Add support for subsumes in tx client

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java

@@ -117,6 +117,13 @@ public class TerminologyClientR2 implements ITerminologyClient {
     p2 = client.operateType(org.hl7.fhir.dstu2.model.ValueSet.class, "validate-code", p2);
     return (Parameters) VersionConvertorFactory_10_50.convertResource(p2);
   }
+  
+  @Override
+  public Parameters subsumes(Parameters pin) throws FHIRException {
+    org.hl7.fhir.dstu2.model.Parameters p2 = (org.hl7.fhir.dstu2.model.Parameters) VersionConvertorFactory_10_50.convertResource(pin);
+    p2 = client.operateType(org.hl7.fhir.dstu2.model.ValueSet.class, "subsumes", p2);
+    return (Parameters) VersionConvertorFactory_10_50.convertResource(p2);
+  }
 
   @Override
   public Parameters validateVS(Parameters pin) throws FHIRException {
@@ -238,4 +245,5 @@ public class TerminologyClientR2 implements ITerminologyClient {
     org.hl7.fhir.dstu2.model.Bundle result = client.search(type, criteria);
     return result == null ? null : (Bundle) VersionConvertorFactory_10_50.convertResource(result);
   }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java

@@ -242,4 +242,11 @@ public class TerminologyClientR3 implements ITerminologyClient {
 
   }
 
+  @Override
+  public Parameters subsumes(Parameters pin) throws FHIRException { 
+    org.hl7.fhir.dstu3.model.Parameters p2 = (org.hl7.fhir.dstu3.model.Parameters) VersionConvertorFactory_30_50.convertResource(pin);
+    p2 = client.operateType(org.hl7.fhir.dstu3.model.CodeSystem.class, "subsumes", p2);
+    return (Parameters) VersionConvertorFactory_30_50.convertResource(p2);
+  }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java

@@ -111,6 +111,25 @@ public class TerminologyClientR4 implements ITerminologyClient {
     }
   }
 
+
+  @Override
+  public Parameters subsumes(Parameters pin) throws FHIRException {
+    try {
+      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(pin);
+      p2 = client.operateType(org.hl7.fhir.r4.model.CodeSystem.class, "subsumes", p2);
+      return (Parameters) VersionConvertorFactory_40_50.convertResource(p2);
+    } catch (EFhirClientException e) {
+      if (e.getServerErrors().size() == 1) {
+        OperationOutcome op =  (OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0));
+        throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getMessage(), op, e);
+      } else {
+        throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getMessage(), e);        
+      }
+    } catch (IOException e) {
+      throw new FHIRException(e);
+    }
+  }
+
   @Override
   public Parameters validateVS(Parameters pin) throws FHIRException {
     try {
@@ -249,6 +268,5 @@ public class TerminologyClientR4 implements ITerminologyClient {
     org.hl7.fhir.r4.model.Bundle result = client.search(type, criteria);
     return result == null ? null : (Bundle) VersionConvertorFactory_40_50.convertResource(result);
   }
-
   
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -1347,7 +1347,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     Set<String> systems = findRelevantSystems(code, vs);
     TerminologyClientContext tc = terminologyClientManager.chooseServer(vs, systems, false);
     
-    String csumm =cachingAllowed && txCache != null ? txCache.summary(code) : null;
+    String csumm = cachingAllowed && txCache != null ? txCache.summary(code) : null;
     if (cachingAllowed && txCache != null) {
       txLog("$validate "+csumm+(vs == null ? "" : " for "+ txCache.summary(vs))+" on "+tc.getAddress());
     } else {
@@ -1377,6 +1377,83 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return res;
   }
 
+
+  /**
+   * ask the terminology system whether parent subsumes child. 
+   * 
+   * @return true if it does, false if it doesn't, and null if it's not know whether it does
+   */
+  public Boolean subsumes(ValidationOptions optionsArg, Coding parent, Coding child) {
+    ValidationOptions options = optionsArg != null ? optionsArg : ValidationOptions.defaults();
+
+    if (parent.hasSystem()) {
+      codeSystemsUsed.add(parent.getSystem());
+    } else {
+      return null;
+    }
+    if (child.hasSystem()) {
+      codeSystemsUsed.add(child.getSystem());
+    } else {
+      return null;
+    }
+
+    final CacheToken cacheToken = cachingAllowed && txCache != null ? txCache.generateSubsumesToken(options, parent, child, expParameters) : null;
+    if (cachingAllowed && txCache != null) {
+      Boolean res = txCache.getSubsumes(cacheToken);
+      if (res != null) {
+        return res;
+      }
+    }
+    
+    if (options.isUseClient() && parent.getSystem().equals(child.getSystem())) {
+      CodeSystem cs = fetchCodeSystem(parent.getSystem());
+      if (cs != null) {
+        Boolean b = CodeSystemUtilities.subsumes(cs, parent.getCode(), child.getCode());
+        if (txCache != null && cachingAllowed) {
+          txCache.cacheSubsumes(cacheToken, b, true);
+        }
+        return b;
+      }
+    }
+
+    if (!terminologyClientManager.hasClient() || !options.isUseServer() || unsupportedCodeSystems.contains(parent.getSystem()) || unsupportedCodeSystems.contains(child.getSystem()) || noTerminologyServer) {
+      return null;      
+    }
+
+    Set<String> systems = new HashSet<>();
+    systems.add(parent.getSystem());
+    systems.add(child.getSystem());
+    TerminologyClientContext tc = terminologyClientManager.chooseServer(null, systems, false);
+    
+    txLog("$subsumes "+parent.toString()+" > "+child.toString()+" on "+tc.getAddress());
+
+    try {
+      Parameters pIn =  new Parameters();
+      pIn.addParameter().setName("codingA").setValue(parent);
+      pIn.addParameter().setName("codingB").setValue(child);
+      if (txLog != null) {
+        txLog.clearLastId();
+      }
+      Parameters pOut = tc.getClient().subsumes(pIn);
+      return processSubsumesResult(pOut, tc.getClient().getAddress());
+    } catch (Exception e) {
+      // e.printStackTrace();
+    }
+    return null;
+  }
+
+
+  public Boolean processSubsumesResult(Parameters pOut, String server) {
+    for (ParametersParameterComponent p : pOut.getParameter()) {
+      if (p.hasValue()) {
+        if (p.getName().equals("outcome")) {
+          return Utilities.existsInList(p.getValue().primitiveValue(), "equivalent", "subsumes");
+        }
+      }
+    }
+    return null;
+  }
+
   protected ValueSetExpander constructValueSetExpanderSimple(ValidationOptions options) {
     return new ValueSetExpander(this, new TerminologyOperationContext(this, options)).setDebug(logger.isDebugLogging());
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java

@@ -640,4 +640,11 @@ public interface IWorkerContext {
   public <T extends Resource> T findTxResource(Class<T> class_, String canonical);
   public <T extends Resource> T findTxResource(Class<T> class_, String canonical, String version);
 
+  /**
+   * ask the terminology system whether parent subsumes child. 
+   * 
+   * @return true if it does, false if it doesn't, and null if it's not know whether it does
+   */
+  public Boolean subsumes(ValidationOptions options, Coding parent, Coding child);
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/ITerminologyClient.java

@@ -54,6 +54,7 @@ public interface ITerminologyClient {
   ValueSet expandValueset(ValueSet vs, Parameters p) throws FHIRException;
   Parameters validateCS(Parameters pin) throws FHIRException;
   Parameters validateVS(Parameters pin) throws FHIRException;
+  Parameters subsumes(Parameters pin) throws FHIRException;
   ITerminologyClient setTimeoutFactor(int i) throws FHIRException;
   ToolingClientLogger getLogger();
   ITerminologyClient setLogger(ToolingClientLogger txLog) throws FHIRException;

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientR5.java

@@ -135,6 +135,11 @@ public class TerminologyClientR5 implements ITerminologyClient {
     return client.operateType(CodeSystem.class, "validate-code", pin);
   }
 
+  @Override
+  public Parameters subsumes(Parameters pin) {
+    return client.operateType(CodeSystem.class, "subsumes", pin);
+  }
+
   @Override
   public Parameters validateVS(Parameters pin) {
     return client.operateType(ValueSet.class, "validate-code", pin);
@@ -256,4 +261,5 @@ public class TerminologyClientR5 implements ITerminologyClient {
     return client.search(type, criteria);
   }
 
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/utilities/TerminologyCache.java

@@ -148,6 +148,21 @@ public class TerminologyCache {
     }
   }
 
+  public static class SubsumesResult {
+    
+    private Boolean result;
+
+    protected SubsumesResult(Boolean result) {
+      super();
+      this.result = result;
+    }
+
+    public Boolean getResult() {
+      return result;
+    }
+    
+  }
+  
   protected SystemNameKeyGenerator getSystemNameKeyGenerator() {
     return systemNameKeyGenerator;
   }
@@ -218,6 +233,7 @@ public class TerminologyCache {
     private boolean persistent;
     private ValidationResult v;
     private ValueSetExpansionOutcome e;
+    private SubsumesResult s;
   }
 
   private class NamedCache {
@@ -381,9 +397,9 @@ public class TerminologyCache {
       if (code.hasSystem()) {
         ct.setName(code.getSystem());
         ct.hasVersion = code.hasVersion();
-      }
+      } else {
-      else
         ct.name = NAME_FOR_NO_SYSTEM;
+      }
       ct.setName(vsUrl);
       JsonParser json = new JsonParser();
       json.setOutputStyle(OutputStyle.PRETTY);
@@ -633,6 +649,9 @@ public class TerminologyCache {
           if (ce.e.getValueset() != null)
             sw.write("  \"valueSet\" : "+json.composeString(ce.e.getValueset()).trim()+",\r\n");
           sw.write("  \"error\" : \""+Utilities.escapeJson(ce.e.getError()).trim()+"\"\r\n}\r\n");
+        } else if (ce.s != null) {
+          sw.write("s: {\r\n");
+          sw.write("  \"result\" : "+ce.s.result+"\r\n}\r\n");
         } else {
           sw.write("v: {\r\n");
           boolean first = true;
@@ -743,15 +762,17 @@ public class TerminologyCache {
     CacheEntry ce = new CacheEntry();
     ce.persistent = true;
     ce.request = request;
-    boolean e = resultString.charAt(0) == 'e';
+    char e = resultString.charAt(0);
     resultString = resultString.substring(3);
     JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(resultString);
     String error = loadJS(o.get("error"));
-    if (e) {
+    if (e == 'e') {
       if (o.has("valueSet"))
         ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN, o.has("from-server"));
       else
         ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN, o.has("from-server"));
+    } else if (e == 's') {
+      ce.s = new SubsumesResult(o.get("result").getAsBoolean());
     } else {
       String t = loadJS(o.get("severity"));
       IssueSeverity severity = t == null ? null :  IssueSeverity.fromCode(t);
@@ -934,15 +955,15 @@ public class TerminologyCache {
 
   public Map<String, String> servers() {
     Map<String, String> servers = new HashMap<>();
-    servers.put("http://local.fhir.org/r2", "tx.fhir.org");
+//    servers.put("http://local.fhir.org/r2", "tx.fhir.org");
-    servers.put("http://local.fhir.org/r3", "tx.fhir.org");
+//    servers.put("http://local.fhir.org/r3", "tx.fhir.org");
-    servers.put("http://local.fhir.org/r4", "tx.fhir.org");
+//    servers.put("http://local.fhir.org/r4", "tx.fhir.org");
-    servers.put("http://local.fhir.org/r5", "tx.fhir.org");
+//    servers.put("http://local.fhir.org/r5", "tx.fhir.org");
-
+//
-    servers.put("http://tx-dev.fhir.org/r2", "tx.fhir.org");
+//    servers.put("http://tx-dev.fhir.org/r2", "tx.fhir.org");
-    servers.put("http://tx-dev.fhir.org/r3", "tx.fhir.org");
+//    servers.put("http://tx-dev.fhir.org/r3", "tx.fhir.org");
-    servers.put("http://tx-dev.fhir.org/r4", "tx.fhir.org");
+//    servers.put("http://tx-dev.fhir.org/r4", "tx.fhir.org");
-    servers.put("http://tx-dev.fhir.org/r5", "tx.fhir.org");
+//    servers.put("http://tx-dev.fhir.org/r5", "tx.fhir.org");
 
     servers.put("http://tx.fhir.org/r2", "tx.fhir.org");
     servers.put("http://tx.fhir.org/r3", "tx.fhir.org");
@@ -1002,5 +1023,58 @@ public class TerminologyCache {
     }
   }
 
+  public CacheToken generateSubsumesToken(ValidationOptions options, Coding parent, Coding child, Parameters expParameters) {
+    try {
+      CacheToken ct = new CacheToken();
+      if (parent.hasSystem()) {
+        ct.setName(parent.getSystem());
+      }
+      if (child.hasSystem()) {
+        ct.setName(child.getSystem());
+      }
+      ct.hasVersion = parent.hasVersion() || child.hasVersion();
+      JsonParser json = new JsonParser();
+      json.setOutputStyle(OutputStyle.PRETTY);
+      String expJS = json.composeString(expParameters);
+      ct.request = "{\"op\": \"subsumes\", \"parent\" : "+json.composeString(parent, "code")+", \"child\" :"+json.composeString(child, "code")+(options == null ? "" : ", "+options.toJson())+", \"profile\": "+expJS+"}";
+      ct.key = String.valueOf(hashJson(ct.request));
+      return ct;
+    } catch (IOException e) {
+      throw new Error(e);
+    }
+  }
+
+  public Boolean getSubsumes(CacheToken cacheToken) {
+   if (cacheToken.key == null) {
+     return null;
+   }
+   synchronized (lock) {
+     requestCount++;
+     NamedCache nc = getNamedCache(cacheToken);
+     CacheEntry e = nc.map.get(cacheToken.key);
+     if (e == null) {
+       networkCount++;
+       return null;
+     } else {
+       hitCount++;
+       return e.s.result;
+     }
+   }
+   
+  }
+
+  public void cacheSubsumes(CacheToken cacheToken, Boolean b, boolean persistent) {
+    if (cacheToken.key != null) {
+      synchronized (lock) {      
+        NamedCache nc = getNamedCache(cacheToken);
+        CacheEntry e = new CacheEntry();
+        e.request = cacheToken.request;
+        e.persistent = persistent;
+        e.s = new SubsumesResult(b);
+        store(cacheToken, persistent, nc, e);
+      }    
+    }
+  }
+
 
 }