more PE work

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Base.java

@@ -228,6 +228,9 @@ public abstract class Base implements Serializable, IBase, IElement {
     throw new FHIRException("Attempt to add child with unknown name "+name);
   }
 
+	public boolean removeChild(String name, Base value) {
+    throw new FHIRException("Attempt to remove child with unknown name "+name);
+	}
   /**
    * Supports iterating the children elements in some generic processor or browser
    * All defined children will be listed, even if they have no value on this instance

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/profilemodel/PEBuilder.java

@@ -20,6 +20,7 @@ import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.ResourceFactory;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.Utilities;
 
@@ -85,6 +86,7 @@ public class PEBuilder {
   private ContextUtilities cu;
   private PEElementPropertiesPolicy elementProps;
   private boolean fixedPropsDefault;
+  private FHIRPathEngine fpe;
 
   /**
    * @param context - must be loaded with R5 definitions
@@ -97,6 +99,28 @@ public class PEBuilder {
     this.fixedPropsDefault = fixedPropsDefault;
     pu = new ProfileUtilities(context, null, null);
     cu = new ContextUtilities(context);
+    fpe = new FHIRPathEngine(context, pu);
+  }
+  
+  /**
+   * Given a profile, return a tree of the elements defined in the profile model. This builds the profile model
+   * for the provided version of the nominated profile
+   * 
+   * The tree of elements in the profile model is different to those defined in the base resource:
+   *  - some elements are removed (max = 0)
+   *  - extensions are turned into named elements 
+   *  - slices are turned into named elements 
+   *  - element properties - doco, cardinality, binding etc is updated for what the profile says
+   * 
+   * Warning: profiles and resources are recursive; you can't iterate this tree until it you get 
+   * to the leaves because there are nodes that don't terminate (extensions have extensions)
+   * 
+   */
+  public PEDefinition buildPEDefinition(StructureDefinition profile) {
+    if (!profile.hasSnapshot()) {
+      throw new DefinitionException("Profile '"+profile.getVersionedUrl()+"' does not have a snapshot");      
+    }
+    return new PEDefinitionResource(this, profile);
   }
   
   /**
@@ -168,6 +192,25 @@ public class PEBuilder {
     return loadInstance(defn, resource);
   }
   
+  /**
+   * Given a resource and a profile, return a tree of instance data as defined by the profile model 
+   * using the provided version of the profile
+   * 
+   * The tree is a facade to the underlying resource - all actual data is stored against the resource,
+   * and retrieved on the fly from the resource, so that applications can work at either level, as 
+   * convenient. 
+   * 
+   * Note that there's a risk that deleting something through the resource while holding 
+   * a handle to a PEInstance that is a facade on what is deleted leaves an orphan facade 
+   * that will continue to function, but is making changes to resource content that is no 
+   * longer part of the resource 
+   * 
+   */
+  public PEInstance buildPEInstance(StructureDefinition profile, Resource resource) {
+    PEDefinition defn = buildPEDefinition(profile);
+    return loadInstance(defn, resource);
+  }
+  
   /**
    * Given a resource and a profile, return a tree of instance data as defined by the profile model 
    * using the nominated version of the profile
@@ -206,6 +249,25 @@ public class PEBuilder {
     return res;
   }
 
+  /**
+   * For the provided version of a profile, construct a resource and fill out any fixed or required elements
+   * 
+   * Note that fixed values are filled out irrespective of the value of fixedProps when the builder is created
+   * 
+   * @param profile  the profile
+   * @param meta whether to mark the profile in Resource.meta.profile 
+   * @return constructed resource
+   */
+  public Resource createResource(StructureDefinition profile, boolean meta) {
+    PEDefinition definition = buildPEDefinition(profile);
+    Resource res = ResourceFactory.createResource(definition.types().get(0).getType());
+    populateByProfile(res, definition);
+    if (meta) {
+      res.getMeta().addProfile(definition.profile.getUrl());
+    }
+    return res;
+  }
+
   /**
    * For the current version of a profile, construct a resource and fill out any fixed or required elements
    * 
@@ -414,7 +476,7 @@ public class PEBuilder {
   }
 
   private PEInstance loadInstance(PEDefinition defn, Resource resource) {
-    throw new NotImplementedException("Not done yet");
+    return new PEInstance(this, defn, resource, resource, defn.name());
   }
 
   public IWorkerContext getContext() {
@@ -496,4 +558,8 @@ public class PEBuilder {
     }
     return getByName(elements, path);
   }
+
+  public List<Base> exec(Resource resource, Base data, String fhirpath) {
+    return fpe.evaluate(this, resource, resource, data, fhirpath);
+  }
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/profilemodel/PEDefinition.java

@@ -229,6 +229,16 @@ public abstract class PEDefinition {
    */
   public abstract String fhirpath();
 
+
+  public boolean isList() {
+    return "*".equals(definition.getBase().getMax());
+  }
+
+
+  public boolean repeats() {
+    return max() > 1;
+  }
+  
 }
 
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/profilemodel/PEDefinitionExtension.java

@@ -57,7 +57,7 @@ public class PEDefinitionExtension extends PEDefinition {
     if (ved.isRequired() || eed.isProhibited()) {
       return "extension('"+extension.getUrl()+"').value";
     } else {
-      return "extension('"+extension.getUrl()+"').extension";      
+      return "extension('"+extension.getUrl()+"')";      
     }
   }
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/profilemodel/PEInstance.java

@@ -1,21 +1,46 @@
 package org.hl7.fhir.r5.profilemodel;
 
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.List;
 
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.model.Base;
+import org.hl7.fhir.r5.model.BaseDateTimeType;
+import org.hl7.fhir.r5.model.CodeableConcept;
+import org.hl7.fhir.r5.model.ContactPoint;
+import org.hl7.fhir.r5.model.Identifier;
 import org.hl7.fhir.r5.model.DataType;
+import org.hl7.fhir.r5.model.DateTimeType;
+import org.hl7.fhir.r5.model.HumanName;
+import org.hl7.fhir.r5.model.Address;
+import org.hl7.fhir.r5.model.PrimitiveType;
+import org.hl7.fhir.r5.model.Quantity;
+import org.hl7.fhir.r5.model.Reference;
 import org.hl7.fhir.r5.model.Resource;
 
-public abstract class PEInstance {
+/**
+ * This class provides a profile centric view of a resource, as driven by a profile
+ * 
+ * This class is also suitable to be used as the base of a POJO 
+ * @author grahamegrieve
+ *
+ */
+public class PEInstance {
 
+  private PEBuilder builder;
   private PEDefinition definition;
+  private Resource resource; // for FHIRPath
   private Base data;
+  private String path;
   
-  protected PEInstance(PEDefinition definition, Base data) {
+  protected PEInstance(PEBuilder builder, PEDefinition definition, Resource resource, Base data, String path) {
     super();
+    this.builder = builder;
     this.definition = definition;
+    this.resource = resource; 
     this.data = data;
+    this.path = path;
   }
   
   /**
@@ -37,60 +62,178 @@ public abstract class PEInstance {
    */
   public List<PEInstance> children() {
     List<PEInstance> res = new ArrayList<>();
-    
+    for (PEDefinition child : definition.children()) {
+      List<Base> instances = builder.exec(resource, data, child.fhirpath());
+      int i = 0;
+      for (Base b : instances) {
+        res.add(new PEInstance(builder, child, resource, b, path+"."+child.name()+(child.repeats() ? "["+i+"]": "")));
+        i++;
+      }
+    }
     return res;
   }
 
+  /**
+   * @return all the single children of this instance data for the named property. An exception if there's more than one, null if there's none
+   */
+  public PEInstance child(String name) {
+    PEDefinition child = byName(definition.children(), name);
+    List<Base> instances = builder.exec(resource, data, child.fhirpath());
+    if (instances.isEmpty()) {
+      return null;
+    } else if (instances.size() == 1) {
+      return new PEInstance(builder, child, resource, instances.get(0), path+"."+child.name()+(child.repeats() ? "[0]": ""));      
+    } else {
+      throw new FHIRException("Found multiple instances for "+name+"@ "+path);
+    }
+  }
+
   /**
    * @return all the children of this instance data for the named property
    */
   public List<PEInstance> children(String name) {
-//    PEDefinition child = definition.childByName(name);
+    PEDefinition child = byName(definition.children(), name);
-//    if (child = null) {
+    List<PEInstance> res = new ArrayList<>();
-//      
+    List<Base> instances = builder.exec(resource, data, child.fhirpath());
-//    }
+    int i = 0;
-    return null;
+    for (Base b : instances) {
+      res.add(new PEInstance(builder, child, resource, b, path+"."+child.name()+(child.repeats() ? "["+i+"]": "")));
+      i++;
+    }
+    return res;
   }
 
-  /**
+  private PEDefinition byName(List<PEDefinition> children, String name) {
-   * @return all the children of this instance data with the named property and the named type (for polymorphic
+    for (PEDefinition defn : children) {
-   */
+      if (defn.name().equals(name)) {
-  public abstract List<PEInstance> children(String name, String type);
+        return defn;
+      }
+    }
+    throw new FHIRException("No children with the name '"+name+"'");
+  }
 
   /**
    * @return make a child, and append it to existing children (if they exist)
    */
-  public abstract PEInstance makeChild(String name);
+  public PEInstance makeChild(String name) {
+    PEDefinition child = byName(definition.children(), name);
+    Base b = data.addChild(child.schemaName());
+    builder.populateByProfile(b, child);
+    return new PEInstance(builder, child, resource, b, path+"."+child.name());
+  }
+  
+  /**
+   * @return get a child. if it doesn't exist, make one
+   */
+  public PEInstance forceChild(String name) {
+    PEDefinition child = byName(definition.children(), name);
+    List<Base> instances = builder.exec(resource, data, child.fhirpath());
+    if (instances.isEmpty()) {
+      Base b = data.addChild(child.schemaName());
+      builder.populateByProfile(b, child);
+      return new PEInstance(builder, child, resource, b, path+"."+child.name()+(child.isList() ? "[0]": ""));
+    } else {
+      return new PEInstance(builder, child, resource, instances.get(0), path+"."+child.name()+(child.repeats() ? "[0]": ""));
+    }
+  }
   
   /**
    * remove the nominated child from the resource
    */
-  public abstract void removeChild(PEInstance child);
+  public boolean removeChild(PEInstance child) {
+    return data.removeChild(child.definition().schemaName(), child.data);
+  }
 
 
   public enum PEInstanceDataKind {
-    Resource, Complex, DataType, PrimitiveValue
+    Resource, Complex, DataType, Primitive
   }
 
   /**
    * @return the kind of data behind this profiled node
    */
-  public abstract PEInstanceDataKind getDataKind();
+  public PEInstanceDataKind getDataKind() {
+    if (data instanceof Resource) {
+      return PEInstanceDataKind.Resource;
+    }
+    if (data instanceof PrimitiveType) {
+      return PEInstanceDataKind.Primitive;
+    }
+    if (data instanceof DataType) {
+      return PEInstanceDataKind.DataType;
+    }
+    return PEInstanceDataKind.Complex;
+  }
+  
+  public Base data() {
+    return data;
+  }
   
   /**
    * @return if dataKind = Resource, get the underlying resource, otherwise an exception
    */
-  public abstract Resource asResource();
+  public Resource asResource() {
+    return (Resource) data;
+  }
   
   /**
    * @return if dataKind = Datatype, get the underlying resource, otherwise an exception
    */
-  public abstract DataType asDataType();
+  public DataType asDataType() {
+    return (DataType) data;
+  }
+  
+  public CodeableConcept asCodeableConcept() {
+    return (CodeableConcept) asDataType();
+  }
+  
+  public Identifier Identifier() {
+    return (Identifier) asDataType();
+  }
+  
+  public Quantity asQuantity() {
+    return (Quantity) asDataType();
+  }
+  
+  public HumanName asHumanName() {
+    return (HumanName) asDataType();
+  }
+  
+  public Address Address() {
+    return (Address) asDataType();
+  }
+  
+  public ContactPoint asContactPoint() {
+    return (ContactPoint) asDataType();
+  }
+  
+  public Reference asReference() {
+    return (Reference) asDataType();
+  }
+  
   
   /**
    * @return if dataKind = PrimitiveValue, get the underlying resource, otherwise an exception
    * 
    * Note that this is for e.g. String.value, not String itself
    */
-  public abstract String getPrimitiveValue(); 
+  public String getPrimitiveAsString() {
+    return data.primitiveValue();
+  }
+  
+  public Date getPrimitiveAsDate() {
+    if (data instanceof BaseDateTimeType) {
+      return ((DateTimeType) data).getValue();
+    }
+    return null;
+  }
+  
+  public void setPrimitiveValue(String value) {
+    PrimitiveType<?> pt = (PrimitiveType<?>) data;
+    pt.setValueAsString(value);
+  }
+
+  public String getPath() {
+    return path;
+  }
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/profilemodel/gen/PEGeneratedBase.java

@@ -0,0 +1,17 @@
+package org.hl7.fhir.r5.profilemodel.gen;
+
+import org.hl7.fhir.r5.profilemodel.PEInstance;
+
+public class PEGeneratedBase {
+
+  protected PEInstance instance;
+  
+  protected void removeChild(String string) {
+    PEInstance child = instance.child("simple");
+    if (child != null) {
+      instance.removeChild(child);
+    }
+  }
+  
+}
+

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/profilemodel/gen/ProfileExample.java

@@ -0,0 +1,49 @@
+package org.hl7.fhir.r5.profilemodel.gen;
+
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.model.CodeType;
+import org.hl7.fhir.r5.model.Observation;
+import org.hl7.fhir.r5.profilemodel.PEBuilder;
+import org.hl7.fhir.r5.profilemodel.PEBuilder.PEElementPropertiesPolicy;
+import org.hl7.fhir.r5.profilemodel.PEInstance;
+
+/**
+ * This class is a manually written example of the code that a POJO code
+ * generator for Profiles would produce 
+ * 
+ * @author grahamegrieve
+ *
+ */
+public class ProfileExample extends PEGeneratedBase {
+
+  public ProfileExample(IWorkerContext context, Observation observation) {
+    super();
+    PEBuilder builder = new PEBuilder(context, PEElementPropertiesPolicy.EXTENSION_ID, true);
+    instance = builder.buildPEInstance("http://hl7.org/fhir/test/StructureDefinition/pe-profile1", "0.1", observation);
+  }
+  
+  /**
+   * Extension http://hl7.org/fhir/test/StructureDefinition/pe-extension-simple, type code
+   * @return
+   */
+  public CodeType getSimple() {
+    return (CodeType) instance.forceChild("simple").asDataType();
+  }
+  
+  public boolean hasSimple() {
+    return instance.child("simple") != null;    
+  }
+  
+  public ProfileExample clearSimple() {
+    removeChild("simple");
+    return this;
+  }
+
+  /*
+   * this doesn't exist, because of the way infrastructure works.
+   * You get the value and set the properties
+   */
+//  public void setSimple() {
+//    return (CodeType) instance.forceChild("simple").asDataType();
+//  }
+}

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/profiles/PETests.java

@@ -6,12 +6,15 @@ import java.util.List;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
+import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.Observation;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.profilemodel.PEDefinition;
+import org.hl7.fhir.r5.profilemodel.PEInstance;
 import org.hl7.fhir.r5.profilemodel.PEType;
 import org.hl7.fhir.r5.profilemodel.PEBuilder;
 import org.hl7.fhir.r5.profilemodel.PEBuilder.PEElementPropertiesPolicy;
+import org.hl7.fhir.r5.profilemodel.PEInstance.PEInstanceDataKind;
 import org.hl7.fhir.r5.test.utils.TestPackageLoader;
 import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
@@ -66,7 +69,7 @@ public class PETests {
     checkElement(children.get(4), "contained", "contained", 0, Integer.MAX_VALUE, false, "http://hl7.org/fhir/StructureDefinition/Resource", 4, "contained");
     checkElement(children.get(5), "extension", "extension", 0, Integer.MAX_VALUE, false, "http://hl7.org/fhir/StructureDefinition/Extension", 3, "extension.where(((url = 'http://hl7.org/fhir/test/StructureDefinition/pe-extension-simple') or (url = 'http://hl7.org/fhir/test/StructureDefinition/pe-extension-complex')).not())");
     checkElement(children.get(6), "extension", "simple", 0, 1, false, "http://hl7.org/fhir/StructureDefinition/code", 2, "extension('http://hl7.org/fhir/test/StructureDefinition/pe-extension-simple').value");
-    checkElement(children.get(7), "extension", "complex", 0, 1, false, "http://hl7.org/fhir/StructureDefinition/Extension", 4, "extension('http://hl7.org/fhir/test/StructureDefinition/pe-extension-complex').extension");
+    checkElement(children.get(7), "extension", "complex", 0, 1, false, "http://hl7.org/fhir/StructureDefinition/Extension", 4, "extension('http://hl7.org/fhir/test/StructureDefinition/pe-extension-complex')");
     checkElement(children.get(8), "identifier", "identifier", 0, 1, false, "http://hl7.org/fhir/StructureDefinition/Identifier", 7, "identifier");
     checkElement(children.get(9), "status", "status", 1, 1, true, "http://hl7.org/fhir/StructureDefinition/code", 2, "status");
     checkElement(children.get(10), "category", "category", 0, Integer.MAX_VALUE, false, "http://hl7.org/fhir/StructureDefinition/CodeableConcept", 3, "category");
@@ -287,7 +290,6 @@ public class PETests {
     }
   }   
 
-
   @Test
   public void testCreate() throws IOException {
     load();
@@ -301,4 +303,50 @@ public class PETests {
     System.out.println(json);
   }
 
+
+  @Test
+  public void testLoad() throws IOException {
+    load();
+    
+    Resource res = new JsonParser().parse(TestingUtilities.loadTestResource("R5", "pe-observation-1.json"));
+    PEInstance obs = new PEBuilder(ctxt, PEElementPropertiesPolicy.EXTENSION, true).buildPEInstance("http://hl7.org/fhir/test/StructureDefinition/pe-profile1", res);
+    
+    PEInstance status = obs.child("status");
+    Assertions.assertNotNull(status);
+    Assertions.assertEquals("TestProfile.status", status.getPath());
+    Assertions.assertEquals(PEInstanceDataKind.Primitive, status.getDataKind());
+    Assertions.assertEquals("final", status.asDataType().primitiveValue());
+    Assertions.assertEquals("final", status.getPrimitiveAsString());
+
+    PEInstance code = obs.child("code");
+    Assertions.assertNotNull(code);
+    Assertions.assertEquals("TestProfile.code", code.getPath());
+    Assertions.assertEquals(PEInstanceDataKind.DataType, code.getDataKind());
+    Assertions.assertEquals("76690-7", code.asCodeableConcept().getCodingFirstRep().getCode());
+
+    PEInstance simple = obs.child("simple");
+    Assertions.assertNotNull(simple);
+    Assertions.assertEquals("TestProfile.simple", simple.getPath());
+    Assertions.assertEquals(PEInstanceDataKind.Primitive, simple.getDataKind());
+    Assertions.assertEquals("14647-2", simple.getPrimitiveAsString());
+
+    PEInstance complex = obs.child("complex");
+    Assertions.assertNotNull(complex);
+    Assertions.assertEquals("TestProfile.complex", complex.getPath());
+    Assertions.assertEquals(PEInstanceDataKind.DataType, complex.getDataKind());
+
+    PEInstance slice1 = complex.child("slice1");
+    Assertions.assertNotNull(slice1);
+    Assertions.assertEquals("TestProfile.complex.slice1[0]", slice1.getPath());
+    Assertions.assertEquals(PEInstanceDataKind.DataType, slice1.getDataKind());
+    Assertions.assertEquals("18767-4", ((Coding) slice1.asDataType()).getCode());
+    
+    PEInstance slice2 = complex.child("slice2");
+    Assertions.assertNotNull(slice2);
+    Assertions.assertEquals("TestProfile.complex.slice2[0]", slice2.getPath());
+    Assertions.assertEquals(PEInstanceDataKind.Primitive, slice2.getDataKind());
+    Assertions.assertEquals("A string value", slice2.getPrimitiveAsString());
+  }
+
+  
 }