mirror of
https://github.com/hapifhir/org.hl7.fhir.core.git
synced 2025-03-03 18:09:08 +00:00
validation documentation improvements, and batch loading
This commit is contained in:
Grahame Grieve
parent
cb70afed0c
commit
0fcb97aa2f
@ -23,6 +23,7 @@ package org.hl7.fhir.r4.utils;
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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.IOException;
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import java.net.URISyntaxException;
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import java.util.UUID;
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@ -30,113 +31,155 @@ import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.r4.formats.IParser;
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import org.hl7.fhir.r4.formats.JsonParser;
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import org.hl7.fhir.r4.formats.XmlParser;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.r4.model.Bundle.BundleType;
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import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
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import org.hl7.fhir.r4.model.Resource;
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import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
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import org.hl7.fhir.r4.utils.client.ToolingClientLogger;
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import org.hl7.fhir.utilities.IniFile;
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import org.hl7.fhir.utilities.Utilities;
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public class BatchLoader {
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public static void main(String[] args) throws IOException, Exception {
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if (args.length < 4) {
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System.out.println("Batch uploader takes 4 parameters in order: server base url, file/folder to upload, xml/json, and batch size");
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if (args.length < 3) {
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System.out.println("Batch uploader takes 3 parameters in order: server base url, file/folder to upload, and batch size");
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} else {
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String server = args[0];
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String file = args[1];
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IParser p = new JsonParser(); // args[2].equals("json") ? new JsonParser() : new XmlParser();
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int size = Integer.parseInt(args[3]);
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size = 500;
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int size = Integer.parseInt(args[2]);
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if (file.endsWith(".xml")) {
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throw new FHIRException("Unimplemented file type "+file);
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} else if (file.endsWith(".json")) {
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throw new FHIRException("Unimplemented file type "+file);
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} else if (file.endsWith(".zip")) {
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LoadZipFile(server, file, p, size, 0, -1);
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// } else if (file.endsWith(".zip")) {
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// LoadZipFile(server, file, p, size, 0, -1);
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} else if (new File(file).isDirectory()) {
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LoadDirectory(server, file, p, size);
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LoadDirectory(server, file, size);
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} else
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throw new FHIRException("Unknown file type "+file);
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}
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}
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private static void LoadDirectory(String server, String file, IParser p, int size) throws IOException, Exception {
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// LoadZipFile(server, Utilities.path(file, "Patient.json.zip"), p, size, 1000, -1);
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// LoadZipFile(server, Utilities.path(file, "Binary.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "DocumentReference.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "Encounter.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "Organization.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "Procedure.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "AllergyIntolerance.json.zip"), p, size, 1500, -1);
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// LoadZipFile(server, Utilities.path(file, "Condition.json.zip"), p, size, 0, -1);
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LoadZipFile(server, Utilities.path(file, "Immunization.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "MedicationStatement.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "Observation-res.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "Observation-sh.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "Observation-vs.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "Observation-gen.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "List.json.zip"), p, size, 6500, -1);
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// LoadZipFile(server, Utilities.path(file, "List-res.json.zip"), p, size, 0, -1);
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// LoadZipFile(server, Utilities.path(file, "List-vs.json.zip"), p, size, 0, -1);
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private static void LoadDirectory(String server, String folder, int size) throws IOException, Exception {
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System.out.print("Connecting to "+server+".. ");
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FHIRToolingClient client = new FHIRToolingClient(server);
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System.out.println("Done");
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IniFile ini = new IniFile(Utilities.path(folder, "batch-load-progress.ini"));
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for (File f : new File(folder).listFiles()) {
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if (f.getName().endsWith(".json") || f.getName().endsWith(".xml")) {
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if (!ini.getBooleanProperty("finished", f.getName())) {
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sendFile(client, f, size, ini);
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}
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}
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}
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}
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private static void LoadZipFile(String server, String file, IParser p, int size, int start, int end) throws IOException, Exception {
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System.out.println("Load Zip file "+file);
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Bundle b = new Bundle();
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b.setType(BundleType.COLLECTION);
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b.setId(UUID.randomUUID().toString().toLowerCase());
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ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
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ZipEntry entry;
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while((entry = zip.getNextEntry())!=null)
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{
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try {
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Resource r = p.parse(zip);
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b.addEntry().setResource(r);
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} catch (Exception e) {
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throw new Exception("Error parsing "+entry.getName()+": "+e.getMessage(), e);
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}
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}
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loadBundle(server, b, size, start, end);
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}
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private static void sendFile(FHIRToolingClient client, File f, int size, IniFile ini) throws FHIRFormatError, FileNotFoundException, IOException {
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System.out.print("Loading "+f.getName()+".. ");
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IParser parser = f.getName().endsWith(".json") ? new JsonParser() : new XmlParser();
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Resource res = parser.parse(new FileInputStream(f));
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System.out.println("Done. Size = "+size);
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if (res instanceof Bundle) {
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Bundle bnd = (Bundle) res;
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int cursor = ini.hasProperty("progress", f.getName()) ? ini.getIntegerProperty("progress", f.getName()) : 0;
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while (cursor < bnd.getEntry().size()) {
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Bundle bt = new Bundle();
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bt.setType(BundleType.BATCH);
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bt.setId(UUID.randomUUID().toString().toLowerCase());
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for (int i = cursor; i < Math.min(bnd.getEntry().size(), cursor+size); i++) {
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BundleEntryComponent be = bt.addEntry();
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be.setResource(bnd.getEntry().get(i).getResource());
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be.getRequest().setMethod(HTTPVerb.PUT);
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be.getRequest().setUrl(be.getResource().getResourceType().toString()+"/"+be.getResource().getId());
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}
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System.out.print(f.getName()+" ("+cursor+"/"+bnd.getEntry().size()+"): ");
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long ms = System.currentTimeMillis();
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Bundle resp = client.transaction(bt);
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private static int loadBundle(String server, Bundle b, int size, int start, int end) throws URISyntaxException {
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System.out.println("Post to "+server+". size = "+Integer.toString(size)+", start = "+Integer.toString(start)+", total = "+Integer.toString(b.getEntry().size()));
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FHIRToolingClient client = new FHIRToolingClient(server);
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int c = start;
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if (end == -1)
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end = b.getEntry().size();
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while (c < end) {
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Bundle bt = new Bundle();
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bt.setType(BundleType.BATCH);
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bt.setId(UUID.randomUUID().toString().toLowerCase());
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for (int i = c; i < Math.min(b.getEntry().size(), c+size); i++) {
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BundleEntryComponent be = bt.addEntry();
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be.setResource(b.getEntry().get(i).getResource());
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be.getRequest().setMethod(HTTPVerb.PUT);
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be.getRequest().setUrl(be.getResource().getResourceType().toString()+"/"+be.getResource().getId());
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}
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System.out.print(" posting..");
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long ms = System.currentTimeMillis();
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Bundle resp = client.transaction(bt);
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for (int i = 0; i < resp.getEntry().size(); i++) {
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BundleEntryComponent t = resp.getEntry().get(i);
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if (!t.getResponse().getStatus().startsWith("2")) {
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System.out.println("failed status at "+Integer.toString(i)+": "+t.getResponse().getStatus());
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return c+i;
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}
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}
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c = c + size;
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System.out.println(" ..done: "+Integer.toString(c)+". ("+Long.toString(System.currentTimeMillis()-ms)+" ms)");
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}
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System.out.println(" done");
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return c;
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}
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cursor = cursor+size;
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for (int i = 0; i < resp.getEntry().size(); i++) {
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BundleEntryComponent t = resp.getEntry().get(i);
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if (!t.getResponse().getStatus().startsWith("2")) {
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System.out.println("failed status at "+Integer.toString(i)+": "+t.getResponse().getStatus());
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cursor = cursor+i-1;
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break;
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}
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}
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System.out.println(" .. done: ("+Long.toString(System.currentTimeMillis()-ms)+" ms)");
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ini.setIntegerProperty("progress", f.getName(), cursor, null);
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ini.save();
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}
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ini.setBooleanProperty("finished", f.getName(), true, null);
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ini.save();
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} else {
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client.update(res);
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ini.setBooleanProperty("finished", f.getName(), true, null);
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ini.save();
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}
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}
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//
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// private static void LoadZipFile(String server, String file, IParser p, int size, int start, int end) throws IOException, Exception {
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// System.out.println("Load Zip file "+file);
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// Bundle b = new Bundle();
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// b.setType(BundleType.COLLECTION);
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// b.setId(UUID.randomUUID().toString().toLowerCase());
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// ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
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// ZipEntry entry;
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// while((entry = zip.getNextEntry())!=null)
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// {
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// try {
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// Resource r = p.parse(zip);
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// b.addEntry().setResource(r);
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// } catch (Exception e) {
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// throw new Exception("Error parsing "+entry.getName()+": "+e.getMessage(), e);
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// }
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// }
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// loadBundle(server, b, size, start, end);
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// }
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//
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//
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// private static int loadBundle(String server, Bundle b, int size, int start, int end) throws URISyntaxException {
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// System.out.println("Post to "+server+". size = "+Integer.toString(size)+", start = "+Integer.toString(start)+", total = "+Integer.toString(b.getEntry().size()));
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// FHIRToolingClient client = new FHIRToolingClient(server);
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// int c = start;
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// if (end == -1)
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// end = b.getEntry().size();
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// while (c < end) {
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// Bundle bt = new Bundle();
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// bt.setType(BundleType.BATCH);
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// bt.setId(UUID.randomUUID().toString().toLowerCase());
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// for (int i = c; i < Math.min(b.getEntry().size(), c+size); i++) {
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// BundleEntryComponent be = bt.addEntry();
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// be.setResource(b.getEntry().get(i).getResource());
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// be.getRequest().setMethod(HTTPVerb.PUT);
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// be.getRequest().setUrl(be.getResource().getResourceType().toString()+"/"+be.getResource().getId());
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// }
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// System.out.print(" posting..");
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// long ms = System.currentTimeMillis();
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// Bundle resp = client.transaction(bt);
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//
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// for (int i = 0; i < resp.getEntry().size(); i++) {
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// BundleEntryComponent t = resp.getEntry().get(i);
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// if (!t.getResponse().getStatus().startsWith("2")) {
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// System.out.println("failed status at "+Integer.toString(i)+": "+t.getResponse().getStatus());
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// return c+i;
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// }
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// }
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// c = c + size;
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// System.out.println(" ..done: "+Integer.toString(c)+". ("+Long.toString(System.currentTimeMillis()-ms)+" ms)");
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// }
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// System.out.println(" done");
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// return c;
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// }
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}
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@ -263,35 +263,64 @@ public class FHIRToolingClient {
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return (T) bnd.getEntry().get(0).getResource();
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}
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//
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// public <T extends Resource> T update(Class<T> resourceClass, T resource, String id) {
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// ResourceRequest<T> result = null;
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// try {
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// List<Header> headers = null;
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// result = utils.issuePutRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers, proxy);
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// result.addErrorStatus(410);//gone
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// result.addErrorStatus(404);//unknown
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// result.addErrorStatus(405);
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// result.addErrorStatus(422);//Unprocessable Entity
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// result.addSuccessStatus(200);
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// result.addSuccessStatus(201);
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// if(result.isUnsuccessfulRequest()) {
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// throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
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// }
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// } catch(Exception e) {
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// throw new EFhirClientException("An error has occurred while trying to update this resource", e);
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// }
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// // TODO oe 26.1.2015 could be made nicer if only OperationOutcome locationheader is returned with an operationOutcome would be returned (and not the resource also) we make another read
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// try {
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// OperationOutcome operationOutcome = (OperationOutcome)result.getPayload();
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// ResourceAddress.ResourceVersionedIdentifier resVersionedIdentifier = ResourceAddress.parseCreateLocation(result.getLocation());
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// return this.vread(resourceClass, resVersionedIdentifier.getId(),resVersionedIdentifier.getVersionId());
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// } catch(ClassCastException e) {
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// // if we fall throught we have the correct type already in the create
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// }
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//
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// return result.getPayload();
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// }
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public Resource update(Resource resource) {
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ResourceRequest<Resource> result = null;
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try {
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List<Header> headers = null;
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result = utils.issuePutRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resource.getClass(), resource.getId()),utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers);
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result.addErrorStatus(410);//gone
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result.addErrorStatus(404);//unknown
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result.addErrorStatus(405);
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result.addErrorStatus(422);//Unprocessable Entity
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result.addSuccessStatus(200);
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result.addSuccessStatus(201);
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if(result.isUnsuccessfulRequest()) {
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throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
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}
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} catch(Exception e) {
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throw new EFhirClientException("An error has occurred while trying to update this resource", e);
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}
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// TODO oe 26.1.2015 could be made nicer if only OperationOutcome locationheader is returned with an operationOutcome would be returned (and not the resource also) we make another read
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try {
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OperationOutcome operationOutcome = (OperationOutcome)result.getPayload();
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ResourceAddress.ResourceVersionedIdentifier resVersionedIdentifier = ResourceAddress.parseCreateLocation(result.getLocation());
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return this.vread(resource.getClass(), resVersionedIdentifier.getId(),resVersionedIdentifier.getVersionId());
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} catch(ClassCastException e) {
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// if we fall throught we have the correct type already in the create
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}
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return result.getPayload();
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}
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public <T extends Resource> T update(Class<T> resourceClass, T resource, String id) {
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ResourceRequest<T> result = null;
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try {
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List<Header> headers = null;
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result = utils.issuePutRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers);
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result.addErrorStatus(410);//gone
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result.addErrorStatus(404);//unknown
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result.addErrorStatus(405);
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result.addErrorStatus(422);//Unprocessable Entity
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result.addSuccessStatus(200);
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result.addSuccessStatus(201);
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if(result.isUnsuccessfulRequest()) {
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throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
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}
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} catch(Exception e) {
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throw new EFhirClientException("An error has occurred while trying to update this resource", e);
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}
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// TODO oe 26.1.2015 could be made nicer if only OperationOutcome locationheader is returned with an operationOutcome would be returned (and not the resource also) we make another read
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try {
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OperationOutcome operationOutcome = (OperationOutcome)result.getPayload();
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ResourceAddress.ResourceVersionedIdentifier resVersionedIdentifier = ResourceAddress.parseCreateLocation(result.getLocation());
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return this.vread(resourceClass, resVersionedIdentifier.getId(),resVersionedIdentifier.getVersionId());
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} catch(ClassCastException e) {
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// if we fall throught we have the correct type already in the create
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}
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return result.getPayload();
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}
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//
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// public <T extends Resource> boolean delete(Class<T> resourceClass, String id) {
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@ -58,6 +58,7 @@ public class Constants {
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public final static String NS_SYSTEM_TYPE = "http://hl7.org/fhirpath/System.";
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public final static String VERSION = "4.1.0";
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public final static String VERSION_MM = "4.1";
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public final static String BUILD_ID = "2ce21320c7";
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public final static String DATE = "Thu Oct 17 19:56:09 AEDT 2019";
|
||||
public final static String URI_REGEX = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AdministrableProductDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CapabilityStatement2|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|ClinicalUseIssue|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|ConditionDefinition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|Ingredient|InsurancePlan|Invoice|Library|Linkage|List|Location|ManufacturedItemDefinition|Measure|MeasureReport|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationUsage|MedicinalProductDefinition|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionIntake|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|PackagedProductDefinition|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RegulatedAuthorization|RelatedPerson|RequestGroup|ResearchStudy|ResearchSubject|RiskAssessment|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceDefinition|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|Topic|ValueSet|VerificationResult|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?";
|
||||
|
||||
@ -1526,4 +1526,8 @@ public final class IniFile
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
public boolean hasProperty(String section, String name) {
|
||||
return getStringProperty(section, name) != null;
|
||||
}
|
||||
}
|
||||
|
||||
@ -160,8 +160,8 @@ public class Validator {
|
||||
System.out.println("");
|
||||
System.out.println("The FHIR validation tool validates a FHIR resource or bundle.");
|
||||
System.out.println("Schema and schematron checking is performed, then some additional checks are performed. ");
|
||||
System.out.println("* XML & Json (FHIR versions 1.0, 1.4, 3.0, 3.4)");
|
||||
System.out.println("* Turtle (FHIR versions 3.0, 3.4)");
|
||||
System.out.println("* XML & Json (FHIR versions 1.0, 1.4, 3.0, 4.0, "+Constants.VERSION_MM+")");
|
||||
System.out.println("* Turtle (FHIR versions 3.0, 4.0, "+Constants.VERSION_MM+")");
|
||||
System.out.println("");
|
||||
System.out.println("If requested, instances will also be verified against the appropriate schema");
|
||||
System.out.println("W3C XML Schema, JSON schema or ShEx, as appropriate");
|
||||
@ -264,8 +264,8 @@ public class Validator {
|
||||
if (v == null) v = Constants.VERSION;
|
||||
else if ("1.0".equals(v)) v = "1.0.2";
|
||||
else if ("1.4".equals(v)) v = "1.4.0";
|
||||
else if ("3.0".equals(v)) v = "3.0.1";
|
||||
else if ("4.0".equals(v)) v = "4.0.0";
|
||||
else if ("3.0".equals(v)) v = "3.0.2";
|
||||
else if ("4.0".equals(v)) v = "4.0.1";
|
||||
else if (v.startsWith(Constants.VERSION)) v = Constants.VERSION;
|
||||
String definitions = "hl7.fhir.core#"+v;
|
||||
System.out.println("Loading (v = "+v+", tx server http://tx.fhir.org)");
|
||||
|
||||
2
pom.xml
2
pom.xml
@ -17,7 +17,7 @@
|
||||
|
||||
<properties>
|
||||
<hapi_fhir_version>4.1.0-SNAPSHOT</hapi_fhir_version>
|
||||
<validator_test_case_version>1.0.3-SNAPSHOT</validator_test_case_version>
|
||||
<validator_test_case_version>1.0.4-SNAPSHOT</validator_test_case_version>
|
||||
</properties>
|
||||
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
@echo off
|
||||
|
||||
set oldver=4.0.30
|
||||
set newver=4.0.31
|
||||
set oldver=4.0.31
|
||||
set newver=4.0.32
|
||||
|
||||
echo ..
|
||||
echo =====================================================================
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user