Merge branch 'release' into merge_branch
This commit is contained in:
Mark Iantorno
GitHub
commit
f5455bb9e9
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@ -1,7 +1,8 @@
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* Override extension methods in BackboneElement to look in modifierExtensions as well as extensions
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* Override extension methods in BackboneElement to look in modifierExtensions as well as extensions
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* First draft of Profile Comparison tools (org.hl7.fhir.r5.comparison)
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* First draft of Profile Comparison tools (org.hl7.fhir.r5.comparison)
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* Improved error messages when snapshot generation fails when slicing something that doesn't repeat
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* Improved error messages when snapshot generation fails when slicing something that doesn't repeat
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* Improvements for CDA round-tripping (XML esacping issues, xsi:type related issues, namespacing issues)
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* Improvements for CDA round-tripping (XML esacping issues, xsi:type related issues, namespacing issues)
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* Fix bug rendering DiagnosticReports with multiple categories
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* Fix bug rendering DiagnosticReports with multiple categories
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* adjust check on Attachment to only be an warning (when no meaningful content exists)
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* adjust check on Attachment to only be an warning (when no meaningful content exists)
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* add security check mode to Validator
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* add security check mode to Validator
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@ -1,212 +1,213 @@
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package org.hl7.fhir.r5.comparison;
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package org.hl7.fhir.r5.comparison;
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import java.io.FileOutputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashMap;
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import java.util.List;
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import java.util.List;
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import java.util.Map;
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import java.util.Map;
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import java.util.Set;
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import java.util.Set;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.PathEngineException;
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import org.hl7.fhir.exceptions.PathEngineException;
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import org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison;
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import org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison;
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import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
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import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
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import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
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import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
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import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
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import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
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import org.hl7.fhir.r5.conformance.ProfileUtilities;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.conformance.ProfileUtilities;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.model.Base;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
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import org.hl7.fhir.r5.model.Base;
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import org.hl7.fhir.r5.model.StringType;
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import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
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import org.hl7.fhir.r5.model.Tuple;
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import org.hl7.fhir.r5.model.StringType;
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import org.hl7.fhir.r5.model.TypeDetails;
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import org.hl7.fhir.r5.model.Tuple;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
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import org.hl7.fhir.r5.model.TypeDetails;
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import org.hl7.fhir.r5.utils.LiquidEngine;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;
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import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.r5.utils.LiquidEngine;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;
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import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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public class ComparisonRenderer implements IEvaluationContext {
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import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
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private IWorkerContext context;
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public class ComparisonRenderer implements IEvaluationContext {
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private ComparisonSession session;
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private Map<String, String> templates = new HashMap<>();
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private IWorkerContext context;
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private String folder;
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private ComparisonSession session;
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private Map<String, String> templates = new HashMap<>();
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public ComparisonRenderer(IWorkerContext context, String folder, ComparisonSession session) {
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private String folder;
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super();
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this.context = context;
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public ComparisonRenderer(IWorkerContext context, String folder, ComparisonSession session) {
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this.folder = folder;
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super();
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this.session = session;
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this.context = context;
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}
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this.folder = folder;
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this.session = session;
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public Map<String, String> getTemplates() {
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}
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return templates;
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}
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public Map<String, String> getTemplates() {
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return templates;
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public void render() throws IOException {
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}
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dumpBinaries();
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StringBuilder b = new StringBuilder();
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public void render() throws IOException {
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dumpBinaries();
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for (String id : sorted(session.getCompares().keySet())) {
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StringBuilder b = new StringBuilder();
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ResourceComparison comp = session.getCompares().get(id);
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renderComparison(id, comp);
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for (String id : sorted(session.getCompares().keySet())) {
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b.append("<li><a href=\""+comp.getId()+".html\">"+Utilities.escapeXml(comp.summary())+"</a></li>\r\n");
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ResourceComparison comp = session.getCompares().get(id);
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}
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renderComparison(id, comp);
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Map<String, Base> vars = new HashMap<>();
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b.append("<li><a href=\""+comp.getId()+".html\">"+Utilities.escapeXml(comp.summary())+"</a></li>\r\n");
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CodeSystemComparer cs = new CodeSystemComparer(session);
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}
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vars.put("title", new StringType(session.getTitle()));
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Map<String, Base> vars = new HashMap<>();
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vars.put("list", new StringType(b.toString()));
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CodeSystemComparer cs = new CodeSystemComparer(session);
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String template = templates.get("Index");
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vars.put("title", new StringType(session.getTitle()));
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String cnt = processTemplate(template, "CodeSystem", vars);
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vars.put("list", new StringType(b.toString()));
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TextFile.stringToFile(cnt, file("index.html"));
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String template = templates.get("Index");
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}
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String cnt = processTemplate(template, "CodeSystem", vars);
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TextFile.stringToFile(cnt, file("index.html"));
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private List<String> sorted(Set<String> keySet) {
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}
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List<String> list = new ArrayList<>();
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list.addAll(keySet);
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private List<String> sorted(Set<String> keySet) {
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Collections.sort(list);
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List<String> list = new ArrayList<>();
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return list;
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list.addAll(keySet);
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}
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Collections.sort(list);
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return list;
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private void dumpBinaries() throws IOException {
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}
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for (String k : context.getBinaries().keySet()) {
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TextFile.bytesToFile(context.getBinaries().get(k), Utilities.path(folder, k));
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private void dumpBinaries() throws IOException {
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}
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for (String k : context.getBinaries().keySet()) {
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TextFile.bytesToFile(context.getBinaries().get(k), Utilities.path(folder, k));
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}
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}
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}
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private void renderComparison(String id, ResourceComparison comp) throws IOException {
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if (comp instanceof ProfileComparison) {
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private void renderComparison(String id, ResourceComparison comp) throws IOException {
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renderProfile(id, (ProfileComparison) comp);
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if (comp instanceof ProfileComparison) {
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} else if (comp instanceof ValueSetComparison) {
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renderProfile(id, (ProfileComparison) comp);
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renderValueSet(id, (ValueSetComparison) comp);
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} else if (comp instanceof ValueSetComparison) {
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} else if (comp instanceof CodeSystemComparison) {
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renderValueSet(id, (ValueSetComparison) comp);
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renderCodeSystem(id, (CodeSystemComparison) comp);
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} else if (comp instanceof CodeSystemComparison) {
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}
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renderCodeSystem(id, (CodeSystemComparison) comp);
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}
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}
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}
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private void renderCodeSystem(String id, CodeSystemComparison comp) throws IOException {
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String template = templates.get("CodeSystem");
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private void renderCodeSystem(String id, CodeSystemComparison comp) throws IOException {
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Map<String, Base> vars = new HashMap<>();
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String template = templates.get("CodeSystem");
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CodeSystemComparer cs = new CodeSystemComparer(session);
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Map<String, Base> vars = new HashMap<>();
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vars.put("left", new StringType(comp.getLeft().present()));
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CodeSystemComparer cs = new CodeSystemComparer(session);
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vars.put("right", new StringType(comp.getRight().present()));
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vars.put("left", new StringType(comp.getLeft().present()));
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vars.put("leftId", new StringType(comp.getLeft().getId()));
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vars.put("right", new StringType(comp.getRight().present()));
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vars.put("rightId", new StringType(comp.getRight().getId()));
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vars.put("leftId", new StringType(comp.getLeft().getId()));
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vars.put("leftUrl", new StringType(comp.getLeft().getUrl()));
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vars.put("rightId", new StringType(comp.getRight().getId()));
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vars.put("rightUrl", new StringType(comp.getRight().getUrl()));
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vars.put("leftUrl", new StringType(comp.getLeft().getUrl()));
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vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
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vars.put("rightUrl", new StringType(comp.getRight().getUrl()));
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vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
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vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
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vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
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vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
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String cnt = processTemplate(template, "CodeSystem", vars);
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vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
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TextFile.stringToFile(cnt, file(comp.getId()+".html"));
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String cnt = processTemplate(template, "CodeSystem", vars);
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
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TextFile.stringToFile(cnt, file(comp.getId()+".html"));
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
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}
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
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}
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private String file(String name) throws IOException {
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return Utilities.path(folder, name);
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private String file(String name) throws IOException {
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}
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return Utilities.path(folder, name);
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}
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private void renderValueSet(String id, ValueSetComparison comp) throws FHIRException, IOException {
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String template = templates.get("ValueSet");
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private void renderValueSet(String id, ValueSetComparison comp) throws FHIRException, IOException {
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Map<String, Base> vars = new HashMap<>();
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String template = templates.get("ValueSet");
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ValueSetComparer cs = new ValueSetComparer(session);
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Map<String, Base> vars = new HashMap<>();
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||||||
vars.put("left", new StringType(comp.getLeft().present()));
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ValueSetComparer cs = new ValueSetComparer(session);
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||||||
vars.put("right", new StringType(comp.getRight().present()));
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vars.put("left", new StringType(comp.getLeft().present()));
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||||||
vars.put("leftId", new StringType(comp.getLeft().getId()));
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vars.put("right", new StringType(comp.getRight().present()));
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vars.put("rightId", new StringType(comp.getRight().getId()));
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vars.put("leftId", new StringType(comp.getLeft().getId()));
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vars.put("leftUrl", new StringType(comp.getLeft().getUrl()));
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vars.put("rightId", new StringType(comp.getRight().getId()));
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||||||
vars.put("rightUrl", new StringType(comp.getRight().getUrl()));
|
vars.put("leftUrl", new StringType(comp.getLeft().getUrl()));
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||||||
vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
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vars.put("rightUrl", new StringType(comp.getRight().getUrl()));
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vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
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vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
|
||||||
vars.put("compose", new StringType(new XhtmlComposer(true).compose(cs.renderCompose(comp, "", ""))));
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vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
|
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vars.put("expansion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
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vars.put("compose", new StringType(new XhtmlComposer(true).compose(cs.renderCompose(comp, "", ""))));
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String cnt = processTemplate(template, "ValueSet", vars);
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vars.put("expansion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
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TextFile.stringToFile(cnt, file(comp.getId()+".html"));
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String cnt = processTemplate(template, "ValueSet", vars);
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new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
|
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
|
||||||
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
|
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
|
||||||
}
|
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
|
||||||
|
}
|
||||||
private void renderProfile(String id, ProfileComparison comp) throws IOException {
|
|
||||||
String template = templates.get("Profile");
|
private void renderProfile(String id, ProfileComparison comp) throws IOException {
|
||||||
Map<String, Base> vars = new HashMap<>();
|
String template = templates.get("Profile");
|
||||||
ProfileComparer cs = new ProfileComparer(session, new ProfileUtilities(session.getContext(), null, null));
|
Map<String, Base> vars = new HashMap<>();
|
||||||
vars.put("left", new StringType(comp.getLeft().present()));
|
ProfileComparer cs = new ProfileComparer(session, new ProfileUtilities(session.getContext(), null, null));
|
||||||
vars.put("right", new StringType(comp.getRight().present()));
|
vars.put("left", new StringType(comp.getLeft().present()));
|
||||||
vars.put("leftId", new StringType(comp.getLeft().getId()));
|
vars.put("right", new StringType(comp.getRight().present()));
|
||||||
vars.put("rightId", new StringType(comp.getRight().getId()));
|
vars.put("leftId", new StringType(comp.getLeft().getId()));
|
||||||
vars.put("leftUrl", new StringType(comp.getLeft().getUrl()));
|
vars.put("rightId", new StringType(comp.getRight().getId()));
|
||||||
vars.put("rightUrl", new StringType(comp.getRight().getUrl()));
|
vars.put("leftUrl", new StringType(comp.getLeft().getUrl()));
|
||||||
vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
|
vars.put("rightUrl", new StringType(comp.getRight().getUrl()));
|
||||||
vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
|
vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
|
||||||
vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
|
vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
|
||||||
String cnt = processTemplate(template, "CodeSystem", vars);
|
vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
|
||||||
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
|
String cnt = processTemplate(template, "CodeSystem", vars);
|
||||||
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
|
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
|
||||||
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
|
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-union.json")), comp.getUnion());
|
||||||
}
|
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
|
||||||
|
}
|
||||||
private String processTemplate(String template, String name, Map<String, Base> vars) {
|
|
||||||
LiquidEngine engine = new LiquidEngine(context, this);
|
private String processTemplate(String template, String name, Map<String, Base> vars) {
|
||||||
LiquidDocument doc = engine.parse(template, name+".template");
|
LiquidEngine engine = new LiquidEngine(context, this);
|
||||||
return engine.evaluate(doc, Tuple.fromMap(vars), vars);
|
LiquidDocument doc = engine.parse(template, name+".template");
|
||||||
}
|
return engine.evaluate(doc, Tuple.fromMap(vars), vars);
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
|
@Override
|
||||||
@SuppressWarnings("unchecked")
|
public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
|
||||||
Map<String, Base> vars = (Map<String, Base>) appContext;
|
@SuppressWarnings("unchecked")
|
||||||
return vars.get(name);
|
Map<String, Base> vars = (Map<String, Base>) appContext;
|
||||||
}
|
return vars.get(name);
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
|
@Override
|
||||||
@SuppressWarnings("unchecked")
|
public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
|
||||||
Map<String, Base> vars = (Map<String, Base>) appContext;
|
@SuppressWarnings("unchecked")
|
||||||
Base b = vars.get(name);
|
Map<String, Base> vars = (Map<String, Base>) appContext;
|
||||||
return new TypeDetails(CollectionStatus.SINGLETON, b == null ? "Base" : b.fhirType());
|
Base b = vars.get(name);
|
||||||
}
|
return new TypeDetails(CollectionStatus.SINGLETON, b == null ? "Base" : b.fhirType());
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public boolean log(String argument, List<Base> focus) {
|
@Override
|
||||||
return false;
|
public boolean log(String argument, List<Base> focus) {
|
||||||
}
|
return false;
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public FunctionDetails resolveFunction(String functionName) {
|
@Override
|
||||||
return null;
|
public FunctionDetails resolveFunction(String functionName) {
|
||||||
}
|
return null;
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
|
@Override
|
||||||
return null;
|
public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
|
||||||
}
|
return null;
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
|
@Override
|
||||||
return null;
|
public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
|
||||||
}
|
return null;
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public Base resolveReference(Object appContext, String url, Base refContext) throws FHIRException {
|
@Override
|
||||||
return null;
|
public Base resolveReference(Object appContext, String url, Base refContext) throws FHIRException {
|
||||||
}
|
return null;
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
|
@Override
|
||||||
return false;
|
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
|
||||||
}
|
return false;
|
||||||
|
}
|
||||||
@Override
|
|
||||||
public ValueSet resolveValueSet(Object appContext, String url) {
|
@Override
|
||||||
return null;
|
public ValueSet resolveValueSet(Object appContext, String url) {
|
||||||
}
|
return null;
|
||||||
|
}
|
||||||
}
|
|
||||||
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,122 +1,114 @@
|
||||||
package org.hl7.fhir.r5.comparison;
|
package org.hl7.fhir.r5.comparison;
|
||||||
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
import java.util.UUID;
|
import java.util.UUID;
|
||||||
|
|
||||||
import org.hl7.fhir.exceptions.DefinitionException;
|
import org.hl7.fhir.exceptions.DefinitionException;
|
||||||
import org.hl7.fhir.exceptions.FHIRException;
|
import org.hl7.fhir.exceptions.FHIRException;
|
||||||
import org.hl7.fhir.exceptions.FHIRFormatError;
|
import org.hl7.fhir.exceptions.FHIRFormatError;
|
||||||
import org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison;
|
import org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison;
|
||||||
import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
|
import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
|
||||||
import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
|
import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
|
||||||
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
|
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
|
||||||
import org.hl7.fhir.r5.conformance.ProfileUtilities;
|
import org.hl7.fhir.r5.conformance.ProfileUtilities;
|
||||||
import org.hl7.fhir.r5.context.IWorkerContext;
|
import org.hl7.fhir.r5.context.IWorkerContext;
|
||||||
import org.hl7.fhir.r5.model.CanonicalResource;
|
import org.hl7.fhir.r5.model.CanonicalResource;
|
||||||
import org.hl7.fhir.r5.model.CodeSystem;
|
import org.hl7.fhir.r5.model.CodeSystem;
|
||||||
import org.hl7.fhir.r5.model.Resource;
|
import org.hl7.fhir.r5.model.Resource;
|
||||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||||
import org.hl7.fhir.r5.model.ValueSet;
|
import org.hl7.fhir.r5.model.ValueSet;
|
||||||
import org.hl7.fhir.utilities.Utilities;
|
import org.hl7.fhir.utilities.Utilities;
|
||||||
|
|
||||||
public class ComparisonSession {
|
public class ComparisonSession {
|
||||||
|
|
||||||
private Map<String, ResourceComparison> compares = new HashMap<>();
|
private Map<String, ResourceComparison> compares = new HashMap<>();
|
||||||
private IWorkerContext context;
|
private IWorkerContext context;
|
||||||
private String sessiondId;
|
private String sessiondId;
|
||||||
private int count;
|
private int count;
|
||||||
private boolean debug;
|
private boolean debug;
|
||||||
private String title;
|
private String title;
|
||||||
|
|
||||||
public ComparisonSession(IWorkerContext context, String title) {
|
public ComparisonSession(IWorkerContext context, String title) {
|
||||||
super();
|
super();
|
||||||
this.context = context;
|
this.context = context;
|
||||||
this.sessiondId = UUID.randomUUID().toString().toLowerCase();
|
this.sessiondId = UUID.randomUUID().toString().toLowerCase();
|
||||||
this.title = title;
|
this.title = title;
|
||||||
// debug = true;
|
// debug = true;
|
||||||
}
|
}
|
||||||
|
|
||||||
public IWorkerContext getContext() {
|
public IWorkerContext getContext() {
|
||||||
return context;
|
return context;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public String getTitle() {
|
||||||
|
return title;
|
||||||
public String getTitle() {
|
}
|
||||||
return title;
|
|
||||||
}
|
public ResourceComparison compare(String left, String right) throws DefinitionException, FHIRFormatError, IOException {
|
||||||
|
CanonicalResource l = (CanonicalResource) context.fetchResource(Resource.class, left);
|
||||||
public ResourceComparison compare(String left, String right) throws DefinitionException, FHIRFormatError, IOException {
|
if (l == null) {
|
||||||
CanonicalResource l = (CanonicalResource) context.fetchResource(Resource.class, left);
|
throw new DefinitionException("Unable to resolve "+left);
|
||||||
if (l == null) {
|
}
|
||||||
throw new DefinitionException("Unable to resolve "+left);
|
CanonicalResource r = (CanonicalResource) context.fetchResource(Resource.class, right);
|
||||||
}
|
if (r == null) {
|
||||||
CanonicalResource r = (CanonicalResource) context.fetchResource(Resource.class, right);
|
throw new DefinitionException("Unable to resolve "+right);
|
||||||
if (r == null) {
|
}
|
||||||
throw new DefinitionException("Unable to resolve "+right);
|
return compare(l, r);
|
||||||
}
|
}
|
||||||
return compare(l, r);
|
|
||||||
}
|
public ResourceComparison compare(CanonicalResource left, CanonicalResource right) throws DefinitionException, FHIRFormatError, IOException {
|
||||||
|
String key = key(left.getUrl(), left.getVersion(), right.getUrl(), right.getVersion());
|
||||||
public ResourceComparison compare(CanonicalResource left, CanonicalResource right) throws DefinitionException, FHIRFormatError, IOException {
|
if (compares.containsKey(key)) {
|
||||||
String key = key(left.getUrl(), left.getVersion(), right.getUrl(), right.getVersion());
|
// if null then the comparison is in progress.
|
||||||
if (compares.containsKey(key)) {
|
// this can happen when profiles refer to each other
|
||||||
// if null then the comparison is in progress.
|
return compares.get(key);
|
||||||
// this can happen when profiles refer to each other
|
}
|
||||||
return compares.get(key);
|
compares.put(key, null);
|
||||||
}
|
if (left instanceof CodeSystem && right instanceof CodeSystem) {
|
||||||
compares.put(key, null);
|
CodeSystemComparer cs = new CodeSystemComparer(this);
|
||||||
if (left instanceof CodeSystem && right instanceof CodeSystem) {
|
CodeSystemComparison csc = cs.compare((CodeSystem) left, (CodeSystem) right);
|
||||||
CodeSystemComparer cs = new CodeSystemComparer(this);
|
compares.put(key, csc);
|
||||||
CodeSystemComparison csc = cs.compare((CodeSystem) left, (CodeSystem) right);
|
return csc;
|
||||||
compares.put(key, csc);
|
} else if (left instanceof ValueSet && right instanceof ValueSet) {
|
||||||
return csc;
|
ValueSetComparer cs = new ValueSetComparer(this);
|
||||||
} else if (left instanceof ValueSet && right instanceof ValueSet) {
|
ValueSetComparison csc = cs.compare((ValueSet) left, (ValueSet) right);
|
||||||
ValueSetComparer cs = new ValueSetComparer(this);
|
compares.put(key, csc);
|
||||||
ValueSetComparison csc = cs.compare((ValueSet) left, (ValueSet) right);
|
return csc;
|
||||||
compares.put(key, csc);
|
} else if (left instanceof StructureDefinition && right instanceof StructureDefinition) {
|
||||||
return csc;
|
ProfileComparer cs = new ProfileComparer(this, new ProfileUtilities(context, null, null));
|
||||||
} else if (left instanceof StructureDefinition && right instanceof StructureDefinition) {
|
ProfileComparison csc = cs.compare((StructureDefinition) left, (StructureDefinition) right);
|
||||||
ProfileComparer cs = new ProfileComparer(this, new ProfileUtilities(context, null, null));
|
compares.put(key, csc);
|
||||||
ProfileComparison csc = cs.compare((StructureDefinition) left, (StructureDefinition) right);
|
return csc;
|
||||||
compares.put(key, csc);
|
} else {
|
||||||
return csc;
|
throw new FHIRException("Unable to compare ");
|
||||||
} else {
|
}
|
||||||
throw new FHIRException("Unable to compare ");
|
}
|
||||||
}
|
|
||||||
}
|
private String key(String urlL, String verL, String urlR, String verR) {
|
||||||
|
return urlL+"|"+verL+"||"+urlR+"|"+verR;
|
||||||
private String key(String urlL, String verL, String urlR, String verR) {
|
}
|
||||||
return urlL+"|"+verL+"||"+urlR+"|"+verR;
|
|
||||||
}
|
public void identify(CanonicalResource res) {
|
||||||
|
count++;
|
||||||
|
res.setId(sessiondId+"-"+count);
|
||||||
public void identify(CanonicalResource res) {
|
res.setUrl("http://hl7.org/fhir/comparison/"+res.fhirType()+"/"+res.getId());
|
||||||
count++;
|
}
|
||||||
res.setId(sessiondId+"-"+count);
|
|
||||||
res.setUrl("http://hl7.org/fhir/comparison/"+res.fhirType()+"/"+res.getId());
|
public void identify(ResourceComparison res) {
|
||||||
}
|
count++;
|
||||||
|
}
|
||||||
public void identify(ResourceComparison res) {
|
|
||||||
count++;
|
public boolean isDebug() {
|
||||||
}
|
return debug;
|
||||||
|
}
|
||||||
public boolean isDebug() {
|
|
||||||
return debug;
|
public void setDebug(boolean debug) {
|
||||||
}
|
this.debug = debug;
|
||||||
|
}
|
||||||
public void setDebug(boolean debug) {
|
|
||||||
this.debug = debug;
|
public Map<String, ResourceComparison> getCompares() {
|
||||||
}
|
return compares;
|
||||||
|
}
|
||||||
public Map<String, ResourceComparison> getCompares() {
|
|
||||||
return compares;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -1,117 +1,118 @@
|
||||||
package org.hl7.fhir.r5.test;
|
package org.hl7.fhir.r5.test;
|
||||||
|
|
||||||
import static org.junit.Assert.assertTrue;
|
import static org.junit.Assert.assertTrue;
|
||||||
|
|
||||||
import java.io.ByteArrayOutputStream;
|
import java.io.ByteArrayOutputStream;
|
||||||
import java.io.FileInputStream;
|
import java.io.FileInputStream;
|
||||||
import java.io.FileNotFoundException;
|
import java.io.FileNotFoundException;
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.List;
|
import java.util.ArrayList;
|
||||||
import java.util.stream.Stream;
|
import java.util.List;
|
||||||
|
import java.util.stream.Stream;
|
||||||
import javax.xml.parsers.ParserConfigurationException;
|
|
||||||
|
import javax.xml.parsers.ParserConfigurationException;
|
||||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
|
||||||
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
|
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||||
import org.hl7.fhir.r5.formats.IParser;
|
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
|
||||||
import org.hl7.fhir.r5.model.Resource;
|
import org.hl7.fhir.r5.formats.IParser;
|
||||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
import org.hl7.fhir.r5.model.Resource;
|
||||||
import org.hl7.fhir.r5.model.StructureMap;
|
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
import org.hl7.fhir.r5.model.StructureMap;
|
||||||
import org.hl7.fhir.utilities.TextFile;
|
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||||
import org.hl7.fhir.utilities.Utilities;
|
import org.hl7.fhir.utilities.TextFile;
|
||||||
import org.hl7.fhir.utilities.xml.XMLUtil;
|
import org.hl7.fhir.utilities.Utilities;
|
||||||
import org.hl7.fhir.validation.ValidationEngine;
|
import org.hl7.fhir.utilities.xml.XMLUtil;
|
||||||
import org.hl7.fhir.validation.instance.InstanceValidatorFactory;
|
import org.hl7.fhir.validation.ValidationEngine;
|
||||||
import org.junit.jupiter.api.BeforeAll;
|
|
||||||
import org.junit.jupiter.params.ParameterizedTest;
|
import org.hl7.fhir.validation.instance.InstanceValidatorFactory;
|
||||||
import org.junit.jupiter.params.provider.Arguments;
|
import org.junit.jupiter.api.BeforeAll;
|
||||||
import org.junit.jupiter.params.provider.MethodSource;
|
import org.junit.jupiter.params.ParameterizedTest;
|
||||||
import org.w3c.dom.Document;
|
import org.junit.jupiter.params.provider.Arguments;
|
||||||
import org.w3c.dom.Element;
|
import org.junit.jupiter.params.provider.MethodSource;
|
||||||
import org.xml.sax.SAXException;
|
import org.w3c.dom.Document;
|
||||||
|
import org.w3c.dom.Element;
|
||||||
public class FHIRMappingLanguageTests {
|
import org.xml.sax.SAXException;
|
||||||
|
|
||||||
private List<Resource> outputs = new ArrayList<Resource>();
|
public class FHIRMappingLanguageTests {
|
||||||
|
|
||||||
static private ValidationEngine validationEngine;
|
private List<Resource> outputs = new ArrayList<Resource>();
|
||||||
|
|
||||||
static private SimpleWorkerContext context;
|
static private ValidationEngine validationEngine;
|
||||||
|
|
||||||
public static Stream<Arguments> data()
|
static private SimpleWorkerContext context;
|
||||||
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
|
|
||||||
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "fml", "manifest.xml"));
|
public static Stream<Arguments> data()
|
||||||
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
|
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
|
||||||
List<Arguments> objects = new ArrayList<>();
|
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "fml", "manifest.xml"));
|
||||||
while (test != null && test.getNodeName().equals("test")) {
|
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
|
||||||
objects.add(Arguments.of(test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
|
List<Arguments> objects = new ArrayList<>();
|
||||||
test.getAttribute("output")));
|
while (test != null && test.getNodeName().equals("test")) {
|
||||||
test = XMLUtil.getNextSibling(test);
|
objects.add(Arguments.of(test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
|
||||||
}
|
test.getAttribute("output")));
|
||||||
return objects.stream();
|
test = XMLUtil.getNextSibling(test);
|
||||||
}
|
}
|
||||||
|
return objects.stream();
|
||||||
@BeforeAll
|
}
|
||||||
public static void setUp() throws Exception {
|
|
||||||
validationEngine = new ValidationEngine("hl7.fhir.r4.core#4.0.1");
|
@BeforeAll
|
||||||
context = validationEngine.getContext();
|
public static void setUp() throws Exception {
|
||||||
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null);
|
validationEngine = new ValidationEngine("hl7.fhir.r4.core#4.0.1");
|
||||||
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null);
|
context = validationEngine.getContext();
|
||||||
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cd.xml"), "cd.xml", null);
|
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null);
|
||||||
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ce.xml"), "ce.xml", null);
|
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null);
|
||||||
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ed.xml"), "ed.xml", null);
|
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cd.xml"), "cd.xml", null);
|
||||||
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "st.xml"), "st.xml", null);
|
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ce.xml"), "ce.xml", null);
|
||||||
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cda.xml"), "cda.xml", null);
|
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ed.xml"), "ed.xml", null);
|
||||||
for (StructureDefinition sd : context.getStructures()) {
|
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "st.xml"), "st.xml", null);
|
||||||
if (!sd.hasSnapshot()) {
|
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cda.xml"), "cda.xml", null);
|
||||||
System.out.println("generate snapshot for " + sd.getUrl());
|
for (StructureDefinition sd : context.getStructures()) {
|
||||||
context.generateSnapshot(sd, true);
|
if (!sd.hasSnapshot()) {
|
||||||
}
|
System.out.println("generate snapshot for " + sd.getUrl());
|
||||||
}
|
context.generateSnapshot(sd, true);
|
||||||
if (context.getValidatorFactory() == null) {
|
}
|
||||||
context.setValidatorFactory(new InstanceValidatorFactory());
|
}
|
||||||
}
|
if (context.getValidatorFactory() == null) {
|
||||||
}
|
context.setValidatorFactory(new InstanceValidatorFactory());
|
||||||
|
}
|
||||||
@ParameterizedTest(name = "{index}: {0}")
|
}
|
||||||
@MethodSource("data")
|
|
||||||
public void test(String name, String source, String map, String output) throws Exception {
|
@ParameterizedTest(name = "{index}: {0}")
|
||||||
|
@MethodSource("data")
|
||||||
byte[] byteSource = TestingUtilities.loadTestResourceBytes("r5", "fml", source);
|
public void test(String name, String source, String map, String output) throws Exception {
|
||||||
String stringMap = TestingUtilities.loadTestResource("r5", "fml", map);
|
|
||||||
String outputJson = TestingUtilities.loadTestResource("r5", "fml", output);
|
byte[] byteSource = TestingUtilities.loadTestResourceBytes("r5", "fml", source);
|
||||||
String fileOutputRes = TestingUtilities.tempFile("fml", output) + ".out";
|
String stringMap = TestingUtilities.loadTestResource("r5", "fml", map);
|
||||||
String fileOutputResOrig = TestingUtilities.tempFile("fml", output) + ".orig.out";
|
String outputJson = TestingUtilities.loadTestResource("r5", "fml", output);
|
||||||
ByteArrayOutputStream s = null;
|
String fileOutputRes = TestingUtilities.tempFile("fml", output) + ".out";
|
||||||
outputs.clear();
|
String fileOutputResOrig = TestingUtilities.tempFile("fml", output) + ".orig.out";
|
||||||
|
ByteArrayOutputStream s = null;
|
||||||
String msg = null;
|
outputs.clear();
|
||||||
try {
|
|
||||||
StructureMap r = new org.hl7.fhir.r5.utils.StructureMapUtilities(context).parse(stringMap, map);
|
String msg = null;
|
||||||
context.cacheResource(r);
|
try {
|
||||||
org.hl7.fhir.r5.elementmodel.Element element = validationEngine.transform(byteSource, FhirFormat.JSON, r.getUrl());
|
StructureMap r = new org.hl7.fhir.r5.utils.StructureMapUtilities(context).parse(stringMap, map);
|
||||||
s = new ByteArrayOutputStream();
|
context.cacheResource(r);
|
||||||
if (output.endsWith(".json"))
|
org.hl7.fhir.r5.elementmodel.Element element = validationEngine.transform(byteSource, FhirFormat.JSON, r.getUrl());
|
||||||
new org.hl7.fhir.r5.elementmodel.JsonParser(context).compose(element, s, IParser.OutputStyle.PRETTY, null);
|
s = new ByteArrayOutputStream();
|
||||||
else
|
if (output.endsWith(".json"))
|
||||||
new org.hl7.fhir.r5.elementmodel.XmlParser(context).compose(element, s, IParser.OutputStyle.PRETTY, null);
|
new org.hl7.fhir.r5.elementmodel.JsonParser(context).compose(element, s, IParser.OutputStyle.PRETTY, null);
|
||||||
context.dropResource(r);
|
else
|
||||||
} catch (Exception e) {
|
new org.hl7.fhir.r5.elementmodel.XmlParser(context).compose(element, s, IParser.OutputStyle.PRETTY, null);
|
||||||
assertTrue(e.getMessage(), false);
|
context.dropResource(r);
|
||||||
}
|
} catch (Exception e) {
|
||||||
if (output.endsWith("json")) {
|
assertTrue(e.getMessage(), false);
|
||||||
msg = TestingUtilities.checkJsonSrcIsSame(s.toString(), outputJson);
|
}
|
||||||
} else {
|
if (output.endsWith("json")) {
|
||||||
TextFile.bytesToFile(s.toByteArray(), fileOutputRes);
|
msg = TestingUtilities.checkJsonSrcIsSame(s.toString(), outputJson);
|
||||||
TextFile.bytesToFile(outputJson.getBytes(), fileOutputResOrig);
|
} else {
|
||||||
msg = TestingUtilities.checkXMLIsSame(new FileInputStream(fileOutputRes), new FileInputStream(fileOutputResOrig));
|
TextFile.bytesToFile(s.toByteArray(), fileOutputRes);
|
||||||
}
|
TextFile.bytesToFile(outputJson.getBytes(), fileOutputResOrig);
|
||||||
if (!Utilities.noString(msg)) {
|
msg = TestingUtilities.checkXMLIsSame(new FileInputStream(fileOutputRes), new FileInputStream(fileOutputResOrig));
|
||||||
System.out.print(s.toString());
|
}
|
||||||
}
|
if (!Utilities.noString(msg)) {
|
||||||
assertTrue(msg, Utilities.noString(msg));
|
System.out.print(s.toString());
|
||||||
}
|
}
|
||||||
|
assertTrue(msg, Utilities.noString(msg));
|
||||||
|
}
|
||||||
}
|
}
|
||||||
Loading…
Reference in New Issue