Minimal example showing segfault on model flattening over multiple di…

…rectories (with some debugging).
cellml · Nov 20, 2024 · c9f69b1 · c9f69b1
1 parent d84057b
commit c9f69b1
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Showing 12 changed files with 203 additions and 107 deletions.
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -245,7 +245,7 @@ set_target_properties(cellml_debug_utilities PROPERTIES
   VISIBILITY_INLINES_HIDDEN 1
 )
 
-target_link_libraries(cellml PRIVATE debug $<BUILD_INTERFACE:cellml_debug_utilities>)
+target_link_libraries(cellml PUBLIC debug $<BUILD_INTERFACE:cellml_debug_utilities>)
 
 group_source_to_dir_structure(
   ${DEBUG_SOURCE_FILES}

diff --git a/src/debug.cpp b/src/debug.cpp
@@ -768,4 +768,102 @@ void listModelsUnits(const ModelPtr &model)
     }
 }
 
+static const std::string FIXED_INDENT = "    ";
+
+void printComponent(const libcellml::ComponentPtr &component, size_t c, const std::string &indent, bool includeMaths)
+{
+    if (c == -1) {
+        std::cout << "COMPONENT: '" << component->name() << "'";
+    } else {
+        std::cout << indent << "[" << c + 1 << "]: " << component->name();
+    }
+
+    if (component->id() != "") {
+        std::cout << ", id: " << component->id();
+    }
+
+    std::cout << std::endl;
+    std::cout << indent << FIXED_INDENT << "VARIABLES: " << component->variableCount() << " variables" << std::endl;
+
+    // Printing the variables within the component.
+    for (size_t v = 0; v < component->variableCount(); ++v) {
+        std::cout << indent << FIXED_INDENT << FIXED_INDENT;
+        std::cout << "[" << v + 1 << "]: " << component->variable(v)->name();
+        if (component->variable(v)->units() != nullptr) {
+            std::cout << " [" << component->variable(v)->units()->name() << "]";
+        }
+        if (component->variable(v)->initialValue() != "") {
+            std::cout << ", initial = " << component->variable(v)->initialValue();
+        }
+        std::cout << std::endl;
+        if (component->variable(v)->equivalentVariableCount() > 0) {
+            std::cout << indent << FIXED_INDENT << FIXED_INDENT << FIXED_INDENT;
+            std::string con = "  └──> ";
+            for (size_t e = 0; e < component->variable(v)->equivalentVariableCount(); ++e) {
+                auto ev = component->variable(v)->equivalentVariable(e);
+                if (ev == nullptr) {
+                    std::cout << "WHOOPS! Null equivalent variable!";
+                    continue;
+                }
+                libcellml::ComponentPtr ev_parent = std::dynamic_pointer_cast<libcellml::Component>(ev->parent());
+                if (ev_parent == nullptr) {
+                    std::cout << "WHOOPS! Null parent component for equivalent variable!";
+                    continue;
+                }
+                std::cout << con << ev_parent->name() << ":" << ev->name();
+                if (ev->units() != nullptr) {
+                    std::cout << " [" << ev->units()->name() << "]";
+                }
+                con = ", ";
+            }
+            std::cout << std::endl;
+        }
+    }
+
+    // Print the maths within the component.
+    if (includeMaths) {
+        if (component->math() != "") {
+            std::cout << indent << "  Maths in the component is:" << std::endl;
+            std::cout << component->math() << std::endl;
+        }
+    }
+
+    // Print the encapsulated components
+    if (component->componentCount() > 0) {
+        std::cout << indent << FIXED_INDENT << "CHILD COMPONENTS: " << component->componentCount()
+                  << " child components" << std::endl;
+        std::string newIndent = indent + FIXED_INDENT + FIXED_INDENT;
+
+        for (size_t c2 = 0; c2 < component->componentCount(); ++c2) {
+            auto child = component->component(c2);
+            printComponent(child, c2, newIndent, includeMaths);
+        }
+    }
+}
+
+void printComponent(const ComponentPtr &component, bool includeMaths)
+{
+    printComponent(component, -1, {}, includeMaths);
+}
+
+void printModel(const ModelPtr &model, bool includeMaths)
+{
+    std::cout << "MODEL: '" << model->name() << "'";
+    if (model->id() != "") {
+        std::cout << ", id: '" << model->id() << "'";
+    }
+    std::cout << std::endl;
+
+    std::cout << FIXED_INDENT << "UNITS: " << model->unitsCount() << " custom units" << std::endl;
+    for (size_t u = 0; u < model->unitsCount(); ++u) {
+        std::cout << FIXED_INDENT << FIXED_INDENT << "[" << u + 1 << "]: " << model->units(u)->name() << std::endl;
+    }
+
+    std::cout << FIXED_INDENT << "COMPONENTS: " << model->componentCount() << " components" << std::endl;
+    for (size_t c = 0; c < model->componentCount(); ++c) {
+        auto component = model->component(c);
+        printComponent(component, c, FIXED_INDENT + FIXED_INDENT, includeMaths);
+    }
+}
+
 } // namespace libcellml
diff --git a/src/debug.h b/src/debug.h
@@ -93,24 +93,26 @@ struct Debug
     bool mNewLine;
 };
 
+void listModelsUnits(const ModelPtr &model);
 void printAnalyserModelEquations(const AnalyserModelPtr &model);
 void printAnalyserModelVariables(const AnalyserModelPtr &model);
 void printAstAsTree(const AnalyserEquationAstPtr &ast);
 void printAstAsCode(const AnalyserEquationAstPtr &ast);
+void printComponent(const ComponentPtr &component, bool includeMaths = true);
 void printComponentMap(const ComponentMap &map);
 void printConnectionMap(const ConnectionMap &map);
 void printEquivalenceMap(const EquivalenceMap &map);
 void printEquivalenceMapWithModelInfo(const EquivalenceMap &map, const ModelPtr &model);
+void printEquivalences(const VariablePtr &variable);
 void printHistory(const History &history);
 void printHistoryEpoch(const HistoryEpochPtr &historyEpoch);
 void printImportLibrary(const ImportLibrary &importlibrary);
+void printModel(const ModelPtr &model, bool includeMaths = true);
+void printNamedPath(const ParentedEntityPtr &parented);
 void printStack(const IndexStack &stack);
 void printStackWithModelInfo(const IndexStack &stack, const ModelPtr &model);
 void printStringStringMap(const StringStringMap &map);
-void printVariableMap(const VariableMap &map);
 void printUnits(const UnitsPtr &units);
-void listModelsUnits(const ModelPtr &model);
-void printNamedPath(const ParentedEntityPtr &parented);
-void printEquivalences(const VariablePtr &variable);
+void printVariableMap(const VariableMap &map);
 
 } // namespace libcellml
diff --git a/src/importer.cpp b/src/importer.cpp
@@ -18,6 +18,7 @@ limitations under the License.
 
 #include <algorithm>
 #include <cmath>
+#include <filesystem>
 #include <fstream>
 #include <libxml/uri.h>
 #include <sstream>
@@ -37,6 +38,8 @@ limitations under the License.
 #include "logger_p.h"
 #include "utilities.h"
 
+#include "debug.h"
+
 namespace libcellml {
 
 /**
@@ -329,14 +332,18 @@ std::string pathFromUrl(const std::string &url)
  */
 std::string resolvePath(const std::string &filename, const std::string &base)
 {
-    return pathFromUrl(base) + filename;
+    return std::filesystem::canonical(pathFromUrl(base) + filename).generic_string();
 }
 
 bool Importer::ImporterImpl::fetchModel(const ImportSourcePtr &importSource, const std::string &baseFile)
 {
     std::string url = normaliseDirectorySeparator(importSource->url());
+    Debug() << "Fetch model: " << importSource->url();
+    Debug() << " norm: " << url;
     if (mLibrary.count(url) == 0) {
         url = resolvePath(url, baseFile);
+        Debug() << "Resolved path: " << url;
+        Debug() << "now: " << std::filesystem::canonical(url);
     }
 
     ModelPtr model;
@@ -481,6 +488,7 @@ bool Importer::ImporterImpl::fetchComponent(const ComponentPtr &importComponent,
     }
 
     std::string resolvingUrl = ImporterImpl::resolvingUrl(importComponent->importSource());
+    Debug() << "Component -> resolvingUrl: " << resolvingUrl;
 
     if (encounteredRelatedError) {
         auto issue = Issue::IssueImpl::create();
@@ -572,6 +580,7 @@ bool Importer::ImporterImpl::fetchUnits(const UnitsPtr &importUnits, const std::
     }
 
     std::string resolvingUrl = ImporterImpl::resolvingUrl(importUnits->importSource());
+    Debug() << "Units -> resolvingUrl: " << resolvingUrl;
 
     if (encounteredRelatedError) {
         auto issue = Issue::IssueImpl::create();
@@ -653,6 +662,7 @@ bool Importer::resolveImports(ModelPtr &model, const std::string &basePath)
 
     clearImports(model);
     auto normalisedBasePath = normalisePath(basePath);
+    Debug() << "normalisedBasePath: " << normalisedBasePath;
 
     for (const UnitsPtr &units : getImportedUnits(model)) {
         history.clear();
@@ -670,6 +680,7 @@ bool Importer::resolveImports(ModelPtr &model, const std::string &basePath)
             status = false;
         }
     }
+    printImportLibrary(pFunc()->mLibrary);
 
     return status;
 }
@@ -842,6 +853,8 @@ ComponentPtr flattenComponent(const ComponentEntityPtr &parent, ComponentPtr &co
         }
 
         // Get list of required units from component's variables and math cn elements.
+        printModel(clonedImportModel);
+        printComponent(importedComponentCopy);
         std::vector<UnitsPtr> requiredUnits = unitsUsed(clonedImportModel, importedComponentCopy);
 
         std::vector<UnitsPtr> uniqueRequiredUnits;

diff --git a/src/utilities.cpp b/src/utilities.cpp
@@ -38,6 +38,8 @@ limitations under the License.
 #include "xmldoc.h"
 #include "xmlutils.h"
 
+#include "debug.h"
+
 namespace libcellml {
 
 static const std::map<std::string, int> standardPrefixList = {
@@ -749,6 +751,9 @@ std::vector<UnitsPtr> unitsUsed(const ModelPtr &model, const ComponentConstPtr &
         auto u = v->units();
         if ((u != nullptr) && !isStandardUnitName(u->name()) && (model != nullptr)) {
             auto modelUnits = model->units(u->name());
+            Debug() << "Info:";
+            Debug() << model->name();
+            Debug() << u->name();
             auto availableUnits = modelUnits ? modelUnits : u;
             auto requiredUnits = referencedUnits(model, availableUnits);
             usedUnits.insert(usedUnits.end(), requiredUnits.begin(), requiredUnits.end());

diff --git a/tests/importer/model_flattening.cpp b/tests/importer/model_flattening.cpp
@@ -1918,3 +1918,28 @@ TEST(ModelFlattening, modelWithCnUnitsNotDefinedInImportedComponent)
     EXPECT_EQ(size_t(1), importer->errorCount());
     EXPECT_EQ("The model is not fully defined.", importer->error(0)->description());
 }
+
+TEST(Experiment, periodicStimulus)
+{
+    auto parser = libcellml::Parser::create(false);
+    auto model = parser->parseModel(fileContents("importer/periodicstimulus/experiments/periodic-stimulus.xml"));
+
+    EXPECT_EQ(size_t(0), parser->errorCount());
+
+    auto validator = libcellml::Validator::create();
+
+    validator->validateModel(model);
+
+    EXPECT_EQ(size_t(0), validator->issueCount());
+    EXPECT_TRUE(model->hasUnresolvedImports());
+
+    auto importer = libcellml::Importer::create(false);
+
+    importer->resolveImports(model, resourcePath("importer/periodicstimulus/experiments"));
+
+    EXPECT_FALSE(model->hasUnresolvedImports());
+
+    auto flattenModel = importer->flattenModel(model);
+
+    EXPECT_NE(nullptr, flattenModel);
+}
diff --git a/tests/resources/importer/periodicstimulus/components/INa.xml b/tests/resources/importer/periodicstimulus/components/INa.xml
@@ -0,0 +1,9 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<model name="INa" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
+    <import xlink:href="units.xml">
+        <units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
+    </import>
+    <component name="INa">
+        <variable name="INa" private_interface="out" public_interface="out" units="uA_per_cmsq"/>
+    </component>
+</model>
diff --git a/tests/resources/importer/periodicstimulus/components/stimulated.xml b/tests/resources/importer/periodicstimulus/components/stimulated.xml
@@ -0,0 +1,23 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<model name="stimulated" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
+    <import xlink:href="units.xml">
+        <units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
+    </import>
+    <import xlink:href="INa.xml">
+        <component component_ref="INa" name="INa"/>
+    </import>
+    <component name="action_potential">
+<!--        <variable name="Istim" private_interface="out" public_interface="in" units="uA_per_cmsq"/>-->
+        <variable name="INa" private_interface="in" public_interface="out" units="uA_per_cmsq"/>
+    </component>
+    <group>
+        <relationship_ref relationship="encapsulation"/>
+        <component_ref component="action_potential">
+            <component_ref component="INa"/>
+        </component_ref>
+    </group>
+    <connection>
+        <map_components component_1="action_potential" component_2="INa"/>
+        <map_variables variable_1="INa" variable_2="INa"/>
+    </connection>
+</model>
diff --git a/tests/resources/importer/periodicstimulus/components/units.xml b/tests/resources/importer/periodicstimulus/components/units.xml
@@ -0,0 +1,13 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<model name="units" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
+    <units name="cm">
+        <unit prefix="centi" units="metre"/>
+    </units>
+    <units name="uA">
+        <unit prefix="micro" units="ampere"/>
+    </units>
+    <units name="uA_per_cmsq">
+        <unit units="uA"/>
+        <unit exponent="-2" units="cm"/>
+    </units>
+</model>
diff --git a/tests/resources/importer/periodicstimulus/experiments/periodic-stimulus.xml b/tests/resources/importer/periodicstimulus/experiments/periodic-stimulus.xml
@@ -0,0 +1,9 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<model name="periodic_stimulus" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
+    <import xlink:href="../components/units.xml">
+        <units name="uA_per_cmsq" units_ref="uA_per_cmsq"/>
+    </import>
+    <import xlink:href="../components/stimulated.xml">
+        <component component_ref="action_potential" name="_model"/>
+    </import>
+</model>