NUP-2514: Fix traversal limit

src/nupic/bindings/algorithms.i

@@ -42,6 +42,8 @@ else:
   from nupic.proto.SvmProto_capnp import (SvmDenseProto, Svm01Proto)
   from nupic.proto.TemporalMemoryProto_capnp import TemporalMemoryProto
 
+# Capnp reader traveral limit (see capnp::ReaderOptions)
+_TRAVERSAL_LIMIT_IN_WORDS = 1 << 63
 
 _ALGORITHMS = _algorithms
 %}
@@ -338,7 +340,8 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
 
       :param: Destination SvmDenseProto message builder
       """
-      reader = SvmDenseProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = SvmDenseProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
     @classmethod
@@ -450,7 +453,8 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
 
       :param: Destination Svm01Proto message builder
       """
-      reader = Svm01Proto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = Svm01Proto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
     @classmethod
@@ -899,7 +903,8 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
 
       :param: Destination Cells4Proto message builder
       """
-      reader = Cells4Proto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = Cells4Proto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
   %}
@@ -1148,7 +1153,8 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
 
       :param: Destination SpatialPoolerProto message builder
       """
-      reader = SpatialPoolerProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = SpatialPoolerProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
 
@@ -1465,7 +1471,8 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
 
       :param: Destination SdrClassifierProto message builder
       """
-      reader = SdrClassifierProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = SdrClassifierProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
     @classmethod
@@ -1581,7 +1588,8 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
 
       :param: Destination ConnectionsProto message builder
       """
-      reader = ConnectionsProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = ConnectionsProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
 
@@ -1782,7 +1790,8 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
 
       :param: Destination TemporalMemoryProto message builder
       """
-      reader = TemporalMemoryProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = TemporalMemoryProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
 

src/nupic/bindings/engine_internal.i

@@ -35,6 +35,9 @@ except ImportError:
 else:
   from nupic.proto.NetworkProto_capnp import NetworkProto
   from nupic.proto.PyRegionProto_capnp import PyRegionProto
+
+# Capnp reader traveral limit (see capnp::ReaderOptions)
+_TRAVERSAL_LIMIT_IN_WORDS = 1 << 63
 %}
 
 %{
@@ -287,7 +290,8 @@ class IterablePair(object):
 
       :param: Destination NetworkProto message builder
       """
-      reader = NetworkProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      reader = NetworkProto.from_bytes(self._writeAsCapnpPyBytes(), 
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
       pyBuilder.from_dict(reader.to_dict())  # copy
 
 
@@ -364,7 +368,8 @@ class _PyCapnpHelper(object):
 
     :returns: The deserialized python region instance.
     """
-    pyRegionProto = PyRegionProto.from_bytes(pyRegionProtoBytes)
+    pyRegionProto = PyRegionProto.from_bytes(pyRegionProtoBytes,
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
 
     return getattr(regionCls, methodName)(pyRegionProto)
 

src/nupic/bindings/math.i

@@ -33,6 +33,9 @@ except ImportError:
 else:
   from nupic.proto.RandomProto_capnp import RandomProto
 
+# Capnp reader traveral limit (see capnp::ReaderOptions)
+_TRAVERSAL_LIMIT_IN_WORDS = 1 << 63
+
 _MATH = _math
 %}
 
@@ -195,7 +198,8 @@ def write(self, pyBuilder):
 
   :param: Destination RandomProto message builder
   """
-  reader = RandomProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+  reader = RandomProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
   pyBuilder.from_dict(reader.to_dict())  # copy
 
 

src/nupic/bindings/sparse_matrix.i

@@ -45,6 +45,9 @@ except ImportError:
 else:
   from nupic.proto.SparseMatrixProto_capnp import SparseMatrixProto
   from nupic.proto.SparseBinaryMatrixProto_capnp import SparseBinaryMatrixProto
+
+# Capnp reader traveral limit (see capnp::ReaderOptions)
+_TRAVERSAL_LIMIT_IN_WORDS = 1 << 63
 %}
 
 
@@ -423,7 +426,8 @@ def write(self, pyBuilder):
 
   :param: Destination SparseMatrixProto message builder
   """
-  reader = SparseMatrixProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+  reader = SparseMatrixProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
   pyBuilder.from_dict(reader.to_dict())  # copy
 
 @classmethod
@@ -2973,7 +2977,8 @@ def write(self, pyBuilder):
 
   :param: Destination SparseBinaryMatrixProto message builder
   """
-  reader = SparseBinaryMatrixProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+  reader = SparseBinaryMatrixProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
   pyBuilder.from_dict(reader.to_dict())  # copy
 
 def read(self, proto):
@@ -3484,7 +3489,8 @@ def write(self, pyBuilder):
 
   :param: Destination SparseBinaryMatrixProto message builder
   """
-  reader = SparseBinaryMatrixProto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+  reader = SparseBinaryMatrixProto.from_bytes(self._writeAsCapnpPyBytes(),
+                            traversal_limit_in_words=_TRAVERSAL_LIMIT_IN_WORDS)
   pyBuilder.from_dict(reader.to_dict())  # copy
 
 def read(self, proto):

src/nupic/engine/Region.cpp

@@ -436,79 +436,14 @@ const Timer &Region::getExecuteTimer() const { return executeTimer_; }
 
 bool Region::operator==(const Region &o) const {
 
-  if (name_ != o.name_ || type_ != o.type_ || dims_ != o.dims_ ||
-      phases_ != o.phases_ || dimensionInfo_ != o.dimensionInfo_ ||
-      initialized_ != o.initialized_ || outputs_.size() != o.outputs_.size() ||
+  if (initialized_ != o.initialized_ || outputs_.size() != o.outputs_.size() ||
       inputs_.size() != o.inputs_.size()) {
     return false;
   }
-  if (spec_ != nullptr && o.spec_ != nullptr) {
-    // Compare specs
-    if (spec_->singleNodeOnly != o.spec_->singleNodeOnly ||
-        spec_->description != o.spec_->description) {
-      return false;
-    }
-
-    // Parameters
-    for (size_t i = 0; i < spec_->parameters.getCount(); ++i) {
-      const std::pair<std::string, ParameterSpec> &p1 =
-          spec_->parameters.getByIndex(i);
-      const std::pair<std::string, ParameterSpec> &p2 =
-          o.spec_->parameters.getByIndex(i);
-      if (p1.first != p2.first || p1.second.count != p2.second.count ||
-          p1.second.description != p2.second.description ||
-          p1.second.constraints != p2.second.constraints ||
-          p1.second.defaultValue != p2.second.defaultValue ||
-          p1.second.dataType != p2.second.dataType ||
-          p1.second.accessMode != p2.second.accessMode) {
-        return false;
-      }
-    }
-    // Outputs
-    for (size_t i = 0; i < spec_->outputs.getCount(); ++i) {
-      const std::pair<std::string, OutputSpec> &p1 =
-          spec_->outputs.getByIndex(i);
-      const std::pair<std::string, OutputSpec> &p2 =
-          o.spec_->outputs.getByIndex(i);
-      if (p1.first != p2.first || p1.second.count != p2.second.count ||
-          p1.second.regionLevel != p2.second.regionLevel ||
-          p1.second.isDefaultOutput != p2.second.isDefaultOutput ||
-          p1.second.sparse != p2.second.sparse ||
-          p1.second.description != p2.second.description ||
-          p1.second.dataType != p2.second.dataType) {
-        return false;
-      }
-    }
 
-    // Outputs
-    for (size_t i = 0; i < spec_->inputs.getCount(); ++i) {
-      const std::pair<std::string, InputSpec> &p1 = spec_->inputs.getByIndex(i);
-      const std::pair<std::string, InputSpec> &p2 =
-          o.spec_->inputs.getByIndex(i);
-      if (p1.first != p2.first || p1.second.count != p2.second.count ||
-          p1.second.regionLevel != p2.second.regionLevel ||
-          p1.second.isDefaultInput != p2.second.isDefaultInput ||
-          p1.second.sparse != p2.second.sparse ||
-          p1.second.requireSplitterMap != p2.second.requireSplitterMap ||
-          p1.second.required != p2.second.required ||
-          p1.second.description != p2.second.description ||
-          p1.second.dataType != p2.second.dataType) {
-        return false;
-      }
-    }
-    // Commands
-    for (size_t i = 0; i < spec_->commands.getCount(); ++i) {
-      const std::pair<std::string, CommandSpec> &p1 =
-          spec_->commands.getByIndex(i);
-      const std::pair<std::string, CommandSpec> &p2 =
-          o.spec_->commands.getByIndex(i);
-      if (p1.first != p2.first ||
-          p1.second.description != p2.second.description) {
-        return false;
-      }
-    }
-  } else if (spec_ != o.spec_) {
-    // One of them is not null
+  if (name_ != o.name_ || type_ != o.type_ || dims_ != o.dims_ ||
+      spec_ != o.spec_ || phases_ != o.phases_ ||
+      dimensionInfo_ != o.dimensionInfo_) {
     return false;
   }
 
@@ -552,6 +487,6 @@ bool Region::operator==(const Region &o) const {
   }
 
   return true;
-}
+} // namespace nupic
 
 } // namespace nupic

src/nupic/engine/Spec.cpp

@@ -31,7 +31,14 @@ Implementation of Spec API
 namespace nupic {
 
 Spec::Spec() : singleNodeOnly(false), description("") {}
-
+bool Spec::operator==(const Spec &o) const {
+  if (singleNodeOnly != o.singleNodeOnly || description != o.description ||
+      parameters != o.parameters || outputs != o.outputs ||
+      inputs != o.inputs || commands != o.commands) {
+    return false;
+  }
+  return true;
+}
 std::string Spec::getDefaultInputName() const {
   if (inputs.getCount() == 0)
     return "";
@@ -87,16 +94,29 @@ InputSpec::InputSpec(std::string description, NTA_BasicType dataType,
       required(required), regionLevel(regionLevel),
       isDefaultInput(isDefaultInput), requireSplitterMap(requireSplitterMap),
       sparse(sparse) {}
-
+bool InputSpec::operator==(const InputSpec &o) const {
+  return required == o.required && regionLevel == o.regionLevel &&
+         isDefaultInput == o.isDefaultInput && sparse == o.sparse &&
+         requireSplitterMap == o.requireSplitterMap && dataType == o.dataType &&
+         count == o.count && description == o.description;
+}
 OutputSpec::OutputSpec(std::string description, NTA_BasicType dataType,
                        size_t count, bool regionLevel, bool isDefaultOutput,
                        bool sparse)
     : description(std::move(description)), dataType(dataType), count(count),
       regionLevel(regionLevel), isDefaultOutput(isDefaultOutput),
       sparse(sparse) {}
+bool OutputSpec::operator==(const OutputSpec &o) const {
+  return regionLevel == o.regionLevel && isDefaultOutput == o.isDefaultOutput &&
+         sparse == o.sparse && dataType == o.dataType && count == o.count &&
+         description == o.description;
+}
 
 CommandSpec::CommandSpec(std::string description)
     : description(std::move(description)) {}
+bool CommandSpec::operator==(const CommandSpec &o) const {
+  return description == o.description;
+}
 
 ParameterSpec::ParameterSpec(std::string description, NTA_BasicType dataType,
                              size_t count, std::string constraints,
@@ -109,6 +129,11 @@ ParameterSpec::ParameterSpec(std::string description, NTA_BasicType dataType,
   if (dataType == NTA_BasicType_Byte && count > 0)
     NTA_THROW << "Parameters of type 'byte' are not supported";
 }
+bool ParameterSpec::operator==(const ParameterSpec &o) const {
+  return dataType == o.dataType && count == o.count &&
+         description == o.description && constraints == o.constraints &&
+         defaultValue == o.defaultValue && accessMode == o.accessMode;
+}
 
 std::string Spec::toString() const {
   // TODO -- minimal information here; fill out with the rest of

src/nupic/engine/Spec.hpp

@@ -39,7 +39,10 @@ class InputSpec {
   InputSpec(std::string description, NTA_BasicType dataType, UInt32 count,
             bool required, bool regionLevel, bool isDefaultInput,
             bool requireSplitterMap = true, bool sparse = false);
-
+  bool operator==(const InputSpec &other) const;
+  inline bool operator!=(const InputSpec &other) const {
+    return !operator==(other);
+  }
   std::string description;
   NTA_BasicType dataType;
   // TBD: Omit? isn't it always of unknown size?
@@ -59,7 +62,10 @@ class OutputSpec {
   OutputSpec(std::string description, const NTA_BasicType dataType,
              size_t count, bool regionLevel, bool isDefaultOutput,
              bool sparse = false);
-
+  bool operator==(const OutputSpec &other) const;
+  inline bool operator!=(const OutputSpec &other) const {
+    return !operator==(other);
+  }
   std::string description;
   NTA_BasicType dataType;
   // Size, in number of elements. If size is fixed, specify it here.
@@ -74,7 +80,10 @@ class CommandSpec {
 public:
   CommandSpec() {}
   CommandSpec(std::string description);
-
+  bool operator==(const CommandSpec &other) const;
+  inline bool operator!=(const CommandSpec &other) const {
+    return !operator==(other);
+  }
   std::string description;
 };
 
@@ -89,7 +98,10 @@ class ParameterSpec {
   ParameterSpec(std::string description, NTA_BasicType dataType, size_t count,
                 std::string constraints, std::string defaultValue,
                 AccessMode accessMode);
-
+  bool operator==(const ParameterSpec &other) const;
+  inline bool operator!=(const ParameterSpec &other) const {
+    return !operator==(other);
+  }
   std::string description;
 
   // [open: current basic types are bytes/{u}int16/32/64, real32/64, BytePtr. Is
@@ -109,7 +121,8 @@ struct Spec {
   // TODO: should this be in the base API or layered? In the API right
   // now since we do not build layered libraries.
   std::string toString() const;
-
+  bool operator==(const Spec &other) const;
+  inline bool operator!=(const Spec &other) const { return !operator==(other); }
   // Some RegionImpls support only a single node in a region.
   // Such regions always have dimension [1]
   bool singleNodeOnly;

src/nupic/ntypes/Collection.cpp

@@ -42,7 +42,14 @@ namespace nupic {
 template <typename T> Collection<T>::Collection() {}
 
 template <typename T> Collection<T>::~Collection() {}
-
+template <typename T>
+bool Collection<T>::operator==(const Collection<T> &o) const {
+  const static auto compare = [](std::pair<std::string, T> a,
+                                 std::pair<std::string, T> b) {
+    return a.first == b.first && a.second == b.second;
+  };
+  return std::equal(vec_.begin(), vec_.end(), o.vec_.begin(), compare);
+}
 template <typename T> size_t Collection<T>::getCount() const {
   return vec_.size();
 }