Merge branch 'master' into refresh-messaging-improvements

cqframework · Jan 26, 2024 · 53ec57a · 53ec57a
2 parents cb6ef87 + 28963bb
commit 53ec57a
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Showing 32 changed files with 795 additions and 738 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -6,8 +6,18 @@
         "ASLP",
         "Careand",
         "conceptmap",
+        "Cqfm",
+        "cqloptions",
+        "DEPENDSON",
+        "Dstu",
+        "Fhir",
+        "opencds",
         "pagecontent",
         "plandefinition",
+        "qicore",
+        "stripcontent",
         "testng"
-    ]
+    ],
+    "java.compile.nullAnalysis.mode": "automatic",
+    "java.jdt.ls.vmargs": "-XX:+UseParallelGC -XX:GCTimeRatio=4 -XX:AdaptiveSizePolicyWeight=90 -Dsun.zip.disableMemoryMapping=true -Xmx2G -Xms100m -Xlog:disable"
 }
diff --git a/pom.xml b/pom.xml
@@ -5,15 +5,15 @@
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling-parent</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.2.0-SNAPSHOT</version>
 
     <packaging>pom</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <cql.version>3.5.1</cql.version>
-        <hapi.version>6.10.0</hapi.version>
+        <cql.version>3.6.0</cql.version>
+        <hapi.version>6.10.2</hapi.version>
         <core.version>6.1.2.2</core.version>
         <spring-boot.version>2.1.5.RELEASE</spring-boot.version>
         <slf4j.version>2.0.5</slf4j.version>

diff --git a/scripts/deploy.sh b/scripts/deploy.sh
@@ -24,7 +24,7 @@ fi
 # Import maven settings
 cp .travis.settings.xml $HOME/.m2/settings.xml
 
-CMD="mvn deploy -DskipTests=true -Dmaven.test.skip=true -B"
+CMD="./mvnw deploy -DskipTests=true -Dmaven.test.skip=true -B"
 
 # Import signing key and publish a release on a tag
 if [[ ! -z "$TRAVIS_TAG" ]]

diff --git a/scripts/install.sh b/scripts/install.sh
@@ -4,4 +4,4 @@
 set -euxo pipefail
 bash -n "$0"
 
-mvn install -U -DskipTests=true -Dmaven.javadoc.skip=true -B -V
+./mvnw install -U -DskipTests=true -Dmaven.javadoc.skip=true -B -V
diff --git a/scripts/maintenance.sh b/scripts/maintenance.sh
@@ -4,4 +4,4 @@
 set -euxo pipefail
 bash -n "$0"
 
-mvn versions:update-properties versions:use-releases versions:use-latest-releases -Dexcludes=com.github.ben-manes.caffeine:caffeine:jar:\*,org.slf4j:\*,org.glassfish.jaxb:\*,com.sun.istack:\*,com.sun.xml.fastinfoset:\*,net.sf.jopt-simple:\*,ch.qos.logback:\*
+./mvnw versions:update-properties versions:use-releases versions:use-latest-releases -Dexcludes=com.github.ben-manes.caffeine:caffeine:jar:\*,org.slf4j:\*,org.glassfish.jaxb:\*,com.sun.istack:\*,com.sun.xml.fastinfoset:\*,net.sf.jopt-simple:\*,ch.qos.logback:\*
diff --git a/scripts/setversion.sh b/scripts/setversion.sh
@@ -1,4 +1,4 @@
 #!/usr/bin/env sh
 
 # usage ./scripts/setversion.sh N.N.N (or N.N.N-SNAPSHOT)
-mvn versions:set -DnewVersion=$1
+./mvnw versions:set -DnewVersion=$1
diff --git a/tooling-cli/pom.xml b/tooling-cli/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>3.1.0-SNAPSHOT</version>
+        <version>3.2.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>tooling-cli</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.2.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <description>CQF Tooling CLI</description>
@@ -27,7 +27,7 @@
         <dependency>
             <groupId>org.opencds.cqf</groupId>
             <artifactId>tooling</artifactId>
-            <version>3.1.0-SNAPSHOT</version>
+            <version>3.2.0-SNAPSHOT</version>
         </dependency>
 
         <dependency>

diff --git a/tooling-ui/pom.xml b/tooling-ui/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>3.1.0-SNAPSHOT</version>
+        <version>3.2.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>tooling-ui</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.2.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <description>CQF Tooling UI</description>
@@ -19,7 +19,7 @@
         <dependency>
             <groupId>org.opencds.cqf</groupId>
             <artifactId>tooling</artifactId>
-            <version>3.1.0-SNAPSHOT</version>
+            <version>3.2.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>org.openjfx</groupId>

diff --git a/tooling/pom.xml b/tooling/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>3.1.0-SNAPSHOT</version>
+        <version>3.2.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>tooling</artifactId>
-    <version>3.1.0-SNAPSHOT</version>
+    <version>3.2.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <dependencies>

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java b/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/constants/Api.java b/tooling/src/main/java/org/opencds/cqf/tooling/constants/Api.java
@@ -4,7 +4,7 @@ public class Api {
 
    private Api() {}
 
-   public static final String RXMIX_WORKFLOW_URL = "https://mor.nlm.nih.gov/RxMix/executeConfig.do";
+   public static final String RXMIX_WORKFLOW_URL = "https://rxmix-legacy.nlm.nih.gov/RxMix/executeConfig.do";
    public static final String LOINC_HIERARCHY_QUERY_URL = "https://loinc.regenstrief.org/searchapi/hierarchy/component-system/search?searchString=";
    public static final String LOINC_FHIR_SERVER_URL = "https://fhir.loinc.org";
    public static final String FHIR_LOOKUP_OPERATION_NAME = "$lookup";

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/cql_generation/context/ElmContext.java b/tooling/src/main/java/org/opencds/cqf/tooling/cql_generation/context/ElmContext.java
@@ -7,11 +7,10 @@
 import java.util.Stack;
 
 import org.apache.commons.lang3.tuple.Pair;
-import org.cqframework.cql.cql2elm.CqlCompilerOptions;
-import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
+import org.cqframework.cql.elm.IdObjectFactory;
 import org.fhir.ucum.UcumEssenceService;
 import org.fhir.ucum.UcumException;
 import org.fhir.ucum.UcumService;
@@ -60,8 +59,7 @@ public void newLibraryBuilder(Pair<VersionedIdentifier, ContextDef> libraryInfo)
             UcumService ucumService = new UcumEssenceService(
                     UcumEssenceService.class.getResourceAsStream("/ucum-essence.xml"));
             libraryManager.setUcumService(ucumService);
-            this.libraryBuilder = new LibraryBuilder(libraryManager);
-            this.libraryBuilder.setCompilerOptions(CqlCompilerOptions.defaultOptions());
+            this.libraryBuilder = new LibraryBuilder(libraryManager, new IdObjectFactory());
             this.libraryBuilder.setLibraryIdentifier(libraryInfo.getLeft());
             this.libraryBuilder.getModel(new UsingDef().withUri(modelBuilder.getModelUri())
                     .withLocalIdentifier(modelBuilder.getModelIdentifier()).withVersion(modelBuilder.getModelVersion()));

diff --git a/...g/src/main/java/org/opencds/cqf/tooling/cql_generation/drool/visitor/ElmToCqlVisitor.java b/...g/src/main/java/org/opencds/cqf/tooling/cql_generation/drool/visitor/ElmToCqlVisitor.java
@@ -4,7 +4,7 @@
 import java.util.Stack;
 import java.util.stream.Collectors;
 
-import org.cqframework.cql.elm.visiting.ElmBaseLibraryVisitor;
+import org.cqframework.cql.elm.visiting.BaseElmLibraryVisitor;
 import org.hl7.elm.r1.*;
 import org.hl7.elm.r1.Library.Statements;
 import org.opencds.cqf.tooling.cql_generation.context.ElmContext;
@@ -19,7 +19,7 @@
  * @author Joshua Reynolds
  * @since 2021-04-05
  */
-public class ElmToCqlVisitor extends ElmBaseLibraryVisitor<Void, ElmContext> {
+public class ElmToCqlVisitor extends BaseElmLibraryVisitor<Void, ElmContext> {
     private static final Logger logger = LoggerFactory.getLogger(ElmToCqlVisitor.class);
     private boolean useSpaces = true;
 
@@ -864,7 +864,7 @@ public Void visitQuery(Query query, ElmContext context) {
                 query.getRelationship().stream().forEach(relationship -> visitRelationshipClause(relationship, context));
             }
             if (query.getWhere() != null) {
-                visitWhereClause(query.getWhere(), context);
+                visitExpression(query.getWhere(), context);
             }
             if (query.getReturn() != null) {
                 visitReturnClause(query.getReturn(), context);
@@ -961,27 +961,6 @@ public Void visitLetClause(LetClause let, ElmContext context) {
         return null;
     }
 
-    /**
-     * Visit WhereClause. This method will be called for
-     * WhereClause expression nodes.
-     *
-     * @param where     the Expression
-     * @param context the context passed to the visitor
-     * @return the visitor result
-     */
-    @Override
-    public Void visitWhereClause(Expression where, ElmContext context) {
-        try {
-            enterClause();
-            output.append("where");
-            visitElement(where, context);
-            return null;
-        }
-        finally {
-            exitClause();
-        }
-    }
-
     /**
      * Visit ReturnClause. This method will be called for
      * every node in the tree that is a ReturnClause.

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/library/LibraryProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/library/LibraryProcessor.java
@@ -3,9 +3,11 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Queue;
+import java.util.Set;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ConcurrentLinkedQueue;
 import java.util.regex.Pattern;
@@ -14,6 +16,7 @@
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions.Format;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.Attachment;
 import org.hl7.fhir.r5.model.CodeableConcept;
@@ -198,14 +201,17 @@ protected Library refreshGeneratedContent(Library sourceLibrary) {
             sourceLibrary.getContent().clear();
             sourceLibrary.getContent().add(attachment);
             setLibraryType(sourceLibrary);
+
+            var translatorOptions = getCqlProcessor().getCqlTranslatorOptions();
+            var formats = translatorOptions.getFormats();
             CqlProcessor.CqlSourceFileInformation info = getCqlProcessor().getFileInformation(attachment.getUrl());
             attachment.setUrlElement(null);
             if (info != null) {
                 //f.getErrors().addAll(info.getErrors());
-                if (info.getElm() != null) {
+                if (info.getElm() != null && emptyIfNull(formats).contains(Format.XML)) {
                     sourceLibrary.addContent().setContentType("application/elm+xml").setData(info.getElm());
                 }
-                if (info.getJsonElm() != null) {
+                if (info.getJsonElm() != null && emptyIfNull(formats).contains(Format.JSON)) {
                     sourceLibrary.addContent().setContentType("application/elm+json").setData(info.getJsonElm());
                 }
                 sourceLibrary.getDataRequirement().clear();
@@ -215,7 +221,7 @@ protected Library refreshGeneratedContent(Library sourceLibrary) {
                 sourceLibrary.getParameter().clear();
                 sourceLibrary.getParameter().addAll(info.getParameters());
                 getCqlProcessor().getCqlTranslatorOptions();
-                setTranslatorOptions(sourceLibrary, getCqlProcessor().getCqlTranslatorOptions());
+                setTranslatorOptions(sourceLibrary, translatorOptions);
             } else {
                 logMessage(String.format("No cql info found for %s", fileName));
                 //f.getErrors().add(new ValidationMessage(ValidationMessage.Source.Publisher, ValidationMessage.IssueType.NOTFOUND, "Library", "No cql info found for "+f.getName(), ValidationMessage.IssueSeverity.ERROR));
@@ -225,6 +231,10 @@ protected Library refreshGeneratedContent(Library sourceLibrary) {
         return sourceLibrary;
     }
 
+    private <T> Set<T> emptyIfNull(Set<T> set) {
+        return set != null ? set : Collections.emptySet();
+    }
+
     protected void setTranslatorOptions(Library sourceLibrary, CqlTranslatorOptions options) {
         Extension optionsExtension = sourceLibrary.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/cqf-cqlOptions");
         if (optionsExtension == null) {