Update to support new packages, new NPM specification
This commit is contained in:
Grahame Grieve
parent
f60bb8a9c6
commit
888356999e
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@ -393,10 +393,8 @@ public class ExtensionDefinitionGenerator {
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else if (sourceVersion == FHIRVersion._1_0_2)
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context = SimpleWorkerContext.fromPackage(npm, new R2ToR4Loader());
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pu = new ProfileUtilities(context, null, null);
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for (String fn : npm.list("package")) {
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if (fn.endsWith(".json") && fn.startsWith("StructureDefinition-")) {
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list.add((StructureDefinition) loadResource(npm.load("package", fn), sourceVersion));
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}
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for (String fn : npm.listResources("StructureDefinition")) {
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list.add((StructureDefinition) loadResource(npm.load("package", fn), sourceVersion));
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}
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for (StructureDefinition sd : list)
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if (sd.getName().equals("Extension")) {
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@ -281,13 +281,8 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
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public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
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if (types.length == 0)
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types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire","ConceptMap","StructureMap", "NamingSystem"};
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for (String s : pi.list("package")) {
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if (s.contains("-") && s.endsWith(".json")) {
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String t = s.substring(0, s.indexOf("-"));
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if (Utilities.existsInList(t, types)) {
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loadDefinitionItem(s, pi.load("package", s), loader);
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}
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}
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for (String s : pi.listResources(types)) {
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loadDefinitionItem(s, pi.load("package", s), loader);
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}
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version = pi.version();
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}
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@ -286,13 +286,8 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
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public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
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if (types.length == 0)
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types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire","ConceptMap","StructureMap", "NamingSystem"};
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for (String s : pi.list("package")) {
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if (s.contains("-") && s.endsWith(".json")) {
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String t = s.substring(0, s.indexOf("-"));
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if (Utilities.existsInList(t, types)) {
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loadDefinitionItem(s, pi.load("package", s), loader);
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}
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}
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for (String s : pi.listResources(types)) {
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loadDefinitionItem(s, pi.load("package", s), loader);
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}
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version = pi.version();
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}
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@ -69,7 +69,7 @@ public class TestingUtilities {
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PackageCacheManager pcm;
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try {
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pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
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fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
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fcontext.setUcumService(new UcumEssenceService(TestingUtilities.loadTestResourceStream("ucum", "ucum-essence.xml")));
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fcontext.setExpansionProfile(new Parameters());
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} catch (Exception e) {
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@ -63,6 +63,7 @@ import com.google.gson.Gson;
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import com.google.gson.GsonBuilder;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonObject;
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import com.google.gson.JsonPrimitive;
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public class NPMPackageGenerator {
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@ -177,11 +178,21 @@ public class NPMPackageGenerator {
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npm.addProperty("title", ig.getTitle());
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if (ig.hasDescription())
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npm.addProperty("description", ig.getDescription()+ " (built "+dtHuman+timezone()+")");
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JsonArray vl = new JsonArray();
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npm.add("fhirVersions", vl);
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for (String v : fhirVersion) {
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vl.add(new JsonPrimitive(v));
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}
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if (kind != PackageType.CORE) {
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JsonObject dep = new JsonObject();
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npm.add("dependencies", dep);
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for (String v : fhirVersion) { // TODO: fix for multiple versions
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dep.addProperty("hl7.fhir.core", v);
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for (String v : fhirVersion) {
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String vp = packageForVersion(v);
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if (vp != null ) {
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dep.addProperty(vp, v);
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}
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}
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for (ImplementationGuideDependsOnComponent d : ig.getDependsOn()) {
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dep.addProperty(d.getPackageId(), d.getVersion());
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@ -228,6 +239,20 @@ public class NPMPackageGenerator {
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}
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private String packageForVersion(String v) {
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if (v == null)
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return null;
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if (v.startsWith("1.0"))
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return "hl7.fhir.r2.core";
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if (v.startsWith("1.4"))
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return "hl7.fhir.r2b.core";
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if (v.startsWith("3.0"))
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return "hl7.fhir.r3.core";
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if (v.startsWith("4.0"))
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return "hl7.fhir.r4.core";
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return null;
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}
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private String timezone() {
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TimeZone tz = TimeZone.getDefault();
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Calendar cal = GregorianCalendar.getInstance(tz);
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@ -484,7 +484,10 @@ public class SnapShotGenerationTests {
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new NarrativeGenerator("", "http://hl7.org/fhir", TestingUtilities.context()).setPkp(new TestPKP()).generate(output, null);
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test.output = output;
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TestingUtilities.context().cacheResource(output);
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IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", test.getId()+"-expected.xml"), new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId()+"-expected.xml")));
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File dst = new File(TestingUtilities.tempFile("snapshot", test.getId()+"-expected.xml"));
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if (dst.exists())
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dst.delete();
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IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", test.getId()+"-expected.xml"), new FileOutputStream(dst));
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new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId()+"-actual.xml")), output);
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StructureDefinition t1 = test.expected.copy();
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t1.setText(null);
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@ -71,6 +71,8 @@ import com.google.gson.JsonObject;
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private Map<String, byte[]> content = new HashMap<String, byte[]>();
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private JsonObject npm;
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private IniFile cache;
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private Map<String, List<String>> types = new HashMap<>();
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private Map<String, String> urls = new HashMap<>();
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public NpmPackage(JsonObject npm, Map<String, byte[]> content, List<String> folders) {
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this.path = null;
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@ -88,10 +90,30 @@ import com.google.gson.JsonObject;
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}
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}
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npm = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(Utilities.path(path, "package", "package.json")));
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File ji = new File(Utilities.path(path, "package", ".index.json"));
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if (ji.exists()) {
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readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(ji)));
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}
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cache = new IniFile(Utilities.path(path, "cache.ini"));
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}
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}
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private void readIndexFile(JsonObject index) throws IOException {
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for (JsonElement e : index.getAsJsonArray("files")) {
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JsonObject file = (JsonObject) e;
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String type = file.get("resourceType").getAsString();
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String name = file.get("filename").getAsString();
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String url = file.has("url") ? file.get("url").getAsString() : null;
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String version = file.has("version") ? file.get("version").getAsString() : null;
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if (!types.containsKey(type))
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types.put(type, new ArrayList<>());
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types.get(type).add(name);
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if (version != null)
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url = url + "|" + version;
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urls.put(url, name);
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}
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}
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private List<String> sorted(String[] keys) {
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List<String> names = new ArrayList<String>();
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for (String s : keys)
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@ -101,7 +123,12 @@ import com.google.gson.JsonObject;
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}
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private static final int BUFFER_SIZE = 1024;
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public static NpmPackage fromPackage(InputStream tgz) throws IOException {
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return fromPackage(tgz, false);
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}
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public static NpmPackage fromPackage(InputStream tgz, boolean progress) throws IOException {
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NpmPackage res = new NpmPackage(null);
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GzipCompressorInputStream gzipIn = new GzipCompressorInputStream(tgz);
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try (TarArchiveInputStream tarIn = new TarArchiveInputStream(gzipIn)) {
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@ -126,6 +153,16 @@ import com.google.gson.JsonObject;
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fos.close();
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res.content.put(entry.getName(), fos.toByteArray());
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}
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i++;
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if (progress && i % 50 == 0) {
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c++;
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System.out.print(".");
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if (c == 120) {
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System.out.println("");
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System.out.print(" ");
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c = 2;
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}
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}
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}
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}
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res.npm = JsonTrackingParser.parseJson(res.content.get("package/package.json"));
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@ -159,6 +196,8 @@ import com.google.gson.JsonObject;
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}
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zip.close();
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res.npm = (JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/package.json")));
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if (res.content.containsKey("package/.index.json"))
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res.readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/.index.json"))));
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return res;
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}
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@ -187,12 +226,19 @@ import com.google.gson.JsonObject;
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}
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public List<String> listResources(String... types) throws IOException {
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List<String> files = list("package");
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List<String> res = new ArrayList<String>();
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for (String s : files) {
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String[] n = s.split("\\-");
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if (Utilities.existsInList(n[0], types))
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res.add(s);
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if (this.types.size() > 0) {
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for (String s : types) {
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if (this.types.containsKey(s))
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res.addAll(this.types.get(s));
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}
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} else {
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List<String> files = list("package");
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for (String s : files) {
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String[] n = s.split("\\-");
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if (Utilities.existsInList(n[0], types))
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res.add(s);
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}
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}
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return res;
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}
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@ -295,18 +341,25 @@ import com.google.gson.JsonObject;
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public String fhirVersion() {
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if ("hl7.fhir.core".equals(npm.get("name").getAsString()))
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return npm.get("version").getAsString();
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else if (npm.get("name").getAsString().startsWith("hl7.fhir.r2.") || npm.get("name").getAsString().startsWith("hl7.fhir.r2b.") || npm.get("name").getAsString().startsWith("hl7.fhir.r3.") || npm.get("name").getAsString().startsWith("hl7.fhir.r4."))
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return npm.get("version").getAsString();
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else {
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JsonObject dep = npm.getAsJsonObject("dependencies");
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if (dep == null)
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throw new FHIRException("no dependencies found in the Package definition");
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JsonElement core = dep.get("hl7.fhir.core");
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if (core == null)
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throw new FHIRException("no dependency on hl7.fhir.core found in the Package definition");
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return core.getAsString();
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for (Entry<String, JsonElement> e : dep.entrySet()) {
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if (Utilities.existsInList(e.getKey(), "hl7.fhir.r2.core", "hl7.fhir.r2b.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core"))
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return e.getValue().getAsString();
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if (Utilities.existsInList(e.getKey(), "hl7.fhir.core")) // while all packages are updated
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return e.getValue().getAsString();
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}
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if (npm.has("fhirVersions"))
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return npm.getAsJsonArray("fhirVersions").get(0).getAsString();
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throw new FHIRException("no core dependency or FHIR Version found in the Package definition");
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}
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}
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public String description() {
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public String summary() {
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if (path != null)
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return path;
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else
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@ -321,6 +374,10 @@ import com.google.gson.JsonObject;
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return npm.get("type").getAsString();
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}
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public String description() {
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return npm.has("description") ? npm.get("description").getAsString() : null;
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}
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public String getPath() {
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return path;
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}
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@ -127,6 +127,10 @@ public class NpmPackageIndexBuilder {
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new NpmPackageIndexBuilder().executeWithStatus("C:\\work\\org.hl7.fhir\\packages\\fhir.tx.support\\fhir.tx.support.r2");
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new NpmPackageIndexBuilder().executeWithStatus("C:\\work\\org.hl7.fhir\\packages\\fhir.tx.support\\fhir.tx.support.r3");
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new NpmPackageIndexBuilder().executeWithStatus("C:\\work\\org.hl7.fhir\\packages\\fhir.tx.support\\fhir.tx.support.r4");
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new NpmPackageIndexBuilder().executeWithStatus("C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.core#1.0.2");
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new NpmPackageIndexBuilder().executeWithStatus("C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.core#1.4.0");
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new NpmPackageIndexBuilder().executeWithStatus("C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.core#3.0.2");
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new NpmPackageIndexBuilder().executeWithStatus("C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.core#4.0.1");
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}
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}
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@ -37,6 +37,7 @@ import java.util.Collections;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
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@ -106,7 +107,7 @@ public class PackageCacheManager {
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public static final String PACKAGE_VERSION_REGEX = "^[a-z][a-z0-9\\_\\-]*(\\.[a-z0-9\\_\\-]+)+\\#[a-z0-9\\-\\_]+(\\.[a-z0-9\\-\\_]+)*$";
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private static final int BUFFER_SIZE = 1024;
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private static final String CACHE_VERSION = "2"; // second version - see wiki page
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private static final String CACHE_VERSION = "3"; // second version - see wiki page
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private static final int ANALYSIS_VERSION = 2;
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private String cacheFolder;
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@ -129,19 +130,172 @@ public class PackageCacheManager {
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TextFile.stringToFile("[cache]\r\nversion="+CACHE_VERSION+"\r\n\r\n[urls]\r\n\r\n[local]\r\n\r\n", Utilities.path(cacheFolder, "packages.ini"), false);
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IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
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boolean save = false;
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String v = ini.getStringProperty("cache", "version");
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if ("1".equals(v)) {
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convertPackageCacheFrom1To2();
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ini.setStringProperty("cache", "version", "2", null);
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v = ini.getStringProperty("cache", "version");
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save = true;
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}
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String v = ini.getStringProperty("cache", "version");
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if (!CACHE_VERSION.equals(v)) {
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clearCache();
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ini.setStringProperty("cache", "version", CACHE_VERSION, null);
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save = true;
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}
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save = initUrlMaps(ini, save);
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if (save) {
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if (!CACHE_VERSION.equals(ini.getStringProperty("cache", "version"))) {
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throw new Error("what?");
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}
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ini.save();
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}
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}
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public static String userDir() throws IOException {
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return Utilities.path(System.getProperty("user.home"), ".fhir", "packages");
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}
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// ========================= Utilities ============================================================================
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private List<String> sorted(String[] keys) {
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List<String> names = new ArrayList<String>();
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for (String s : keys)
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names.add(s);
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Collections.sort(names);
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return names;
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}
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private NpmPackage loadPackageInfo(String path) throws IOException {
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NpmPackage pi = new NpmPackage(path);
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return pi;
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}
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public String getFolder() {
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return cacheFolder;
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}
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private void analysePackage(String dir) throws IOException {
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NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
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indexer.start();
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int i = 0;
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int c = 0;
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File[] packages = new File(Utilities.path(dir, "package")).listFiles();
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for (File f : packages) {
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indexer.seeFile(f.getName(), TextFile.fileToBytes(f));
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i++;
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if (progress && i % 50 == 0) {
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c++;
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System.out.print(".");
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if (c == 120) {
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System.out.println("");
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System.out.print(" ");
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c = 2;
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}
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}
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}
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TextFile.stringToFile(indexer.build(), Utilities.path(dir, "package", ".index.json"));
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}
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private NpmPackage checkCurrency(String id, NpmPackage p) {
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// special case: current versions roll over, and we have to check their currency
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try {
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String url = ciList.get(id);
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JsonObject json = fetchJson(Utilities.pathURL(url, "package.manifest.json"));
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String currDate = json.get("date").getAsString();
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String packDate = p.date();
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if (!currDate.equals(packDate))
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return null; // nup, we need a new copy
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return p;
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} catch (Exception e) {
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return p;
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}
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}
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private JsonObject fetchJson(String source) throws IOException {
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URL url = new URL(source);
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URLConnection c = url.openConnection();
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return (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(c.getInputStream()));
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}
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private InputStream fetchFromUrlSpecific(String source, boolean optional) throws FHIRException {
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try {
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URL url = new URL(source);
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URLConnection c = url.openConnection();
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return c.getInputStream();
|
||||
} catch (Exception e) {
|
||||
if (optional)
|
||||
return null;
|
||||
else
|
||||
throw new FHIRException(e.getMessage(), e);
|
||||
}
|
||||
}
|
||||
|
||||
// ========================= Full Cache Management ============================================================================
|
||||
|
||||
private void clearCache() throws IOException {
|
||||
for (File f : new File(cacheFolder).listFiles()) {
|
||||
if (f.isDirectory())
|
||||
FileUtils.deleteDirectory(f);
|
||||
else if (!f.getName().equals("packages.ini"))
|
||||
FileUtils.forceDelete(f);
|
||||
}
|
||||
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
|
||||
ini.removeSection("packages");
|
||||
ini.save();
|
||||
}
|
||||
|
||||
// private void checkDeleteVersion(String id, String ver, int minVer) {
|
||||
// if (hasPackage(id, ver)) {
|
||||
// boolean del = true;
|
||||
// NpmPackage pck;
|
||||
// try {
|
||||
// pck = loadPackageFromCacheOnly(id, ver);
|
||||
// if (pck.getNpm().has("tools-version")) {
|
||||
// del = pck.getNpm().get("tools-version").getAsInt() < minVer;
|
||||
// }
|
||||
// } catch (Exception e) {
|
||||
// }
|
||||
// if (del)
|
||||
// try {
|
||||
// removePackage(id, ver);
|
||||
// } catch (IOException e) {
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
|
||||
//private void convertPackageCacheFrom1To2() throws IOException {
|
||||
//for (File f : new File(cacheFolder).listFiles()) {
|
||||
// if (f.isDirectory() && f.getName().contains("-")) {
|
||||
// String s = f.getName();
|
||||
// int i = s.lastIndexOf("-");
|
||||
// s = s.substring(0, i)+"#"+s.substring(i+1);
|
||||
// File nf = new File(Utilities.path(cacheFolder, s));
|
||||
// if (!f.renameTo(nf))
|
||||
// throw new IOException("Unable to rename "+f.getAbsolutePath()+" to "+nf.getAbsolutePath());
|
||||
// }
|
||||
//}
|
||||
//}
|
||||
|
||||
// ========================= URL maps (while waiting for package registry) ============================================================================
|
||||
|
||||
public boolean initUrlMaps(IniFile ini, boolean save) {
|
||||
save = checkIniHasMapping("hl7.fhir.core", "http://hl7.org/fhir", ini) || save;
|
||||
|
||||
save = checkIniHasMapping("hl7.fhir.r2.core", "http://hl7.org/fhir/DSTU2/hl7.fhir.r2.core.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r2.examples", "http://hl7.org/fhir/DSTU2/hl7.fhir.r2.examples.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r2.elements", "http://hl7.org/fhir/DSTU2/hl7.fhir.r2.elements.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r2.expansions", "http://hl7.org/fhir/DSTU2/hl7.fhir.r2.expansions.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r2b.core", "http://hl7.org/fhir/2016May/hl7.fhir.r2b.core.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r2b.examples", "http://hl7.org/fhir/2016May/hl7.fhir.r2b.examples.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r2b.elements", "http://hl7.org/fhir/2016May/hl7.fhir.r2b.elements.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r2b.expansions", "http://hl7.org/fhir/2016May/hl7.fhir.r2b.expansions.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r3.core", "http://hl7.org/fhir/STU3/hl7.fhir.r3.core.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r3.examples", "http://hl7.org/fhir/STU3/hl7.fhir.r3.examples.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r3.elements", "http://hl7.org/fhir/STU3/hl7.fhir.r3.elements.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r3.expansions", "http://hl7.org/fhir/STU3/hl7.fhir.r3.expansions.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r4.core", "http://hl7.org/fhir/R4/hl7.fhir.r4.core.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r4.examples", "http://hl7.org/fhir/R4/hl7.fhir.r4.examples.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r4.elements", "http://hl7.org/fhir/R4/hl7.fhir.r4.elements.tgz", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.r4.expansions", "http://hl7.org/fhir/R4/hl7.fhir.r4.expansions.tgz", ini) || save;
|
||||
|
||||
save = checkIniHasMapping("hl7.fhir.r5.core", "http://build.fhir.org/package.tgz", ini) || save;
|
||||
|
||||
save = checkIniHasMapping("fhir.argonaut.ehr", "http://fhir.org/guides/argonaut", ini) || save;
|
||||
save = checkIniHasMapping("fhir.argonaut.pd", "http://fhir.org/guides/argonaut-pd", ini) || save;
|
||||
save = checkIniHasMapping("fhir.argonaut.scheduling", "http://fhir.org/guides/argonaut-scheduling", ini) || save;
|
||||
|
|
@ -172,59 +326,8 @@ public class PackageCacheManager {
|
|||
save = checkIniHasMapping("hl7.fhir.uv.vhdir", "http://hl7.org/fhir/ig/vhdir", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.vn.base", "http://hl7.org/fhir/ig/vietnam", ini) || save;
|
||||
save = checkIniHasMapping("hl7.fhir.vocabpoc", "http://hl7.org/fhir/ig/vocab-poc", ini) || save;
|
||||
if (save) {
|
||||
if (!CACHE_VERSION.equals(ini.getStringProperty("cache", "version"))) {
|
||||
throw new Error("what?");
|
||||
}
|
||||
ini.save();
|
||||
}
|
||||
checkDeleteVersion("hl7.fhir.core", "1.0.2", 2);
|
||||
checkDeleteVersion("hl7.fhir.core", "1.4.0", 2);
|
||||
checkDeleteVersion("hl7.fhir.core", "current", toolsVersion);
|
||||
checkDeleteVersion("hl7.fhir.core", "4.0.0", toolsVersion);
|
||||
return save;
|
||||
}
|
||||
|
||||
|
||||
private void checkDeleteVersion(String id, String ver, int minVer) {
|
||||
if (hasPackage(id, ver)) {
|
||||
boolean del = true;
|
||||
NpmPackage pck;
|
||||
try {
|
||||
pck = loadPackageFromCacheOnly(id, ver);
|
||||
if (pck.getNpm().has("tools-version")) {
|
||||
del = pck.getNpm().get("tools-version").getAsInt() < minVer;
|
||||
}
|
||||
} catch (Exception e) {
|
||||
}
|
||||
if (del)
|
||||
try {
|
||||
removePackage(id, ver);
|
||||
} catch (IOException e) {
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public void removePackage(String id, String ver) throws IOException {
|
||||
String f = Utilities.path(cacheFolder, id+"#"+ver);
|
||||
Utilities.clearDirectory(f);
|
||||
new File(f).delete();
|
||||
}
|
||||
|
||||
|
||||
private void convertPackageCacheFrom1To2() throws IOException {
|
||||
for (File f : new File(cacheFolder).listFiles()) {
|
||||
if (f.isDirectory() && f.getName().contains("-")) {
|
||||
String s = f.getName();
|
||||
int i = s.lastIndexOf("-");
|
||||
s = s.substring(0, i)+"#"+s.substring(i+1);
|
||||
File nf = new File(Utilities.path(cacheFolder, s));
|
||||
if (!f.renameTo(nf))
|
||||
throw new IOException("Unable to rename "+f.getAbsolutePath()+" to "+nf.getAbsolutePath());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private boolean checkIniHasMapping(String pid, String curl, IniFile ini) {
|
||||
if (curl.equals(ini.getStringProperty("urls", pid)))
|
||||
|
|
@ -233,17 +336,6 @@ public class PackageCacheManager {
|
|||
return true;
|
||||
}
|
||||
|
||||
|
||||
private void clearCache() throws IOException {
|
||||
for (File f : new File(cacheFolder).listFiles()) {
|
||||
if (f.isDirectory())
|
||||
FileUtils.deleteDirectory(f);
|
||||
else if (!f.getName().equals("packages.ini"))
|
||||
FileUtils.forceDelete(f);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public void recordMap(String url, String id) throws IOException {
|
||||
if (url == null)
|
||||
return;
|
||||
|
|
@ -280,12 +372,89 @@ public class PackageCacheManager {
|
|||
return null;
|
||||
}
|
||||
|
||||
private List<String> sorted(String[] keys) {
|
||||
List<String> names = new ArrayList<String>();
|
||||
for (String s : keys)
|
||||
names.add(s);
|
||||
Collections.sort(names);
|
||||
return names;
|
||||
public JsonArray loadFromBuildServer() throws IOException {
|
||||
buildLoaded = true; // whether it succeeds or not
|
||||
URL url = new URL("https://build.fhir.org/ig/qas.json?nocache=" + System.currentTimeMillis());
|
||||
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
|
||||
connection.setRequestMethod("GET");
|
||||
InputStream json = connection.getInputStream();
|
||||
buildInfo = (JsonArray) new com.google.gson.JsonParser().parse(TextFile.streamToString(json));
|
||||
|
||||
for (JsonElement n : buildInfo) {
|
||||
JsonObject o = (JsonObject) n;
|
||||
if (o.has("url") && o.has("package-id") && o.get("package-id").getAsString().contains(".")) {
|
||||
String u = o.get("url").getAsString();
|
||||
if (u.contains("/ImplementationGuide/"))
|
||||
u = u.substring(0, u.indexOf("/ImplementationGuide/"));
|
||||
recordMap(u, o.get("package-id").getAsString());
|
||||
ciList.put(o.get("package-id").getAsString(), "https://build.fhir.org/ig/"+o.get("repo").getAsString());
|
||||
}
|
||||
}
|
||||
return buildInfo;
|
||||
}
|
||||
|
||||
public boolean isBuildLoaded() {
|
||||
return buildLoaded;
|
||||
}
|
||||
|
||||
|
||||
public String buildPath(String url) {
|
||||
for (JsonElement e : buildInfo) {
|
||||
JsonObject j = (JsonObject) e;
|
||||
if (j.has("url") && (url.equals(j.get("url").getAsString()) || j.get("url").getAsString().startsWith(url+"/ImplementationGuide"))) {
|
||||
return "https://build.fhir.org/ig/"+j.get("repo").getAsString();
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
public boolean checkBuildLoaded() throws IOException {
|
||||
if (isBuildLoaded())
|
||||
return true;
|
||||
loadFromBuildServer();
|
||||
return false;
|
||||
}
|
||||
|
||||
public Map<String, String> getCiList() {
|
||||
return ciList;
|
||||
}
|
||||
|
||||
public List<String> getUrls() throws IOException {
|
||||
if (allUrls == null)
|
||||
{
|
||||
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
|
||||
allUrls = new ArrayList<>();
|
||||
for (String s : ini.getPropertyNames("urls"))
|
||||
allUrls.add(ini.getStringProperty("urls", s));
|
||||
try {
|
||||
URL url = new URL("https://raw.githubusercontent.com/FHIR/ig-registry/master/fhir-ig-list.json?nocache=" + System.currentTimeMillis());
|
||||
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
|
||||
connection.setRequestMethod("GET");
|
||||
InputStream json = connection.getInputStream();
|
||||
JsonObject packages = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(json));
|
||||
JsonArray guides = packages.getAsJsonArray("guides");
|
||||
for (JsonElement g : guides) {
|
||||
JsonObject gi = (JsonObject) g;
|
||||
if (gi.has("canonical"))
|
||||
if (!allUrls.contains(gi.get("canonical").getAsString()))
|
||||
allUrls.add(gi.get("canonical").getAsString());
|
||||
}
|
||||
} catch (Exception e) {
|
||||
System.out.println("Listing known Implementation Guides failed: "+e.getMessage());
|
||||
}
|
||||
}
|
||||
return allUrls;
|
||||
}
|
||||
|
||||
// ========================= Package API ============================================================================
|
||||
|
||||
public void removePackage(String id, String ver) throws IOException {
|
||||
String f = Utilities.path(cacheFolder, id+"#"+ver);
|
||||
Utilities.clearDirectory(f);
|
||||
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
|
||||
ini.removeProperty("packages", id+"#"+ver);
|
||||
ini.save();
|
||||
new File(f).delete();
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -295,7 +464,6 @@ public class PackageCacheManager {
|
|||
* @throws IOException
|
||||
*/
|
||||
public NpmPackage loadPackageFromCacheOnly(String id) throws IOException {
|
||||
String match = null;
|
||||
List<String> l = sorted(new File(cacheFolder).list());
|
||||
for (int i = l.size()-1; i >= 0; i--) {
|
||||
String f = l.get(i);
|
||||
|
|
@ -321,7 +489,6 @@ public class PackageCacheManager {
|
|||
if (p.name().equals(id) && ("current".equals(version) || "dev".equals(version) || p.version().equals(version)))
|
||||
return p;
|
||||
}
|
||||
String match = null;
|
||||
for (String f : sorted(new File(cacheFolder).list())) {
|
||||
if (f.equals(id+"#"+version)) {
|
||||
return loadPackageInfo(Utilities.path(cacheFolder, f));
|
||||
|
|
@ -332,130 +499,49 @@ public class PackageCacheManager {
|
|||
else
|
||||
return null;
|
||||
}
|
||||
|
||||
private NpmPackage loadPackageInfo(String path) throws IOException {
|
||||
NpmPackage pi = new NpmPackage(path);
|
||||
return pi;
|
||||
}
|
||||
|
||||
/**
|
||||
* Add an already fetched package to the cache
|
||||
*/
|
||||
public NpmPackage addPackageToCache(String id, String version, InputStream tgz) throws IOException {
|
||||
if (progress ) {
|
||||
System.out.println("Installing "+id+"#"+(version == null ? "?" : version)+" to the package cache");
|
||||
System.out.print(" Fetching:");
|
||||
}
|
||||
List<PackageEntry> files = new ArrayList<PackageEntry>();
|
||||
|
||||
long size = unPackage(tgz, files);
|
||||
|
||||
byte[] npmb = null;
|
||||
for (PackageEntry e : files) {
|
||||
if (e.name.equals("package/package.json"))
|
||||
npmb = e.bytes;
|
||||
}
|
||||
if (npmb == null)
|
||||
throw new IOException("Unable to find package/package.json in the package file");
|
||||
NpmPackage npm = NpmPackage.fromPackage(tgz, true);
|
||||
|
||||
if (progress )
|
||||
System.out.print("|");
|
||||
JsonObject npm = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.bytesToString(npmb));
|
||||
if (npm.get("name") == null || id == null || !id.equals(npm.get("name").getAsString()))
|
||||
// work around for stupid core-r4 problem
|
||||
if (!npm.get("name").getAsString().startsWith(id))
|
||||
throw new IOException("Attempt to import a mis-identified package. Expected "+id+", got "+npm.get("name").getAsString());
|
||||
if (npm.name() == null || id == null || !id.equals(npm.name())) {
|
||||
if (!id.equals("hl7.fhir.r5.core")) {// temporary work around
|
||||
throw new IOException("Attempt to import a mis-identified package. Expected "+id+", got "+npm.name());
|
||||
}
|
||||
}
|
||||
if (version == null)
|
||||
version = npm.get("version").getAsString();
|
||||
version = npm.version();
|
||||
|
||||
String packRoot = Utilities.path(cacheFolder, id+"#"+version);
|
||||
Utilities.createDirectory(packRoot);
|
||||
Utilities.clearDirectory(packRoot);
|
||||
|
||||
for (PackageEntry e : files) {
|
||||
if (e.bytes == null) {
|
||||
File f = new File(Utilities.path(packRoot, e.name));
|
||||
if (!f.mkdir())
|
||||
throw new IOException("Unable to create directory '%s', during extraction of archive contents: "+ f.getAbsolutePath());
|
||||
} else {
|
||||
String fn = Utilities.path(packRoot, e.name);
|
||||
String dir = Utilities.getDirectoryForFile(fn);
|
||||
if (!(new File(dir).exists()))
|
||||
Utilities.createDirectory(dir);
|
||||
TextFile.bytesToFile(e.bytes, fn);
|
||||
}
|
||||
}
|
||||
if (progress) {
|
||||
System.out.println("");
|
||||
System.out.print(" Analysing");
|
||||
}
|
||||
|
||||
Map<String, String> profiles = new HashMap<String, String>();
|
||||
Map<String, String> canonicals = new HashMap<String, String>();
|
||||
if ("hl7.fhir.core".equals(npm.get("name").getAsString()))
|
||||
analysePackage(packRoot, npm.get("version").getAsString(), profiles, canonicals);
|
||||
else if (npm.has("dependencies")) // templates do not
|
||||
analysePackage(packRoot, npm.getAsJsonObject("dependencies").get("hl7.fhir.core").getAsString(), profiles, canonicals);
|
||||
IniFile ini = new IniFile(Utilities.path(packRoot, "cache.ini"));
|
||||
ini.setTimeStampFormat("dd/MM/yyyy h:mm:ss a");
|
||||
ini.setLongProperty("Package", "size", size, null);
|
||||
ini.setTimestampProperty("Package", "install", Timestamp.from(Instant.now()), null);
|
||||
for (String p : profiles.keySet())
|
||||
ini.setStringProperty("Profiles", p, profiles.get(p), null);
|
||||
for (String p : canonicals.keySet())
|
||||
ini.setStringProperty("Canonicals", p, canonicals.get(p), null);
|
||||
ini.setIntegerProperty("Packages", "analysis", ANALYSIS_VERSION, null);
|
||||
ini.save();
|
||||
if (progress )
|
||||
System.out.println(" done.");
|
||||
return loadPackageInfo(packRoot);
|
||||
}
|
||||
|
||||
|
||||
public long unPackage(InputStream tgz, List<PackageEntry> files) throws IOException {
|
||||
long size = 0;
|
||||
GzipCompressorInputStream gzipIn = new GzipCompressorInputStream(tgz);
|
||||
try (TarArchiveInputStream tarIn = new TarArchiveInputStream(gzipIn)) {
|
||||
TarArchiveEntry entry;
|
||||
|
||||
int i = 0;
|
||||
int c = 12;
|
||||
while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
|
||||
i++;
|
||||
if (progress && i % 20 == 0) {
|
||||
c++;
|
||||
System.out.print(".");
|
||||
if (c == 120) {
|
||||
System.out.println("");
|
||||
System.out.print(" ");
|
||||
c = 2;
|
||||
}
|
||||
}
|
||||
if (entry.isDirectory()) {
|
||||
files.add(new PackageEntry(entry.getName()));
|
||||
} else {
|
||||
int count;
|
||||
byte data[] = new byte[BUFFER_SIZE];
|
||||
|
||||
ByteArrayOutputStream fos = new ByteArrayOutputStream();
|
||||
try (BufferedOutputStream dest = new BufferedOutputStream(fos, BUFFER_SIZE)) {
|
||||
while ((count = tarIn.read(data, 0, BUFFER_SIZE)) != -1) {
|
||||
dest.write(data, 0, count);
|
||||
}
|
||||
}
|
||||
fos.close();
|
||||
files.add(new PackageEntry(entry.getName(), fos.toByteArray()));
|
||||
size = size + fos.size();
|
||||
}
|
||||
}
|
||||
}
|
||||
return size;
|
||||
}
|
||||
|
||||
private void analysePackage(String dir, String v, Map<String, String> profiles, Map<String, String> canonicals) throws IOException {
|
||||
int i = 0;
|
||||
int c = 11;
|
||||
File[] packages = new File(Utilities.path(dir, "package")).listFiles();
|
||||
for (File f : packages) {
|
||||
int c = 0;
|
||||
for (Entry<String, byte[]> e : npm.getContent().entrySet()) {
|
||||
// if (e.getValue() == null) {
|
||||
// thorw
|
||||
// File f = new File(Utilities.path(packRoot, e.name));
|
||||
// if (!f.mkdir())
|
||||
// throw new IOException("Unable to create directory '%s', during extraction of archive contents: "+ f.getAbsolutePath());
|
||||
// } else {
|
||||
String fn = Utilities.path(packRoot, e.getKey());
|
||||
String dir = Utilities.getDirectoryForFile(fn);
|
||||
if (!(new File(dir).exists()))
|
||||
Utilities.createDirectory(dir);
|
||||
TextFile.bytesToFile(e.getValue(), fn);
|
||||
// }
|
||||
i++;
|
||||
if (progress && i % 20 == 0) {
|
||||
if (progress && i % 50 == 0) {
|
||||
c++;
|
||||
System.out.print(".");
|
||||
if (c == 120) {
|
||||
|
|
@ -464,117 +550,26 @@ public class PackageCacheManager {
|
|||
c = 2;
|
||||
}
|
||||
}
|
||||
if (!f.getName().startsWith("Bundle-")) {
|
||||
try {
|
||||
JsonObject j = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(f));
|
||||
if (!Utilities.noString(j.get("url").getAsString()) && !Utilities.noString(j.get("resourceType").getAsString()))
|
||||
canonicals.put(j.get("url").getAsString(), f.getName());
|
||||
if ("StructureDefinition".equals(j.get("resourceType").getAsString()) && "resource".equals(j.get("kind").getAsString())) {
|
||||
String bd = null;
|
||||
if ("1.0.2".equals(v))
|
||||
bd = j.get("constrainedType").getAsString();
|
||||
else
|
||||
bd = j.get("type").getAsString();
|
||||
if (Utilities.noString(bd))
|
||||
bd = j.get("name").getAsString();
|
||||
if (!"Extension".equals(bd))
|
||||
profiles.put(j.get("url").getAsString(), bd);
|
||||
}
|
||||
} catch (Exception e) {
|
||||
// nothing
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public NpmPackage extractLocally(String filename) throws IOException {
|
||||
return extractLocally(new FileInputStream(filename), filename);
|
||||
}
|
||||
|
||||
public NpmPackage extractLocally(InputStream tgz, String name) throws IOException {
|
||||
if (progress ) {
|
||||
System.out.println("Loading "+name+" to the package cache");
|
||||
System.out.print(" Fetching:");
|
||||
}
|
||||
List<PackageEntry> files = new ArrayList<PackageEntry>();
|
||||
if (progress) {
|
||||
System.out.println("");
|
||||
System.out.print(" Analysing");
|
||||
}
|
||||
|
||||
unPackage(tgz, files);
|
||||
analysePackage(packRoot); // do this whether there's an index.json or not.
|
||||
|
||||
byte[] npmb = null;
|
||||
for (PackageEntry e : files) {
|
||||
if (e.name.equals("package/package.json"))
|
||||
npmb = e.bytes;
|
||||
}
|
||||
if (npmb == null)
|
||||
throw new IOException("Unable to find package/package.json in the package file");
|
||||
|
||||
JsonObject npm = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.bytesToString(npmb));
|
||||
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
|
||||
ini.setTimeStampFormat("yyyyMMddhhmmss");
|
||||
ini.setTimestampProperty("packages", id+"#"+version, Timestamp.from(Instant.now()), null);
|
||||
ini.save();
|
||||
if (progress)
|
||||
System.out.println(" done.");
|
||||
|
||||
Map<String, byte[]> content = new HashMap<String, byte[]>();
|
||||
List<String> folders = new ArrayList<String>();
|
||||
|
||||
for (PackageEntry e : files) {
|
||||
if (e.bytes == null) {
|
||||
folders.add(e.name);
|
||||
} else {
|
||||
content.put(e.name, e.bytes);
|
||||
}
|
||||
}
|
||||
System.out.println(" done.");
|
||||
NpmPackage p = new NpmPackage(npm, content, folders);
|
||||
recordMap(p.canonical(), p.name());
|
||||
return p;
|
||||
//todo: load dependencies
|
||||
NpmPackage pck = loadPackageInfo(packRoot);
|
||||
return pck;
|
||||
}
|
||||
|
||||
public String getFolder() {
|
||||
return cacheFolder;
|
||||
}
|
||||
|
||||
|
||||
public JsonArray loadFromBuildServer() throws IOException {
|
||||
buildLoaded = true; // whether it succeeds or not
|
||||
URL url = new URL("https://build.fhir.org/ig/qas.json?nocache=" + System.currentTimeMillis());
|
||||
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
|
||||
connection.setRequestMethod("GET");
|
||||
InputStream json = connection.getInputStream();
|
||||
buildInfo = (JsonArray) new com.google.gson.JsonParser().parse(TextFile.streamToString(json));
|
||||
|
||||
for (JsonElement n : buildInfo) {
|
||||
JsonObject o = (JsonObject) n;
|
||||
if (o.has("url") && o.has("package-id") && o.get("package-id").getAsString().contains(".")) {
|
||||
String u = o.get("url").getAsString();
|
||||
if (u.contains("/ImplementationGuide/"))
|
||||
u = u.substring(0, u.indexOf("/ImplementationGuide/"));
|
||||
recordMap(u, o.get("package-id").getAsString());
|
||||
ciList.put(o.get("package-id").getAsString(), "https://build.fhir.org/ig/"+o.get("repo").getAsString());
|
||||
}
|
||||
}
|
||||
return buildInfo;
|
||||
}
|
||||
|
||||
|
||||
public boolean isBuildLoaded() {
|
||||
return buildLoaded;
|
||||
}
|
||||
|
||||
|
||||
public String buildPath(String url) {
|
||||
for (JsonElement e : buildInfo) {
|
||||
JsonObject j = (JsonObject) e;
|
||||
if (j.has("url") && (url.equals(j.get("url").getAsString()) || j.get("url").getAsString().startsWith(url+"/ImplementationGuide"))) {
|
||||
return "https://build.fhir.org/ig/"+j.get("repo").getAsString();
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
public boolean checkBuildLoaded() throws IOException {
|
||||
if (isBuildLoaded())
|
||||
return true;
|
||||
loadFromBuildServer();
|
||||
return false;
|
||||
}
|
||||
|
||||
public NpmPackage loadPackage(String id) throws FHIRException, IOException {
|
||||
throw new Error("Not done yet");
|
||||
}
|
||||
|
|
@ -600,6 +595,12 @@ public class PackageCacheManager {
|
|||
String url = getPackageUrl(id);
|
||||
if (url == null)
|
||||
throw new FHIRException("Unable to resolve the package '"+id+"'");
|
||||
if (url.contains(".tgz")) {
|
||||
InputStream stream = fetchFromUrlSpecific(url, true);
|
||||
if (stream != null)
|
||||
return addPackageToCache(id, v, stream);
|
||||
throw new FHIRException("Unable to find the package source for '"+id+"' at "+url);
|
||||
}
|
||||
if (v == null) {
|
||||
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(url, "package.tgz"), true);
|
||||
if (stream == null && isBuildLoaded()) {
|
||||
|
|
@ -642,62 +643,21 @@ public class PackageCacheManager {
|
|||
}
|
||||
|
||||
|
||||
private NpmPackage checkCurrency(String id, NpmPackage p) {
|
||||
// special case: current versions roll over, and we have to check their currency
|
||||
try {
|
||||
String url = ciList.get(id);
|
||||
JsonObject json = fetchJson(Utilities.pathURL(url, "package.manifest.json"));
|
||||
String currDate = json.get("date").getAsString();
|
||||
String packDate = p.date();
|
||||
if (!currDate.equals(packDate))
|
||||
return null; // nup, we need a new copy
|
||||
return p;
|
||||
} catch (Exception e) {
|
||||
return p;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// !!!
|
||||
// if (packageId != null) {
|
||||
// return loadPackage();
|
||||
// } else
|
||||
// return loadPackage(pcm.extractLocally(stream));
|
||||
|
||||
|
||||
private JsonObject fetchJson(String source) throws IOException {
|
||||
URL url = new URL(source);
|
||||
URLConnection c = url.openConnection();
|
||||
return (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(c.getInputStream()));
|
||||
}
|
||||
|
||||
private InputStream fetchFromUrlSpecific(String source, boolean optional) throws FHIRException {
|
||||
try {
|
||||
URL url = new URL(source);
|
||||
URLConnection c = url.openConnection();
|
||||
return c.getInputStream();
|
||||
} catch (Exception e) {
|
||||
if (optional)
|
||||
return null;
|
||||
else
|
||||
throw new FHIRException(e.getMessage(), e);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public void loadFromFolder(String packagesFolder) throws IOException {
|
||||
for (File f : new File(packagesFolder).listFiles()) {
|
||||
if (f.getName().endsWith(".tgz")) {
|
||||
temporaryPackages.add(extractLocally(new FileInputStream(f), f.getName()));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public Map<String, String> getCiList() {
|
||||
return ciList;
|
||||
}
|
||||
|
||||
// public void loadFromFolder(String packagesFolder) throws IOException {
|
||||
// for (File f : new File(packagesFolder).listFiles()) {
|
||||
// if (f.getName().endsWith(".tgz")) {
|
||||
// temporaryPackages.add(extractLocally(new FileInputStream(f), f.getName()));
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
//
|
||||
|
||||
/**
|
||||
* turn true if a package exists
|
||||
* @param id
|
||||
* @param version
|
||||
* @return
|
||||
*/
|
||||
public boolean hasPackage(String id, String version) {
|
||||
for (NpmPackage p : temporaryPackages) {
|
||||
if (p.name().equals(id) && ("current".equals(version) || "dev".equals(version) || p.version().equals(version)))
|
||||
|
|
@ -715,33 +675,13 @@ public class PackageCacheManager {
|
|||
}
|
||||
|
||||
|
||||
public List<String> getUrls() throws IOException {
|
||||
if (allUrls == null)
|
||||
{
|
||||
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
|
||||
allUrls = new ArrayList<>();
|
||||
for (String s : ini.getPropertyNames("urls"))
|
||||
allUrls.add(ini.getStringProperty("urls", s));
|
||||
try {
|
||||
URL url = new URL("https://raw.githubusercontent.com/FHIR/ig-registry/master/fhir-ig-list.json?nocache=" + System.currentTimeMillis());
|
||||
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
|
||||
connection.setRequestMethod("GET");
|
||||
InputStream json = connection.getInputStream();
|
||||
JsonObject packages = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(json));
|
||||
JsonArray guides = packages.getAsJsonArray("guides");
|
||||
for (JsonElement g : guides) {
|
||||
JsonObject gi = (JsonObject) g;
|
||||
if (gi.has("canonical"))
|
||||
if (!allUrls.contains(gi.get("canonical").getAsString()))
|
||||
allUrls.add(gi.get("canonical").getAsString());
|
||||
}
|
||||
} catch (Exception e) {
|
||||
System.out.println("Listing known Implementation Guides failed: "+e.getMessage());
|
||||
}
|
||||
}
|
||||
return allUrls;
|
||||
}
|
||||
|
||||
/**
|
||||
* List which versions of a package are available
|
||||
*
|
||||
* @param url
|
||||
* @return
|
||||
* @throws IOException
|
||||
*/
|
||||
|
||||
public VersionHistory listVersions(String url) throws IOException {
|
||||
if (historyCache.containsKey(url))
|
||||
|
|
@ -767,18 +707,13 @@ public class PackageCacheManager {
|
|||
}
|
||||
|
||||
|
||||
/**
|
||||
* Clear the cache
|
||||
*
|
||||
* @throws IOException
|
||||
*/
|
||||
public void clear() throws IOException {
|
||||
for (File f : new File(cacheFolder).listFiles()) {
|
||||
if (f.isDirectory()) {
|
||||
Utilities.clearDirectory(f.getAbsolutePath());
|
||||
f.delete();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public static String userDir() throws IOException {
|
||||
return Utilities.path(System.getProperty("user.home"), ".fhir", "packages");
|
||||
clearCache();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -505,14 +505,13 @@ public class ValidationEngine {
|
|||
}
|
||||
|
||||
private Map<String, byte[]> loadPackage(InputStream stream, String name) throws FileNotFoundException, IOException {
|
||||
return loadPackage(pcm.extractLocally(stream, name));
|
||||
return loadPackage(NpmPackage.fromPackage(stream));
|
||||
}
|
||||
|
||||
public Map<String, byte[]> loadPackage(NpmPackage pi) throws IOException {
|
||||
Map<String, byte[]> res = new HashMap<String, byte[]>();
|
||||
for (String s : pi.list("package")) {
|
||||
if (s.startsWith("CodeSystem-") || s.startsWith("ConceptMap-") || s.startsWith("ImplementationGuide-") || s.startsWith("StructureMap-") || s.startsWith("ValueSet-") || s.startsWith("StructureDefinition-"))
|
||||
res.put(s, TextFile.streamToBytes(pi.load("package", s)));
|
||||
for (String s : pi.listResources("CodeSystem", "ConceptMap", "ImplementationGuide", "StructureMap", "ValueSet", "StructureDefinition")) {
|
||||
res.put(s, TextFile.streamToBytes(pi.load("package", s)));
|
||||
}
|
||||
String ini = "[FHIR]\r\nversion="+pi.fhirVersion()+"\r\n";
|
||||
res.put("version.info", ini.getBytes());
|
||||
|
|
|
|||
|
|
@ -415,13 +415,13 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
|||
private IContextResourceLoader loaderForVersion() {
|
||||
if (Utilities.noString(version))
|
||||
return null;
|
||||
if (version.equals("1.0.2"))
|
||||
if (version.startsWith("1.0"))
|
||||
return new R2ToR5Loader();
|
||||
if (version.equals("1.4.0"))
|
||||
if (version.startsWith("1.4"))
|
||||
return new R2016MayToR5Loader(); // special case
|
||||
if (version.equals("3.0.1"))
|
||||
if (version.startsWith("3.0"))
|
||||
return new R3ToR5Loader();
|
||||
if (version.equals("4.0.0"))
|
||||
if (version.startsWith("4.0"))
|
||||
return new R4ToR5Loader();
|
||||
return null;
|
||||
}
|
||||
|
|
@ -613,14 +613,13 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
|||
}
|
||||
|
||||
private Map<String, byte[]> loadPackage(InputStream stream, String name) throws FileNotFoundException, IOException {
|
||||
return loadPackage(pcm.extractLocally(stream, name));
|
||||
return loadPackage(NpmPackage.fromPackage(stream));
|
||||
}
|
||||
|
||||
public Map<String, byte[]> loadPackage(NpmPackage pi) throws IOException {
|
||||
Map<String, byte[]> res = new HashMap<String, byte[]>();
|
||||
for (String s : pi.list("package")) {
|
||||
if (s.startsWith("CodeSystem-") || s.startsWith("ConceptMap-") || s.startsWith("ImplementationGuide-") || s.startsWith("CapabilityStatement-") || s.startsWith("StructureMap-") || s.startsWith("ValueSet-") || s.startsWith("StructureDefinition-"))
|
||||
res.put(s, TextFile.streamToBytes(pi.load("package", s)));
|
||||
for (String s : pi.listResources("CodeSystem", "ConceptMap", "ImplementationGuide", "CapabilityStatement", "Conformance", "StructureMap", "ValueSet", "StructureDefinition")) {
|
||||
res.put(s, TextFile.streamToBytes(pi.load("package", s)));
|
||||
}
|
||||
String ini = "[FHIR]\r\nversion="+pi.fhirVersion()+"\r\n";
|
||||
res.put("version.info", ini.getBytes());
|
||||
|
|
@ -787,7 +786,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
|||
System.out.print("* load file: "+fn);
|
||||
Resource r = null;
|
||||
try {
|
||||
if (version.equals("3.0.1") || version.equals("3.0.0")) {
|
||||
if (version.startsWith("3.0")) {
|
||||
org.hl7.fhir.dstu3.model.Resource res;
|
||||
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
|
||||
res = new org.hl7.fhir.dstu3.formats.XmlParser().parse(new ByteArrayInputStream(t.getValue()));
|
||||
|
|
@ -798,7 +797,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
|||
else
|
||||
throw new Exception("Unsupported format for "+fn);
|
||||
r = VersionConvertor_30_50.convertResource(res, false);
|
||||
} else if (version.equals("4.0.0")) {
|
||||
} else if (version.startsWith("4.0")) {
|
||||
org.hl7.fhir.r4.model.Resource res;
|
||||
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
|
||||
res = new org.hl7.fhir.r4.formats.XmlParser().parse(new ByteArrayInputStream(t.getValue()));
|
||||
|
|
@ -809,7 +808,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
|||
else
|
||||
throw new Exception("Unsupported format for "+fn);
|
||||
r = VersionConvertor_40_50.convertResource(res);
|
||||
} else if (version.equals("1.4.0")) {
|
||||
} else if (version.startsWith("1.4")) {
|
||||
org.hl7.fhir.dstu2016may.model.Resource res;
|
||||
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
|
||||
res = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new ByteArrayInputStream(t.getValue()));
|
||||
|
|
@ -818,7 +817,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
|||
else
|
||||
throw new Exception("Unsupported format for "+fn);
|
||||
r = VersionConvertor_14_50.convertResource(res);
|
||||
} else if (version.equals("1.0.2")) {
|
||||
} else if (version.startsWith("1.0")) {
|
||||
org.hl7.fhir.dstu2.model.Resource res;
|
||||
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
|
||||
res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(new ByteArrayInputStream(t.getValue()));
|
||||
|
|
|
|||
|
|
@ -372,12 +372,26 @@ public class Validator {
|
|||
definitions = args[++i];
|
||||
else if (args[i].equals("-version")) {
|
||||
sv = args[++i];
|
||||
if ("1.0".equals(sv)) sv = "1.0.2";
|
||||
if ("1.4".equals(sv)) sv = "1.4.0";
|
||||
if ("3.0".equals(sv)) sv = "3.0.1";
|
||||
if ("4.0".equals(sv)) sv = "4.0.0";
|
||||
if (sv.startsWith(Constants.VERSION)) sv = Constants.VERSION;
|
||||
definitions = "hl7.fhir.core#"+sv;
|
||||
if (sv.startsWith("1.0")) {
|
||||
sv = "1.0.2";
|
||||
definitions = "hl7.fhir.r2.core#"+sv;
|
||||
}
|
||||
if (sv.startsWith("1.4")) {
|
||||
sv = "1.4.0";
|
||||
definitions = "hl7.fhir.r2b.core#"+sv;
|
||||
}
|
||||
if (sv.startsWith("3.0")) {
|
||||
sv = "3.0.2";
|
||||
definitions = "hl7.fhir.r3.core#"+sv;
|
||||
}
|
||||
if (sv.startsWith("4.0")) {
|
||||
sv = "4.0.1";
|
||||
definitions = "hl7.fhir.r4.core#"+sv;
|
||||
}
|
||||
if (sv.startsWith(Constants.VERSION)) {
|
||||
sv = Constants.VERSION;
|
||||
definitions = "hl7.fhir.r5.core#"+sv;
|
||||
}
|
||||
} else if (args[i].equals("-output"))
|
||||
if (i+1 == args.length)
|
||||
throw new Error("Specified -output without indicating output file");
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ public class ProfileComparisonTests {
|
|||
public void testCurrentComparison() throws Exception {
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println("Compare US Patient Core with AU Patient Base");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.R4);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r3.core#3.0.1", DEF_TX, null, FhirPublication.R4);
|
||||
ve.loadIg("hl7.fhir.us.core#1.0.1", false);
|
||||
ve.loadIg("hl7.fhir.au.base#dev", false);
|
||||
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ public class ValidationEngineTests {
|
|||
public void testCurrentXml() throws Exception {
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println("Validate patient-example.xml in Current version");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#4.0.0", DEF_TX, null, FhirPublication.R4);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, null, FhirPublication.R4);
|
||||
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient-example.xml"), null);
|
||||
int e = errors(op);
|
||||
int w = warnings(op);
|
||||
|
|
@ -47,7 +47,7 @@ public class ValidationEngineTests {
|
|||
public void testCurrentJson() throws Exception {
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println("Validate patient-example.json in Current version");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#4.0.0", DEF_TX, null, FhirPublication.R4);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, null, FhirPublication.R4);
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "patient-example.json"), null);
|
||||
int e = errors(op);
|
||||
int w = warnings(op);
|
||||
|
|
@ -67,7 +67,7 @@ public class ValidationEngineTests {
|
|||
}
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println("Validate patient-example.xml in v1.4.0 version");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#1.4.0", DEF_TX, null, FhirPublication.DSTU2016May);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2b.core#1.4.0", DEF_TX, null, FhirPublication.DSTU2016May);
|
||||
ve.setNoInvariantChecks(true);
|
||||
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient140.xml"), null);
|
||||
if (!TestUtilities.silent)
|
||||
|
|
@ -92,7 +92,7 @@ public class ValidationEngineTests {
|
|||
}
|
||||
if (!org.hl7.fhir.validation.tests.utilities.TestUtilities.silent)
|
||||
System.out.println("Validate patient-example.xml in v1.0.2 version");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2);
|
||||
ve.setNoInvariantChecks(true);
|
||||
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient102.xml"), null);
|
||||
if (!TestUtilities.silent)
|
||||
|
|
@ -117,7 +117,7 @@ public class ValidationEngineTests {
|
|||
}
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println("Validate patient-example.xml in v1.0.2 version");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2);
|
||||
ve.setNoInvariantChecks(true);
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "observation102.json"), null);
|
||||
if (!TestUtilities.silent)
|
||||
|
|
@ -139,7 +139,7 @@ public class ValidationEngineTests {
|
|||
public void test301() throws Exception {
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println("Validate observation301.xml against Core");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.STU3);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, null, FhirPublication.STU3);
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println(" .. load USCore");
|
||||
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "observation301.xml"), null);
|
||||
|
|
@ -158,7 +158,7 @@ public class ValidationEngineTests {
|
|||
public void test301USCore() throws Exception {
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println("Validate patient300.xml against US-Core");
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.STU3);
|
||||
ValidationEngine ve = new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, null, FhirPublication.STU3);
|
||||
if (!TestUtilities.silent)
|
||||
System.out.println(" .. load USCore");
|
||||
ve.loadIg("hl7.fhir.us.core#1.0.1", false);
|
||||
|
|
|
|||
|
|
@ -93,14 +93,14 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
|
|||
v = content.get("version").getAsString();
|
||||
|
||||
if (ve == null || !v.equals(veVersion)) {
|
||||
if (v.equals("5.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.core#current", DEF_TX, null, FhirPublication.R5, true);
|
||||
else if (v.equals("3.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.STU3, true);
|
||||
else if (v.equals("4.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.core#4.0.0", DEF_TX, null, FhirPublication.R4, true);
|
||||
else if (v.equals("1.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, true);
|
||||
if (v.startsWith("5.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.r5.core#current", DEF_TX, null, FhirPublication.R5, true);
|
||||
else if (v.startsWith("3.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, null, FhirPublication.STU3, true);
|
||||
else if (v.startsWith("4.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, null, FhirPublication.R4, true);
|
||||
else if (v.startsWith("1.0"))
|
||||
ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, true);
|
||||
else
|
||||
throw new Exception("unknown version "+v);
|
||||
TestingUtilities.fcontext = ve.getContext();
|
||||
|
|
|
|||
Loading…
Reference in New Issue