Remove shared pointer behaviour

README.md

@@ -32,15 +32,18 @@ void create_example_ro_crate() {
     // --------------------------------------------------------------------------
     // Add description to the root metadata entity (ro-crate-metadata.json) as 
     // this is currently missing
+    // 
+    // Shows two methods for updating entities already in a crate A) and B)
 
     // Get the root metadata entity from the crate and set the description
-    Entity root = crate.getEntity("ro-crate-metadata.json");
+    // A) Get a reference to allow mutability
+    Entity& root = crate.getEntity("ro-crate-metadata.json");
     root.set("description", "RO-Crate Metadata File Descriptor (this file)");
 
     // Add name, description to the root data entity (./)
-    Entity rootData = crate.getEntity("./");
-    rootData.set("name", "Example RO-Crate");
-    rootData.set("description", "The RO-Crate Root Data Entity");
+    // B) Directly edit in the crate
+    crate.getEntity("./").set("name", "Example RO-Crate");
+    crate.getEntity("./").set("description", "The RO-Crate Root Data Entity");
 
     // --------------------------------------------------------------------------
     // Create the person, which is a contextual entity, and add it to the crate
@@ -63,11 +66,11 @@ void create_example_ro_crate() {
     data1.set("author", alice);
     data1.set("contentLocation", catalinaPark);
     crate.addEntity("data1.txt", data1);
-    rootData.set("hasPart", data1); // Ensure that the root data entity has a hasPart relationship to data1
+    crate.getEntity("./").set("hasPart", data1); // Ensure that the root data entity has a hasPart relationship to data1
 
     Entity data2({"File"});
     crate.addEntity("data2.txt", data2);
-    rootData.set("hasPart", data2); 
+    crate.getEntity("./").set("hasPart", data2); 
 
     // --------------------------------------------------------------------------
     // Write out
@@ -166,50 +169,33 @@ relationships between entities.
 When an entity is created, it is not automatically added to the RO-Crate. The user 
 must explicitly add the entity to the RO-Crate using the `addEntity` method.
 
-When an entity is added to the RO-Crate, it is stored in a map of entities.
+When an entity is added to the RO-Crate, a copy is stored in a map of entities.
 
-For maximum flexiblity, an already added entity may still be updated on the 
-original entity object. The RO-Crate shares the same entity object, so any changes 
-made to the original entity will be reflected in the RO-Crate.
-
-Worked example:
+Updates to the copy will not be reflected in the RO-Crate. If you want to update 
+an entity, you must retrieve it. See below for an example:
 
 ```cpp
 ROCrate crate;
 
 Entity alice({"Person"});
-alice.set("name", "Alice");
-
 crate.addEntity("#alice", alice);
 
-/* Crate state: 
-{
-  "#alice": {
-    "type": ["Person"],
-    "name": "Alice"
-  }
-}
-*/
-
-// Add an additional property to the crate entity
-Entity crateAlice = crate.getEntity("#alice");
-crateAlice.set("description", "One of hopefully many Contextual Entities");
+// Update the entity, use & to allow modifications
+Entity& aliceCopy = crate.getEntity("#alice");
+aliceCopy.set("name", "Alice Smith");
 
-// Add an additional property to the original entity object
-alice.set("occupation", "Software Engineer");
-
-/* Crate state:
+/* Output
 {
-  "#alice": {
-    "type": ["Person"],
-    "name": "Alice",
-    "description": "One of hopefully many Contextual Entities",
-    "occupation": "Software Engineer"
-  }
+  "@id": "#alice",
+  "@type": [
+    "Person"
+  ],
+  "name": "Alice Smith"
 }
 */
 ```
 
+
 ## Reference
 
 Reference documentation generated by [doxide](doxide.org) is available [here](http://esciencelab.org.uk/ro-crate-cpp/).

include/ro-crate.hpp

@@ -3,7 +3,6 @@
 #include <nlohmann/json.hpp>
 
 #include <fstream>
-#include <memory>
 #include <stdexcept>
 #include <string>
 #include <map>
@@ -79,11 +78,10 @@ namespace rocrate {
      * @throw std::invalid_argument if the id is empty.
      */
     void assignId(const std::string& id);
-    std::shared_ptr<Properties> properties_;
+    Properties properties_;
   };
 
-  inline Entity::Entity(std::vector<std::string> types)
-    : properties_(std::make_shared<Properties>()) {
+  inline Entity::Entity(std::vector<std::string> types) {
 
     // Validate types (reject empty)
     if ( types.empty() ) {
@@ -94,7 +92,7 @@ namespace rocrate {
     std::vector<PropertyValue> typeValues;
     for (const auto& type : types)
       typeValues.push_back({type, ValueType::Literal});
-    properties_->emplace("@type", typeValues);
+    properties_.emplace("@type", typeValues);
   }
 
   inline void Entity::set(Property property, Value value, ValueType valueType) {
@@ -108,7 +106,7 @@ namespace rocrate {
                                   "Use ROCrate::addEntity to assign an ID.");
 
     // Add the value to the property in the properties map
-    (*properties_)[property].push_back({value, valueType});
+    properties_[property].push_back({value, valueType});
   }
 
   inline void Entity::set(Property property, const Entity& entity) {
@@ -117,13 +115,20 @@ namespace rocrate {
       throw std::invalid_argument("Property name cannot be empty.");
     }
 
-    // Check if the entity has an '@id' property set
-    const auto id = entity.properties_->find("@id");
-    if (id == entity.properties_->end() || id->second.empty())
-      throw std::runtime_error("Entity does not have an '@id' property set.");
+    // Check if the entity has an '@id' property 
+    auto it = entity.properties_.find("@id");
+    if ( it == entity.properties_.end()) {
+      throw std::runtime_error("Referenced entity must have an '@id' property.");
+    }
 
-    // Add JSON reference to the entity's '@id' to the property in the properties map
-    set(property, id->second.front().value, ValueType::Reference);
+    // Get the ID and check it isn't empty
+    const auto& idValues = it->second;
+    if (idValues.empty()) {
+      throw std::runtime_error("Referenced entity must have a non-empty '@id' property.");
+    }
+
+    // Add the reference to the property in the properties map
+    set(property, idValues[0].value, ValueType::Reference);
   }
 
   inline void Entity::assignId(const std::string& id) {
@@ -133,7 +138,7 @@ namespace rocrate {
     }
 
     // Assign the '@id' property to the entity's properties map
-    (*properties_)["@id"] = {{id, ValueType::Literal}};
+    properties_["@id"] = {{id, ValueType::Literal}};
   }
 
   // ---------------------------------------------------------------------------
@@ -169,7 +174,7 @@ namespace rocrate {
     void addEntity(const std::string& id, Entity& entity);
 
     /**
-     * Retrieves an entity from the RO-Crate's entity register by its id.
+     * Retrieves an entity reference from the RO-Crate's entity register by its id.
      *
      * @param id The identifier of the entity to retrieve.
      * @return A reference to the entity with the specified id.
@@ -213,14 +218,14 @@ namespace rocrate {
         "https://w3id.org/ro/crate/1.1",
         ValueType::Reference
     );
-    addEntity("ro-crate-metadata.json", rootEntity);
 
     // Create the root dataset entity
     Entity datasetEntity({"Dataset"});
     addEntity("./", datasetEntity);
 
     // Add the root dataset entity to the root metadata entity
     rootEntity.set("about", datasetEntity);
+    addEntity("ro-crate-metadata.json", rootEntity);
   }
 
   inline void ROCrate::addEntity(const std::string& id, Entity& entity) {
@@ -301,7 +306,7 @@ namespace rocrate {
     nlohmann::json serialized;
     serialized["@id"] = id;
 
-    for (const auto& [property, values] : *entity.properties_) {
+    for (const auto& [property, values] : entity.properties_) {
       if (property == "@id") {
         continue;
       }

tests/example.cpp

@@ -15,16 +15,19 @@ void create_example_ro_crate() {
     // --------------------------------------------------------------------------
     // Add description to the root metadata entity (ro-crate-metadata.json) as 
     // this is currently missing
+    // 
+    // Shows two methods for updating entities already in a crate A) and B)
 
     // Get the root metadata entity from the crate and set the description
-    Entity root = crate.getEntity("ro-crate-metadata.json");
+    // A) Get a reference to allow mutability
+    Entity& root = crate.getEntity("ro-crate-metadata.json");
     root.set("description", "RO-Crate Metadata File Descriptor (this file)");
 
     // Add name, description to the root data entity (./)
-    Entity rootData = crate.getEntity("./");
-    rootData.set("name", "Example RO-Crate");
-    rootData.set("description", "The RO-Crate Root Data Entity");
-
+    // B) Directly edit in the crate
+    crate.getEntity("./").set("name", "Example RO-Crate");
+    crate.getEntity("./").set("description", "The RO-Crate Root Data Entity");
+    
     // --------------------------------------------------------------------------
     // Create the person, which is a contextual entity, and add it to the crate
 
@@ -46,11 +49,11 @@ void create_example_ro_crate() {
     data1.set("author", alice);
     data1.set("contentLocation", catalinaPark);
     crate.addEntity("data1.txt", data1);
-    rootData.set("hasPart", data1); // Ensure that the root data entity has a hasPart relationship to data1
+    crate.getEntity("./").set("hasPart", data1); // Ensure that the root data entity has a hasPart relationship to data1
 
     Entity data2({"File"});
     crate.addEntity("data2.txt", data2);
-    rootData.set("hasPart", data2); 
+    crate.getEntity("./").set("hasPart", data2); 
 
     // --------------------------------------------------------------------------
     // Write out

tests/integration.cpp

@@ -12,7 +12,7 @@ TEST_CASE("Minimal RO-Crate", "[integration]")
   ROCrate crate;
 
   // Add metadata to root data entity
-  Entity rootData = crate.getEntity("./");
+  Entity& rootData = crate.getEntity("./");
   rootData.set("identifier", "https://doi.org/10.4225/59/59672c09f4a4b");
   rootData.set("datePublished", "2017");
   rootData.set("name", "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...");
@@ -47,12 +47,12 @@ TEST_CASE("Example with file, author, location", "[integration]")
     ROCrate crate;
 
     // Add description to the root metadata entity (ro-crate-metadata.json)
-    Entity root = crate.getEntity("ro-crate-metadata.json");
+    Entity& root = crate.getEntity("ro-crate-metadata.json");
     root.set("description", "RO-Crate Metadata File Descriptor (this file)");
     REQUIRE_NOTHROW(crate.getEntity("ro-crate-metadata.json"));
 
     // Add name, description to the root data entity (./)
-    Entity rootData = crate.getEntity("./");
+    Entity& rootData = crate.getEntity("./");
     rootData.set("name", "Example RO-Crate");
     rootData.set("description", "The RO-Crate Root Data Entity");
     REQUIRE_NOTHROW(crate.getEntity("./"));
@@ -116,7 +116,7 @@ TEST_CASE("Example with web resources", "[integration]")
   crate.addEntity("https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf", roCrateSpec);
 
   // Add to root data entity
-  Entity rootData = crate.getEntity("./");
+  Entity& rootData = crate.getEntity("./");
   rootData.set("hasPart", surveyResponses);
   rootData.set("hasPart", roCrateSpec);
 

tests/unit.cpp

@@ -100,18 +100,6 @@ TEST_CASE("RO-Crate initilises with valid root metadata and dataset entities", "
   REQUIRE_NOTHROW(crate.getEntity("./"));
 }
 
-TEST_CASE("Crate and builder observe shared entity updates", "[unit]") {
-  rocrate::ROCrate crate;
-  Entity alice({"Person"});
-
-  crate.addEntity("#alice", alice);
-
-  alice.set("name", "Alice");  
-  crate.getEntity("#alice").set("description", "Updated");
-
-  SUCCEED("No exceptions thrown, can't currently assert on entity values as they are not exposed in the API");
-}
-
 TEST_CASE("Add entity rejects entities with duplicate IDs", "[unit]") {
   // Create a crate and add an entity
   rocrate::ROCrate crate;