Issue #1980 - updates

Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
LinuxForHealth · Mar 10, 2021 · 9bac1af · 9bac1af
1 parent 9e914ee
commit 9bac1af
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Showing 9 changed files with 158 additions and 46 deletions.
diff --git a/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/FHIRTermGraph.java b/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/FHIRTermGraph.java
@@ -28,4 +28,5 @@ default Stream<Result<JanusGraphVertex>> indexQuery(String query) {
     Stream<Result<JanusGraphVertex>> indexQuery(String query, int limit);
     void close();
     void drop();
+    void dropAllVertices();
 }
diff --git a/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/impl/FHIRTermGraphImpl.java b/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/impl/FHIRTermGraphImpl.java
@@ -194,4 +194,13 @@ public void drop() {
             graph = null;
         }
     }
+
+    @Override
+    public void dropAllVertices() {
+        log.info("Dropping all vertices...");
+        if (traversal != null) {
+            traversal.V().drop().iterate();
+            traversal.tx().commit();
+        }
+    }
 }
diff --git a/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/FHIRTermGraphLoader.java b/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/FHIRTermGraphLoader.java
@@ -10,6 +10,8 @@
 
 import org.apache.commons.cli.Options;
 
+import com.ibm.fhir.term.graph.FHIRTermGraph;
+
 public interface FHIRTermGraphLoader {
     enum Type {
         CODESYSTEM {
@@ -49,4 +51,5 @@ public Options options() {
     void load();
     void close();
     Map<String, String> options();
+    FHIRTermGraph getGraph();
 }
diff --git a/...term-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/AbstractTermGraphLoader.java b/...term-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/AbstractTermGraphLoader.java
@@ -11,6 +11,7 @@
 import java.util.Map;
 import java.util.Objects;
 
+import org.apache.commons.configuration.Configuration;
 import org.apache.tinkerpop.gremlin.process.traversal.dsl.graph.GraphTraversalSource;
 import org.janusgraph.core.JanusGraph;
 
@@ -35,11 +36,30 @@ public AbstractTermGraphLoader(Map<String, String> options) {
         g = graph.traversal();
 
         // create label filter
-        if (options.containsKey("labels")) {
-            labelFilter = new LabelFilter(new HashSet<>(Arrays.asList(options.get("labels").split(","))));
-        } else {
-            labelFilter = LabelFilter.ACCEPT_ALL;
-        }
+        labelFilter = createLabelFilter(options);
+    }
+
+    public AbstractTermGraphLoader(Map<String, String> options, Configuration configuration) {
+        this.options = Objects.requireNonNull(options, "options");
+        Objects.requireNonNull(configuration, "configuration");
+
+        graph = FHIRTermGraphFactory.open(configuration);
+        janusGraph = graph.getJanusGraph();
+        g = graph.traversal();
+
+        // create label filter
+        labelFilter = createLabelFilter(options);
+    }
+
+    public AbstractTermGraphLoader(Map<String, String> options, FHIRTermGraph graph) {
+        this.options = Objects.requireNonNull(options, "options");
+
+        this.graph = Objects.requireNonNull(graph, "graph");
+        janusGraph = graph.getJanusGraph();
+        g = graph.traversal();
+
+        // create label filter
+        labelFilter = createLabelFilter(options);
     }
 
     @Override
@@ -54,4 +74,15 @@ public final void close() {
     public final Map<String, String> options() {
         return options;
     }
+
+    @Override
+    public final FHIRTermGraph getGraph() {
+        return graph;
+    }
+
+    protected LabelFilter createLabelFilter(Map<String, String> options) {
+        return options.containsKey("labels") ?
+                new LabelFilter(new HashSet<>(Arrays.asList(options.get("labels").split(",")))) :
+                    LabelFilter.ACCEPT_ALL;
+    }
 }
diff --git a/...rm-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/CodeSystemTermGraphLoader.java b/...rm-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/CodeSystemTermGraphLoader.java
@@ -7,14 +7,14 @@
 package com.ibm.fhir.term.graph.loader.impl;
 
 import static com.ibm.fhir.term.graph.loader.util.FHIRTermGraphLoaderUtil.toMap;
-import static com.ibm.fhir.term.graph.util.FHIRTermGraphUtil.toObject;
 import static com.ibm.fhir.term.graph.util.FHIRTermGraphUtil.normalize;
 import static com.ibm.fhir.term.graph.util.FHIRTermGraphUtil.toLong;
+import static com.ibm.fhir.term.graph.util.FHIRTermGraphUtil.toObject;
 import static com.ibm.fhir.term.util.CodeSystemSupport.getConcepts;
-import static com.ibm.fhir.term.util.CodeSystemSupport.isCaseSensitive;
 
 import java.io.FileInputStream;
 import java.io.InputStream;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
@@ -27,6 +27,7 @@
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.MissingOptionException;
 import org.apache.commons.cli.Options;
+import org.apache.commons.configuration.Configuration;
 import org.apache.tinkerpop.gremlin.structure.Vertex;
 
 import com.ibm.fhir.model.format.Format;
@@ -72,6 +73,22 @@ public CodeSystemTermGraphLoader(Map<String, String> options) {
         conceptVertexMap = new HashMap<>();
     }
 
+    public CodeSystemTermGraphLoader(Configuration configuration, CodeSystem codeSystem) {
+        super(Collections.emptyMap(), configuration);
+
+        this.codeSystem = Objects.requireNonNull(codeSystem, "codeSystem");
+        concepts = getConcepts(codeSystem);
+        conceptVertexMap = new HashMap<>();
+    }
+
+    public CodeSystemTermGraphLoader(FHIRTermGraph graph, CodeSystem codeSystem) {
+        super(Collections.emptyMap(), graph);
+
+        this.codeSystem = Objects.requireNonNull(codeSystem, "codeSystem");
+        concepts = getConcepts(codeSystem);
+        conceptVertexMap = new HashMap<>();
+    }
+
     @Override
     public void load() {
         createCodeSystemVertex();
@@ -88,7 +105,7 @@ private void createCodeSystemVertex() {
 
         codeSystemVertex = g.addV("CodeSystem")
                 .property("url", url)
-                .property("caseSensitive", isCaseSensitive(codeSystem))
+                .property("count", concepts.size())
                 .next();
 
         if (codeSystem.getVersion() != null) {

diff --git a/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/provider/GraphTermServiceProvider.java b/fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/provider/GraphTermServiceProvider.java
@@ -53,12 +53,18 @@
 import com.ibm.fhir.term.spi.FHIRTermServiceProvider;
 
 public class GraphTermServiceProvider implements FHIRTermServiceProvider {
+    private static final int DEFAULT_COUNT = 1000;
     private final FHIRTermGraph graph;
 
     public GraphTermServiceProvider(Configuration configuration) {
+        Objects.requireNonNull(configuration, "configuration");
         graph = FHIRTermGraphFactory.open(configuration);
     }
 
+    public GraphTermServiceProvider(FHIRTermGraph graph) {
+        this.graph = Objects.requireNonNull(graph, "graph");
+    }
+
     @Override
     public Set<Concept> closure(CodeSystem codeSystem, Code code) {
         Objects.requireNonNull(codeSystem.getUrl(), "CodeSystem.url");
@@ -84,13 +90,13 @@ public Concept getConcept(CodeSystem codeSystem, Code code) {
     @Override
     public Set<Concept> getConcepts(CodeSystem codeSystem) {
         Objects.requireNonNull(codeSystem.getUrl(), "CodeSystem.url");
-        List<Concept> concepts = new ArrayList<>(getCount(codeSystem));
+        Set<Concept> concepts = new LinkedHashSet<>(getCount(codeSystem));
         hasVersion(hasUrl(vertices(), codeSystem.getUrl()), codeSystem.getVersion())
             .out("concept")
             .elementMap()
             .toStream()
             .forEach(elementMap -> concepts.add(createConcept(elementMap)));
-        return Collections.emptySet();
+        return concepts;
     }
 
     @SuppressWarnings("unchecked")
@@ -325,7 +331,7 @@ private int getCount(CodeSystem codeSystem) {
         if (optional.isPresent()) {
             return (Integer) optional.get().get("count");
         }
-        return -1;
+        return DEFAULT_COUNT;
     }
 
     private List<Designation> getDesignations(CodeSystem codeSystem, String code) {
@@ -393,29 +399,20 @@ private Element getValue(Map<Object, Object> elementMap) {
     }
 
     private GraphTraversal<Vertex, Vertex> hasCode(GraphTraversal<Vertex, Vertex> g, String code, boolean caseSensitive) {
-        if (caseSensitive) {
-            return g.has("code", code);
-        }
-        return g.has("codeLowerCase", normalize(code));
+        return caseSensitive ? g.has("code", code) : g.has("codeLowerCase", normalize(code));
     }
 
     // anonymous graph traversal
     private GraphTraversal<Vertex, Vertex> hasCode(String code, boolean caseSensitive) {
-        if (caseSensitive) {
-            return __.has("code", code);
-        }
-        return __.has("codeLowerCase", normalize(code));
+        return caseSensitive ? __.has("code", code) : __.has("codeLowerCase", normalize(code));
     }
 
     private GraphTraversal<Vertex, Vertex> hasUrl(GraphTraversal<Vertex, Vertex> g, Uri url) {
         return g.has("url", url.getValue());
     }
 
     private GraphTraversal<Vertex, Vertex> hasVersion(GraphTraversal<Vertex, Vertex> g, com.ibm.fhir.model.type.String version) {
-        if (version != null) {
-            return g.has("version", version.getValue());
-        }
-        return g;
+        return (version != null) ? g.has("version", version.getValue()) : g;
     }
 
     private GraphTraversal<Vertex, Vertex> vertices(Object... vertexIds) {

diff --git a/...-term-graph/src/test/java/com/ibm/fhir/term/graph/test/CodeSystemTermGraphLoaderTest.java b/...-term-graph/src/test/java/com/ibm/fhir/term/graph/test/CodeSystemTermGraphLoaderTest.java
@@ -7,22 +7,62 @@
 package com.ibm.fhir.term.graph.test;
 
 import java.io.InputStream;
+import java.util.Collections;
+import java.util.LinkedHashSet;
+import java.util.Set;
 
 import org.apache.commons.configuration.PropertiesConfiguration;
+import org.locationtech.jts.util.Assert;
+import org.testng.annotations.Test;
 
 import com.ibm.fhir.model.format.Format;
 import com.ibm.fhir.model.parser.FHIRParser;
 import com.ibm.fhir.model.resource.CodeSystem;
-import com.ibm.fhir.model.type.Code;
+import com.ibm.fhir.model.resource.CodeSystem.Concept;
+import com.ibm.fhir.term.graph.FHIRTermGraph;
+import com.ibm.fhir.term.graph.factory.FHIRTermGraphFactory;
+import com.ibm.fhir.term.graph.loader.FHIRTermGraphLoader;
+import com.ibm.fhir.term.graph.loader.impl.CodeSystemTermGraphLoader;
 import com.ibm.fhir.term.graph.provider.GraphTermServiceProvider;
+import com.ibm.fhir.term.graph.util.FHIRTermGraphUtil;
+import com.ibm.fhir.term.spi.FHIRTermServiceProvider;
+import com.ibm.fhir.term.util.CodeSystemSupport;
+
+import ch.qos.logback.classic.Level;
 
 public class CodeSystemTermGraphLoaderTest {
-    public static void main(String[] args) throws Exception {
-        InputStream in = CodeSystemTermGraphLoaderTest.class.getClassLoader().getResourceAsStream("JSON/CodeSystem-cs5.json");
-        CodeSystem codeSystem = FHIRParser.parser(Format.JSON).parse(in);
-        GraphTermServiceProvider provider = new GraphTermServiceProvider(new PropertiesConfiguration("conf/janusgraph-berkeleyje-lucene.properties"));
-        System.out.println(provider.subsumes(codeSystem, Code.of("m"), Code.of("p")));
-        System.out.println(provider.getConcept(codeSystem, Code.of("o")));
-        provider.getGraph().close();
+    @Test
+    public void testCodeSystemTermGraphLoader() throws Exception {
+        FHIRTermGraphUtil.setRootLoggerLevel(Level.INFO);
+
+        FHIRTermGraph graph = null;
+        try (InputStream in = CodeSystemTermGraphLoaderTest.class.getClassLoader().getResourceAsStream("JSON/CodeSystem-cs5.json")) {
+            graph = FHIRTermGraphFactory.open(new PropertiesConfiguration("conf/janusgraph-berkeleyje-lucene.properties"));
+            graph.dropAllVertices();
+
+            CodeSystem codeSystem = FHIRParser.parser(Format.JSON).parse(in);
+            FHIRTermGraphLoader loader = new CodeSystemTermGraphLoader(graph, codeSystem);
+            loader.load();
+
+            FHIRTermServiceProvider provider = new GraphTermServiceProvider(graph);
+
+            Set<Concept> expected = new LinkedHashSet<>();
+            for (Concept concept : CodeSystemSupport.getConcepts(codeSystem)) {
+                expected.add(concept.toBuilder()
+                    .concept(Collections.emptyList())
+                    .build());
+            }
+
+            Set<Concept> actual = new LinkedHashSet<>();
+            for (Concept concept : provider.getConcepts(codeSystem)) {
+                actual.add(provider.getConcept(codeSystem, concept.getCode()));
+            }
+
+            Assert.equals(expected, actual);
+        } finally {
+            if (graph != null) {
+                graph.close();
+            }
+        }
     }
-}
+}
diff --git a/fhir-term-graph/src/test/java/com/ibm/fhir/term/graph/test/FHIRTermGraphTest.java b/fhir-term-graph/src/test/java/com/ibm/fhir/term/graph/test/FHIRTermGraphTest.java
@@ -29,7 +29,7 @@ public static void main(String[] args) throws Exception {
         GraphTraversalSource g = graph.traversal();
 
         g.V().drop().iterate();
-        g.E().drop().iterate();
+//      g.E().drop().iterate();
 
         Vertex v1 = g.addV("Concept").property("code", "a").next();
         System.out.println(v1.id());