mirror of
https://github.com/hapifhir/org.hl7.fhir.core.git
synced 2025-03-05 19:09:11 +00:00
fixing broken links, and r4/r5 map testing
This commit is contained in:
Grahame Grieve
parent
b5bbe5108b
commit
824f51f82e
@ -323,48 +323,48 @@ public class AdditionalBindingsRenderer {
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boolean r5 = context == null || context.getWorker() == null ? false : VersionUtilities.isR5Plus(context.getWorker().getVersion());
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switch (purpose) {
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case "maximum":
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-maximum" : corePath+"extension-elementdefinition-maxvalueset.html", "A required binding, for use when the binding strength is 'extensible' or 'preferred'").tx("Max Binding");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-maximum" : corePath+"extension-elementdefinition-maxvalueset.html", "A required binding, for use when the binding strength is 'extensible' or 'preferred'").tx("Max Binding");
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break;
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case "minimum":
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-minimum" : corePath+"extension-elementdefinition-minvalueset.html", "The minimum allowable value set - any conformant system SHALL support all these codes").tx("Min Binding");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-minimum" : corePath+"extension-elementdefinition-minvalueset.html", "The minimum allowable value set - any conformant system SHALL support all these codes").tx("Min Binding");
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break;
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case "required" :
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-required" : corePath+"terminologies.html#strength", "Validators will check this binding (strength = required)").tx("Required Binding");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-required" : corePath+"terminologies.html#strength", "Validators will check this binding (strength = required)").tx("Required Binding");
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break;
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case "extensible" :
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-extensible" : corePath+"terminologies.html#strength", "Validators will check this binding (strength = extensible)").tx("Extensible Binding");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-extensible" : corePath+"terminologies.html#strength", "Validators will check this binding (strength = extensible)").tx("Extensible Binding");
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break;
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case "current" :
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if (r5) {
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-current" : corePath+"terminologies.html#strength", "New records are required to use this value set, but legacy records may use other codes").tx("Current Binding");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-current" : corePath+"terminologies.html#strength", "New records are required to use this value set, but legacy records may use other codes").tx("Current Binding");
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} else {
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td.span(null, "New records are required to use this value set, but legacy records may use other codes").tx("Required");
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}
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break;
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case "preferred" :
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if (r5) {
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-preferred" : corePath+"terminologies.html#strength", "This is the value set that is recommended (documentation should explain why)").tx("Preferred Binding");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-preferred" : corePath+"terminologies.html#strength", "This is the value set that is recommended (documentation should explain why)").tx("Preferred Binding");
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} else {
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td.span(null, "This is the value set that is recommended (documentation should explain why)").tx("Recommended");
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}
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break;
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case "ui" :
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if (r5) {
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-ui" : corePath+"terminologies.html#strength", "This value set is provided to user look up in a given context").tx("UI Binding");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-ui" : corePath+"terminologies.html#strength", "This value set is provided to user look up in a given context").tx("UI Binding");
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} else {
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td.span(null, "This value set is provided to user look up in a given context").tx("UI");
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}
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break;
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case "starter" :
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if (r5) {
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-starter" : corePath+"terminologies.html#strength", "This value set is a good set of codes to start with when designing your system").tx("Starter Set");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-starter" : corePath+"terminologies.html#strength", "This value set is a good set of codes to start with when designing your system").tx("Starter Set");
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} else {
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td.span(null, "This value set is a good set of codes to start with when designing your system").tx("Starter");
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}
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break;
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case "component" :
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if (r5) {
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td.ah(r5 ? "valueset-additional-binding-purpose.html#additional-binding-purpose-component" : corePath+"terminologies.html#strength", "This value set is a component of the base value set").tx("Component");
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td.ah(r5 ? corePath+"valueset-additional-binding-purpose.html#additional-binding-purpose-component" : corePath+"terminologies.html#strength", "This value set is a component of the base value set").tx("Component");
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} else {
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td.span(null, "This value set is a component of the base value set").tx("Component");
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}
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@ -243,8 +243,9 @@ public abstract class ParserBase {
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return logical;
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}
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public void setLogical(StructureDefinition logical) {
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public ParserBase setLogical(StructureDefinition logical) {
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this.logical = logical;
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return this;
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}
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}
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@ -2761,4 +2761,30 @@ public class StructureMapUtilities {
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return null;
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}
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public ResolvedGroup getGroupForUrl(StructureMap map, String url, StructureMapInputMode mode) {
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for (StructureMapGroupComponent grp : map.getGroup()) {
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if (grp.getTypeMode() != StructureMapGroupTypeMode.NULL) {
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for (StructureMapGroupInputComponent p : grp.getInput()) {
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if (mode == null || mode == p.getMode()) {
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String t = resolveInputType(p, map);
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if (url.equals(t)) {
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return new ResolvedGroup(map, grp);
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}
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}
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}
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}
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}
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return null;
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}
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public String getInputType(ResolvedGroup grp, StructureMapInputMode mode) {
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if (grp.getTargetGroup().getInput().size() != 2 || grp.getTargetGroup().getInput().get(0).getMode() == grp.getTargetGroup().getInput().get(1).getMode()) {
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return null;
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} else if (grp.getTargetGroup().getInput().get(0).getMode() == mode) {
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return resolveInputType(grp.getTargetGroup().getInput().get(0), grp.getTargetMap());
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} else {
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return resolveInputType(grp.getTargetGroup().getInput().get(1), grp.getTargetMap());
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}
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}
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}
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@ -47,7 +47,7 @@ public class ValidatorUtils {
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}
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}
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protected static IWorkerContext.IContextResourceLoader loaderForVersion(String version) {
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public static IWorkerContext.IContextResourceLoader loaderForVersion(String version) {
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if (Utilities.noString(version)) {
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return null;
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}
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@ -1,26 +1,96 @@
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package org.hl7.fhir.validation.special;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
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import org.hl7.fhir.r5.model.StructureMap;
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import org.hl7.fhir.r5.model.StructureMap.StructureMapInputMode;
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import org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader;
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import org.hl7.fhir.exceptions.DefinitionException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.r4.formats.IParser.OutputStyle;
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import org.hl7.fhir.r4.model.Resource;
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import org.hl7.fhir.r4.model.ResourceFactory;
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import org.hl7.fhir.r4.test.utils.TestingUtilities;
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import org.hl7.fhir.r5.context.SimpleWorkerContext;
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import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
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import org.hl7.fhir.r5.context.SimpleWorkerContext.SimpleWorkerContextBuilder;
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import org.hl7.fhir.r5.elementmodel.Element;
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import org.hl7.fhir.r5.utils.structuremap.ResolvedGroup;
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import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
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import org.hl7.fhir.r5.utils.structuremap.VariableMode;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.VersionUtilities;
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import org.hl7.fhir.utilities.json.JsonException;
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import org.hl7.fhir.utilities.json.model.JsonElement;
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import org.hl7.fhir.utilities.json.model.JsonObject;
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import org.hl7.fhir.utilities.json.model.JsonProperty;
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import org.hl7.fhir.utilities.json.parser.JsonParser;
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import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.npm.NpmPackage;
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import org.hl7.fhir.validation.IgLoader;
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import org.hl7.fhir.validation.ValidatorUtils;
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import org.hl7.fhir.validation.special.R4R5MapTester.Stats;
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public class R4R5MapTester {
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public class Stats {
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private Set<String> errors = new HashSet<>();
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private int total;
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private int parsed;
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private int forward;
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public void example() {
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total++;
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}
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public void parsed() {
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parsed++;
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}
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public void error(String s) {
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errors.add(s);
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}
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public void forward() {
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forward++;
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}
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public int totalCount() {
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return total;
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}
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public int parseCount() {
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return parsed;
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}
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public String summary() {
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if (errors.size() == 0) {
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return "All OK";
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} else {
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return String.join(", ", errors);
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}
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}
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public boolean ok() {
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return errors.size() == 0;
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}
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}
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private boolean saveProcess = false;
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private SimpleWorkerContext context;
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private FilesystemPackageCacheManager pcm;
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private StructureMapUtilities utils;
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@ -32,18 +102,29 @@ public class R4R5MapTester {
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new R4R5MapTester().testMaps(args[0]);
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}
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private void testMaps(String src) throws JsonException, IOException {
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public void testMaps(String src) throws JsonException, IOException {
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log("Load Test Outcomes");
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JsonObject json = JsonParser.parseObjectFromFile(Utilities.path(src, "input", "_data", "conversions.json"));
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log("Load R5");
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pcm = new FilesystemPackageCacheManager(true);
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context = new SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(pcm.loadPackage("hl7.fhir.r5.core#current"));
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log("Load Maps");
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context.loadFromPackage(pcm.loadPackage("hl7.fhir.uv.extensions#dev"), null);
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// context.loadFromPackage(pcm.loadPackage(), null);
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loadPackage("hl7.fhir.uv.extensions#dev");
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loadPackage("hl7.fhir.r4.core#4.0.1");
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loadPackage("hl7.fhir.r4b.core#4.3.0");
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log("Load R4 Examples");
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NpmPackage r4Examples = pcm.loadPackage("hl7.fhir.r4.examples");
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log("Load R4B Examples");
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NpmPackage r4bExamples = pcm.loadPackage("hl7.fhir.r4b.examples");
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utils = new StructureMapUtilities(context);
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allMaps = context.fetchResourcesByType(StructureMap.class);
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log("Resource Count = "+context.getResourceNames().size());
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log("Go. "+context.getResourceNames().size()+" types of resources");
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log("Map Count = "+allMaps.size());
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boolean changed = false;
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for (JsonProperty jp : json.getProperties()) {
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@ -53,8 +134,8 @@ public class R4R5MapTester {
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StructureDefinition sd = context.fetchTypeDefinition(rn);
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List<StructureMap> mapSrc = utils.getMapsForUrl(allMaps, sd.getUrl(), StructureMapInputMode.SOURCE);
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List<StructureMap> mapTgt = utils.getMapsForUrl(allMaps, sd.getUrl(), StructureMapInputMode.TARGET);
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changed = checkMaps(rn, o.getJsonObject("r4"), "http://hl7.org/fhir/4.0", mapSrc, mapTgt) || changed;
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changed = checkMaps(rn, o.getJsonObject("r4b"), "http://hl7.org/fhir/4.0", mapSrc, mapTgt) || changed;
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changed = checkMaps(sd, o.getJsonObject("r4"), "http://hl7.org/fhir/4.0", mapSrc, mapTgt, r4Examples) || changed;
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changed = checkMaps(sd, o.getJsonObject("r4b"), "http://hl7.org/fhir/4.3", mapSrc, mapTgt, r4bExamples) || changed;
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}
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if (changed) {
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JsonParser.compose(json, new FileOutputStream(Utilities.path(src, "input", "_data", "conversions.json")), true);
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@ -76,7 +157,15 @@ public class R4R5MapTester {
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}
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private boolean checkMaps(String rn, JsonObject json, String ns, List<StructureMap> mapSrc, List<StructureMap> mapTgt) {
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private void loadPackage(String pid) throws FHIRException, IOException {
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log("Load "+pid);
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NpmPackage npm = pcm.loadPackage(pid);
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IContextResourceLoader loader = ValidatorUtils.loaderForVersion(npm.fhirVersion());
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loader.setPatchUrls(VersionUtilities.isCorePackage(npm.id()));
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int count = context.loadFromPackage(npm, loader);
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}
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private boolean checkMaps(StructureDefinition sd, JsonObject json, String ns, List<StructureMap> mapSrc, List<StructureMap> mapTgt, NpmPackage examples) throws IOException {
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List<StructureMap> src = utils.getMapsForUrlPrefix(mapSrc, ns, StructureMapInputMode.TARGET);
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List<StructureMap> tgt = utils.getMapsForUrlPrefix(mapTgt, ns, StructureMapInputMode.SOURCE);
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if (src.size() + tgt.size() == 0) {
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@ -92,9 +181,30 @@ public class R4R5MapTester {
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isDraft = map.getStatus() == PublicationStatus.DRAFT || isDraft;
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}
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json.set("status", ""+(src.size()+tgt.size())+" Maps Defined"+(isDraft ? " (draft)" : ""));
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if (context.getResourceNames().contains(rn)) {
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json.set("testColor", "#ffcccc");
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json.set("testMessage", "To Do");
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json.set("testColor", "#ffcccc");
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if (sd.getKind() == StructureDefinitionKind.RESOURCE) {
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if (tgt.size() == 1 && src.size() == 1) {
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StructureMap tgtM = tgt.get(0);
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ResolvedGroup tgtG = utils.getGroupForUrl(tgtM, sd.getUrl(), StructureMapInputMode.TARGET);
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String tgtU = utils.getInputType(tgtG, StructureMapInputMode.SOURCE);
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assert tgtU.startsWith(ns);
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StructureMap srcM = src.get(0);
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ResolvedGroup srcG = utils.getGroupForUrl(srcM, sd.getUrl(), StructureMapInputMode.SOURCE);
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String srcU = utils.getInputType(srcG, StructureMapInputMode.TARGET);
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assert srcU.startsWith(ns);
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if (!srcU.equals(tgtU)) {
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json.set("testMessage", "Maps do not round trip to same resource ("+Utilities.tail(srcU)+" -> "+Utilities.tail(tgtU)+") - can't test");
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} else {
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StructureDefinition tsd = context.fetchResource(StructureDefinition.class, srcU);
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if (tsd == null) {
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json.set("testMessage", "Undefined type "+srcU);
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} else {
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testRoundTrips(sd, json, tgtG, srcG, tsd, examples);
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}
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}
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} else {
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json.set("testMessage", "Multiple matching maps ("+src.size()+"/"+tgt.size()+") - no tests performed");
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}
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} else {
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json.set("testColor", "#eeeeee");
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json.set("testMessage", "n/a");
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@ -103,6 +213,44 @@ public class R4R5MapTester {
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return true;
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}
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private void testRoundTrips(StructureDefinition sd, JsonObject json, ResolvedGroup tgtG, ResolvedGroup srcG, StructureDefinition tsd, NpmPackage examples) throws IOException {
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Stats stats = new Stats();
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for (String s : examples.listResources(tsd.getType())) {
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log(" Test "+examples.id()+"::"+s);
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try {
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testRoundTrip(sd, tsd, tgtG, srcG, stats, examples.load("package", s));
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} catch (Exception e) {
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log("error: "+e.getMessage());
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stats.error("Error: "+e.getMessage());
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}
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}
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json.set("total", stats.totalCount());
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json.set("parsed", stats.parseCount());
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json.set("testMessage", stats.summary());
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if (stats.ok()) {
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json.set("testColor", "#d4ffdf");
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}
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}
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private void testRoundTrip(StructureDefinition sd, StructureDefinition tsd, ResolvedGroup tgtG, ResolvedGroup srcG, Stats stats, InputStream stream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
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stats.example();
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Element r4 = new org.hl7.fhir.r5.elementmodel.JsonParser(context).setLogical(tsd).parseSingle(stream);
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stats.parsed();
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String id = r4.getIdBase();
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checkSave(id, "src.loaded", r4);
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Resource r5 = ResourceFactory.createResource(sd.getType());
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utils.transform(context, r4, tgtG.getTargetMap(), r4);
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stats.forward();
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}
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private void checkSave(String id, String state, Element e) {
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if (saveProcess) {
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// new org.hl7.fhir.r4.elementmodel.JsonParser(context).compose(r3, bso, OutputStyle.PRETTY, null);
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}
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}
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private void log(String msg) {
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System.out.println(msg);
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}
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2
pom.xml
2
pom.xml
@ -19,7 +19,7 @@
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<properties>
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<hapi_fhir_version>6.2.1</hapi_fhir_version>
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<validator_test_case_version>1.2.20</validator_test_case_version>
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<validator_test_case_version>1.2.21-SNAPSHOT</validator_test_case_version>
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<junit_jupiter_version>5.7.1</junit_jupiter_version>
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<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
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<maven_surefire_version>3.0.0-M5</maven_surefire_version>
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