ENH: Add retrieval and queries to Extern C interface

Summary

See https://gitlab.indiscale.com/caosdb/customers/lfpb/management/-/issues/411. Extends the Extern C interface by retrieving single and multiple entities and executing queries.

Focus

There is a lot of repetitive new code for create, delete, set, and get functions in ccaosdb.cpp. Some aspects of the c++ objects of Entities, Parents, and Propeties had to be changed in order to comply with the C interface, mainly because of memory management.

The most important new parts is that entities, transactions, properties and parents can now be created and deleted via the C interface, and that their properties can be set and gotten.

Test Environment

In principle, unit tests should be sufficient. Check whether you are content with the extent of the tests. Queries and retrievals are checked in the integration tests.

Check List for the Author

Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab comments for the reviewer. They should guide the reviewer through the changes, explain your changes and also point out open questions. For further good practices have a look at our review guidelines

• All automated tests pass
• Reference related Issues
• [ ] Up-to-date CHANGELOG.md
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• [ ] Up-to-date CHANGELOG.md
• The test environment setup works and the intended behavior is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?

For further good practices have a look at our review guidelines.

include/caosdb/entity.h

@@ -43,11 +43,11 @@
 #include <google/protobuf/message.h>                   // for RepeatedPtrField
 #include <google/protobuf/util/json_util.h>            // for MessageToJson...
 #include <iosfwd>                                      // for streamsize
-#include <iterator>                         // for iterator, output_iterato...
-#include <map>                              // for map
-#include <random>                                      // for mt19937, rand...
-#include <stdexcept>                                   // for out_of_range
-#include <string>                                      // for string, basic...
+#include <iterator>  // for iterator, output_iterato...
+#include <map>       // for map
+#include <random>    // for mt19937, rand...
+#include <stdexcept> // for out_of_range
+#include <string>    // for string, basic...
 
 namespace caosdb::entity {
 using boost::filesystem::exists;
@@ -58,10 +58,10 @@ using ProtoProperty = caosdb::entity::v1alpha1::Property;
 using ProtoEntity = caosdb::entity::v1alpha1::Entity;
 using ProtoFileDescriptor = caosdb::entity::v1alpha1::FileDescriptor;
 using ProtoMessage = caosdb::entity::v1alpha1::Message;
-using ::google::protobuf::RepeatedPtrField;
 using caosdb::StatusCode;
 using caosdb::entity::v1alpha1::EntityResponse;
 using caosdb::entity::v1alpha1::FileTransmissionId;
+using ::google::protobuf::RepeatedPtrField;
 using google::protobuf::RepeatedPtrField;
 
 static const std::string logger_name = "caosdb::entity";
@@ -84,11 +84,11 @@ public:
   /**
    * Return the current size of the container.
    */
-  [[nodiscard]] inline auto Size() const -> int { return wrapped->size(); }
+  [[nodiscard]] inline auto size() const -> int { return wrapped->size(); }
   /**
    * Return a const reference to the element at the given index.
    */
-  [[nodiscard]] inline auto At(int index) const -> const T & {
+  [[nodiscard]] inline auto at(int index) const -> const T & {
     return *mutable_at(index);
   }
 
@@ -96,8 +96,8 @@ public:
    * Return a mutable pointer to the element at the given index.
    */
   [[nodiscard]] inline auto mutable_at(int index) const -> T * {
-    if (index >= Size() || index < 0) {
-      throw std::out_of_range("Container has size " + std::to_string(Size()));
+    if (index >= size() || index < 0) {
+      throw std::out_of_range("Container has size " + std::to_string(size()));
     }
     if (cache.count(index) == 0) {
       cache.emplace(index, T(&(wrapped->at(index))));
@@ -157,7 +157,7 @@ protected:
 
     // shift all indices in the cache above index (such that the values do not
     // get deleted/copied because this could destroy pointers (c-interface).
-    for (int i = index + 1; i < Size(); i++) {
+    for (int i = index + 1; i < size(); i++) {
       if (cache.count(i) > 0) {
         auto handle = cache.extract(i);
         handle.key()--;
@@ -225,7 +225,7 @@ auto RepeatedPtrFieldWrapper<T, P>::begin()
 template <typename T, typename P>
 auto RepeatedPtrFieldWrapper<T, P>::end()
   -> RepeatedPtrFieldWrapper<T, P>::iterator {
-  return RepeatedPtrFieldWrapper<T, P>::iterator(this, Size());
+  return RepeatedPtrFieldWrapper<T, P>::iterator(this, size());
 }
 
 template <typename T, typename P>
@@ -237,7 +237,7 @@ auto RepeatedPtrFieldWrapper<T, P>::begin() const
 template <typename T, typename P>
 auto RepeatedPtrFieldWrapper<T, P>::end() const
   -> const RepeatedPtrFieldWrapper<T, P>::iterator {
-  return RepeatedPtrFieldWrapper<T, P>::iterator(this, Size());
+  return RepeatedPtrFieldWrapper<T, P>::iterator(this, size());
 }
 
 /**