath == null))
for (BundleEntryComponent be : bnd.getEntry())
result.add(be.getResource());
else {
FHIRPathEngine fpe = new FHIRPathEngine(context);
ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
for (BundleEntryComponent be : bnd.getEntry())
if (fpe.evaluateToBoolean(null, be.getResource(), be.getResource(), node))
result.add(be.getResource());
}
}
return result;
}
private List<Resource> filterResources(Argument fhirpath, List<IBaseResource> list) throws EGraphQLException, FHIRException {
List<Resource> result = new ArrayList<>();
if (list.size() > 0) {
if ((fhirpath == null))
for (IBaseResource v : list)
result.add((Resource) v);
else {
FHIRPathEngine fpe = new FHIRPathEngine(context);
ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
for (IBaseResource v : list)
if (fpe.evaluateToBoolean(null, (Resource)v, (Resource)v, node))
result.add((Resource) v);
}
}
return result;
}
private boolean hasArgument(List<Argument> arguments, String name, String value) {
for (Argument arg : arguments)
if ((arg.getName().equals(name)) && arg.hasValue(value))
return true;
return false;
}
private void processValues(Resource context, Selection sel, Property prop, ObjectValue target, List<Base> values, boolean extensionMode, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
boolean il = false;
Argument arg = null;
ExpressionNode expression = null;
if (sel.getField().hasDirective("slice")) {
Directive dir = sel.getField().directive("slice");
String s = ((StringValue) dir.getArguments().get(0).getValues().get(0)).getValue();
if (s.equals("$index"))
expression = magicExpression;
else
expression = fpe.parse(s);
}
if (sel.getField().hasDirective("flatten")) // special: instruction to drop this node...
il = prop.isList() && !sel.getField().hasDirective("first");
else if (sel.getField().hasDirective("first")) {
if (expression != null)
throw new FHIRException("You cannot mix @slice and @first");
arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), inheritedList));
} else if (expression == null)
arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
int index = 0;
for (Base value : values) {
String ss = "";
if (expression != null) {
if (expression == magicExpression)
ss = suffix+'.'+Integer.toString(index);
else
ss = suffix+'.'+fpe.evaluateToString(null, null, value, expression);
if (!sel.getField().hasDirective("flatten"))
arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
}
if (value.isPrimitive() && !extensionMode) {
if (!sel.getField().getSelectionSet().isEmpty())
throw new EGraphQLException("Encountered a selection set on a scalar field type");
processPrimitive(arg, value);
} else {
if (sel.getField().getSelectionSet().isEmpty())
throw new EGraphQLException("No Fields selected on a complex object");
if (arg == null)
processObject(context, value, target, sel.getField().getSelectionSet(), il, ss);
else {
ObjectValue n = new ObjectValue();
arg.addValue(n);
processObject(context, value, n, sel.getField().getSelectionSet(), il, ss);
}
}
if (sel.getField().hasDirective("first"))
return;
index++;
}
}
private void processVariables(Operation op) throws EGraphQLException {
for (Variable varRef : op.getVariables()) {
Argument varDef = null;
for (Argument v : graphQL.getVariables())
if (v.getName().equals(varRef.getName()))
varDef = v;
if (varDef != null)
workingVariables.put(varRef.getName(), varDef); // todo: check type?
else if (varRef.getDefaultValue() != null)
workingVariables.put(varRef.getName(), new Argument(varRef.getName(), varRef.getDefaultValue()));
else
throw new EGraphQLException("No value found for variable ");
}
}
private boolean isPrimitive(String typename) {
return Utilities.existsInList(typename, "boolean", "integer", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime", "time", "code", "oid", "id", "markdown", "unsignedInt", "positiveInt", "url", "canonical");
}
private boolean isResourceName(String name, String suffix) {
if (!name.endsWith(suffix))
return false;
name = name.substring(0, name.length()-suffix.length());
return context.getResourceNamesAsSet().contains(name);
}
private void processObject(Resource context, Base source, ObjectValue target, List<Selection> selection, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
for (Selection sel : selection) {
if (sel.getField() != null) {
if (checkDirectives(sel.getField().getDirectives())) {
Property prop = source.getNamedProperty(sel.getField().getName());
if ((prop == null) && sel.getField().getName().startsWith("_"))
prop = source.getNamedProperty(sel.getField().getName().substring(1));
if (prop == null) {
if ((sel.getField().getName().equals("resourceType") && source instanceof Resource))
target.addField("resourceType", listStatus(sel.getField(), false)).addValue(new StringValue(source.fhirType()));
else if ((sel.getField().getName().equals("resource") && source.fhirType().equals("Reference")))
processReference(context, source, sel.getField(), target, inheritedList, suffix);
else if ((sel.getField().getName().equals("resource") && source.fhirType().equals("canonical")))
processCanonicalReference(context, source, sel.getField(), target, inheritedList, suffix);
else if (isResourceName(sel.getField().getName(), "List") && (source instanceof Resource))
processReverseReferenceList((Resource) source, sel.getField(), target, inheritedList, suffix);
else if (isResourceName(sel.getField().getName(), "Connection") && (source instanceof Resource))
processReverseReferenceSearch((Resource) source, sel.getField(), target, inheritedList, suffix);
else
throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
} else {
if (!isPrimitive(prop.getTypeCode()) && sel.getField().getName().startsWith("_"))
throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
List<Base> vl = filter(context, prop, sel.getField().getArguments(), prop.getValues(), sel.getField().getName().startsWith("_"));
if (!vl.isEmpty())
processValues(context, sel, prop, target, vl, sel.getField().getName().startsWith("_"), inheritedList, suffix);
}
}
} else if (sel.getInlineFragment() != null) {
if (checkDirectives(sel.getInlineFragment().getDirectives())) {
if (Utilities.noString(sel.getInlineFragment().getTypeCondition()))
throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
if (source.fhirType().equals(sel.getInlineFragment().getTypeCondition()))
processObject(context, source, target, sel.getInlineFragment().getSelectionSet(), inheritedList, suffix);
}
} else if (checkDirectives(sel.getFragmentSpread().getDirectives())) {
Fragment fragment = graphQL.getDocument().fragment(sel.getFragmentSpread().getName());
if (fragment == null)
throw new EGraphQLException("Unable to resolve fragment "+sel.getFragmentSpread().getName());
if (Utilities.noString(fragment.getTypeCondition()))
throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
if (source.fhirType().equals(fragment.getTypeCondition()))
processObject(context, source, target, fragment.getSelectionSet(), inheritedList, suffix);
}
}
}
private void processPrimitive(Argument arg, Base value) {
String s = value.fhirType();
if (s.equals("integer") || s.equals("decimal") || s.equals("unsignedInt") || s.equals("positiveInt"))
arg.addValue(new NumberValue(value.primitiveValue()));
else if (s.equals("boolean"))
arg.addValue(new NameValue(value.primitiveValue()));
else
arg.addValue(new StringValue(value.primitiveValue()));
}
private void processReference(Resource context, Base source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (!(source instanceof Reference))
throw new EGraphQLException("Not done yet");
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
Reference ref = (Reference) source;
ReferenceResolution res = services.lookup(appInfo, context, ref);
if (res != null) {
if (targetTypeOk(field.getArguments(), res.getTarget())) {
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
}
}
else if (!hasArgument(field.getArguments(), "optional", "true"))
throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
}
private void processCanonicalReference(Resource context, Base source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
Reference ref = new Reference(source.primitiveValue());
ReferenceResolution res = services.lookup(appInfo, context, ref);
if (res != null) {
if (targetTypeOk(field.getArguments(), res.getTarget())) {
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
}
}
else if (!hasArgument(field.getArguments(), "optional", "true"))
throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
}
private ArgumentListStatus listStatus(Field field, boolean isList) {
if (field.hasDirective("singleton"))
return ArgumentListStatus.SINGLETON;
else if (isList)
return ArgumentListStatus.REPEATING;
else
return ArgumentListStatus.NOT_SPECIFIED;
}
private void processReverseReferenceList(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<IBaseResource> list = new ArrayList<>();
List<Argument> params = new ArrayList<>();
Argument parg = null;
for (Argument a : field.getArguments())
if (!(a.getName().equals("_reference")))
params.add(a);
else if ((parg == null))
parg = a;
else
throw new EGraphQLException("Duplicate parameter _reference");
if (parg == null)
throw new EGraphQLException("Missing parameter _reference");
Argument arg = new Argument();
params.add(arg);
arg.setName(getSingleValue(parg));
arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
arg = null;
ObjectValue obj = null;
List<Resource> vl = filterResources(field.argument("fhirpath"), list);
if (!vl.isEmpty()) {
arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
for (Resource v : vl) {
obj = new ObjectValue();
arg.addValue(obj);
processObject(v, v, obj, field.getSelectionSet(), inheritedList, suffix);
}
}
}
private void processReverseReferenceSearch(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<Argument> params = new ArrayList<Argument>();
Argument parg = null;
for (Argument a : field.getArguments())
if (!(a.getName().equals("_reference")))
params.add(a);
else if ((parg == null))
parg = a;
else
throw new EGraphQLException("Duplicate parameter _reference");
if (parg == null)
throw new EGraphQLException("Missing parameter _reference");
Argument arg = new Argument();
params.add(arg);
arg.setName(getSingleValue(parg));
arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
Base bndWrapper = new SearchWrapper(field.getName(), bnd);
arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
}
private void processSearch(ObjectValue target, List<Selection> selection, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
for (Selection sel : selection) {
if ((sel.getField() == null))
throw new EGraphQLException("Only field selections are allowed in this context");
checkNoDirectives(sel.getField().getDirectives());
if ((isResourceName(sel.getField().getName(), "")))
processSearchSingle(target, sel.getField(), inheritedList, suffix);
else if ((isResourceName(sel.getField().getName(), "List")))
processSearchSimple(target, sel.getField(), inheritedList, suffix);
else if ((isResourceName(sel.getField().getName(), "Connection")))
processSearchFull(target, sel.getField(), inheritedList, suffix);
}
}
private void processSearchSingle(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
String id = "";
for (Argument arg : field.getArguments())
if ((arg.getName().equals("id")))
id = getSingleValue(arg);
else
throw new EGraphQLException("Unknown/invalid parameter "+arg.getName());
if (Utilities.noString(id))
throw new EGraphQLException("No id found");
Resource res = (Resource) services.lookup(appInfo, field.getName(), id);
if (res == null)
throw new EGraphQLException("Resource "+field.getName()+"/"+id+" not found");
Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(res, res, obj, field.getSelectionSet(), inheritedList, suffix);
}
private void processSearchSimple(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<IBaseResource> list = new ArrayList<>();
services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), field.getArguments(), list);
Argument arg = null;
ObjectValue obj = null;
List<Resource> vl = filterResources(field.argument("fhirpath"), list);
if (!vl.isEmpty()) {
arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
for (Resource v : vl) {
obj = new ObjectValue();
arg.addValue(obj);
processObject(v, v, obj, field.getSelectionSet(), inheritedList, suffix);
}
}
}
private void processSearchFull(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<Argument> params = new ArrayList<Argument>();
Argument carg = null;
for ( Argument arg : field.getArguments())
if (arg.getName().equals("cursor"))
carg = arg;
else
params.add(arg);
if ((carg != null)) {
params.clear();;
String[] parts = getSingleValue(carg).split(":");
params.add(new Argument("search-id", new StringValue(parts[0])));
params.add(new Argument("search-offset", new StringValue(parts[1])));
}
Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
SearchWrapper bndWrapper = new SearchWrapper(field.getName(), bnd);
Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
}
private String getSingleValue(Argument arg) throws EGraphQLException {
List<Value> vl = resolveValues(arg, 1);
if (vl.size() == 0)
return "";
return vl.get(0).toString();
}
private List<Value> resolveValues(Argument arg) throws EGraphQLException {
return resolveValues(arg, -1, "");
}
private List<Value> resolveValues(Argument arg, int max) throws EGraphQLException {
return resolveValues(arg, max, "");
}
private List<Value> resolveValues(Argument arg, int max, String vars) throws EGraphQLException {
List<Value> result = new ArrayList<Value>();
for (Value v : arg.getValues()) {
if (! (v instanceof VariableValue))
result.add(v);
else {
if (vars.contains(":"+v.toString()+":"))
throw new EGraphQLException("Recursive reference to variable "+v.toString());
Argument a = workingVariables.get(v.toString());
if (a == null)
throw new EGraphQLException("No value found for variable \""+v.toString()+"\" in \""+arg.getName()+"\"");
List<Value> vl = resolveValues(a, -1, vars+":"+v.toString()+":");
result.addAll(vl);
}
}
if ((max != -1 && result.size() > max))
throw new EGraphQLException("Only "+Integer.toString(max)+" values are allowed for \""+arg.getName()+"\", but "+Integer.toString(result.size())+" enoucntered");
return result;
}
public Object getAppInfo() {
return appInfo;
}
public void setAppInfo(Object appInfo) {
this.appInfo = appInfo;
}
public Resource getFocus() {
return focus;
}
@Override
public void setFocus(IBaseResource focus) {
this.focus = (Resource) focus;
}
public Package getGraphQL() {
return graphQL;
}
@Override
public void setGraphQL(Package graphQL) {
this.graphQL = graphQL;
}
public ObjectValue getOutput() {
return output;
}
public IGraphQLStorageServices getServices() {
return services;
}
@Override
public void setServices(IGraphQLStorageServices services) {
this.services = services;
}
//
//{ GraphQLSearchWrapper }
//
//constructor GraphQLSearchWrapper.Create(bundle : Bundle);
//var
// s : String;
//{
// inherited Create;
// FBundle = bundle;
// s = bundle_List.Matches["self"];
// FParseMap = TParseMap.create(s.Substring(s.IndexOf("?")+1));
//}
//
//destructor GraphQLSearchWrapper.Destroy;
//{
// FParseMap.free;
// FBundle.Free;
// inherited;
//}
//
//function GraphQLSearchWrapper.extractLink(name: String): String;
//var
// s : String;
// pm : TParseMap;
//{
// s = FBundle_List.Matches[name];
// if (s == "")
// result = null
// else
// {
// pm = TParseMap.create(s.Substring(s.IndexOf("?")+1));
// try
// result = String.Create(pm.GetVar("search-id")+":"+pm.GetVar("search-offset"));
// finally
// pm.Free;
// }
// }
//}
//
//function GraphQLSearchWrapper.extractParam(name: String; int : boolean): Base;
//var
// s : String;
//{
// s = FParseMap.GetVar(name);
// if (s == "")
// result = null
// else if (int)
// result = Integer.Create(s)
// else
// result = String.Create(s);
//}
//
//function GraphQLSearchWrapper.fhirType(): String;
//{
// result = "*Connection";
//}
//
// // http://test.fhir.org/r4/Patient?_format==text/xhtml&search-id==77c97e03-8a6c-415f-a63d-11c80cf73f&&active==true&_sort==_id&search-offset==50&_count==50
//
//function GraphQLSearchWrapper.getPropertyValue(propName: string): Property;
//var
// list : List<GraphQLSearchEdge>;
// be : BundleEntry;
//{
// if (propName == "first")
// result = Property.Create(self, propname, "string", false, String, extractLink("first"))
// else if (propName == "previous")
// result = Property.Create(self, propname, "string", false, String, extractLink("previous"))
// else if (propName == "next")
// result = Property.Create(self, propname, "string", false, String, extractLink("next"))
// else if (propName == "last")
// result = Property.Create(self, propname, "string", false, String, extractLink("last"))
// else if (propName == "count")
// result = Property.Create(self, propname, "integer", false, String, FBundle.totalElement)
// else if (propName == "offset")
// result = Property.Create(self, propname, "integer", false, Integer, extractParam("search-offset", true))
// else if (propName == "pagesize")
// result = Property.Create(self, propname, "integer", false, Integer, extractParam("_count", true))
// else if (propName == "edges")
// {
// list = ArrayList<GraphQLSearchEdge>();
// try
// for be in FBundle.getEntry() do
// list.add(GraphQLSearchEdge.create(be));
// result = Property.Create(self, propname, "integer", true, Integer, List<Base>(list));
// finally
// list.Free;
// }
// }
// else
// result = null;
//}
//
//private void GraphQLSearchWrapper.SetBundle(const Value: Bundle);
//{
// FBundle.Free;
// FBundle = Value;
//}
//
//{ GraphQLSearchEdge }
//
//constructor GraphQLSearchEdge.Create(entry: BundleEntry);
//{
// inherited Create;
// FEntry = entry;
//}
//
//destructor GraphQLSearchEdge.Destroy;
//{
// FEntry.Free;
// inherited;
//}
//
//function GraphQLSearchEdge.fhirType(): String;
//{
// result = "*Edge";
//}
//
//function GraphQLSearchEdge.getPropertyValue(propName: string): Property;
//{
// if (propName == "mode")
// {
// if (FEntry.search != null)
// result = Property.Create(self, propname, "code", false, Enum, FEntry.search.modeElement)
// else
// result = Property.Create(self, propname, "code", false, Enum, Base(null));
// }
// else if (propName == "score")
// {
// if (FEntry.search != null)
// result = Property.Create(self, propname, "decimal", false, Decimal, FEntry.search.scoreElement)
// else
// result = Property.Create(self, propname, "decimal", false, Decimal, Base(null));
// }
// else if (propName == "resource")
// result = Property.Create(self, propname, "resource", false, Resource, FEntry.getResource())
// else
// result = null;
//}
//
//private void GraphQLSearchEdge.SetEntry(const Value: BundleEntry);
//{
// FEntry.Free;
// FEntry = value;
//}
//
}

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

580
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/GraphQLEngine.java
View File

@ -21,6 +21,18 @@ package org.hl7.fhir.r4.utils;
*/
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.*;
import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
import org.hl7.fhir.utilities.graphql.Package;
import org.hl7.fhir.utilities.graphql.Operation.OperationType;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.ArrayList;
@ -28,239 +40,41 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.model.BackboneElement;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.Element;
import org.hl7.fhir.r4.model.ExpressionNode;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Property;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.utils.GraphQLEngine.IGraphQLStorageServices.ReferenceResolution;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
import org.hl7.fhir.utilities.graphql.Directive;
import org.hl7.fhir.utilities.graphql.EGraphEngine;
import org.hl7.fhir.utilities.graphql.EGraphQLException;
import org.hl7.fhir.utilities.graphql.Field;
import org.hl7.fhir.utilities.graphql.Fragment;
import org.hl7.fhir.utilities.graphql.NameValue;
import org.hl7.fhir.utilities.graphql.NumberValue;
import org.hl7.fhir.utilities.graphql.ObjectValue;
import org.hl7.fhir.utilities.graphql.Operation;
import org.hl7.fhir.utilities.graphql.Operation.OperationType;
import org.hl7.fhir.utilities.graphql.Package;
import org.hl7.fhir.utilities.graphql.Selection;
import org.hl7.fhir.utilities.graphql.StringValue;
import org.hl7.fhir.utilities.graphql.Value;
import org.hl7.fhir.utilities.graphql.Variable;
import org.hl7.fhir.utilities.graphql.VariableValue;
import static org.hl7.fhir.utilities.graphql.IGraphQLStorageServices.ReferenceResolution;
public class GraphQLEngine {
public class SearchEdge extends Base {
public class GraphQLEngine implements IGraphQLEngine {
private BundleEntryComponent be;
private String type;
public SearchEdge(String type, BundleEntryComponent be) {
this.type = type;
this.be = be;
}
@Override
public String fhirType() {
return type;
}
@Override
protected void listChildren(List<Property> result) {
throw new Error("Not Implemented");
}
@Override
public String getIdBase() {
throw new Error("Not Implemented");
}
@Override
public void setIdBase(String value) {
throw new Error("Not Implemented");
}
@Override
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
switch (_hash) {
case 3357091: /*mode*/ return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasMode() ? be.getSearch().getModeElement() : null);
case 109264530: /*score*/ return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasScore() ? be.getSearch().getScoreElement() : null);
case -341064690: /*resource*/ return new Property(_name, "resource", "n/a", 0, 1, be.hasResource() ? be.getResource() : null);
default: return super.getNamedProperty(_hash, _name, _checkValid);
}
}
}
public class SearchWrapper extends Base {
private Bundle bnd;
private String type;
private Map<String, String> map;
public SearchWrapper(String type, Bundle bnd) throws FHIRException {
this.type = type;
this.bnd = bnd;
for (BundleLinkComponent bl : bnd.getLink())
if (bl.getRelation().equals("self"))
map = parseURL(bl.getUrl());
}
@Override
public String fhirType() {
return type;
}
@Override
protected void listChildren(List<Property> result) {
throw new Error("Not Implemented");
}
@Override
public String getIdBase() {
throw new Error("Not Implemented");
}
@Override
public void setIdBase(String value) {
throw new Error("Not Implemented");
}
@Override
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
switch (_hash) {
case 97440432: /*first*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case -1273775369: /*previous*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 3377907: /*next*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 3314326: /*last*/ return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 94851343: /*count*/ return new Property(_name, "integer", "n/a", 0, 1, bnd.getTotalElement());
case -1019779949:/*offset*/ return new Property(_name, "integer", "n/a", 0, 1, extractParam("search-offset"));
case 860381968: /*pagesize*/ return new Property(_name, "integer", "n/a", 0, 1, extractParam("_count"));
case 96356950: /*edges*/ return new Property(_name, "edge", "n/a", 0, Integer.MAX_VALUE, getEdges());
default: return super.getNamedProperty(_hash, _name, _checkValid);
}
}
private List<Base> getEdges() {
List<Base> list = new ArrayList<>();
for (BundleEntryComponent be : bnd.getEntry())
list.add(new SearchEdge(type.substring(0, type.length()-10)+"Edge", be));
return list;
}
private Base extractParam(String name) throws FHIRException {
return map != null ? new IntegerType(map.get(name)) : null;
}
private Map<String, String> parseURL(String url) throws FHIRException {
try {
Map<String, String> map = new HashMap<String, String>();
String[] pairs = url.split("&");
for (String pair : pairs) {
int idx = pair.indexOf("=");
String key;
key = idx > 0 ? URLDecoder.decode(pair.substring(0, idx), "UTF-8") : pair;
String value = idx > 0 && pair.length() > idx + 1 ? URLDecoder.decode(pair.substring(idx + 1), "UTF-8") : null;
map.put(key, value);
}
return map;
} catch (UnsupportedEncodingException e) {
throw new FHIRException(e);
}
}
private Base extractLink(String _name) throws FHIRException {
for (BundleLinkComponent bl : bnd.getLink()) {
if (bl.getRelation().equals(_name)) {
Map<String, String> map = parseURL(bl.getUrl());
return new StringType(map.get("search-id")+':'+map.get("search-offset"));
}
}
return null;
}
}
public interface IGraphQLStorageServices {
public class ReferenceResolution {
private Resource targetContext;
private Resource target;
public ReferenceResolution(Resource targetContext, Resource target) {
super();
this.targetContext = targetContext;
this.target = target;
}
}
// given a reference inside a context, return what it references (including resolving internal references (e.g. start with #)
public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException;
// just get the identified resource
public Resource lookup(Object appInfo, String type, String id) throws FHIRException;
// list the matching resources. searchParams are the standard search params.
// this instanceof different to search because the server returns all matching resources, or an error. There instanceof no paging on this search
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException;
// just perform a standard search, and return the bundle as you return to the client
public Bundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException;
}
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 focus;
/**
* The package that describes the graphQL to be executed, operation name, and variables
*/
private Package graphQL;
/**
* where the output from executing the query instanceof going to go
*/
private ObjectValue output;
/**
* Application provided reference resolution services
*/
private IGraphQLStorageServices services;
// internal stuff
private Map<String, Argument> workingVariables = new HashMap<String, Argument>();
private FHIRPathEngine fpe;
private ExpressionNode magicExpression;
public GraphQLEngine(IWorkerContext context) {
super();
this.context = 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 focus;
/**
* The package that describes the graphQL to be executed, operation name, and variables
*/
private Package graphQL;
/**
* where the output from executing the query instanceof going to go
*/
private ObjectValue output;
/**
* Application provided reference resolution services
*/
private IGraphQLStorageServices services;
// internal stuff
private Map<String, Argument> workingVariables = new HashMap<String, Argument>();
private FHIRPathEngine fpe;
private ExpressionNode magicExpression;
public void execute() throws EGraphEngine, EGraphQLException, FHIRException {
if (graphQL == null)
throw new EGraphEngine("Unable to process graphql - graphql document missing");
@ -274,7 +88,7 @@ public class GraphQLEngine {
if (!Utilities.noString(graphQL.getOperationName())) {
op = graphQL.getDocument().operation(graphQL.getOperationName());
if (op == null)
throw new EGraphEngine("Unable to find operation \""+graphQL.getOperationName()+"\"");
throw new EGraphEngine("Unable to find operation \"" + graphQL.getOperationName() + "\"");
} else if ((graphQL.getDocument().getOperations().size() == 1))
op = graphQL.getDocument().getOperations().get(0);
else
@ -293,9 +107,9 @@ public class GraphQLEngine {
private boolean checkBooleanDirective(Directive dir) throws EGraphQLException {
if (dir.getArguments().size() != 1)
throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
throw new EGraphQLException("Unable to process @" + dir.getName() + ": expected a single argument \"if\"");
if (!dir.getArguments().get(0).getName().equals("if"))
throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
throw new EGraphQLException("Unable to process @" + dir.getName() + ": expected a single argument \"if\"");
List<Value> vl = resolveValues(dir.getArguments().get(0), 1);
return vl.get(0).toString().equals("true");
}
@ -314,9 +128,8 @@ public class GraphQLEngine {
include = dir;
else
throw new EGraphQLException("Duplicate @include directives");
}
else if (!Utilities.existsInList(dir.getName(), "flatten", "first", "singleton", "slice"))
throw new EGraphQLException("Directive \""+dir.getName()+"\" instanceof not recognised");
} else if (!Utilities.existsInList(dir.getName(), "flatten", "first", "singleton", "slice"))
throw new EGraphQLException("Directive \"" + dir.getName() + "\" instanceof not recognised");
}
if ((skip != null && include != null))
throw new EGraphQLException("Cannot mix @skip and @include directives");
@ -332,7 +145,7 @@ public class GraphQLEngine {
}
private boolean targetTypeOk(List<Argument> arguments, Resource dest) throws EGraphQLException {
private boolean targetTypeOk(List<Argument> arguments, IBaseResource dest) throws EGraphQLException {
List<String> list = new ArrayList<String>();
for (Argument arg : arguments) {
if ((arg.getName().equals("type"))) {
@ -350,12 +163,12 @@ public class GraphQLEngine {
private boolean hasExtensions(Base obj) {
if (obj instanceof BackboneElement)
return ((BackboneElement) obj).getExtension().size() > 0 || ((BackboneElement) obj).getModifierExtension().size() > 0;
else if (obj instanceof DomainResource)
return ((DomainResource)obj).getExtension().size() > 0 || ((DomainResource)obj).getModifierExtension().size() > 0;
else if (obj instanceof Element)
return ((Element)obj).getExtension().size() > 0;
else
return false;
else if (obj instanceof DomainResource)
return ((DomainResource) obj).getExtension().size() > 0 || ((DomainResource) obj).getModifierExtension().size() > 0;
else if (obj instanceof Element)
return ((Element) obj).getExtension().size() > 0;
else
return false;
}
private boolean passesExtensionMode(Base obj, boolean extensionMode) {
@ -378,9 +191,9 @@ public class GraphQLEngine {
if ((vl.size() != 1))
throw new EGraphQLException("Incorrect number of arguments");
if (values.get(0).isPrimitive())
throw new EGraphQLException("Attempt to use a filter ("+arg.getName()+") on a primtive type ("+prop.getTypeCode()+")");
throw new EGraphQLException("Attempt to use a filter (" + arg.getName() + ") on a primtive type (" + prop.getTypeCode() + ")");
if ((arg.getName().equals("fhirpath")))
fp.append(" and "+vl.get(0).toString());
fp.append(" and " + vl.get(0).toString());
else if ((arg.getName().equals("_count")))
count = Integer.valueOf(vl.get(0).toString());
else if ((arg.getName().equals("_offset")))
@ -388,8 +201,8 @@ public class GraphQLEngine {
else {
Property p = values.get(0).getNamedProperty(arg.getName());
if (p == null)
throw new EGraphQLException("Attempt to use an unknown filter ("+arg.getName()+") on a type ("+prop.getTypeCode()+")");
fp.append(" and "+arg.getName()+" = '"+vl.get(0).toString()+"'");
throw new EGraphQLException("Attempt to use an unknown filter (" + arg.getName() + ") on a type (" + prop.getTypeCode() + ")");
fp.append(" and " + arg.getName() + " = '" + vl.get(0).toString() + "'");
}
}
int i = 0;
@ -403,18 +216,19 @@ public class GraphQLEngine {
break;
}
i++;
} else {
ExpressionNode node = fpe.parse(fp.toString().substring(5));
for (Base v : values) {
if ((i >= offset) && passesExtensionMode(v, extensionMode) && fpe.evaluateToBoolean(null, context, v, node)) {
result.add(v);
t++;
if (t >= count)
break;
}
i++;
}
}
else {
ExpressionNode node = fpe.parse(fp.toString().substring(5));
for (Base v : values) {
if ((i >= offset) && passesExtensionMode(v, extensionMode) && fpe.evaluateToBoolean(null, context, v, node)) {
result.add(v);
t++;
if (t >= count)
break;
}
i++;
}
}
}
return result;
}
@ -436,18 +250,18 @@ public class GraphQLEngine {
return result;
}
private List<Resource> filterResources(Argument fhirpath, List<Resource> list) throws EGraphQLException, FHIRException {
private List<Resource> filterResources(Argument fhirpath, List<IBaseResource> list) throws EGraphQLException, FHIRException {
List<Resource> result = new ArrayList<Resource>();
if (list.size() > 0) {
if ((fhirpath == null))
for (Resource v : list)
result.add(v);
for (IBaseResource v : list)
result.add((Resource) v);
else {
FHIRPathEngine fpe = new FHIRPathEngine(context);
ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
for (Resource v : list)
if (fpe.evaluateToBoolean(null, v, v, node))
result.add(v);
for (IBaseResource v : list)
if (fpe.evaluateToBoolean(null, (Resource) v, (Base) v, node))
result.add((Resource) v);
}
}
return result;
@ -475,23 +289,23 @@ public class GraphQLEngine {
if (sel.getField().hasDirective("flatten")) // special: instruction to drop this node...
il = prop.isList() && !sel.getField().hasDirective("first");
else if (sel.getField().hasDirective("first")) {
if (expression != null)
if (expression != null)
throw new FHIRException("You cannot mix @slice and @first");
arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), inheritedList));
arg = target.addField(sel.getField().getAlias() + suffix, listStatus(sel.getField(), inheritedList));
} else if (expression == null)
arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
arg = target.addField(sel.getField().getAlias() + suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
int index = 0;
for (Base value : values) {
String ss = "";
if (expression != null) {
if (expression == magicExpression)
ss = suffix+'.'+Integer.toString(index);
ss = suffix + '.' + Integer.toString(index);
else
ss = suffix+'.'+fpe.evaluateToString(null, null, null, value, expression);
if (!sel.getField().hasDirective("flatten"))
arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
arg = target.addField(sel.getField().getAlias() + suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
}
if (value.isPrimitive() && !extensionMode) {
@ -518,7 +332,7 @@ public class GraphQLEngine {
private void processVariables(Operation op) throws EGraphQLException {
for (Variable varRef : op.getVariables()) {
Argument varDef = null;
for (Argument v : graphQL.getVariables())
for (Argument v : graphQL.getVariables())
if (v.getName().equals(varRef.getName()))
varDef = v;
if (varDef != null)
@ -537,7 +351,7 @@ public class GraphQLEngine {
private boolean isResourceName(String name, String suffix) {
if (!name.endsWith(suffix))
return false;
name = name.substring(0, name.length()-suffix.length());
name = name.substring(0, name.length() - suffix.length());
return context.getResourceNamesAsSet().contains(name);
}
@ -560,10 +374,10 @@ public class GraphQLEngine {
else if (isResourceName(sel.getField().getName(), "Connection") && (source instanceof Resource))
processReverseReferenceSearch((Resource) source, sel.getField(), target, inheritedList, suffix);
else
throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
throw new EGraphQLException("Unknown property " + sel.getField().getName() + " on " + source.fhirType());
} else {
if (!isPrimitive(prop.getTypeCode()) && sel.getField().getName().startsWith("_"))
throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
throw new EGraphQLException("Unknown property " + sel.getField().getName() + " on " + source.fhirType());
List<Base> vl = filter(context, prop, sel.getField().getArguments(), prop.getValues(), sel.getField().getName().startsWith("_"));
if (!vl.isEmpty())
@ -574,13 +388,13 @@ public class GraphQLEngine {
if (checkDirectives(sel.getInlineFragment().getDirectives())) {
if (Utilities.noString(sel.getInlineFragment().getTypeCondition()))
throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
if (source.fhirType().equals(sel.getInlineFragment().getTypeCondition()))
if (source.fhirType().equals(sel.getInlineFragment().getTypeCondition()))
processObject(context, source, target, sel.getInlineFragment().getSelectionSet(), inheritedList, suffix);
}
} else if (checkDirectives(sel.getFragmentSpread().getDirectives())) {
Fragment fragment = graphQL.getDocument().fragment(sel.getFragmentSpread().getName());
if (fragment == null)
throw new EGraphQLException("Unable to resolve fragment "+sel.getFragmentSpread().getName());
throw new EGraphQLException("Unable to resolve fragment " + sel.getFragmentSpread().getName());
if (Utilities.noString(fragment.getTypeCondition()))
throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
@ -609,15 +423,14 @@ public class GraphQLEngine {
Reference ref = (Reference) source;
ReferenceResolution res = services.lookup(appInfo, context, ref);
if (res != null) {
if (targetTypeOk(field.getArguments(), res.target)) {
if (targetTypeOk(field.getArguments(), res.getTarget())) {
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
processObject((Resource) res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
}
}
else if (!hasArgument(field.getArguments(), "optional", "true"))
throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
} else if (!hasArgument(field.getArguments(), "optional", "true"))
throw new EGraphQLException("Unable to resolve reference to " + ref.getReference());
}
private void processCanonicalReference(Resource context, Base source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
@ -629,15 +442,14 @@ public class GraphQLEngine {
Reference ref = new Reference(source.primitiveValue());
ReferenceResolution res = services.lookup(appInfo, context, ref);
if (res != null) {
if (targetTypeOk(field.getArguments(), res.target)) {
if (targetTypeOk(field.getArguments(), res.getTarget())) {
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
processObject((Resource) res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
}
}
else if (!hasArgument(field.getArguments(), "optional", "true"))
throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
} else if (!hasArgument(field.getArguments(), "optional", "true"))
throw new EGraphQLException("Unable to resolve reference to " + ref.getReference());
}
private ArgumentListStatus listStatus(Field field, boolean isList) {
@ -652,7 +464,7 @@ public class GraphQLEngine {
private void processReverseReferenceList(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<Resource> list = new ArrayList<Resource>();
List<IBaseResource> list = new ArrayList<>();
List<Argument> params = new ArrayList<Argument>();
Argument parg = null;
for (Argument a : field.getArguments())
@ -667,14 +479,14 @@ public class GraphQLEngine {
Argument arg = new Argument();
params.add(arg);
arg.setName(getSingleValue(parg));
arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
arg.addValue(new StringValue(source.fhirType() + "/" + source.getId()));
services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
arg = null;
ObjectValue obj = null;
List<Resource> vl = filterResources(field.argument("fhirpath"), list);
if (!vl.isEmpty()) {
arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
arg = target.addField(field.getAlias() + suffix, listStatus(field, true));
for (Resource v : vl) {
obj = new ObjectValue();
arg.addValue(obj);
@ -682,7 +494,7 @@ public class GraphQLEngine {
}
}
}
private void processReverseReferenceSearch(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
@ -700,10 +512,10 @@ public class GraphQLEngine {
Argument arg = new Argument();
params.add(arg);
arg.setName(getSingleValue(parg));
arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
arg.addValue(new StringValue(source.fhirType() + "/" + source.getId()));
Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length() - 10), params);
Base bndWrapper = new SearchWrapper(field.getName(), bnd);
arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
arg = target.addField(field.getAlias() + suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
@ -732,13 +544,13 @@ public class GraphQLEngine {
if ((arg.getName().equals("id")))
id = getSingleValue(arg);
else
throw new EGraphQLException("Unknown/invalid parameter "+arg.getName());
throw new EGraphQLException("Unknown/invalid parameter " + arg.getName());
if (Utilities.noString(id))
throw new EGraphQLException("No id found");
Resource res = services.lookup(appInfo, field.getName(), id);
Resource res = (Resource) services.lookup(appInfo, field.getName(), id);
if (res == null)
throw new EGraphQLException("Resource "+field.getName()+"/"+id+" not found");
Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
throw new EGraphQLException("Resource " + field.getName() + "/" + id + " not found");
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(res, res, obj, field.getSelectionSet(), inheritedList, suffix);
@ -747,14 +559,14 @@ public class GraphQLEngine {
private void processSearchSimple(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<Resource> list = new ArrayList<Resource>();
List<IBaseResource> list = new ArrayList<>();
services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), field.getArguments(), list);
Argument arg = null;
ObjectValue obj = null;
List<Resource> vl = filterResources(field.argument("fhirpath"), list);
if (!vl.isEmpty()) {
arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
arg = target.addField(field.getAlias() + suffix, listStatus(field, true));
for (Resource v : vl) {
obj = new ObjectValue();
arg.addValue(obj);
@ -762,27 +574,28 @@ public class GraphQLEngine {
}
}
}
private void processSearchFull(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<Argument> params = new ArrayList<Argument>();
Argument carg = null;
for ( Argument arg : field.getArguments())
for (Argument arg : field.getArguments())
if (arg.getName().equals("cursor"))
carg = arg;
else
params.add(arg);
if ((carg != null)) {
params.clear();;
params.clear();
;
String[] parts = getSingleValue(carg).split(":");
params.add(new Argument("search-id", new StringValue(parts[0])));
params.add(new Argument("search-offset", new StringValue(parts[1])));
}
Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length() - 10), params);
SearchWrapper bndWrapper = new SearchWrapper(field.getName(), bnd);
Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
@ -798,34 +611,31 @@ public class GraphQLEngine {
private List<Value> resolveValues(Argument arg) throws EGraphQLException {
return resolveValues(arg, -1, "");
}
private List<Value> resolveValues(Argument arg, int max) throws EGraphQLException {
return resolveValues(arg, max, "");
}
private List<Value> resolveValues(Argument arg, int max, String vars) throws EGraphQLException {
List<Value> result = new ArrayList<Value>();
for (Value v : arg.getValues()) {
if (! (v instanceof VariableValue))
if (!(v instanceof VariableValue))
result.add(v);
else {
if (vars.contains(":"+v.toString()+":"))
throw new EGraphQLException("Recursive reference to variable "+v.toString());
if (vars.contains(":" + v.toString() + ":"))
throw new EGraphQLException("Recursive reference to variable " + v.toString());
Argument a = workingVariables.get(v.toString());
if (a == null)
throw new EGraphQLException("No value found for variable \""+v.toString()+"\" in \""+arg.getName()+"\"");
List<Value> vl = resolveValues(a, -1, vars+":"+v.toString()+":");
throw new EGraphQLException("No value found for variable \"" + v.toString() + "\" in \"" + arg.getName() + "\"");
List<Value> vl = resolveValues(a, -1, vars + ":" + v.toString() + ":");
result.addAll(vl);
}
}
if ((max != -1 && result.size() > max))
throw new EGraphQLException("Only "+Integer.toString(max)+" values are allowed for \""+arg.getName()+"\", but "+Integer.toString(result.size())+" enoucntered");
throw new EGraphQLException("Only " + Integer.toString(max) + " values are allowed for \"" + arg.getName() + "\", but " + Integer.toString(result.size()) + " enoucntered");
return result;
}
public Object getAppInfo() {
return appInfo;
}
@ -838,14 +648,16 @@ public class GraphQLEngine {
return focus;
}
public void setFocus(Resource focus) {
this.focus = focus;
@Override
public void setFocus(IBaseResource focus) {
this.focus = (Resource) focus;
}
public Package getGraphQL() {
return graphQL;
}
@Override
public void setGraphQL(Package graphQL) {
this.graphQL = graphQL;
}
@ -858,10 +670,154 @@ public class GraphQLEngine {
return services;
}
@Override
public void setServices(IGraphQLStorageServices services) {
this.services = services;
}
public static class SearchEdge extends Base {
private BundleEntryComponent be;
private String type;
SearchEdge(String type, BundleEntryComponent be) {
this.type = type;
this.be = be;
}
@Override
public String fhirType() {
return type;
}
@Override
protected void listChildren(List<Property> result) {
throw new Error("Not Implemented");
}
@Override
public String getIdBase() {
throw new Error("Not Implemented");
}
@Override
public void setIdBase(String value) {
throw new Error("Not Implemented");
}
@Override
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
switch (_hash) {
case 3357091: /*mode*/
return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasMode() ? be.getSearch().getModeElement() : null);
case 109264530: /*score*/
return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasScore() ? be.getSearch().getScoreElement() : null);
case -341064690: /*resource*/
return new Property(_name, "resource", "n/a", 0, 1, be.hasResource() ? be.getResource() : null);
default:
return super.getNamedProperty(_hash, _name, _checkValid);
}
}
}
public static class SearchWrapper extends Base {
private Bundle bnd;
private String type;
private Map<String, String> map;
SearchWrapper(String type, Bundle bnd) throws FHIRException {
this.type = type;
this.bnd = bnd;
for (BundleLinkComponent bl : bnd.getLink())
if (bl.getRelation().equals("self"))
map = parseURL(bl.getUrl());
}
@Override
public String fhirType() {
return type;
}
@Override
protected void listChildren(List<Property> result) {
throw new Error("Not Implemented");
}
@Override
public String getIdBase() {
throw new Error("Not Implemented");
}
@Override
public void setIdBase(String value) {
throw new Error("Not Implemented");
}
@Override
public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
switch (_hash) {
case 97440432: /*first*/
return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case -1273775369: /*previous*/
return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 3377907: /*next*/
return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 3314326: /*last*/
return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
case 94851343: /*count*/
return new Property(_name, "integer", "n/a", 0, 1, bnd.getTotalElement());
case -1019779949:/*offset*/
return new Property(_name, "integer", "n/a", 0, 1, extractParam("search-offset"));
case 860381968: /*pagesize*/
return new Property(_name, "integer", "n/a", 0, 1, extractParam("_count"));
case 96356950: /*edges*/
return new Property(_name, "edge", "n/a", 0, Integer.MAX_VALUE, getEdges());
default:
return super.getNamedProperty(_hash, _name, _checkValid);
}
}
private List<Base> getEdges() {
List<Base> list = new ArrayList<>();
for (BundleEntryComponent be : bnd.getEntry())
list.add(new SearchEdge(type.substring(0, type.length() - 10) + "Edge", be));
return list;
}
private Base extractParam(String name) throws FHIRException {
return map != null ? new IntegerType(map.get(name)) : null;
}
private Map<String, String> parseURL(String url) throws FHIRException {
try {
Map<String, String> map = new HashMap<String, String>();
String[] pairs = url.split("&");
for (String pair : pairs) {
int idx = pair.indexOf("=");
String key;
key = idx > 0 ? URLDecoder.decode(pair.substring(0, idx), "UTF-8") : pair;
String value = idx > 0 && pair.length() > idx + 1 ? URLDecoder.decode(pair.substring(idx + 1), "UTF-8") : null;
map.put(key, value);
}
return map;
} catch (UnsupportedEncodingException e) {
throw new FHIRException(e);
}
}
private Base extractLink(String _name) throws FHIRException {
for (BundleLinkComponent bl : bnd.getLink()) {
if (bl.getRelation().equals(_name)) {
Map<String, String> map = parseURL(bl.getUrl());
return new StringType(map.get("search-id") + ':' + map.get("search-offset"));
}
}
return null;
}
}
//
//{ GraphQLSearchWrapper }

40
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/GraphQLEngineTests.java
View File

@ -1,32 +1,22 @@
package org.hl7.fhir.r4.test;
import static org.junit.Assert.assertTrue;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.r4.model.Bundle.SearchEntryMode;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.GraphQLEngine;
import org.hl7.fhir.r4.utils.GraphQLEngine.IGraphQLStorageServices;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.graphql.NameValue;
import org.hl7.fhir.utilities.graphql.Parser;
import org.hl7.fhir.utilities.xml.XMLUtil;
@ -38,6 +28,16 @@ import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import static org.junit.Assert.assertTrue;
@RunWith(Parameterized.class)
public class GraphQLEngineTests implements IGraphQLStorageServices {
@ -127,18 +127,18 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
}
@Override
public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException {
public ReferenceResolution lookup(Object appInfo, IBaseResource context, IBaseReference reference) throws FHIRException {
try {
if (reference.getReference().startsWith("#")) {
if (!(context instanceof DomainResource))
if (reference.getReferenceElement().isLocal()) {
if (!(context instanceof DomainResource))
return null;
for (Resource r : ((DomainResource)context).getContained()) {
if (('#'+r.getId()).equals(reference.getReference())) {
if (('#'+r.getId()).equals(reference.getReferenceElement().getValue())) {
return new ReferenceResolution(context, r);
}
}
} else {
String[] parts = reference.getReference().split("/");
String[] parts = reference.getReferenceElement().getValue().split("/");
String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase()+'-'+parts[1].toLowerCase()+".xml");
if (new File(filename).exists())
return new ReferenceResolution(null, new XmlParser().parse(new FileInputStream(filename)));
@ -150,7 +150,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
}
@Override
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException {
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
try {
if (type.equals("Condition"))
matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("condition-example.xml"))));

2
org.hl7.fhir.r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

133
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLEngine.java
View File

@ -21,6 +21,18 @@ package org.hl7.fhir.r5.utils;
*/
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.*;
import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
import org.hl7.fhir.utilities.graphql.Package;
import org.hl7.fhir.utilities.graphql.Operation.OperationType;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.ArrayList;
@ -28,51 +40,16 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.BackboneElement;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Element;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.Property;
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.r5.utils.GraphQLEngine.IGraphQLStorageServices.ReferenceResolution;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
import org.hl7.fhir.utilities.graphql.Directive;
import org.hl7.fhir.utilities.graphql.EGraphEngine;
import org.hl7.fhir.utilities.graphql.EGraphQLException;
import org.hl7.fhir.utilities.graphql.Field;
import org.hl7.fhir.utilities.graphql.Fragment;
import org.hl7.fhir.utilities.graphql.NameValue;
import org.hl7.fhir.utilities.graphql.NumberValue;
import org.hl7.fhir.utilities.graphql.ObjectValue;
import org.hl7.fhir.utilities.graphql.Operation;
import org.hl7.fhir.utilities.graphql.Operation.OperationType;
import org.hl7.fhir.utilities.graphql.Package;
import org.hl7.fhir.utilities.graphql.Selection;
import org.hl7.fhir.utilities.graphql.StringValue;
import org.hl7.fhir.utilities.graphql.Value;
import org.hl7.fhir.utilities.graphql.Variable;
import org.hl7.fhir.utilities.graphql.VariableValue;
import static org.hl7.fhir.utilities.graphql.IGraphQLStorageServices.ReferenceResolution;
public class GraphQLEngine {
public class GraphQLEngine implements IGraphQLEngine {
public class SearchEdge extends Base {
public static class SearchEdge extends Base {
private BundleEntryComponent be;
private String type;
public SearchEdge(String type, BundleEntryComponent be) {
SearchEdge(String type, BundleEntryComponent be) {
this.type = type;
this.be = be;
}
@ -107,13 +84,13 @@ public class GraphQLEngine {
}
}
public class SearchWrapper extends Base {
public static class SearchWrapper extends Base {
private Bundle bnd;
private String type;
private Map<String, String> map;
public SearchWrapper(String type, Bundle bnd) throws FHIRException {
SearchWrapper(String type, Bundle bnd) throws FHIRException {
this.type = type;
this.bnd = bnd;
for (BundleLinkComponent bl : bnd.getLink())
@ -159,7 +136,7 @@ public class GraphQLEngine {
private List<Base> getEdges() {
List<Base> list = new ArrayList<>();
for (BundleEntryComponent be : bnd.getEntry())
list.add(new SearchEdge(type.substring(0, type.length()-10)+"Edge", be));
list.add(new SearchEdge(type.substring(0, type.length() - 10) + "Edge", be));
return list;
}
@ -195,32 +172,6 @@ public class GraphQLEngine {
}
}
public interface IGraphQLStorageServices {
public class ReferenceResolution {
private Resource targetContext;
private Resource target;
public ReferenceResolution(Resource targetContext, Resource target) {
super();
this.targetContext = targetContext;
this.target = target;
}
}
// given a reference inside a context, return what it references (including resolving internal references (e.g. start with #)
public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException;
// just get the identified resource
public Resource lookup(Object appInfo, String type, String id) throws FHIRException;
// list the matching resources. searchParams are the standard search params.
// this instanceof different to search because the server returns all matching resources, or an error. There instanceof no paging on this search
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException;
// just perform a standard search, and return the bundle as you return to the client
public Bundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException;
}
private IWorkerContext context;
@ -260,7 +211,8 @@ public class GraphQLEngine {
private FHIRPathEngine fpe;
private ExpressionNode magicExpression;
@Override
public void execute() throws EGraphEngine, EGraphQLException, FHIRException {
if (graphQL == null)
throw new EGraphEngine("Unable to process graphql - graphql document missing");
@ -332,7 +284,7 @@ public class GraphQLEngine {
}
private boolean targetTypeOk(List<Argument> arguments, Resource dest) throws EGraphQLException {
private boolean targetTypeOk(List<Argument> arguments, IBaseResource dest) throws EGraphQLException {
List<String> list = new ArrayList<String>();
for (Argument arg : arguments) {
if ((arg.getName().equals("type"))) {
@ -436,18 +388,18 @@ public class GraphQLEngine {
return result;
}
private List<Resource> filterResources(Argument fhirpath, List<Resource> list) throws EGraphQLException, FHIRException {
private List<Resource> filterResources(Argument fhirpath, List<IBaseResource> list) throws EGraphQLException, FHIRException {
List<Resource> result = new ArrayList<Resource>();
if (list.size() > 0) {
if ((fhirpath == null))
for (Resource v : list)
result.add(v);
for (IBaseResource v : list)
result.add((Resource) v);
else {
FHIRPathEngine fpe = new FHIRPathEngine(context);
ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
for (Resource v : list)
if (fpe.evaluateToBoolean(null, v, v, node))
result.add(v);
for (IBaseResource v : list)
if (fpe.evaluateToBoolean(null, (Resource)v, (Base) v, node))
result.add((Resource) v);
}
}
return result;
@ -609,11 +561,11 @@ public class GraphQLEngine {
Reference ref = (Reference) source;
ReferenceResolution res = services.lookup(appInfo, context, ref);
if (res != null) {
if (targetTypeOk(field.getArguments(), res.target)) {
if (targetTypeOk(field.getArguments(), res.getTarget())) {
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
}
}
else if (!hasArgument(field.getArguments(), "optional", "true"))
@ -629,11 +581,11 @@ public class GraphQLEngine {
Reference ref = new Reference(source.primitiveValue());
ReferenceResolution res = services.lookup(appInfo, context, ref);
if (res != null) {
if (targetTypeOk(field.getArguments(), res.target)) {
if (targetTypeOk(field.getArguments(), res.getTarget())) {
Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
ObjectValue obj = new ObjectValue();
arg.addValue(obj);
processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
}
}
else if (!hasArgument(field.getArguments(), "optional", "true"))
@ -652,8 +604,8 @@ public class GraphQLEngine {
private void processReverseReferenceList(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<Resource> list = new ArrayList<Resource>();
List<Argument> params = new ArrayList<Argument>();
List<IBaseResource> list = new ArrayList<>();
List<Argument> params = new ArrayList<>();
Argument parg = null;
for (Argument a : field.getArguments())
if (!(a.getName().equals("_reference")))
@ -701,7 +653,7 @@ public class GraphQLEngine {
params.add(arg);
arg.setName(getSingleValue(parg));
arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
Base bndWrapper = new SearchWrapper(field.getName(), bnd);
arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
@ -735,7 +687,7 @@ public class GraphQLEngine {
throw new EGraphQLException("Unknown/invalid parameter "+arg.getName());
if (Utilities.noString(id))
throw new EGraphQLException("No id found");
Resource res = services.lookup(appInfo, field.getName(), id);
Resource res = (Resource) services.lookup(appInfo, field.getName(), id);
if (res == null)
throw new EGraphQLException("Resource "+field.getName()+"/"+id+" not found");
Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
@ -747,7 +699,7 @@ public class GraphQLEngine {
private void processSearchSimple(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
if (services == null)
throw new EGraphQLException("Resource Referencing services not provided");
List<Resource> list = new ArrayList<Resource>();
List<IBaseResource> list = new ArrayList<>();
services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), field.getArguments(), list);
Argument arg = null;
ObjectValue obj = null;
@ -780,7 +732,7 @@ public class GraphQLEngine {
params.add(new Argument("search-offset", new StringValue(parts[1])));
}
Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
SearchWrapper bndWrapper = new SearchWrapper(field.getName(), bnd);
Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
ObjectValue obj = new ObjectValue();
@ -830,6 +782,7 @@ public class GraphQLEngine {
return appInfo;
}
@Override
public void setAppInfo(Object appInfo) {
this.appInfo = appInfo;
}
@ -838,18 +791,21 @@ public class GraphQLEngine {
return focus;
}
public void setFocus(Resource focus) {
this.focus = focus;
@Override
public void setFocus(IBaseResource focus) {
this.focus = (Resource) focus;
}
public Package getGraphQL() {
return graphQL;
}
@Override
public void setGraphQL(Package graphQL) {
this.graphQL = graphQL;
}
@Override
public ObjectValue getOutput() {
return output;
}
@ -858,6 +814,7 @@ public class GraphQLEngine {
return services;
}
@Override
public void setServices(IGraphQLStorageServices services) {
this.services = services;
}

39
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/GraphQLEngineTests.java
View File

@ -1,32 +1,21 @@
package org.hl7.fhir.r5.test;
import static org.junit.Assert.assertTrue;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.r5.model.Bundle.SearchEntryMode;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.GraphQLEngine;
import org.hl7.fhir.r5.utils.GraphQLEngine.IGraphQLStorageServices;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.graphql.NameValue;
import org.hl7.fhir.utilities.graphql.Parser;
import org.hl7.fhir.utilities.xml.XMLUtil;
@ -38,6 +27,16 @@ import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import static org.junit.Assert.assertTrue;
@RunWith(Parameterized.class)
public class GraphQLEngineTests implements IGraphQLStorageServices {
@ -127,18 +126,18 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
}
@Override
public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException {
public ReferenceResolution lookup(Object appInfo, IBaseResource context, IBaseReference reference) throws FHIRException {
try {
if (reference.getReference().startsWith("#")) {
if (reference.getReferenceElement().isLocal()) {
if (!(context instanceof DomainResource))
return null;
for (Resource r : ((DomainResource)context).getContained()) {
if (('#'+r.getId()).equals(reference.getReference())) {
if (('#'+r.getId()).equals(reference.getReferenceElement().getValue())) {
return new ReferenceResolution(context, r);
}
}
} else {
String[] parts = reference.getReference().split("/");
String[] parts = reference.getReferenceElement().getValue().split("/");
String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase()+'-'+parts[1].toLowerCase()+".xml");
if (new File(filename).exists())
return new ReferenceResolution(null, new XmlParser().parse(new FileInputStream(filename)));
@ -150,7 +149,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
}
@Override
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException {
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
try {
if (type.equals("Condition"))
matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("condition-example.xml"))));

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

39
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/graphql/IGraphQLEngine.java Normal file
View File

@ -0,0 +1,39 @@
package org.hl7.fhir.utilities.graphql;
/*-
* #%L
* org.hl7.fhir.utilities
* %%
* Copyright (C) 2014 - 2019 Health Level 7
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
public interface IGraphQLEngine {
void execute() throws EGraphEngine, EGraphQLException, FHIRException;
ObjectValue getOutput();
void setAppInfo(Object appInfo);
void setFocus(IBaseResource focus);
void setGraphQL(Package graphQL);
void setServices(IGraphQLStorageServices services);
}

73
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/graphql/IGraphQLStorageServices.java Normal file
View File

@ -0,0 +1,73 @@
package org.hl7.fhir.utilities.graphql;
/*-
* #%L
* org.hl7.fhir.utilities
* %%
* Copyright (C) 2014 - 2019 Health Level 7
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.List;
public interface IGraphQLStorageServices {
/**
* given a reference inside a context, return what it references (including resolving internal references (e.g. start with #)
*/
ReferenceResolution lookup(Object appInfo, IBaseResource context, IBaseReference reference) throws FHIRException;
/**
* just get the identified resource
*/
IBaseResource lookup(Object appInfo, String type, String id) throws FHIRException;
/**
* list the matching resources. searchParams are the standard search params.
* this instanceof different to search because the server returns all matching resources, or an error. There instanceof no paging on this search
*/
void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException;
/**
* just perform a standard search, and return the bundle as you return to the client
*/
IBaseBundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException;
class ReferenceResolution {
private IBaseResource targetContext;
private IBaseResource target;
public ReferenceResolution(IBaseResource targetContext, IBaseResource target) {
super();
this.targetContext = targetContext;
this.target = target;
}
public IBaseResource getTargetContext() {
return targetContext;
}
public IBaseResource getTarget() {
return target;
}
}
}

2
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

22
org.hl7.fhir.validation.cli/src/main/java/Marker.java Normal file
View File

@ -0,0 +1,22 @@
/*-
* #%L
* org.hl7.fhir.validation.cli
* %%
* Copyright (C) 2014 - 2019 Health Level 7
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public class Marker {
// This class is just here to force a javadoc build in order to satisfy maven central
}

2
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

6
pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>3.8.0-SNAPSHOT</version>
<version>4.0.0</version>
</parent>
<!--
@ -13,10 +13,10 @@
each other. It is fine to bump the point version of this POM without affecting
HAPI FHIR.
-->
<version>3.8.24-SNAPSHOT</version>
<version>4.0.1-SNAPSHOT</version>
<properties>
<hapi_fhir_version>4.0.0-SNAPSHOT</hapi_fhir_version>
<hapi_fhir_version>4.0.0</hapi_fhir_version>
</properties>
<artifactId>org.hl7.fhir.core</artifactId>