Shorten column names in Search table for JPA

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

@@ -1539,6 +1539,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		/*
 		 * Update the "search param present" table which is used for the
 		 * ?foo:missing=true queries
+		 * 
+		 * Note that we're only populating this for reference params
+		 * because the index tables for all other types have a MISSING column
+		 * right on them for handling the :missing queries. We can't use the
+		 * index table for resource links (reference indexes) because we index
+		 * those by path and not by parameter name.
 		 */
 		if (thePerformIndexing) {
 			Map<String, Boolean> presentSearchParams = new HashMap<String, Boolean>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseResourceIndexedSearchParam.java

@@ -23,15 +23,8 @@ package ca.uhn.fhir.jpa.entity;
 import java.io.Serializable;
 import java.util.Date;
 
-import javax.persistence.Column;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.MappedSuperclass;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import javax.persistence.*;
 
-import org.hibernate.annotations.ColumnDefault;
-import org.hibernate.annotations.Columns;
 import org.hibernate.search.annotations.ContainedIn;
 import org.hibernate.search.annotations.Field;
 
@@ -44,7 +37,6 @@ public abstract class BaseResourceIndexedSearchParam implements Serializable {
 
 	@Field()
 	@Column(name = "SP_MISSING", nullable = true)
-	@ColumnDefault("false")
 	private boolean myMissing;
 
 	@Field

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Search.java

@@ -42,8 +42,8 @@ import ca.uhn.fhir.rest.param.DateRangeParam;
 @Table(name = "HFJ_SEARCH", uniqueConstraints= {
 	@UniqueConstraint(name="IDX_SEARCH_UUID", columnNames="SEARCH_UUID")
 }, indexes= {
-	@Index(name="JDX_SEARCH_LASTRETURNED", columnList="SEARCH_LAST_RETURNED"),
-	@Index(name="JDX_SEARCH_RESTYPE_STRINGHASHCREATED", columnList="RESOURCE_TYPE,SEARCH_QUERY_STRING_HASH,CREATED")
+	@Index(name="IDX_SEARCH_LASTRETURNED", columnList="SEARCH_LAST_RETURNED"),
+	@Index(name="IDX_SEARCH_RESTYPE_HASHS", columnList="RESOURCE_TYPE,SEARCH_QUERY_STRING_HASH,CREATED")
 })
 public class Search implements Serializable {
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/SearchParam.java

@@ -52,5 +52,8 @@ public class SearchParam {
 		myResourceName = theResourceName;
 	}
 
+	public Long getId() {
+		return myId;
+	}
 	
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/SearchParamPresent.java

@@ -54,6 +54,13 @@ public class SearchParamPresent implements Serializable {
 	@JoinColumn(name = "SP_ID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_RESPARMPRES_SPID"))
 	private SearchParam mySearchParam;
 
+	/**
+	 * Constructor
+	 */
+	public SearchParamPresent() {
+		super();
+	}
+	
 	public ResourceTable getResource() {
 		return myResource;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java

@@ -80,9 +80,7 @@ import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.method.PageMethodBinding;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.SimpleBundleProvider;
-import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.*;
 
 public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 	static final int DEFAULT_SYNC_SIZE = 250;
@@ -475,7 +473,22 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				ourLog.info("Completed search for {} resources in {}ms", mySyncedPids.size(), sw.getMillis());
 
 			} catch (Throwable t) {
-				ourLog.error("Failed during search loading after {}ms", sw.getMillis(), t);
+				
+				/*
+				 * Don't print a stack trace for client errors.. that's just noisy
+				 */
+				boolean logged = false;
+				if (t instanceof BaseServerResponseException) {
+					BaseServerResponseException exception = (BaseServerResponseException) t;
+					if (exception.getStatusCode() >= 400 && exception.getStatusCode() < 500) {
+						logged = true;
+						ourLog.warn("Failed during search due to invalid request: {}", t.toString());
+					}
+				} 
+				
+				if (!logged) {
+					ourLog.error("Failed during search loading after {}ms", sw.getMillis(), t);
+				}
 				myUnsyncedPids.clear();
 
 				Throwable rootCause = ExceptionUtils.getRootCause(t);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java

@@ -82,7 +82,8 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 					searchParam = new SearchParam();
 					searchParam.setResourceName(resourceType);
 					searchParam.setParamName(paramName);
-					mySearchParamDao.save(searchParam);
+					searchParam = mySearchParamDao.saveAndFlush(searchParam);
+					ourLog.info("Added search param {} with pid {}", paramName, searchParam.getId());
 					// Don't add the newly saved entity to the map in case the save fails
 				}
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java

@@ -0,0 +1,98 @@
+package ca.uhn.fhir.jpa.util;
+
+import java.io.IOException;
+import java.lang.reflect.AnnotatedElement;
+import java.lang.reflect.Field;
+
+import javax.persistence.*;
+
+import org.apache.commons.lang3.Validate;
+
+import com.google.common.collect.ImmutableSet;
+import com.google.common.reflect.ClassPath;
+import com.google.common.reflect.ClassPath.ClassInfo;
+
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+
+public class TestUtil {
+	private static final int MAX_LENGTH = 30;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestUtil.class);
+
+	/** non instantiable */
+	private TestUtil() {
+		super();
+	}
+	
+	/**
+	 * This is really only useful for unit tests, do not call otherwise
+	 */
+	public static void scanEntities(String packageName) throws IOException, ClassNotFoundException {
+		ImmutableSet<ClassInfo> classes = ClassPath.from(TestUtil.class.getClassLoader()).getTopLevelClasses(packageName);
+		
+		if (classes.size() <= 1) {
+			throw new InternalErrorException("Found no classes");
+		}
+		
+		for (ClassInfo classInfo : classes) {
+			Class<?> clazz = Class.forName(classInfo.getName());
+			Entity entity = clazz.getAnnotation(Entity.class);
+			if (entity == null) {
+				continue;
+			}
+			
+			ourLog.info("Scanning: {}", clazz.getSimpleName());
+			
+			scan(clazz);
+			
+			for (Field nextField : clazz.getFields()) {
+				scan(nextField);
+			}
+			
+		}
+	}
+
+	private static void scan(AnnotatedElement ae) {
+		Table table = ae.getAnnotation(Table.class);
+		if (table != null) {
+			assertThat(table.name());
+			for (UniqueConstraint nextConstraint : table.uniqueConstraints()) {
+				assertThat(nextConstraint.name());
+			}
+			for (Index nextConstraint : table.indexes()) {
+				assertThat(nextConstraint.name());
+			}
+		}
+		
+		JoinColumn joinColumn = ae.getAnnotation(JoinColumn.class);
+		if (joinColumn != null) {
+			assertThat(joinColumn.name());
+			ForeignKey fk = joinColumn.foreignKey();
+			assertThat(fk.name());
+		}
+
+		Column column = ae.getAnnotation(Column.class);
+		if (column != null) {
+			assertThat(column.name());
+		}
+
+		GeneratedValue gen = ae.getAnnotation(GeneratedValue.class);
+		if (gen != null) {
+			assertThat(gen.generator());
+			SequenceGenerator sg = ae.getAnnotation(SequenceGenerator.class);
+			assertThat(sg.name());
+			assertThat(sg.sequenceName());
+			assertEquals(gen.generator(), sg.name());
+			assertEquals(gen.generator(), sg.sequenceName());
+		}
+
+	}
+
+	private static void assertEquals(String theGenerator, String theName) {
+		Validate.isTrue(theGenerator.equals(theName));
+	}
+
+	private static void assertThat(String theName) {
+		Validate.isTrue(theName.length() <= MAX_LENGTH, "Identifier \"" + theName + "\" is " + theName.length() + " chars long");
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/IdentifierLengthTest.java

@@ -0,0 +1,16 @@
+package ca.uhn.fhir.jpa.config;
+
+import org.junit.Test;
+
+import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.util.TestUtil;
+
+public class IdentifierLengthTest {
+
+	@Test
+	public void testIdentifierLength() throws Exception {
+		TestUtil.scanEntities(ResourceTable.class.getPackage().getName());
+	}
+
+	
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java

@@ -25,6 +25,7 @@ import java.util.List;
 
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Test;
@@ -75,6 +76,21 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu2Test.class);
 
+	/**
+	 * See #638
+	 */
+	@Test
+	public void testTransactionBug638() throws Exception {
+		String input = loadClasspath("/bug638.xml");
+		Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
+		
+		Bundle resp = mySystemDao.transaction(mySrd, request);
+		
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		
+		assertEquals(18, resp.getEntry().size());
+	}
+
 	/**
 	 * Per a message on the mailing list
 	 */

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -3094,6 +3094,28 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		checkParamMissing(Observation.SP_DATE);
 	}
 
+	@Test
+	public void testSearchInvalidParam() throws Exception {
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("urn:system").setValue("0");
+		patient.addName().setFamily("testSearchWithMixedParams").addGiven("Joe");
+		myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+
+		// should be subject._id
+		HttpGet httpPost = new HttpGet(ourServerBase + "/Observation?subject.id=FOO"); 
+
+		CloseableHttpResponse resp = ourHttpClient.execute(httpPost);
+		try {
+			String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(respString);
+			assertThat(respString, containsString("Invalid parameter chain: subject.id"));
+			assertEquals(400, resp.getStatusLine().getStatusCode());
+		} finally {
+			IOUtils.closeQuietly(resp.getEntity().getContent());
+		}
+		ourLog.info("Outgoing post: {}", httpPost);
+	}
+	
 	/**
 	 * See #411
 	 * 

hapi-fhir-jpaserver-base/src/test/resources/bug638.xml

@@ -0,0 +1,651 @@
+<Bundle xmlns="http://hl7.org/fhir">
+	<meta>
+		<lastUpdated value="2017-05-02T11:15:27.998+01:00" />
+		<profile value="http://fhir.nhs.net/StructureDefinition/NewbornBloodSpotScreeningBundlev1" />
+	</meta>
+	<type value="transaction" />
+	<entry>
+		<fullUrl value="urn:uuid:60c88939-6159-45ee-9f78-122c9b56a5bb" />
+		<resource>
+			<Provenance>
+				<id value="60c88939-6159-45ee-9f78-122c9b56a5bb" />
+				<meta>
+					<profile value="http://fhir.nhs.net/StructureDefinition/PCHRProvenancev1" />
+				</meta>
+				<target>
+					<reference value="urn:uuid:be58eb90-74b3-4db6-9a31-c40a6c97e3dc" />
+				</target>
+				<target>
+					<reference value="urn:uuid:3d1cffec-2f6e-4bca-9945-f1ca77bf8949" />
+				</target>
+				<target>
+					<reference value="urn:uuid:f0b5569d-136b-4be8-b5a3-e5db1feead99" />
+				</target>
+				<target>
+					<reference value="urn:uuid:8a3a8adc-747a-4430-8876-d8b4937928b9" />
+				</target>
+				<target>
+					<reference value="urn:uuid:aee71835-b117-4fe5-ad11-4bff7c9adff3" />
+				</target>
+				<target>
+					<reference value="urn:uuid:116799a0-223e-4708-aa5c-010587fabde8" />
+				</target>
+				<target>
+					<reference value="urn:uuid:8b43b707-cab5-42e7-8dd8-2f664c69dee7" />
+				</target>
+				<target>
+					<reference value="urn:uuid:a947c7d3-ea88-4f45-b6ab-a1db471ccd32" />
+				</target>
+				<target>
+					<reference value="urn:uuid:ed9ca84e-86ba-4a1d-9e6f-4a928be7a89c" />
+				</target>
+				<target>
+					<reference value="urn:uuid:51d6a6de-4263-43b5-9fa0-64a41d1f89a1" />
+				</target>
+				<target>
+					<reference value="urn:uuid:acd1e52b-00bb-49b6-af2c-83c592694e86" />
+				</target>
+				<target>
+					<reference value="urn:uuid:80159cb4-9fc2-434f-9fb5-b4da4beb92dc" />
+				</target>
+				<target>
+					<reference value="urn:uuid:463c6bd8-79c8-4982-acef-5312329bba72" />
+				</target>
+				<target>
+					<reference value="urn:uuid:db24d6f9-6110-4ab2-a694-e4c99f5a5838" />
+				</target>
+				<target>
+					<reference value="urn:uuid:c3e671e6-1402-4993-97fc-3e970fa0e1d4" />
+				</target>
+				<target>
+					<reference value="urn:uuid:f7bb659c-fb86-4aed-90c3-a7957459927f" />
+				</target>
+				<recorded value="2017-05-02T11:15:27.998+01:00" />
+				<agent>
+					<role>
+						<system value="http://hl7.org/fhir/provenance-participant-role" />
+						<code value="author" />
+					</role>
+					<actor>
+						<reference value="urn:uuid:89df119a-409d-4e18-a68c-ab75fcecb9c3" />
+					</actor>
+				</agent>
+			</Provenance>
+		</resource>
+		<request>
+			<method value="POST"/>
+			<url value="Provenance"/>
+		</request>
+	</entry>
+	<entry>
+		<fullUrl value="urn:uuid:89df119a-409d-4e18-a68c-ab75fcecb9c3" />
+		<resource>
+			<Organization>
+				<id value="89df119a-409d-4e18-a68c-ab75fcecb9c3" />
+				<meta>
+					<profile value="http://fhir.nhs.net/StructureDefinition/PCHROrganizationv1" />
+				</meta>
+				<identifier>
+					<system value="urn:ietf:rfc:RNS01" />
+					<value value="2.16.840.1.113883.19.5" />
+				</identifier>
+			</Organization>
+		</resource>
+		<request>
+			<method value="POST"/>
+			<url value="Organization"/>
+		</request>
+	</entry>
+	<entry>
+		<fullUrl value="urn:uuid:be58eb90-74b3-4db6-9a31-c40a6c97e3dc" />
+		<resource>
+			<Organization>
+				<id value="be58eb90-74b3-4db6-9a31-c40a6c97e3dc" />
+				<meta>
+					<profile value="http://fhir.nhs.net/StructureDefinition/PCHROrganizationv1" />
+				</meta>
+				<identifier>
+					<system value="http://fhir.nhs.net/id/gcode" />
+					<value value="M87003" />
+				</identifier>
+			</Organization>
+		</resource>
+		<request>
+			<method value="POST"/>
+			<url value="Organization"/>
+		</request>
+	</entry>
+	<entry>
+		<fullUrl value="urn:uuid:3d1cffec-2f6e-4bca-9945-f1ca77bf8949" />
+		<resource>
+			<Patient>
+				<id value="3d1cffec-2f6e-4bca-9945-f1ca77bf8949" />
+				<meta>
+					<profile value="http://fhir.nhs.net/StructureDefinition/NHSPatientv1" />
+				</meta>
+				<extension url="http://fhir.nhs.net/StructureDefinition/BirthDetailsExtensionv1">
+					<extension url="birthTime">
+						<valueTime value="12:05:00" />
+					</extension>
+				</extension>
+				<identifier>
+					<system value="http://fhir.nhs.net/id/nhs-number" />
+					<value value="1935537156" />
+				</identifier>
+				<name>
+					<family value="Gibson" />
+					<given value="Mike" />
+				</name>
+				<gender value="male" />
+				<birthDate value="2014-05-25" />
+				<careProvider>
+					<reference value="urn:uuid:be58eb90-74b3-4db6-9a31-c40a6c97e3dc" />
+				</careProvider>
+			</Patient>
+		</resource>
+		<request>
+			<method value="POST"/>
+			<url value="Patient"/>
+		</request>
+	</entry>
+	<entry>
+		<fullUrl value="urn:uuid:f0b5569d-136b-4be8-b5a3-e5db1feead99" />
+		<resource>
+			<Encounter>
+				<id value="f0b5569d-136b-4be8-b5a3-e5db1feead99" />
+				<meta>
+					<profile value="http://fhir.nhs.net/StructureDefinition/PCHREncounterv1" />
+				</meta>
+				<status value="finished" />
+				<type>
+					<coding>
+						<system value="http://snomed.info/sct" />
+						<code value="428447008" />
+						<display value="Newborn blood spot screening (procedure)" />
+					</coding>
+				</type>
+				<patient>
+					<reference value="urn:uuid:3d1cffec-2f6e-4bca-9945-f1ca77bf8949" />
+				</patient>
+				<period>
+					<start value="2017-05-02" />
+				</period>
+			</Encounter>
+		</resource>
+		<request>
+			<method value="POST"/>
+			<url value="Encounter"/>
+		</request>
+	</entry>
+	<entry>
+		<fullUrl value="urn:uuid:8a3a8adc-747a-4430-8876-d8b4937928b9" />
+		<resource>
+			<Procedure>
+				<id value="8a3a8adc-747a-4430-8876-d8b4937928b9" />
+				<meta>
+					<profile value="http://fhir.nhs.net/StructureDefinition/NewbornBloodSpotScreeningProcedurev1" />
+				</meta>
+				<subject>
+					<reference value="urn:uuid:3d1cffec-2f6e-4bca-9945-f1ca77bf8949" />
+				</subject>
+				<status value="completed" />
+				<code>
+					<coding>
+						<system value="http://snomed.info/sct" />
+						<code value="77262006" />
+						<display value="Heel stick (procedure)" />
+					</coding>
+				</code>
+				<performer>
+					<actor>
+						<reference value="urn:uuid:f7bb659c-fb86-4aed-90c3-a7957459927f" />
+					</actor>
+				</performer>
+				<performedDate value="2014-06-06" />
+				<encounter>
+					<reference value="urn:uuid:f0b5569d-136b-4be8-b5a3-e5db1feead99" />
+				</encounter>
+				<outcome>
+					<coding>
+						<system value="http://snomed.info/sct" />
+						<code value="15501000000100" />
+						<display value="" />
+					</coding>
+				</outcome>
+			</Procedure>
+		</resource>
+		<request>
+			<method value="POST"/>
+			<url value="Procedure"/>
+		</request>
+	</entry>
+	<entry>
+		<fullUrl value="urn:uuid:aee71835-b117-4fe5-ad11-4bff7c9adff3" />
+		<resource>
+			<DiagnosticReport>
+				<id value="aee71835-b117-4fe5-ad11-4bff7c9adff3" />
+				<meta>
+					<profile value="http://fhir.nhs.net/StructureDefinition/NewbornBloodSpotScreeningDiagnosticReportv1" />
+				</meta>
+				<status value="final" />
+				<code>
+					<coding>
+						<system value="http://snomed.info/sct" />
+						<code value="428447008" />
+						<display value="Newborn blood spot screening (procedure)" />
+					</coding>
+				</code>
+				<subject>
+					<reference value="urn:uuid:3d1cffec-2f6e-4bca-9945-f1ca77bf8949" />
+				</subject>
+				<effectiveDateTime value="2014-06-06" />
+				<issued value="2017-05-02T11:15:27.998+01:00" />
+				<performer>
+					<reference value="urn:uuid:f7bb659c-fb86-4aed-90c3-a7957459927f" />
+				</performer>
+				<result>
+					<reference value="urn:uuid:8b43b707-cab5-42e7-8dd8-2f664c69dee7" />
+					<display value="Cystic fibrosis screening test (observable entity)" />
+				</result>
+				<result>
+					<reference value="urn:uuid:a947c7d3-ea88-4f45-b6ab-a1db471ccd32" />
+					<display value="Congenital hypothyroidism screening test (observable entity)" />
+				</result>
+				<result>
+					<reference value="urn:uuid:ed9ca84e-86ba-4a1d-9e6f-4a928be7a89c" />
+					<display value="Blood spot glutaric aciduria type 1 screening test (observable entity)" />
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