Add support for OMEX files that don't specify a master file

VERSION.txt

@@ -1 +1 @@
-1.20261007.0
+1.20261008.0

src/sed/seddocument.cpp

@@ -90,10 +90,17 @@ void SedDocument::Impl::initialiseFromSedmlFile(const SedDocumentPtr &pOwner, co
 
 void SedDocument::Impl::initialiseFromCombineArchive(const SedDocumentPtr &pOwner, const FilePtr &pFile)
 {
-    const auto &masterFile {pFile->pimpl()->mCombineArchive->masterFile()};
+    const auto &combineArchive {pFile->pimpl()->mCombineArchive};
+    const auto &masterFile {combineArchive->masterFile()};
 
     if (masterFile == nullptr) {
-        addError("A simulation experiment description cannot be created using a COMBINE archive with no master file.");
+        if (combineArchive->sedmlFileCount() > 1) {
+            addError("A simulation experiment description cannot be created using a COMBINE archive with no master file and several SED-ML files.");
+        } else if (combineArchive->cellmlFileCount() > 1) {
+            addError("A simulation experiment description cannot be created using a COMBINE archive with no master file, no SED-ML file, and several CellML files.");
+        } else {
+            addError("A simulation experiment description cannot be created using a COMBINE archive with no master file.");
+        }
     } else {
         auto masterFileType {masterFile->type()};
 

src/support/combine/combinearchive.cpp

@@ -22,8 +22,30 @@ limitations under the License.
 #include "combine/combinearchive.h"
 #include "omex/CaContent.h"
 
+#include <regex>
+
 namespace libOpenCOR {
 
+namespace {
+
+bool isCellmlFormat(const std::string &pFormat)
+{
+    // Note: we accept versioned formats (e.g., cellml.1.0 or cellml.2.0).
+
+    static const std::regex CELLML_FORMAT_REGEX {R"(^http://identifiers\.org/combine\.specifications/cellml(\..*)?$)"};
+
+    return std::regex_match(pFormat, CELLML_FORMAT_REGEX);
+}
+
+bool isSedmlFormat(const std::string &pFormat)
+{
+    static const std::string SEDML_FORMAT {"http://identifiers.org/combine.specifications/sed-ml"};
+
+    return pFormat == SEDML_FORMAT;
+}
+
+} // namespace
+
 CombineArchive::Impl::Impl(const FilePtr &pFile, libcombine::CombineArchive *pArchive, UnsignedChars &&pArchiveContents)
     : mArchiveContents(std::move(pArchiveContents))
     , mArchive(pArchive)
@@ -37,6 +59,9 @@ CombineArchive::Impl::Impl(const FilePtr &pFile, libcombine::CombineArchive *pAr
     mFiles.reserve(fileCount);
     mFileNames.reserve(fileCount);
 
+    FilePtr cellmlFile;
+    FilePtr sedmlFile;
+
     for (int i {0}; i < mArchive->getNumEntries(); ++i) {
         const auto *entry {mArchive->getEntry(i)};
         auto location {entry->getLocation()};
@@ -50,6 +75,50 @@ CombineArchive::Impl::Impl(const FilePtr &pFile, libcombine::CombineArchive *pAr
         if (entry->getMaster()) {
             mMasterFile = file;
         }
+
+        // Determine the type of the file using its contents or, if they are not recognised (e.g., malformed XML), using
+        // the format specified in the manifest. This means that a broken SED-ML file is still considered to be a SED-ML
+        // file and, as such, cannot be silently ignored in favour of a CellML file.
+
+        auto fileType {file->type()};
+
+        if (fileType == File::Type::UNKNOWN_FILE) {
+            const auto &format {entry->getFormat()};
+
+            if (isCellmlFormat(format)) {
+                fileType = File::Type::CELLML_FILE;
+            } else if (isSedmlFormat(format)) {
+                fileType = File::Type::SEDML_FILE;
+            }
+        }
+
+        if (fileType == File::Type::CELLML_FILE) {
+            if (mCellmlFileCount == 0) {
+                cellmlFile = file;
+            }
+
+            ++mCellmlFileCount;
+        } else if (fileType == File::Type::SEDML_FILE) {
+            if (mSedmlFileCount == 0) {
+                sedmlFile = file;
+            }
+
+            ++mSedmlFileCount;
+        }
+    }
+
+    // Determine the master file, if none was specified.
+    // Note: the master attribute is optional, so if no master file was specified then we consider the SED-ML file to be
+    //       the master file, if there is only one SED-ML file, or the CellML file to be the master file, if there is no
+    //       SED-ML file and only one CellML file. Otherwise, it is up to the user (or a tool like Web OpenCOR) to decide
+    //       which file should be used.
+
+    if (mMasterFile == nullptr) {
+        if (mSedmlFileCount == 1) {
+            mMasterFile = sedmlFile;
+        } else if ((mSedmlFileCount == 0) && (mCellmlFileCount == 1)) {
+            mMasterFile = cellmlFile;
+        }
     }
 }
 
@@ -63,6 +132,16 @@ const FilePtr &CombineArchive::Impl::masterFile() const
     return mMasterFile;
 }
 
+size_t CombineArchive::Impl::cellmlFileCount() const
+{
+    return mCellmlFileCount;
+}
+
+size_t CombineArchive::Impl::sedmlFileCount() const
+{
+    return mSedmlFileCount;
+}
+
 bool CombineArchive::Impl::hasFiles() const
 {
     return mFiles.empty();
@@ -176,6 +255,16 @@ const FilePtr &CombineArchive::masterFile() const
     return pimpl()->masterFile();
 }
 
+size_t CombineArchive::cellmlFileCount() const
+{
+    return pimpl()->cellmlFileCount();
+}
+
+size_t CombineArchive::sedmlFileCount() const
+{
+    return pimpl()->sedmlFileCount();
+}
+
 bool CombineArchive::hasFiles() const
 {
     return !pimpl()->hasFiles();

src/support/combine/combinearchive.h

@@ -44,6 +44,8 @@ class LIBOPENCOR_UNIT_TESTING_EXPORT CombineArchive: public Logger
     static CombineArchivePtr create(const FilePtr &pFile);
 
     const FilePtr &masterFile() const;
+    size_t cellmlFileCount() const;
+    size_t sedmlFileCount() const;
 
     bool hasFiles() const;
     size_t fileCount() const;

src/support/combine/combinearchive_p.h

@@ -32,11 +32,15 @@ class CombineArchive::Impl: public Logger::Impl
     std::vector<FilePtr> mFiles;
     std::vector<std::string> mFileNames;
     FilePtr mMasterFile;
+    size_t mCellmlFileCount {0};
+    size_t mSedmlFileCount {0};
 
     explicit Impl(const FilePtr &pFile, libcombine::CombineArchive *pArchive, UnsignedChars &&pArchiveContents);
     ~Impl() override;
 
     const FilePtr &masterFile() const;
+    size_t cellmlFileCount() const;
+    size_t sedmlFileCount() const;
     bool hasFiles() const;
     size_t fileCount() const;
     const Strings &fileNames() const;

tests/api/sed/basictests.cpp

@@ -107,13 +107,79 @@ TEST(BasicSedTest, combineArchiveWithNoManifestFile)
     EXPECT_EQ_ISSUES(document, EXPECTED_ISSUES);
 }
 
-TEST(BasicSedTest, combineArchiveWithNoMasterFile)
+TEST(BasicSedTest, combineArchiveWithNoMasterFileAndOneCellmlFile)
+{
+    auto file {libOpenCOR::File::create(libOpenCOR::resourcePath("api/sed/no_master_file_with_one_cellml_file.omex"))};
+    auto document {libOpenCOR::SedDocument::create(file)};
+
+    EXPECT_FALSE(document->hasIssues());
+    EXPECT_EQ(std::dynamic_pointer_cast<libOpenCOR::SedUniformTimeCourse>(document->simulations()[0])->outputEndTime(), 1000.0);
+
+    auto instance {document->instantiate()};
+
+    instance->run();
+
+    EXPECT_FALSE(instance->hasIssues());
+}
+
+TEST(BasicSedTest, combineArchiveWithNoMasterFileAndOneUnknownCellmlFile)
 {
     static const libOpenCOR::ExpectedIssues EXPECTED_ISSUES {{
-        {libOpenCOR::Issue::Type::ERROR, "A simulation experiment description cannot be created using a COMBINE archive with no master file."},
+        {libOpenCOR::Issue::Type::ERROR, "A simulation experiment description cannot be created using a COMBINE archive with an unknown master file (only CellML and SED-ML master files are supported)."},
+    }};
+
+    auto file {libOpenCOR::File::create(libOpenCOR::resourcePath("api/sed/no_master_file_with_one_unknown_cellml_file.omex"))};
+    auto document {libOpenCOR::SedDocument::create(file)};
+
+    EXPECT_EQ_ISSUES(document, EXPECTED_ISSUES);
+}
+
+TEST(BasicSedTest, combineArchiveWithNoMasterFileAndSeveralCellmlFiles)
+{
+    static const libOpenCOR::ExpectedIssues EXPECTED_ISSUES {{
+        {libOpenCOR::Issue::Type::ERROR, "A simulation experiment description cannot be created using a COMBINE archive with no master file, no SED-ML file, and several CellML files."},
+    }};
+
+    auto file {libOpenCOR::File::create(libOpenCOR::resourcePath("api/sed/no_master_file_with_several_cellml_files.omex"))};
+    auto document {libOpenCOR::SedDocument::create(file)};
+
+    EXPECT_EQ_ISSUES(document, EXPECTED_ISSUES);
+}
+
+TEST(BasicSedTest, combineArchiveWithNoMasterFileAndOneSedmlFile)
+{
+    auto file {libOpenCOR::File::create(libOpenCOR::resourcePath("api/sed/no_master_file_with_one_sedml_file.omex"))};
+    auto document {libOpenCOR::SedDocument::create(file)};
+
+    EXPECT_FALSE(document->hasIssues());
+    EXPECT_EQ(std::dynamic_pointer_cast<libOpenCOR::SedUniformTimeCourse>(document->simulations()[0])->outputEndTime(), 50.0);
+
+    auto instance {document->instantiate()};
+
+    instance->run();
+
+    EXPECT_FALSE(instance->hasIssues());
+}
+
+TEST(BasicSedTest, combineArchiveWithNoMasterFileAndOneUnknownSedmlFile)
+{
+    static const libOpenCOR::ExpectedIssues EXPECTED_ISSUES {{
+        {libOpenCOR::Issue::Type::ERROR, "A simulation experiment description cannot be created using a COMBINE archive with an unknown master file (only CellML and SED-ML master files are supported)."},
+    }};
+
+    auto file {libOpenCOR::File::create(libOpenCOR::resourcePath("api/sed/no_master_file_with_one_unknown_sedml_file.omex"))};
+    auto document {libOpenCOR::SedDocument::create(file)};
+
+    EXPECT_EQ_ISSUES(document, EXPECTED_ISSUES);
+}
+
+TEST(BasicSedTest, combineArchiveWithNoMasterFileAndSeveralSedmlFiles)
+{
+    static const libOpenCOR::ExpectedIssues EXPECTED_ISSUES {{
+        {libOpenCOR::Issue::Type::ERROR, "A simulation experiment description cannot be created using a COMBINE archive with no master file and several SED-ML files."},
     }};
 
-    auto file {libOpenCOR::File::create(libOpenCOR::resourcePath("api/sed/no_master_file.omex"))};
+    auto file {libOpenCOR::File::create(libOpenCOR::resourcePath("api/sed/no_master_file_with_several_sedml_files.omex"))};
     auto document {libOpenCOR::SedDocument::create(file)};
 
     EXPECT_EQ_ISSUES(document, EXPECTED_ISSUES);

tests/bindings/javascript/sed.basic.test.js

@@ -129,8 +129,25 @@ test.describe('Sed basic tests', () => {
     ]);
   });
 
-  test('COMBINE archive with no master file', () => {
-    const file = new loc.File(utils.resourcePath('api/sed/no_master_file.omex'));
+  test('COMBINE archive with no master file and one CellML file', () => {
+    const file = new loc.File(utils.resourcePath('api/sed/no_master_file_with_one_cellml_file.omex'));
+
+    file.setContents(utils.fileContents(file.path));
+
+    const document = new loc.SedDocument(file);
+
+    assert.strictEqual(document.hasIssues, false);
+    assert.strictEqual(document.simulations.get(0).outputEndTime, 1000);
+
+    const instance = document.instantiate();
+
+    instance.run();
+
+    assert.strictEqual(instance.hasIssues, false);
+  });
+
+  test('COMBINE archive with no master file and one unknown CellML file', () => {
+    const file = new loc.File(utils.resourcePath('api/sed/no_master_file_with_one_unknown_cellml_file.omex'));
 
     file.setContents(utils.fileContents(file.path));
 
@@ -139,7 +156,69 @@ test.describe('Sed basic tests', () => {
     assertIssues(loc, document, [
       [
         loc.Issue.Type.ERROR,
-        'A simulation experiment description cannot be created using a COMBINE archive with no master file.'
+        'A simulation experiment description cannot be created using a COMBINE archive with an unknown master file (only CellML and SED-ML master files are supported).'
+      ]
+    ]);
+  });
+
+  test('COMBINE archive with no master file and several CellML files', () => {
+    const file = new loc.File(utils.resourcePath('api/sed/no_master_file_with_several_cellml_files.omex'));
+
+    file.setContents(utils.fileContents(file.path));
+
+    const document = new loc.SedDocument(file);
+
+    assertIssues(loc, document, [
+      [
+        loc.Issue.Type.ERROR,
+        'A simulation experiment description cannot be created using a COMBINE archive with no master file, no SED-ML file, and several CellML files.'
+      ]
+    ]);
+  });
+
+  test('COMBINE archive with no master file and one SED-ML file', () => {
+    const file = new loc.File(utils.resourcePath('api/sed/no_master_file_with_one_sedml_file.omex'));
+
+    file.setContents(utils.fileContents(file.path));
+
+    const document = new loc.SedDocument(file);
+
+    assert.strictEqual(document.hasIssues, false);
+    assert.strictEqual(document.simulations.get(0).outputEndTime, 50);
+
+    const instance = document.instantiate();
+
+    instance.run();
+
+    assert.strictEqual(instance.hasIssues, false);
+  });
+
+  test('COMBINE archive with no master file and one unknown SED-ML file', () => {
+    const file = new loc.File(utils.resourcePath('api/sed/no_master_file_with_one_unknown_sedml_file.omex'));
+
+    file.setContents(utils.fileContents(file.path));
+
+    const document = new loc.SedDocument(file);
+
+    assertIssues(loc, document, [
+      [
+        loc.Issue.Type.ERROR,
+        'A simulation experiment description cannot be created using a COMBINE archive with an unknown master file (only CellML and SED-ML master files are supported).'
+      ]
+    ]);
+  });
+
+  test('COMBINE archive with no master file and several SED-ML files', () => {
+    const file = new loc.File(utils.resourcePath('api/sed/no_master_file_with_several_sedml_files.omex'));
+
+    file.setContents(utils.fileContents(file.path));
+
+    const document = new loc.SedDocument(file);
+
+    assertIssues(loc, document, [
+      [
+        loc.Issue.Type.ERROR,
+        'A simulation experiment description cannot be created using a COMBINE archive with no master file and several SED-ML files.'
       ]
     ]);
   });