Work on conditional operations in JPA

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirDao.java

@@ -24,8 +24,10 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.net.URL;
 import java.text.Normalizer;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -636,7 +638,12 @@ public abstract class BaseFhirDao implements IDao {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		List<NameValuePair> parameters;
 		try {
-			parameters = URLEncodedUtils.parse(new URI(theMatchUrl), "UTF-8");
+			String matchUrl = theMatchUrl;
+			if (matchUrl.indexOf('?') == -1) {
+				throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Error was: URL does not contain any parameters ('?' not detected)");
+			}
+			matchUrl = matchUrl.replace("|", "%7C");
+			parameters = URLEncodedUtils.parse(new URI(matchUrl), "UTF-8");
 		} catch (URISyntaxException e) {
 			throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Error was: " + e.toString());
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java

@@ -200,7 +200,10 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
 					String url = extractTransactionUrlOrThrowException(nextEntry, verb);
 
 					UrlParts parts = parseUrl(verb.getCode(), url);
-					if (parts.getResourceId() != null) {
+					if (res.getId().hasIdPart() && isBlank(parts.getResourceId())) {
+						parts.setResourceId(res.getId().getIdPart());
+					}
+					if (isNotBlank(parts.getResourceId())) {
 						res.setId(new IdDt(parts.getResourceType(), parts.getResourceId()));
 						outcome = resourceDao.update(res, null, false);
 					} else {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamExtractorDstu2.java

@@ -446,6 +446,22 @@ class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implements ISea
 					}
 					systems.add(null);
 					codes.add(nextValue.getValueAsString());
+				} else if (nextObject instanceof CodingDt) {
+					CodingDt nextValue = (CodingDt) nextObject;
+					if (nextValue.isEmpty()) {
+						continue;
+					}
+					String nextSystem = nextValue.getSystemElement().getValueAsString();
+					String nextCode = nextValue.getCodeElement().getValue();
+					if (isNotBlank(nextSystem) || isNotBlank(nextCode)) {
+						systems.add(nextSystem);
+						codes.add(nextCode);
+					}
+
+					if (!nextValue.getDisplayElement().isEmpty()) {
+						systems.add(null);
+						codes.add(nextValue.getDisplayElement().getValue());
+					}
 				} else if (nextObject instanceof CodeableConceptDt) {
 					CodeableConceptDt nextCC = (CodeableConceptDt) nextObject;
 					if (!nextCC.getTextElement().isEmpty()) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2Test.java

@@ -217,8 +217,8 @@ public class FhirResourceDaoDstu2Test {
 	}
 
 	@Test
-	public void testCreateWithIfNoneExist() {
+	public void testCreateWithIfNoneExistBasic() {
-		String methodName = "testCreateWithIfNoneExist";
+		String methodName = "testCreateWithIfNoneExistBasic";
 		MethodOutcome results;
 
 		Patient p = new Patient();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -4,7 +4,15 @@ import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.*;
 
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.net.InetSocketAddress;
+import java.net.Socket;
+import java.net.SocketAddress;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashSet;
@@ -13,6 +21,7 @@ import java.util.Set;
 import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.builder.CompareToBuilder;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpDelete;
 import org.apache.http.client.methods.HttpGet;
@@ -31,6 +40,8 @@ import org.junit.BeforeClass;
 import org.junit.Test;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
 
+import com.google.common.net.UrlEscapers;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
@@ -89,6 +100,7 @@ public class ResourceProviderDstu2Test {
 	private static DaoConfig ourDaoConfig;
 	private static CloseableHttpClient ourHttpClient;
 	private static String ourServerBase;
+	private static int ourPort;
 
 	// private static JpaConformanceProvider ourConfProvider;
 
@@ -147,6 +159,7 @@ public class ResourceProviderDstu2Test {
 		String resource = ourFhirCtx.newXmlParser().encodeResourceToString(pt);
 
 		HttpPost post = new HttpPost(ourServerBase + "/Patient");
+		post.addHeader(Constants.HEADER_IF_NONE_EXIST, "Patient?name=" + methodName);
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 		CloseableHttpResponse response = ourHttpClient.execute(post);
 		IdDt id;
@@ -166,7 +179,7 @@ public class ResourceProviderDstu2Test {
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String newIdString = response.getFirstHeader(Constants.HEADER_LOCATION_LC).getValue();
-			assertEquals(id.getValue(), newIdString);
+			assertEquals(id.getValue(), newIdString); // version should match for conditional create
 		} finally {
 			response.close();
 		}
@@ -181,7 +194,7 @@ public class ResourceProviderDstu2Test {
 		pt.addName().addFamily(methodName);
 		String resource = ourFhirCtx.newXmlParser().encodeResourceToString(pt);
 
-		HttpPost post = new HttpPost(ourServerBase + "/Patient");
+		HttpPost post = new HttpPost(ourServerBase + "/Patient?name=" + methodName);
 		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 		CloseableHttpResponse response = ourHttpClient.execute(post);
 		IdDt id;
@@ -200,7 +213,7 @@ public class ResourceProviderDstu2Test {
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			IdDt newId = new IdDt(response.getFirstHeader(Constants.HEADER_LOCATION_LC).getValue());
-			assertEquals(id.toVersionless(), newId.toVersionless());
+			assertEquals(id.toVersionless(), newId.toVersionless()); // version shouldn't match for conditional update
 			assertNotEquals(id, newId);
 		} finally {
 			response.close();
@@ -209,8 +222,8 @@ public class ResourceProviderDstu2Test {
 	}
 
 	@Test
-	public void testDeleteResourceConditional() throws IOException {
+	public void testDeleteResourceConditional1() throws IOException {
-		String methodName = "testDeleteResourceConditional";
+		String methodName = "testDeleteResourceConditional1";
 
 		Patient pt = new Patient();
 		pt.addName().addFamily(methodName);
@@ -248,6 +261,67 @@ public class ResourceProviderDstu2Test {
 
 	}
 
+	/**
+	 * Based on email from Rene Spronk
+	 */
+	@Test
+	public void testDeleteResourceConditional2() throws IOException, Exception {
+		String methodName = "testDeleteResourceConditional2";
+
+		Patient pt = new Patient();
+		pt.addName().addFamily(methodName);
+		pt.addIdentifier().setSystem("http://ghh.org/patient").setValue("555-44-4444");
+		String resource = ourFhirCtx.newXmlParser().encodeResourceToString(pt);
+
+		HttpPost post = new HttpPost(ourServerBase + "/Patient");
+		post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+		CloseableHttpResponse response = ourHttpClient.execute(post);
+		IdDt id;
+		try {
+			assertEquals(201, response.getStatusLine().getStatusCode());
+			String newIdString = response.getFirstHeader(Constants.HEADER_LOCATION_LC).getValue();
+			assertThat(newIdString, startsWith(ourServerBase + "/Patient/"));
+			id = new IdDt(newIdString);
+		} finally {
+			response.close();
+		}
+
+		/*
+		 * Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL
+		 * but we want to make sure that works too..  
+		 */
+		Socket sock = new Socket();
+		try {
+			sock.connect(new InetSocketAddress("localhost", ourPort));
+			sock.getOutputStream().write(("DELETE " + "/fhir/context/Patient?identifier=" + ("http://ghh.org/patient|555-44-4444")).getBytes("UTF-8"));
+			sock.getOutputStream().write("\n\n".getBytes("UTF-8"));
+			sock.getOutputStream().flush();
+			
+			InputStream inputStream = sock.getInputStream();
+
+			byte[] buf = new byte[10000];
+			int count;
+			StringBuilder b = new StringBuilder();
+			while ((count = inputStream.read(buf)) > 0) {
+				b.append(new String(buf, 0, count, Charset.forName("UTF-8")));
+			}
+			String resp = b.toString();
+						
+			ourLog.info("Resp: {}", resp);
+		} finally {
+			sock.close();
+		}
+		HttpGet read = new HttpGet(ourServerBase + "/Patient/" + id.getIdPart());
+		response = ourHttpClient.execute(read);
+		try {
+			ourLog.info(response.toString());
+			assertEquals(Constants.STATUS_HTTP_410_GONE, response.getStatusLine().getStatusCode());
+		} finally {
+			response.close();
+		}
+
+	}
+
 	/**
 	 * Test for issue #60
 	 */
@@ -746,8 +820,7 @@ public class ResourceProviderDstu2Test {
 		p1.addIdentifier().setValue("testSearchByIdentifierWithoutSystem01");
 		IdDt p1Id = ourClient.create().resource(p1).execute().getId();
 
-		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode(null, "testSearchByIdentifierWithoutSystem01")).encodedJson().prettyPrint()
+		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode(null, "testSearchByIdentifierWithoutSystem01")).encodedJson().prettyPrint().execute();
-				.execute();
 		assertEquals(1, actual.size());
 		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getResource().getId().getIdPart());
 
@@ -845,8 +918,7 @@ public class ResourceProviderDstu2Test {
 
 		assertThat(p1Id.getValue(), containsString("Patient/testUpdateWithClientSuppliedIdWhichDoesntExistRpDstu2/_history"));
 
-		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testUpdateWithClientSuppliedIdWhichDoesntExistRpDstu2"))
+		Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testUpdateWithClientSuppliedIdWhichDoesntExistRpDstu2")).encodedJson().prettyPrint().execute();
-				.encodedJson().prettyPrint().execute();
 		assertEquals(1, actual.size());
 		assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getResource().getId().getIdPart());
 
@@ -862,13 +934,13 @@ public class ResourceProviderDstu2Test {
 	@SuppressWarnings("unchecked")
 	@BeforeClass
 	public static void beforeClass() throws Exception {
-		int port = RandomServerPortProvider.findFreePort();
+		ourPort = RandomServerPortProvider.findFreePort();
 
 		RestfulServer restServer = new RestfulServer();
 		ourFhirCtx = FhirContext.forDstu2();
 		restServer.setFhirContext(ourFhirCtx);
 
-		ourServerBase = "http://localhost:" + port + "/fhir/context";
+		ourServerBase = "http://localhost:" + ourPort + "/fhir/context";
 
 		ourAppCtx = new ClassPathXmlApplicationContext("hapi-fhir-server-resourceproviders-dstu2.xml", "fhir-jpabase-spring-test-config.xml");
 
@@ -886,7 +958,7 @@ public class ResourceProviderDstu2Test {
 
 		restServer.setPagingProvider(new FifoMemoryPagingProvider(10));
 
-		ourServer = new Server(port);
+		ourServer = new Server(ourPort);
 
 		ServletContextHandler proxyHandler = new ServletContextHandler();
 		proxyHandler.setContextPath("/");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderTest.java

@@ -41,6 +41,14 @@ public class SystemProviderTest {
 		ourLog.info(response);
 	}
 	
+	@Test
+	public void testTransactionFromBundle2() throws Exception {
+
+		InputStream bundleRes = SystemProviderTest.class.getResourceAsStream("/transaction_link_patient_eve_temp.xml");
+		String bundle = IOUtils.toString(bundleRes);
+		String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
+		ourLog.info(response);
+	}
 	
 	@AfterClass
 	public static void afterClass() throws Exception {

hapi-fhir-jpaserver-base/src/test/resources/transaction_link_patient_eve_temp.xml

@@ -0,0 +1,167 @@
+<Bundle xmlns="http://hl7.org/fhir">
+    <id value="ringholm1430996763590912"/>
+    <type value="transaction"/>
+    <entry>
+        <resource>
+            <Provenance>
+                <id value="ringholm1430996763591053"/>
+                <text>
+                    <status value="generated"/>
+                    <div xmlns="http://www.w3.org/1999/xhtml">Authored on 15-Feb 2015 by GHH.</div>
+                </text>
+                <target>
+                    <!-- unversioned, part of a transaction -->
+                    <reference value="Patient/b555-44-4444"/>
+                </target>
+                <recorded value="2015-05-07T13:06:03+01:00"/>
+                <reason>
+                    <text value="Patient validated demographics."/>
+                </reason>
+                <agent>
+                    <role>
+                        <system value="http://hl7.org/fhir/provenance-participant-role"/>
+                        <code value="author"/>
+                    </role>
+                    <type>
+                        <system value="http://hl7.org/fhir/provenance-participant-type"/>
+                        <code value="patient"/>
+                    </type>
+                    <referenceReference>
+                        <reference value="Patient/b555-44-4444"/>
+                        <display value="Patient Everywoman"/>
+                    </referenceReference>
+                    <display value="Eve Everywoman"/>
+                </agent>
+            </Provenance>
+        </resource>
+        <transaction>
+            <method value="POST"/>
+        </transaction>
+    </entry>
+    <entry>
+        <resource>
+            <Patient>
+                <id value="b555-44-4444"/>
+                <extension url="http://ihe.net/ITI-78/Profile/pdqm#mothersMaidenName">
+                    <valueHumanName>
+                        <family value="Jones"/>
+                    </valueHumanName>
+                </extension>
+                <identifier>
+                    <use value="official"/>
+                    <system value="http://ghh.org/patient"/>
+                    <value value="555-44-4444"/>
+                </identifier>
+                <identifier>
+                    <use value="official"/>
+                    <system value="http://www.ohio.gov/dmv/driverslicence"/>
+                    <value value="67-A4335"/>
+                    <period>
+                        <end value="2003-05-20"/>
+                    </period>
+                </identifier>
+                <name>
+                    <use value="official"/>
+                    <family value="Everywoman"/>
+                    <given value="Eve E."/>
+                </name>
+                <telecom>
+                    <system value="phone"/>
+                    <value value="(206)3345232"/>
+                    <use value="home"/>
+                </telecom>
+                <telecom>
+                    <system value="phone"/>
+                    <value value="(206)752-121"/>
+                    <use value="work"/>
+                </telecom>
+                <gender value="female"/>
+                <birthDate value="1962-03-20"/>
+                <address>
+                    <line value="153 Fernwood Dr."/>
+                    <city value="Statesville"/>
+                    <state value="OH"/>
+                    <postalCode value="35292"/>
+                </address>
+                <managingOrganization>
+                    <reference value="Organization/GHH"/>
+                    <display value="Good Health Hospital"/>
+                </managingOrganization>
+                <link>
+                    <other>
+                        <reference value="Patient/temp6789"/>
+                    </other>
+                    <type value="seealso"/>
+                </link>
+                <active value="true"/>
+            </Patient>
+        </resource>
+        <transaction>
+            <method value="PUT"/>
+            <url value="Patient/?identifier=http://ghh.org/patient%7C555-44-4444"/>
+        </transaction>
+    </entry>
+    <entry>
+        <resource>
+            <Patient>
+                <!-- Jane Doe registered in the emergency department -->
+                <id value="temp6789"/>
+                <identifier>
+                    <use value="temp"/>
+                    <system value="http://ghh.org/patient"/>
+                    <value value="temp6789"/>
+                </identifier>
+                <name>
+                    <use value="temp"/>
+                    <family value="Doe 6789"/>
+                    <given value="Jane"/>
+                </name>
+                <gender value="female"/>
+                <managingOrganization>
+                    <reference value="Organization/GHH"/>
+                    <display value="Good Health Hospital"/>
+                </managingOrganization>
+                <link>
+                    <other>
+                        <reference value="Patient/b555-44-4444"/>
+                    </other>
+                    <type value="replace"/>
+                </link>
+                <active value="true"/>
+            </Patient>
+        </resource>
+        <transaction>
+            <method value="PUT"/>
+            <url value="Patient/?identifier=http://ghh.org/patient%7Ctemp6789"/>
+        </transaction>
+    </entry>
+    <entry>
+        <resource>
+            <Organization> 
+                <id value="GHH"/>
+                <identifier>
+                    <!-- Identifier for the GHH hospital -->
+                    <use value="official"/>
+                    <system value="http://ghh.org/department"/>
+                    <value value="GHH"/>
+                </identifier>
+                <name value="Good Health Hospital"/>
+                <type>
+                    <!-- GHH is a Hospital -->
+                    <coding>
+                        <system value="http://snomed.info/sct"/>
+                        <code value="22232009"/>
+                        <display value="Hospital"/>
+                    </coding>
+                </type>
+                <active value="true"/>
+            </Organization>
+        </resource>
+        <transaction>
+            <method value="POST"/>
+            <url value="Organization"/>
+            <ifNoneExist value="Organization/?identifier=http://ghh.org/department%7CGHH"/>
+        </transaction>
+    </entry>
+</Bundle>
+