Merge branch 'main' of https://github.com/IBM/FHIR into main

LinuxForHealth · Nov 5, 2021 · a4cece3 · a4cece3
2 parents 48ae33e + 9fae77b
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diff --git a/demo/fhir-operation-member-match-demo/README.md b/demo/fhir-operation-member-match-demo/README.md
@@ -0,0 +1,8 @@
+# $member-match operation demo
+The contents in this module are from HL7 FHIR® Da Vinci Health Record Exchange (HRex) 0.2.0 - STU R1 - 2nd ballot. The [$member-match](http://build.fhir.org/ig/HL7/davinci-ehrx/OperationDefinition-member-match.html) operation is used to demonstrate that a custom strategy can and is used.
+
+You must install the fhir-operation-member-match jar in the userlib (hrex, us-core as well).
+
+```
+mvn clean install -DskipTests
+```
diff --git a/demo/fhir-operation-member-match-demo/pom.xml b/demo/fhir-operation-member-match-demo/pom.xml
@@ -0,0 +1,61 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>com.ibm.fhir</groupId>
+        <artifactId>fhir-parent</artifactId>
+        <version>4.10.0-SNAPSHOT</version>
+        <relativePath>../../fhir-parent</relativePath>
+    </parent>
+    <artifactId>fhir-operation-member-match-demo</artifactId>
+    <dependencies>
+        <dependency>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-server-spi</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-server</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-model</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-registry</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-ig-us-core</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-ig-davinci-hrex</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.ibm.fhir</groupId>
+            <artifactId>fhir-operation-member-match</artifactId>
+            <version>4.10.0-SNAPSHOT</version>
+            <scope>provided</scope>
+        </dependency>
+    </dependencies>
+</project>
diff --git a/...mo/src/main/java/demo/ibm/fhir/operation/davinci/hrex/provider/strategy/DemoStrategy.java b/...mo/src/main/java/demo/ibm/fhir/operation/davinci/hrex/provider/strategy/DemoStrategy.java
@@ -0,0 +1,45 @@
+/*
+ * (C) Copyright IBM Corp. 2021
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package demo.ibm.fhir.operation.davinci.hrex.provider.strategy;
+
+import java.util.logging.Logger;
+
+import com.ibm.fhir.config.PropertyGroup;
+import com.ibm.fhir.exception.FHIROperationException;
+import com.ibm.fhir.model.resource.Parameters;
+import com.ibm.fhir.operation.davinci.hrex.configuration.ConfigurationFactory;
+import com.ibm.fhir.operation.davinci.hrex.provider.strategy.DefaultMemberMatchStrategy;
+import com.ibm.fhir.operation.davinci.hrex.provider.strategy.MemberMatchResult;
+
+/**
+ * Used to Demonstrate a custom Strategy
+ */
+public class DemoStrategy extends DefaultMemberMatchStrategy {
+
+    private static final Logger LOG = Logger.getLogger(DemoStrategy.class.getSimpleName());
+
+    @Override
+    public String getMemberMatchIdentifier() {
+        return "demo";
+    }
+
+    @Override
+    public void validate(Parameters input) throws FHIROperationException {
+        LOG.info("Validating Content for strategy - " + this.getMemberMatchIdentifier());
+        super.validate(input);
+    }
+
+    @Override
+    public MemberMatchResult executeMemberMatch() throws FHIROperationException {
+        LOG.info("executeMemberMatch for strategy - " + this.getMemberMatchIdentifier());
+        PropertyGroup group = ConfigurationFactory.factory().getConfigurationAdapter().getExtendedStrategyPropertyGroup();
+        if (group != null) {
+            LOG.info("executeMemberMatch Extend Strategy Config is " + group.getJsonObj());
+        }
+        return super.executeMemberMatch();
+    }
+}
diff --git a/...TA-INF/services/com.ibm.fhir.operation.davinci.hrex.provider.strategy.MemberMatchStrategy b/...TA-INF/services/com.ibm.fhir.operation.davinci.hrex.provider.strategy.MemberMatchStrategy
@@ -0,0 +1 @@
+demo.ibm.fhir.operation.davinci.hrex.provider.strategy.DemoStrategy
diff --git a/docs/src/pages/guides/FHIRServerUsersGuide.md b/docs/src/pages/guides/FHIRServerUsersGuide.md
@@ -2207,9 +2207,9 @@ This section contains reference information about each of the configuration prop
 |`fhirServer/bulkdata/storageProviders/<source>/requiresAccessToken`|boolean|controls the `$bulkdata-status` response to indicate Bulk Data storageprovider requires an accessToken using `requiresAccessToken`.|
 |`fhirServer/operations/erase/enabled`|boolean|Enables the $erase operation|
 |`fhirServer/operations/erase/allowedRoles`|list|The list of allowed roles, allowed entries are: `FHIRUsers` every authenticated user, `FHIROperationAdmin` which is authenticated `FHIRAdmin` users|
-|`fhirServer/operations/member-match/enabled`|boolean|Enables or disables the $member-match|
-|`fhirServer/operations/member-match/strategy`|string|The key identifying the Member Match strategy|
-|`fhirServer/operations/member-match/extendedProps`|object|The extended options for the extended member match implementation|
+|`fhirServer/operations/membermatch/enabled`|boolean|Enables or disables the $member-match|
+|`fhirServer/operations/membermatch/strategy`|string|The key identifying the Member Match strategy|
+|`fhirServer/operations/membermatch/extendedProps`|object|The extended options for the extended member match implementation|
 
 
 ### 5.1.2 Default property values
@@ -2351,9 +2351,9 @@ This section contains reference information about each of the configuration prop
 |`fhirServer/bulkdata/storageProviders/<source>/requiresAccessToken`|false|
 |`fhirServer/operations/erase/enabled`|false|
 |`fhirServer/operations/erase/allowedRoles`|empty, all roles|
-|`fhirServer/operations/member-match/enabled`|true|
-|`fhirServer/operations/member-match/strategy`|default|
-|`fhirServer/operations/member-match/extendedProps`|empty|
+|`fhirServer/operations/membermatch/enabled`|true|
+|`fhirServer/operations/membermatch/strategy`|default|
+|`fhirServer/operations/membermatch/extendedProps`|empty|
 
 ### 5.1.3 Property attributes
 Depending on the context of their use, config properties can be:
@@ -2527,9 +2527,9 @@ must restart the server for that change to take effect.
 |`fhirServer/bulkdata/storageProviders/<source>/requiresAccessToken`|Y|Y|
 |`fhirServer/operations/erase/enabled`|Y|Y|
 |`fhirServer/operations/erase/allowedRoles`|Y|Y|
-|`fhirServer/operations/member-match/enabled`|Y|Y|
-|`fhirServer/operations/member-match/strategy`|Y|Y|
-|`fhirServer/operations/member-match/extendedProps`|Y|Y|
+|`fhirServer/operations/membermatch/enabled`|Y|Y|
+|`fhirServer/operations/membermatch/strategy`|Y|Y|
+|`fhirServer/operations/membermatch/extendedProps`|Y|Y|
 
 ## 5.2 Keystores, truststores, and the IBM FHIR server
 

diff --git a/fhir-persistence-schema/src/main/java/com/ibm/fhir/schema/app/Main.java b/fhir-persistence-schema/src/main/java/com/ibm/fhir/schema/app/Main.java
@@ -46,6 +46,7 @@
 import com.ibm.fhir.database.utils.api.TableSpaceRemovalException;
 import com.ibm.fhir.database.utils.api.TenantStatus;
 import com.ibm.fhir.database.utils.api.UndefinedNameException;
+import com.ibm.fhir.database.utils.api.UniqueConstraintViolationException;
 import com.ibm.fhir.database.utils.common.DataDefinitionUtil;
 import com.ibm.fhir.database.utils.common.JdbcConnectionProvider;
 import com.ibm.fhir.database.utils.common.JdbcPropertyAdapter;
@@ -384,6 +385,9 @@ protected void updateSchemas() {
         IDatabaseAdapter adapter = getDbAdapter(dbType, connectionPool);
         try (ITransaction tx = transactionProvider.getTransaction()) {
             CreateControl.createTableIfNeeded(schema.getAdminSchemaName(), adapter);
+        } catch (UniqueConstraintViolationException x) {
+            // Race condition - two or more instances trying to create the CONTROL table
+            throw new ConcurrentUpdateException("Concurrent update - create control table");
         }
 
         if (updateFhirSchema) {
@@ -2531,6 +2535,9 @@ protected void logStatusMessage(int status) {
         case EXIT_RUNTIME_ERROR:
             logger.severe("SCHEMA CHANGE: RUNTIME ERROR");
             break;
+        case EXIT_CONCURRENT_UPDATE:
+            logger.warning("SCHEMA CHANGE: CONCURRENT UPDATE");
+            break;
         case EXIT_VALIDATION_FAILED:
             logger.warning("SCHEMA CHANGE: FAILED");
             break;
@@ -2582,7 +2589,8 @@ public static void main(String[] args) {
             logger.warning("Tablespace removal is not complete, as an async dependency has not finished dettaching. Please re-try.");
             exitStatus = EXIT_TABLESPACE_REMOVAL_NOT_COMPLETE;
         } catch (ConcurrentUpdateException x) {
-            logger.log(Level.WARNING, "Update is already running. Please re-try later.", x);
+            // We handle this, so no need to log the exception
+            logger.log(Level.WARNING, "Please try again later: update is already running - " + x.getMessage());
             exitStatus = EXIT_CONCURRENT_UPDATE;
         } catch (DatabaseNotReadyException x) {
             logger.log(Level.SEVERE, "The database is not yet available. Please re-try.", x);

diff --git a/fhir-persistence/src/main/java/com/ibm/fhir/persistence/util/InputOutputByteStream.java b/fhir-persistence/src/main/java/com/ibm/fhir/persistence/util/InputOutputByteStream.java
@@ -95,6 +95,9 @@ private class ByteInputStream extends InputStream {
         // each read stream gets its own read offset in the buffer
         private int posn = 0;
 
+        // maintains the position of the last call to mark
+        private int mark = 0;
+
         @Override
         public int read() throws IOException {
             return posn < offset ? (buffer[posn++] & 0xff) : -1;
@@ -139,6 +142,21 @@ public long skip(long n) {
             posn += n;
             return n;
         }
+
+        @Override
+        public void reset() throws IOException {
+            posn = mark;
+        }
+
+        @Override
+        public void mark(int readlimit) {
+            mark = posn;
+        }
+
+        @Override
+        public boolean markSupported() {
+            return true;
+        }
     }
 
     /**
@@ -221,7 +239,7 @@ public InputStream inputStream() {
     public ByteBuffer wrap() {
         return ByteBuffer.wrap(this.buffer, 0, size()).asReadOnlyBuffer();
     }
-    
+
     /**
      * Reset the offset to make the buffer appear empty. Does not change the current
      * length (capacity). Note that any streams currently being used to read the data

diff --git a/fhir-persistence/src/test/java/com/ibm/fhir/test/InputOutputByteStreamTest.java b/fhir-persistence/src/test/java/com/ibm/fhir/test/InputOutputByteStreamTest.java
@@ -49,9 +49,42 @@ public void testBasicOperation() throws IOException {
         assertEquals(compare(source, 0, source.length-1, readBack2, 0, len2-1), 0);
     }
 
+    @Test
+    public void testBasicOperationWithMarkAndReset() throws IOException {
+        InputOutputByteStream iobs = new InputOutputByteStream(10);
+        byte[] source = {0x01, 0x02, 0x03, 0x04};
+        OutputStream os = iobs.outputStream();
+        os.write(source);
+
+        // read back and check
+        InputStream is = iobs.inputStream();
+        byte[] readBack = new byte[8];
+        int len = is.read(readBack);
+        assertEquals(len, source.length);
+        assertEquals(compare(source, 0, source.length-1, readBack, 0, len-1), 0);
+
+        // If it's not supported then it'll throw an exception.
+        is.reset();
+
+        // Read 3 of 4 bytes, and then iterate.
+        byte[] readReset = new byte[3];
+        int lenReset = is.read(readReset);
+        assertEquals(lenReset, 3);
+
+        // Fixing the mark to the current posn
+        is.mark(100);
+        lenReset = is.read(readReset);
+        assertEquals(lenReset, 1);
+
+        // Reset to marked point
+        is.reset();
+        lenReset = is.read(readReset);
+        assertEquals(lenReset, 1);
+    }
+
     /**
      * Check that the two arrays are equal. Can't use {@link Arrays#compare(byte[], int, int, byte[], int, int)}
-     * because that's since J9 and we still supprt J8.
+     * because that's since Java9 and we still support Java8.
      * @param left
      * @param leftFrom
      * @param leftTo

diff --git a/operation/fhir-operation-member-match-demo/README.md b/operation/fhir-operation-member-match-demo/README.md
@@ -0,0 +1,8 @@
+# $member-match operation demo
+The contents in this module are from HL7 FHIR® Da Vinci Health Record Exchange (HRex) 0.2.0 - STU R1 - 2nd ballot. The [$member-match](http://build.fhir.org/ig/HL7/davinci-ehrx/OperationDefinition-member-match.html) operation is used to demonstrate that a custom strategy can and is used.
+
+You must install the fhir-operation-member-match jar in the userlib (hrex, us-core as well).
+
+```
+mvn clean install -DskipTests
+```
diff --git a/operation/fhir-operation-member-match-demo/pom.xml b/operation/fhir-operation-member-match-demo/pom.xml
@@ -0,0 +1,61 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>com.ibm.fhir</groupId>
+        <artifactId>fhir-parent</artifactId>
+        <version>4.10.0-SNAPSHOT</version>
+        <relativePath>../../fhir-parent</relativePath>
+    </parent>
+    <artifactId>fhir-operation-member-match-demo</artifactId>
+    <dependencies>
+        <dependency>
+            <groupId>jakarta.ws.rs</groupId>
+            <artifactId>jakarta.ws.rs-api</artifactId>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-server-spi</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-server</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-model</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-registry</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-ig-us-core</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>fhir-ig-davinci-hrex</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.ibm.fhir</groupId>
+            <artifactId>fhir-operation-member-match</artifactId>
+            <version>4.10.0-SNAPSHOT</version>
+            <scope>provided</scope>
+        </dependency>
+    </dependencies>
+</project>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		demo.ibm.fhir.operation.davinci.hrex.provider.strategy.DemoStrategy