mirror of
https://github.com/hapifhir/org.hl7.fhir.core.git
synced 2025-02-07 21:38:15 +00:00
upgrade tx-task in validator to handle more repackaging functionality
This commit is contained in:
Grahame Grieve
parent
cefb6f64e8
commit
462463cfb0
@ -99,6 +99,15 @@ public class CanonicalType extends UriType {
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}
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return null;
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}
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public boolean hasVersion() {
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return getValue() != null && getValue().contains("|");
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}
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public void addVersion(String version) {
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if (version != null) {
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setValue(getValue()+"|"+version);
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}
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}
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}
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@ -76,6 +76,7 @@ public abstract class JsonElement {
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return type() == JsonElementType.STRING;
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}
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public boolean isJsonNumber() {
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return type() == JsonElementType.NUMBER;
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}
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@ -471,5 +471,12 @@ public class JsonObject extends JsonElement {
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properties.clear();
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propMap.clear();
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}
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public boolean isJsonString(String name) {
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return has(name) && get(name).type() == JsonElementType.STRING;
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}
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public boolean isJsonBoolean(String name) {
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return has(name) && get(name).type() == JsonElementType.BOOLEAN;
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}
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}
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@ -3,10 +3,12 @@ package org.hl7.fhir.validation.cli.model;
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import java.io.FileInputStream;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Locale;
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import java.util.Map;
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import java.util.Objects;
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import java.util.Set;
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import com.google.gson.annotations.SerializedName;
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@ -221,7 +223,7 @@ public class CliContext {
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@JsonProperty("modeParams")
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@SerializedName("modeParams")
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private
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List<String> modeParams = new ArrayList<String>();
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Set<String> modeParams = new HashSet<String>();
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@JsonProperty("mode")
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@SerializedName("mode")
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@ -779,7 +781,7 @@ public class CliContext {
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@SerializedName("modeParams")
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@JsonProperty("modeParams")
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public List<String> getModeParams() {
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public Set<String> getModeParams() {
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return modeParams;
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}
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@ -12,11 +12,11 @@ import org.hl7.fhir.validation.cli.model.CliContext;
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import org.hl7.fhir.validation.cli.services.ValidationService;
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import org.hl7.fhir.validation.cli.utils.Display;
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import org.hl7.fhir.validation.cli.utils.EngineMode;
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import org.hl7.fhir.validation.special.ExpansionPackageGenerator;
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import org.hl7.fhir.validation.special.ExpansionPackageGenerator.ExpansionPackageGeneratorOutputType;
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import org.hl7.fhir.validation.special.ExpansionPackageGenerator.ExpansionPackageGeneratorScope;
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import org.hl7.fhir.validation.special.PackageReGenerator;
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import org.hl7.fhir.validation.special.PackageReGenerator.ExpansionPackageGeneratorOutputType;
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import org.hl7.fhir.validation.special.PackageReGenerator.ExpansionPackageGeneratorScope;
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public class TxPackTask extends ValidationEngineTask {
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public class RePackageTask extends ValidationEngineTask {
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@Override
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public String getName() {
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@ -35,7 +35,7 @@ public class TxPackTask extends ValidationEngineTask {
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@Override
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public boolean shouldExecuteTask(CliContext cliContext, String[] args) {
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return cliContext.getMode() == EngineMode.TX_PACK;
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return cliContext.getMode() == EngineMode.RE_PACKAGE;
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}
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@Override
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@ -45,7 +45,6 @@ public class TxPackTask extends ValidationEngineTask {
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@Override
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public void executeTask(ValidationService validationService, ValidationEngine validationEngine, CliContext cliContext, String[] args, TimeTracker tt, TimeTracker.Session tts) throws Exception {
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String pid = cliContext.getPackageName();
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boolean json = cliContext.getFormat() != FhirFormat.XML;
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String output = cliContext.getOutput();
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File f = ManagedFileAccess.file(output);
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@ -66,13 +65,13 @@ public class TxPackTask extends ValidationEngineTask {
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}
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if (c < args.length - 1) {
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switch (args[c+1].toLowerCase()) {
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case "ig" :
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case "ig" :
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scope = ExpansionPackageGeneratorScope.IG_ONLY;
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break;
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case "igs" :
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scope = ExpansionPackageGeneratorScope.ALL_IGS;
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break;
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case "core" :
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case "core" :
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scope = ExpansionPackageGeneratorScope.EVERYTHING;
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break;
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default:
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@ -80,11 +79,15 @@ public class TxPackTask extends ValidationEngineTask {
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}
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}
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IWorkerContext ctxt = validationEngine.getContext();
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ExpansionPackageGenerator ep = new ExpansionPackageGenerator().setContext(ctxt).setPackageId(pid).setScope(scope);
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PackageReGenerator ep = new PackageReGenerator().setContext(ctxt).setScope(scope);
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for (String s : cliContext.getIgs()) {
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ep.addPackage(s);
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}
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if (cliContext.getExpansionParameters() != null) {
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validationEngine.loadExpansionParameters(cliContext.getExpansionParameters());
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}
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ep.setOutput(output).setOutputType(t);
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ep.setOutput(output).setOutputType(t).setJson(json);
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ep.setModes(cliContext.getModeParams());
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ep.generateExpansionPackage();
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}
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}
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@ -50,7 +50,10 @@ public class Params {
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public static final String HINT_ABOUT_NON_MUST_SUPPORT = "-hintAboutNonMustSupport";
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public static final String TO_VERSION = "-to-version";
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public static final String TX_PACK = "-tx-pack";
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public static final String RE_PACK = "-re-package";
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public static final String PACKAGE_NAME = "-package-name";
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public static final String PIN = "-pin";
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public static final String EXPAND = "-expand";
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public static final String DO_NATIVE = "-do-native";
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public static final String NO_NATIVE = "-no-native";
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public static final String COMPILE = "-compile";
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@ -345,8 +348,38 @@ public class Params {
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cliContext.setPackageName(args[++i]);
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cliContext.setMode(EngineMode.CODEGEN);
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} else if (args[i].equals(TX_PACK)) {
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cliContext.setPackageName(args[++i]);
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cliContext.setMode(EngineMode.TX_PACK);
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cliContext.setMode(EngineMode.RE_PACKAGE);
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String pn = args[++i];
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if (pn != null) {
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if (pn.contains(",")) {
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for (String s : pn.split("\\,")) {
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cliContext.getIgs().add(s);
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}
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} else {
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cliContext.getIgs().add(pn);
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}
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}
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cliContext.getModeParams().add("tx");
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cliContext.getModeParams().add("expansions");
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} else if (args[i].equals(RE_PACK)) {
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cliContext.setMode(EngineMode.RE_PACKAGE);
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String pn = args[++i];
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if (pn != null) {
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if (pn.contains(",")) {
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for (String s : pn.split("\\,")) {
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cliContext.getIgs().add(s);
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}
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} else {
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cliContext.getIgs().add(pn);
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}
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}
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cliContext.getModeParams().add("tx");
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cliContext.getModeParams().add("cnt");
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cliContext.getModeParams().add("api");
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} else if (args[i].equals(PIN)) {
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cliContext.getModeParams().add("pin");
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} else if (args[i].equals(EXPAND)) {
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cliContext.getModeParams().add("expand");
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} else if (args[i].equals(DO_NATIVE)) {
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cliContext.setCanDoNative(true);
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} else if (args[i].equals(NO_NATIVE)) {
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@ -1,409 +0,0 @@
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package org.hl7.fhir.validation.special;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import org.hl7.fhir.convertors.txClient.TerminologyClientFactory;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.context.ContextUtilities;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.context.SimpleWorkerContext;
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import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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import org.hl7.fhir.r5.formats.JsonParser;
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import org.hl7.fhir.r5.formats.XmlParser;
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import org.hl7.fhir.r5.model.CanonicalType;
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import org.hl7.fhir.r5.model.ElementDefinition;
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import org.hl7.fhir.r5.model.Parameters;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpansionOutcome;
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import org.hl7.fhir.r5.utils.NPMPackageGenerator;
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import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
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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.ZipGenerator;
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import org.hl7.fhir.utilities.json.model.JsonObject;
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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.special.ExpansionPackageGenerator.TerminologyResourceEntry;
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/**
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* Given a package id, and an expansion parameters,
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* get a list of all the value sets in the package, optionally with expansions.
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* Parameters:
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*
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* - scope: this ig | all igs | all igs + core
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* - expansions: true | false
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* - output type: folder | zip | tgz
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*/
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public class ExpansionPackageGenerator {
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public static class TerminologyResourceEntry {
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public ValueSet valueSet;
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public Set<String> sources = new HashSet<>();
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public String error;
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}
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public static void main(String[] args) throws Exception {
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new ExpansionPackageGenerator()
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.setPackageId("hl7.fhir.us.davinci-alerts")
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.setJson(true)
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.setOutputType(ExpansionPackageGeneratorOutputType.TGZ)
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.setOutput("/Users/grahamegrieve/temp/vs-output.tgz")
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.generateExpansionPackage();
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}
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public enum ExpansionPackageGeneratorOutputType {
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FOLDER, ZIP, TGZ
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}
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public enum ExpansionPackageGeneratorScope {
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IG_ONLY, ALL_IGS, EVERYTHING
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}
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private String packageId;
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private Parameters expansionParameters = new Parameters();
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private ExpansionPackageGeneratorScope scope = ExpansionPackageGeneratorScope.EVERYTHING;
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private boolean expansions;
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private String output;
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private ExpansionPackageGeneratorOutputType outputType;
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private boolean hierarchical;
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private boolean json;
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private IWorkerContext context;
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public String getPackageId() {
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return packageId;
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}
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public ExpansionPackageGenerator setPackageId(String packageId) {
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this.packageId = packageId;
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return this;
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}
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public Parameters getExpansionParameters() {
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return expansionParameters;
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}
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public ExpansionPackageGenerator setExpansionParameters(Parameters expansionParameters) {
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this.expansionParameters = expansionParameters;
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return this;
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}
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public ExpansionPackageGeneratorScope getScope() {
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return scope;
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}
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public ExpansionPackageGenerator setScope(ExpansionPackageGeneratorScope scope) {
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this.scope = scope;
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return this;
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}
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public boolean isExpansions() {
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return expansions;
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}
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public ExpansionPackageGenerator setExpansions(boolean expansions) {
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this.expansions = expansions;
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return this;
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}
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public String getOutput() {
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return output;
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}
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public ExpansionPackageGenerator setOutput(String output) {
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this.output = output;
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return this;
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}
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public ExpansionPackageGeneratorOutputType getOutputType() {
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return outputType;
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}
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public ExpansionPackageGenerator setOutputType(ExpansionPackageGeneratorOutputType outputType) {
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this.outputType = outputType;
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return this;
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}
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public boolean isHierarchical() {
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return hierarchical;
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}
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public ExpansionPackageGenerator setHierarchical(boolean hierarchical) {
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this.hierarchical = hierarchical;
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return this;
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}
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public boolean isJson() {
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return json;
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}
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public ExpansionPackageGenerator setJson(boolean json) {
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this.json = json;
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return this;
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}
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public IWorkerContext getContext() {
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return context;
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}
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public ExpansionPackageGenerator setContext(IWorkerContext context) {
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this.context = context;
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return this;
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}
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private ContextUtilities cu;
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private Map<String, TerminologyResourceEntry> entries = new HashMap<>();
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public void generateExpansionPackage() throws IOException {
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if (output == null) {
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throw new Error("No output");
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}
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var npm = load();
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System.out.println("Finding ValueSets");
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for (String res : npm.listResources("StructureDefinition")) {
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StructureDefinition sd = (StructureDefinition) new JsonParser().parse(npm.loadResource(res));
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processSD(sd, npm.id());
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}
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System.out.println("Generating Expansions");
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for (String n : Utilities.sorted(entries.keySet())) {
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TerminologyResourceEntry e = entries.get(n);
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try {
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System.out.print("Generate Expansion for "+n+" ... ");
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ValueSetExpansionOutcome exp = context.expandVS(e.valueSet, true, hierarchical);
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if (exp.isOk()) {
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e.valueSet.setExpansion(exp.getValueset().getExpansion());
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System.out.println("OK");
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} else {
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e.valueSet.setExpansion(null);
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e.error = exp.getError();
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System.out.println(exp.getError());
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}
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} catch (Exception ex) {
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System.out.println("Error= "+ex.getMessage());
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e.error = ex.getMessage();
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}
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}
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System.out.println("Producing Output");
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switch (outputType) {
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case FOLDER:
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produceFolder();
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break;
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case TGZ:
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producePackage(npm);
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break;
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case ZIP:
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produceZip();
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break;
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default:
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break;
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}
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System.out.println("Done");
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}
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private void produceZip() throws IOException {
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ZipGenerator zip = new ZipGenerator(output);
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Set<String> names = new HashSet<>();
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names.add("manifest");
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if (json) {
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zip.addBytes("manifest.json", new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters), false);
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} else {
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zip.addBytes("manifest.xml", new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters), false);
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}
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StringBuilder b = new StringBuilder();
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for (String n : Utilities.sorted(entries.keySet())) {
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TerminologyResourceEntry e = entries.get(n);
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String name = e.valueSet.getIdBase();
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int i = 0;
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while (names.contains(name)) {
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i++;
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name = e.valueSet.getIdBase()+i;
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}
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names.add(name);
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if (e.error == null) {
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b.append(name+","+n+", , "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
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} else {
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b.append(name+","+n+", \""+Utilities.escapeCSV(e.error)+"\", "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
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}
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if (json) {
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zip.addBytes(name+".json", new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(e.valueSet), false);
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} else {
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zip.addBytes(name+".xml", new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(e.valueSet), false);
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}
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}
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zip.addBytes("valuesets.csv", b.toString().getBytes(StandardCharsets.UTF_8), false);
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zip.close();
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}
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private void producePackage(NpmPackage npm) throws FHIRException, IOException {
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JsonObject j = new JsonObject();
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j.add("name", npm.id()+".custom.extensions");
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j.add("version", npm.version());
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j.add("tools-version", 3);
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j.add("type", "Conformance");
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j.forceArray("fhirVersions").add(npm.fhirVersion());
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j.forceObject("dependencies").add(VersionUtilities.packageForVersion(npm.fhirVersion()), npm.fhirVersion());
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NPMPackageGenerator gen = new NPMPackageGenerator(output, j, new Date(), true);
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Set<String> names = new HashSet<>();
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names.add("manifest");
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if (json) {
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gen.addFile("package", "manifest.json", new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters));
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} else {
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gen.addFile("package", "manifest.xml", new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters));
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}
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StringBuilder b = new StringBuilder();
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for (String n : Utilities.sorted(entries.keySet())) {
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TerminologyResourceEntry e = entries.get(n);
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String name = e.valueSet.getIdBase();
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int i = 0;
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while (names.contains(name)) {
|
||||
i++;
|
||||
name = e.valueSet.getIdBase()+i;
|
||||
}
|
||||
names.add(name);
|
||||
if (e.error == null) {
|
||||
b.append(name+","+n+", , "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
} else {
|
||||
b.append(name+","+n+", \""+Utilities.escapeCSV(e.error)+"\", "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
}
|
||||
if (json) {
|
||||
gen.addFile("package",name+".json", new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(e.valueSet));
|
||||
} else {
|
||||
gen.addFile("package",name+".xml", new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(e.valueSet));
|
||||
}
|
||||
}
|
||||
gen.addFile("other","valuesets.csv", b.toString().getBytes(StandardCharsets.UTF_8));
|
||||
gen.finish();
|
||||
}
|
||||
|
||||
private void produceFolder() throws IOException {
|
||||
Utilities.createDirectory(output);
|
||||
Utilities.clearDirectory(output);
|
||||
Set<String> names = new HashSet<>();
|
||||
names.add("manifest");
|
||||
if (json) {
|
||||
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(output, "manifest.json")), expansionParameters);
|
||||
} else {
|
||||
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(output, "manifest.xml")), expansionParameters);
|
||||
}
|
||||
StringBuilder b = new StringBuilder();
|
||||
for (String n : Utilities.sorted(entries.keySet())) {
|
||||
TerminologyResourceEntry e = entries.get(n);
|
||||
String name = e.valueSet.getIdBase();
|
||||
int i = 0;
|
||||
while (names.contains(name)) {
|
||||
i++;
|
||||
name = e.valueSet.getIdBase()+i;
|
||||
}
|
||||
names.add(name);
|
||||
if (e.error == null) {
|
||||
b.append(name+","+n+", , "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
} else {
|
||||
b.append(name+","+n+", \""+Utilities.escapeCSV(e.error)+"\", "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
}
|
||||
if (json) {
|
||||
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(output, name+".json")), e.valueSet);
|
||||
} else {
|
||||
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(output, name+".xml")), e.valueSet);
|
||||
}
|
||||
}
|
||||
TextFile.stringToFile(b.toString(), Utilities.path(output, "valuesets.csv"));
|
||||
}
|
||||
|
||||
private void processSD(StructureDefinition sd, String packageId) {
|
||||
// System.out.println("Found Structure: "+sd.getVersionedUrl());
|
||||
for (ElementDefinition ed : sd.getDifferential().getElement()) {
|
||||
if (ed.hasBinding() && ed.getBinding().hasValueSet()) {
|
||||
// TerminologyResourceEntry e = new TerminologyResourceEntry();
|
||||
processValueSet(ed.getBinding().getValueSet(), packageId+":"+sd.getVersionedUrl()+"#"+ed.getId());
|
||||
}
|
||||
}
|
||||
if (scope != ExpansionPackageGeneratorScope.IG_ONLY && sd.getBaseDefinition() != null) {
|
||||
StructureDefinition bsd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
|
||||
if (!bsd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition") || scope == ExpansionPackageGeneratorScope.EVERYTHING) {
|
||||
processSD(bsd, bsd.getSourcePackage().getVID());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void processValueSet(String valueSet, String source) {
|
||||
String url = cu.pinValueSet(valueSet);
|
||||
ValueSet vs = context.fetchResource(ValueSet.class, url);
|
||||
if (vs != null) {
|
||||
TerminologyResourceEntry e = entries.get(vs.getVersionedUrl());
|
||||
if (e == null) {
|
||||
e = new TerminologyResourceEntry();
|
||||
e.sources.add(source);
|
||||
e.valueSet = vs;
|
||||
entries.put(vs.getVersionedUrl(), e);
|
||||
source = vs.getSourcePackage().getVID()+":"+vs.getVersionedUrl();
|
||||
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
|
||||
for (CanonicalType v : inc.getValueSet()) {
|
||||
if (v.hasValue()) {
|
||||
processValueSet(v.primitiveValue(), source);
|
||||
}
|
||||
}
|
||||
}
|
||||
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
|
||||
for (CanonicalType v : inc.getValueSet()) {
|
||||
if (v.hasValue()) {
|
||||
processValueSet(v.primitiveValue(), source);
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
e.sources.add(source);
|
||||
}
|
||||
|
||||
} else {
|
||||
System.out.println("Unable to resolve value set "+valueSet);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private NpmPackage load() throws IOException {
|
||||
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
|
||||
NpmPackage npm = pcm.loadPackage(packageId);
|
||||
if (context == null) {
|
||||
String v = npm.fhirVersion();
|
||||
NpmPackage core = pcm.loadPackage(VersionUtilities.packageForVersion(v));
|
||||
NpmPackage tho = pcm.loadPackage("hl7.terminology");
|
||||
System.out.println("Load FHIR from "+core.name()+"#"+core.version());
|
||||
SimpleWorkerContext ctxt = new SimpleWorkerContext.SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(core);
|
||||
TerminologyClientFactory factory = new TerminologyClientFactory(ctxt.getVersion());
|
||||
ctxt.connectToTSServer(factory, "http://tx.fhir.org", ctxt.getUserAgent(), null, true);
|
||||
var loader = new IgLoader(pcm, ctxt, ctxt.getVersion());
|
||||
loader.loadPackage(tho, true);
|
||||
loader.loadPackage(npm, true);
|
||||
context = ctxt;
|
||||
} else {
|
||||
var loader = new IgLoader(pcm, (SimpleWorkerContext) context, context.getVersion());
|
||||
loader.loadPackage(npm, true);
|
||||
}
|
||||
context.setExpansionParameters(expansionParameters);
|
||||
cu = new ContextUtilities(context);
|
||||
return npm;
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,508 @@
|
||||
package org.hl7.fhir.validation.special;
|
||||
|
||||
import java.io.FileOutputStream;
|
||||
import java.io.IOException;
|
||||
import java.io.OutputStream;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Date;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
|
||||
import org.hl7.fhir.convertors.txClient.TerminologyClientFactory;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.r5.context.ContextUtilities;
|
||||
import org.hl7.fhir.r5.context.IWorkerContext;
|
||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
|
||||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.model.Base;
|
||||
import org.hl7.fhir.r5.model.CanonicalResource;
|
||||
import org.hl7.fhir.r5.model.CanonicalType;
|
||||
import org.hl7.fhir.r5.model.CapabilityStatement;
|
||||
import org.hl7.fhir.r5.model.CodeSystem;
|
||||
import org.hl7.fhir.r5.model.ElementDefinition;
|
||||
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
|
||||
import org.hl7.fhir.r5.model.NamingSystem;
|
||||
import org.hl7.fhir.r5.model.OperationDefinition;
|
||||
import org.hl7.fhir.r5.model.Parameters;
|
||||
import org.hl7.fhir.r5.model.Property;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.model.SearchParameter;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.r5.model.ValueSet;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpansionOutcome;
|
||||
import org.hl7.fhir.r5.utils.NPMPackageGenerator;
|
||||
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.VersionUtilities;
|
||||
import org.hl7.fhir.utilities.ZipGenerator;
|
||||
import org.hl7.fhir.utilities.json.model.JsonObject;
|
||||
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage;
|
||||
import org.hl7.fhir.validation.IgLoader;
|
||||
import org.hl7.fhir.validation.special.PackageReGenerator.TerminologyResourceEntry;
|
||||
|
||||
/**
|
||||
* Given a package id, and an expansion parameters,
|
||||
* get a list of all the value sets in the package, optionally with expansions.
|
||||
* Parameters:
|
||||
*
|
||||
* - scope: this ig | all igs | all igs + core
|
||||
* - expansions: true | false
|
||||
* - output type: folder | zip | tgz
|
||||
*/
|
||||
|
||||
public class PackageReGenerator {
|
||||
|
||||
public static class TerminologyResourceEntry {
|
||||
public ValueSet valueSet;
|
||||
public Set<String> sources = new HashSet<>();
|
||||
public String error;
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
new PackageReGenerator()
|
||||
.addPackage("hl7.fhir.us.davinci-alerts")
|
||||
.setJson(true)
|
||||
.setOutputType(ExpansionPackageGeneratorOutputType.TGZ)
|
||||
.setOutput("/Users/grahamegrieve/temp/vs-output.tgz")
|
||||
.generateExpansionPackage();
|
||||
}
|
||||
|
||||
public enum ExpansionPackageGeneratorOutputType {
|
||||
FOLDER, ZIP, TGZ
|
||||
}
|
||||
|
||||
public enum ExpansionPackageGeneratorScope {
|
||||
IG_ONLY, ALL_IGS, EVERYTHING
|
||||
}
|
||||
|
||||
private List<String> packages = new ArrayList<String>();
|
||||
private Parameters expansionParameters = new Parameters();
|
||||
private ExpansionPackageGeneratorScope scope = ExpansionPackageGeneratorScope.EVERYTHING;
|
||||
private String output;
|
||||
private ExpansionPackageGeneratorOutputType outputType;
|
||||
private boolean hierarchical;
|
||||
private boolean json;
|
||||
private IWorkerContext context;
|
||||
|
||||
|
||||
public PackageReGenerator addPackage(String packageId) {
|
||||
packages.add(packageId);
|
||||
return this;
|
||||
}
|
||||
|
||||
public Parameters getExpansionParameters() {
|
||||
return expansionParameters;
|
||||
}
|
||||
|
||||
public PackageReGenerator setExpansionParameters(Parameters expansionParameters) {
|
||||
this.expansionParameters = expansionParameters;
|
||||
return this;
|
||||
}
|
||||
|
||||
public ExpansionPackageGeneratorScope getScope() {
|
||||
return scope;
|
||||
}
|
||||
|
||||
public PackageReGenerator setScope(ExpansionPackageGeneratorScope scope) {
|
||||
this.scope = scope;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getOutput() {
|
||||
return output;
|
||||
}
|
||||
|
||||
public PackageReGenerator setOutput(String output) {
|
||||
this.output = output;
|
||||
return this;
|
||||
}
|
||||
|
||||
public ExpansionPackageGeneratorOutputType getOutputType() {
|
||||
return outputType;
|
||||
}
|
||||
|
||||
public PackageReGenerator setOutputType(ExpansionPackageGeneratorOutputType outputType) {
|
||||
this.outputType = outputType;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isHierarchical() {
|
||||
return hierarchical;
|
||||
}
|
||||
|
||||
public PackageReGenerator setHierarchical(boolean hierarchical) {
|
||||
this.hierarchical = hierarchical;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isJson() {
|
||||
return json;
|
||||
}
|
||||
|
||||
public PackageReGenerator setJson(boolean json) {
|
||||
this.json = json;
|
||||
return this;
|
||||
}
|
||||
|
||||
|
||||
public IWorkerContext getContext() {
|
||||
return context;
|
||||
}
|
||||
|
||||
public PackageReGenerator setContext(IWorkerContext context) {
|
||||
this.context = context;
|
||||
return this;
|
||||
}
|
||||
|
||||
|
||||
private ContextUtilities cu;
|
||||
|
||||
private Map<String, TerminologyResourceEntry> entries = new HashMap<>();
|
||||
private Set<String> modeParams;
|
||||
private List<CanonicalResource> resources = new ArrayList<CanonicalResource>();
|
||||
|
||||
public void generateExpansionPackage() throws IOException {
|
||||
if (output == null) {
|
||||
throw new Error("No output");
|
||||
}
|
||||
|
||||
var list = load();
|
||||
for (NpmPackage npm : list) {
|
||||
if (modeParams.contains("api")) {
|
||||
System.out.println("Processing CapabilityStatements");
|
||||
for (String res : npm.listResources("CapabilityStatement")) {
|
||||
CapabilityStatement cs = (CapabilityStatement) new JsonParser().parse(npm.loadResource(res));
|
||||
processResource(cs);
|
||||
}
|
||||
System.out.println("Processing OperationDefinitions");
|
||||
for (String res : npm.listResources("OperationDefinition")) {
|
||||
OperationDefinition op = (OperationDefinition) new JsonParser().parse(npm.loadResource(res));
|
||||
processResource(op);
|
||||
}
|
||||
System.out.println("Processing SearchParameters");
|
||||
for (String res : npm.listResources("SearchParameter")) {
|
||||
SearchParameter sp = (SearchParameter) new JsonParser().parse(npm.loadResource(res));
|
||||
processResource(sp);
|
||||
}
|
||||
}
|
||||
if (modeParams.contains("tx")) {
|
||||
System.out.println("Processing CodeSystems");
|
||||
for (String res : npm.listResources("CodeSystem")) {
|
||||
CodeSystem cs = (CodeSystem) new JsonParser().parse(npm.loadResource(res));
|
||||
processResource(cs);
|
||||
}
|
||||
System.out.println("Processing ValueSets");
|
||||
for (String res : npm.listResources("ValueSet")) {
|
||||
ValueSet vs = (ValueSet) new JsonParser().parse(npm.loadResource(res));
|
||||
processResource(vs);
|
||||
}
|
||||
System.out.println("Processing NamingSystems");
|
||||
for (String res : npm.listResources("NamingSystem")) {
|
||||
NamingSystem ns = (NamingSystem) new JsonParser().parse(npm.loadResource(res));
|
||||
processResource(ns);
|
||||
}
|
||||
}
|
||||
if (modeParams.contains("cnt")) {
|
||||
System.out.println("Processing StructureDefinitions");
|
||||
for (String res : npm.listResources("StructureDefinition")) {
|
||||
StructureDefinition cs = (StructureDefinition) new JsonParser().parse(npm.loadResource(res));
|
||||
processResource(cs);
|
||||
}
|
||||
}
|
||||
System.out.println("Processing Bindings");
|
||||
for (String res : npm.listResources("StructureDefinition")) {
|
||||
StructureDefinition sd = (StructureDefinition) new JsonParser().parse(npm.loadResource(res));
|
||||
processSD(sd, npm.id());
|
||||
}
|
||||
if (modeParams.contains("expansions")) {
|
||||
System.out.println("Generating Expansions");
|
||||
for (String n : Utilities.sorted(entries.keySet())) {
|
||||
TerminologyResourceEntry e = entries.get(n);
|
||||
try {
|
||||
System.out.print("Generate Expansion for "+n+" ... ");
|
||||
ValueSetExpansionOutcome exp = context.expandVS(e.valueSet, true, hierarchical);
|
||||
if (exp.isOk()) {
|
||||
e.valueSet.setExpansion(exp.getValueset().getExpansion());
|
||||
System.out.println("OK");
|
||||
} else {
|
||||
e.valueSet.setExpansion(null);
|
||||
e.error = exp.getError();
|
||||
System.out.println(exp.getError());
|
||||
}
|
||||
} catch (Exception ex) {
|
||||
System.out.println("Error= "+ex.getMessage());
|
||||
e.error = ex.getMessage();
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
switch (outputType) {
|
||||
case FOLDER:
|
||||
produceFolder();
|
||||
break;
|
||||
case TGZ:
|
||||
producePackage();
|
||||
break;
|
||||
case ZIP:
|
||||
produceZip();
|
||||
break;
|
||||
default:
|
||||
break;
|
||||
|
||||
}
|
||||
System.out.println("Done");
|
||||
}
|
||||
|
||||
private void processResource(CanonicalResource res) {
|
||||
resources.add(res);
|
||||
if (modeParams.contains("pin")) {
|
||||
processBase(res, res);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void processBase(CanonicalResource src, Base b) {
|
||||
for (Property p : b.children()) {
|
||||
for (Base v : p.getValues()) {
|
||||
processBase(src, v);
|
||||
}
|
||||
}
|
||||
if (b instanceof CanonicalType) {
|
||||
CanonicalType ct = (CanonicalType) b;
|
||||
if (!ct.hasVersion()) {
|
||||
Resource res = context.fetchResource(Resource.class, ct.getValue(), src);
|
||||
if (res != null && res instanceof CanonicalResource) {
|
||||
CanonicalResource cr = (CanonicalResource) res;
|
||||
ct.addVersion(cr.getVersion());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void produceZip() throws IOException {
|
||||
System.out.println("Producing Output in Zip "+output);
|
||||
ZipGenerator zip = new ZipGenerator(output);
|
||||
Set<String> names = new HashSet<>();
|
||||
names.add("manifest");
|
||||
if (json) {
|
||||
zip.addBytes("manifest.json", new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters), false);
|
||||
} else {
|
||||
zip.addBytes("manifest.xml", new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters), false);
|
||||
}
|
||||
if (modeParams.contains("expansions")) {
|
||||
StringBuilder b = new StringBuilder();
|
||||
for (String n : Utilities.sorted(entries.keySet())) {
|
||||
TerminologyResourceEntry e = entries.get(n);
|
||||
String name = e.valueSet.getIdBase();
|
||||
int i = 0;
|
||||
while (names.contains(name)) {
|
||||
i++;
|
||||
name = e.valueSet.getIdBase()+i;
|
||||
}
|
||||
names.add(name);
|
||||
if (e.error == null) {
|
||||
b.append(name+","+n+", , "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
} else {
|
||||
b.append(name+","+n+", \""+Utilities.escapeCSV(e.error)+"\", "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
}
|
||||
zip.addBytes(name+".json", composeResource(e.valueSet), false);
|
||||
}
|
||||
zip.addBytes("valuesets.csv", b.toString().getBytes(StandardCharsets.UTF_8), false);
|
||||
}
|
||||
zip.close();
|
||||
}
|
||||
|
||||
private void producePackage() throws FHIRException, IOException {
|
||||
System.out.println("Producing Output Package in "+output);
|
||||
JsonObject j = new JsonObject();
|
||||
j.add("name", "custom.generated");
|
||||
j.add("version", "0.0.1");
|
||||
j.add("tools-version", 3);
|
||||
j.add("type", "Conformance");
|
||||
j.forceArray("fhirVersions").add(context.getVersion());
|
||||
j.forceObject("dependencies").add(VersionUtilities.packageForVersion(context.getVersion()), context.getVersion());
|
||||
|
||||
NPMPackageGenerator gen = new NPMPackageGenerator(output, j, new Date(), true);
|
||||
|
||||
Set<String> names = new HashSet<>();
|
||||
names.add("manifest");
|
||||
if (json) {
|
||||
gen.addFile("package", "manifest.json", new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters));
|
||||
} else {
|
||||
gen.addFile("package", "manifest.xml", new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(expansionParameters));
|
||||
}
|
||||
if (modeParams.contains("expansions")) {
|
||||
StringBuilder b = new StringBuilder();
|
||||
for (String n : Utilities.sorted(entries.keySet())) {
|
||||
TerminologyResourceEntry e = entries.get(n);
|
||||
String name = e.valueSet.getIdBase();
|
||||
int i = 0;
|
||||
while (names.contains(name)) {
|
||||
i++;
|
||||
name = e.valueSet.getIdBase()+i;
|
||||
}
|
||||
names.add(name);
|
||||
if (e.error == null) {
|
||||
b.append(name+","+n+", , "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
} else {
|
||||
b.append(name+","+n+", \""+Utilities.escapeCSV(e.error)+"\", "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
}
|
||||
gen.addFile("package",name+".json", composeResource(e.valueSet));
|
||||
}
|
||||
gen.addFile("other","valuesets.csv", b.toString().getBytes(StandardCharsets.UTF_8));
|
||||
}
|
||||
gen.finish();
|
||||
}
|
||||
|
||||
private void produceFolder() throws IOException {
|
||||
System.out.println("Producing Output in folder "+output);
|
||||
Utilities.createDirectory(output);
|
||||
Utilities.clearDirectory(output);
|
||||
Set<String> names = new HashSet<>();
|
||||
names.add("manifest");
|
||||
if (json) {
|
||||
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(output, "manifest.json")), expansionParameters);
|
||||
} else {
|
||||
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(output, "manifest.xml")), expansionParameters);
|
||||
}
|
||||
for (CanonicalResource cr : resources) {
|
||||
TextFile.bytesToFile(composeResource(cr), Utilities.path(output, cr.fhirType()+"-"+cr.getIdBase()+(json? ".json" : ".xml")));
|
||||
}
|
||||
if (modeParams.contains("expansions")) {
|
||||
StringBuilder b = new StringBuilder();
|
||||
for (String n : Utilities.sorted(entries.keySet())) {
|
||||
TerminologyResourceEntry e = entries.get(n);
|
||||
String name = "ValueSet-"+e.valueSet.getIdBase()+"-expansion";
|
||||
int i = 0;
|
||||
while (names.contains(name)) {
|
||||
i++;
|
||||
name = e.valueSet.getIdBase()+i;
|
||||
}
|
||||
names.add(name);
|
||||
if (e.error == null) {
|
||||
b.append(name+","+n+", , "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
} else {
|
||||
b.append(name+","+n+", \""+Utilities.escapeCSV(e.error)+"\", "+CommaSeparatedStringBuilder.join(";",e.sources)+"\r\n");
|
||||
}
|
||||
TextFile.bytesToFile(composeResource(e.valueSet), Utilities.path(output, name+(json? ".json" : ".xml")));
|
||||
}
|
||||
TextFile.stringToFile(b.toString(), Utilities.path(output, "expansions.csv"));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private byte[] composeResource(CanonicalResource cr) throws IOException {
|
||||
if (json) {
|
||||
return new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(cr);
|
||||
} else {
|
||||
return new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(cr);
|
||||
}
|
||||
}
|
||||
|
||||
private void processSD(StructureDefinition sd, String packageId) {
|
||||
for (ElementDefinition ed : sd.getDifferential().getElement()) {
|
||||
if (ed.hasBinding() && ed.getBinding().hasValueSet()) {
|
||||
processValueSet(ed.getBinding().getValueSet(), packageId+":"+sd.getVersionedUrl()+"#"+ed.getId());
|
||||
}
|
||||
}
|
||||
if (scope != ExpansionPackageGeneratorScope.IG_ONLY && sd.getBaseDefinition() != null) {
|
||||
StructureDefinition bsd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition(), sd);
|
||||
if (bsd != null) {
|
||||
if (!bsd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition") || scope == ExpansionPackageGeneratorScope.EVERYTHING) {
|
||||
processSD(bsd, bsd.getSourcePackage().getVID());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void processValueSet(String valueSet, String source) {
|
||||
String url = cu.pinValueSet(valueSet);
|
||||
ValueSet vs = context.fetchResource(ValueSet.class, url);
|
||||
if (vs != null) {
|
||||
TerminologyResourceEntry e = entries.get(vs.getVersionedUrl());
|
||||
if (e == null) {
|
||||
e = new TerminologyResourceEntry();
|
||||
e.sources.add(source);
|
||||
e.valueSet = vs;
|
||||
entries.put(vs.getVersionedUrl(), e);
|
||||
source = vs.getSourcePackage().getVID()+":"+vs.getVersionedUrl();
|
||||
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
|
||||
for (CanonicalType v : inc.getValueSet()) {
|
||||
if (v.hasValue()) {
|
||||
processValueSet(v.primitiveValue(), source);
|
||||
}
|
||||
}
|
||||
}
|
||||
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
|
||||
for (CanonicalType v : inc.getValueSet()) {
|
||||
if (v.hasValue()) {
|
||||
processValueSet(v.primitiveValue(), source);
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
e.sources.add(source);
|
||||
}
|
||||
|
||||
} else {
|
||||
System.out.println("Unable to resolve value set "+valueSet);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private List<NpmPackage> load() throws IOException {
|
||||
List<NpmPackage> list = new ArrayList<NpmPackage>();
|
||||
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
|
||||
for (String packageId : packages) {
|
||||
NpmPackage npm = pcm.loadPackage(packageId);
|
||||
if (context == null) {
|
||||
String v = npm.fhirVersion();
|
||||
NpmPackage core = pcm.loadPackage(VersionUtilities.packageForVersion(v));
|
||||
NpmPackage tho = pcm.loadPackage("hl7.terminology");
|
||||
System.out.println("Load FHIR from "+core.name()+"#"+core.version());
|
||||
SimpleWorkerContext ctxt = new SimpleWorkerContext.SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(core);
|
||||
TerminologyClientFactory factory = new TerminologyClientFactory(ctxt.getVersion());
|
||||
ctxt.connectToTSServer(factory, "http://tx.fhir.org", ctxt.getUserAgent(), null, true);
|
||||
var loader = new IgLoader(pcm, ctxt, ctxt.getVersion());
|
||||
loader.loadPackage(tho, true);
|
||||
loader.loadPackage(npm, true);
|
||||
context = ctxt;
|
||||
context.setExpansionParameters(expansionParameters);
|
||||
if (scope == ExpansionPackageGeneratorScope.EVERYTHING) {
|
||||
// list.add(core);
|
||||
// list.add(tho);
|
||||
}
|
||||
} else {
|
||||
var loader = new IgLoader(pcm, (SimpleWorkerContext) context, context.getVersion());
|
||||
loader.loadPackage(npm, true);
|
||||
if (scope == ExpansionPackageGeneratorScope.ALL_IGS) {
|
||||
for (NpmPackage p : loader.getPackageList()) {
|
||||
// nothing?
|
||||
}
|
||||
}
|
||||
}
|
||||
list.add(npm);
|
||||
}
|
||||
if (cu == null) {
|
||||
cu = new ContextUtilities(context);
|
||||
}
|
||||
return list;
|
||||
}
|
||||
|
||||
public void setModes(Set<String> modeParams) {
|
||||
this.modeParams = modeParams;
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
@ -93,7 +93,7 @@ public class ValidatorCliTests {
|
||||
CodeGenTask codeGenTask;
|
||||
|
||||
@Spy
|
||||
TxPackTask txPackTask;
|
||||
RePackageTask txPackTask;
|
||||
|
||||
@Spy
|
||||
InstanceFactoryTask instanceFactoryTask;
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user