add more log statements
This commit is contained in:
Grahame Grieve
parent
662f18e09f
commit
4f048776ba
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@ -286,6 +286,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
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}
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}
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public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
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public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
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System.out.println("Load Package "+pi.name()+"#"+pi.version());
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if (types.length == 0)
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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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types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire","ConceptMap","StructureMap", "NamingSystem"};
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for (String s : pi.listResources(types)) {
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for (String s : pi.listResources(types)) {
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@ -1,94 +0,0 @@
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package org.hl7.fhir.utilities.cache;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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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 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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/**
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* intenral use only - set the file name to edit in main(), and fill out the edit routine
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*
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* @author grahame
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*
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*/
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public class PackageHacker {
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public static void main(String[] args) throws FileNotFoundException, IOException {
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new PackageHacker().edit("C:\\web\\hl7.org\\fhir\\uv\\pocd\\2018Jan\\package.tgz");
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}
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private void edit(String name) throws FileNotFoundException, IOException {
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File f = new File(name);
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if (!f.exists())
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throw new Error("Unable to find "+f.getAbsolutePath());
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NpmPackage pck = NpmPackage.fromPackage(new FileInputStream(f));
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System.out.println("Altering Package "+f.getAbsolutePath());
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System.out.println(nice(pck.getNpm()));
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change(pck.getNpm(), pck.getContent());
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System.out.println("Revised Package");
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System.out.println("=======================");
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System.out.println(nice(pck.getNpm()));
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System.out.println("=======================");
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System.out.print("save? y/n: ");
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int r = System.in.read();
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if (r == 'y') {
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f.renameTo(new File(Utilities.changeFileExt(name, ".tgz.bak")));
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pck.save(new FileOutputStream(f));
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}
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}
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private String nice(JsonObject json) {
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return new GsonBuilder().setPrettyPrinting().create().toJson(json);
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}
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private void change(JsonObject npm, Map<String, byte[]> content) throws FileNotFoundException, IOException {
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// addContentFrom("C:\\web\\hl7.org\\fhir\\us\\meds", content);
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fixNames(content);
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// setProperty(npm, "homepage", "http://hl7.org/fhir");
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}
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private void setProperty(JsonObject npm, String name, String value) {
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npm.remove("homepage");
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npm.addProperty("homepage", "http://hl7.org/fhir");
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}
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private void fixNames(Map<String, byte[]> content) {
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List<String> names = new ArrayList<>();
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names.addAll(content.keySet());
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for (String s : names) {
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if (s.endsWith("json") && !s.endsWith(".json")) {
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String n = s.substring(0, s.length()-4)+".json";
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content.put(n, content.get(s));
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content.remove(s);
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}
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}
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}
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private void addContentFrom(String folder, Map<String, byte[]> content) throws FileNotFoundException, IOException {
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for (File f : new File(folder).listFiles()) {
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if (f.getName().endsWith(".json") && !f.getName().endsWith(".canonical.json")) {
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String cnt = TextFile.fileToString(f);
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if (cnt.contains("\"resourceType\"")) {
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content.put("package/"+f.getName(), TextFile.fileToBytes(f));
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}
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}
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}
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}
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}
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@ -1,219 +0,0 @@
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package org.hl7.fhir.utilities.cache;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map.Entry;
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import org.hl7.fhir.utilities.CSVWriter;
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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.cache.PackageScanner.ResourceInfo;
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import org.hl7.fhir.utilities.json.JsonTrackingParser;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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public class PackageScanner {
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public class ResourceInfo {
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private String filenameRoot;
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private String htmlName;
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private String id;
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public ResourceInfo(String filename, String id) {
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this.filenameRoot = Utilities.changeFileExt(filename, "");
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this.id = id;
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}
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}
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public static void main(String[] args) throws FileNotFoundException, IOException {
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new PackageScanner().scan(new File("C:\\web\\hl7.org\\fhir"), "c:\\temp\\package-scan.csv", "http://hl7.org/fhir");
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}
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private void scan(File folder, String dest, String url) throws IOException {
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CSVWriter csv = new CSVWriter(new FileOutputStream(dest));
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csv.line("path", "error", "name", "version", "fhir-version", "fhir-version-explicit", "canonical", "homepage",
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"url", "type", "#types", "#urls", "dependencies", "spec.internals");
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scanFolders(folder, csv, folder.getAbsolutePath(), url);
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csv.close();
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System.out.println("done");
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}
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private void scanFolders(File folder, CSVWriter csv, String root, String url) {
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System.out.println(folder.getAbsolutePath());
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for (File file : folder.listFiles()) {
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if (file.isDirectory()) {
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scanFolders(file, csv, root, url);
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} else if (file.getName().endsWith(".tgz")) {
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processPackage(file, csv, root, url);
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}
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}
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}
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private void processPackage(File file, CSVWriter csv, String root, String url) {
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try {
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NpmPackage npm = NpmPackage.fromPackage(new FileInputStream(file));
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fix(npm, file, root, url);
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csv.line(file.getAbsolutePath(), "", npm.name(), npm.version(), npm.fhirVersion(), npm.fhirVersionList(), npm.canonical(), npm.homepage(),
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npm.url(), npm.type(), Integer.toString(npm.getTypes().size()), Integer.toString(npm.getUrls().size()), npm.dependencySummary(), Boolean.toString(npm.hasFile("other", "spec.internals")));
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} catch (Exception e) {
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try {
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csv.line(file.getAbsolutePath(), e.getMessage() == null ? "NPE" : e.getMessage());
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} catch (IOException e1) {
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e1.printStackTrace();
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}
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}
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}
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private void fix(NpmPackage npm, File file, String root, String url) throws FileNotFoundException, IOException {
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String u = Utilities.pathURL(url, Utilities.getDirectoryForFile(file.getAbsolutePath()).substring(root.length()).replace("\\", "/"));
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if (Utilities.getDirectoryForFile(file.getAbsolutePath()).equals("C:\\web\\hl7.org\\fhir")) {
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u = "http://hl7.org/fhir/R4";
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}
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boolean save = false;
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List<String> names = new ArrayList<>();
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names.addAll(npm.getContent().keySet());
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for (String s : names) {
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if (!s.startsWith("package/")) {
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save = true;
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String n = "package/"+s;
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npm.getContent().put(n, npm.getContent().get(s));
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npm.getContent().remove(s);
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}
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}
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if (!npm.getNpm().has("fhirVersions")) {
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JsonArray fv = new JsonArray();
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fv.add(npm.fhirVersion());
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npm.getNpm().add("fhirVersions", fv);
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save = true;
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}
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if (npm.getNpm().has("dependencies")) {
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JsonObject dep = npm.getNpm().getAsJsonObject("dependencies");
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for (Entry<String, JsonElement> e : dep.entrySet()) {
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if ("current".equals(e.getValue().getAsString())) {
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save = true;
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if ("hl7.fhir.us.core.r4".equals(e.getKey())) {
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dep.remove("hl7.fhir.us.core.r4");
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dep.addProperty("hl7.fhir.us.core", "3.0.1");
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} else if ("hl7.fhir.us.davinci-pas".equals(e.getKey())) {
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dep.remove("hl7.fhir.us.davinci-pas");
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dep.addProperty("hl7.fhir.us.davinci-pas", "0.1.0");
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} else if ("hl7.fhir.uv.sdc".equals(e.getKey())) {
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dep.remove("hl7.fhir.uv.sdc");
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if ("0.1.0".equals(npm.version()))
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dep.addProperty("hl7.fhir.uv.sdc", "2.5.0");
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else
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dep.addProperty("hl7.fhir.uv.sdc", "2.7.0");
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} else if ("hl7.fhir.us.core".equals(e.getKey())) {
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dep.remove("hl7.fhir.us.core");
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dep.addProperty("hl7.fhir.us.core", "3.0.1");
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} else if ("hl7.fhir.us.ccda.r4".equals(e.getKey())) {
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dep.remove("hl7.fhir.us.ccda.r4");
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dep.addProperty("hl7.fhir.us.ccda", "1.0.0");
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}
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}
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}
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}
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if (!npm.hasFile("other", "spec.internals") && !file.getName().startsWith("hl7.fhir.r")) {
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save = true;
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npm.getContent().put("package/other/spec.internals", buildSpecInternals(npm.canonical(), Utilities.getDirectoryForFile(file.getAbsolutePath())));
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}
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// if (npm.url() == null || !npm.url().equals(u)) {
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// npm.getNpm().remove("url");
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// npm.getNpm().addProperty("url", u);
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// save = true;
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// }
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// if (!npm.canonical().startsWith("http://hl7.org")) {
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// npm.getNpm().remove("canonical");
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// npm.getNpm().addProperty("canonical", "http://hl7.org/fhir/smart-app-launch");
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// save = true;
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// }
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//
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if (save) {
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File bck = new File(Utilities.changeFileExt(file.getAbsolutePath(), ".bcknpm"));
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if (bck.exists()) {
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bck.delete();
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}
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file.renameTo(bck);
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npm.save(new FileOutputStream(file));
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}
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}
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private byte[] buildSpecInternals(String canonical, String dir) throws FileNotFoundException, IOException {
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// the spec internals file contains 2 important things: a map from canonical URL to html path
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// and a list of html target files
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List<ResourceInfo> rl = makeResList(dir);
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List<String> targets = new ArrayList<>();
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for (File f : new File(dir).listFiles()) {
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if (f.getName().endsWith(".html")) {
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targets.add(f.getName());
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String src = TextFile.fileToString(f);
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for (ResourceInfo r : rl) {
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if (r.htmlName == null) {
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if (src.contains(r.filenameRoot+".json")) {
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r.htmlName = f.getName();
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}
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}
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}
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}
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}
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StringBuilder b = new StringBuilder();
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b.append("{\r\n");
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b.append(" \"paths\": {");
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boolean first = true;
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for (ResourceInfo r : rl) {
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String link = r.htmlName;
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if (link == null) {
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System.out.println("No link found for "+r.id);
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} else {
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if (first) first = false; else b.append(",");
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b.append("\r\n \"");
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b.append(Utilities.pathURL(canonical, r.id));
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b.append("\": \"");
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if (link.contains(".json.html") && new File(Utilities.path(dir,link. replace(".json", ""))).exists()) {
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link = link.replace(".json", "");
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}
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b.append(link);
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b.append("\"");
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}
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}
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b.append("\r\n },\r\n");
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b.append(" \"targets\": [");
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first = true;
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for (String s : targets) {
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if (first) first = false; else b.append(",");
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b.append("\r\n \"");
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b.append(s);
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b.append("\"");
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}
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b.append(" ]\r\n");
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b.append("}\r\n");
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return TextFile.stringToBytes(b.toString(), false);
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}
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private List<ResourceInfo> makeResList(String dir) {
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List<ResourceInfo> rl = new ArrayList<>();
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for (File f : new File(dir).listFiles()) {
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if (f.getName().endsWith(".json") && !f.getName().endsWith(".canonical.json")) {
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try {
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JsonObject obj = JsonTrackingParser.parseJson(f);
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if (obj.has("resourceType") && obj.has("id")) {
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rl.add(new ResourceInfo(f.getName(), obj.get("resourceType").getAsString() +"/"+ obj.get("id").getAsString()));
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}
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} catch (IOException e) {
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}
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}
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}
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return rl;
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}
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}
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