Merge branch 'main' into enh_unit_coverage

NeurodataWithoutBorders · Jan 27, 2025 · 52b8e44 · 52b8e44
2 parents ac7e3c1 + 00a529c
commit 52b8e44
Show file tree

Hide file tree

Showing 5 changed files with 135 additions and 9 deletions.
diff --git a/src/Utils.hpp b/src/Utils.hpp
@@ -6,6 +6,7 @@
 #include <cstdint>
 #include <ctime>
 #include <iomanip>
+#include <regex>
 #include <sstream>
 #include <string>
 
@@ -61,6 +62,26 @@ static inline std::string getCurrentTime()
   return currentTime;
 }
 
+/**
+ * @brief Check that a string is formatted in ISO8601 format
+ *
+ * This function only validates the regex pattern but does not check that
+ * the time values specified are indeed valid.
+ *
+ * @return bool indicating whether the string is in ISO8601 form
+ */
+static inline bool isISO8601Date(const std::string& dateStr)
+{
+  // Define the regex pattern for ISO 8601 extended format with timezone offset
+  // Allow one or more fractional seconds digits
+  const std::string iso8601Pattern =
+      R"(^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}\.\d+[+-]\d{2}:\d{2}$)";
+  std::regex pattern(iso8601Pattern);
+
+  // Check if the date string matches the regex pattern
+  return std::regex_match(dateStr, pattern);
+}
+
 /**
  * @brief Factory method to create an IO object.
  * @return A pointer to a BaseIO object

diff --git a/src/nwb/NWBFile.cpp b/src/nwb/NWBFile.cpp
@@ -49,15 +49,42 @@ NWBFile::~NWBFile() {}
 
 Status NWBFile::initialize(const std::string& identifierText,
                            const std::string& description,
-                           const std::string& dataCollection)
+                           const std::string& dataCollection,
+                           const std::string& sessionStartTime,
+                           const std::string& timestampsReferenceTime)
 {
   if (!m_io->isOpen()) {
     return Status::Failure;
   }
+  std::string currentTime = getCurrentTime();
+  // use the current time if sessionStartTime is empty
+  std::string useSessionStartTime =
+      (!sessionStartTime.empty()) ? sessionStartTime : currentTime;
+  // use the current time if timestampsReferenceTime is empty
+  std::string useTimestampsReferenceTime = (!timestampsReferenceTime.empty())
+      ? timestampsReferenceTime
+      : currentTime;
+  // check that sessionStartTime and timestampsReferenceTime are ISO8601
+  if (!isISO8601Date(useSessionStartTime)) {
+    std::cerr << "NWBFile::initialize sessionStartTime not in ISO8601 format: "
+              << useSessionStartTime << std::endl;
+    return Status::Failure;
+  }
+  if (!isISO8601Date(useTimestampsReferenceTime)) {
+    std::cerr
+        << "NWBFile::initialize timestampsReferenceTime not in ISO8601 format: "
+        << useTimestampsReferenceTime << std::endl;
+    return Status::Failure;
+  }
+
   // Check that the file is empty and initialize if it is
   bool fileInitialized = isInitialized();
   if (!fileInitialized) {
-    return createFileStructure(identifierText, description, dataCollection);
+    return createFileStructure(identifierText,
+                               description,
+                               dataCollection,
+                               useSessionStartTime,
+                               useTimestampsReferenceTime);
   } else {
     return Status::Success;  // File is already initialized
   }
@@ -102,7 +129,9 @@ Status NWBFile::finalize()
 
 Status NWBFile::createFileStructure(const std::string& identifierText,
                                     const std::string& description,
-                                    const std::string& dataCollection)
+                                    const std::string& dataCollection,
+                                    const std::string& sessionStartTime,
+                                    const std::string& timestampsReferenceTime)
 {
   if (!m_io->canModifyObjects()) {
     return Status::Failure;
@@ -133,12 +162,12 @@ Status NWBFile::createFileStructure(const std::string& identifierText,
   cacheSpecifications("hdmf-experimental",
                       AQNWB::SPEC::HDMF_EXPERIMENTAL::version,
                       AQNWB::SPEC::HDMF_EXPERIMENTAL::specVariables);
-  std::string time = getCurrentTime();
-  std::vector<std::string> timeVec = {time};
+  std::vector<std::string> timeVec = {sessionStartTime};
   m_io->createStringDataSet("/file_create_date", timeVec);
   m_io->createStringDataSet("/session_description", description);
-  m_io->createStringDataSet("/session_start_time", time);
-  m_io->createStringDataSet("/timestamps_reference_time", time);
+  m_io->createStringDataSet("/session_start_time", sessionStartTime);
+  m_io->createStringDataSet("/timestamps_reference_time",
+                            timestampsReferenceTime);
   m_io->createStringDataSet("/identifier", identifierText);
   return Status::Success;
 }

diff --git a/src/nwb/NWBFile.hpp b/src/nwb/NWBFile.hpp
@@ -67,10 +67,16 @@ class NWBFile : public Container
    * @param identifierText The identifier text for the NWBFile.
    * @param description A description of the NWBFile session.
    * @param dataCollection Information about the data collection methods.
+   * @param sessionStartTime ISO formatted time string with the session start
+   * time. If empty (default), then the getCurrentTime() will be used.
+   * @param timestampsReferenceTime ISO formatted time string with the timestamp
+   * reference time. If empty (default), then the getCurrentTime() will be used.
    */
   Status initialize(const std::string& identifierText,
                     const std::string& description = "a recording session",
-                    const std::string& dataCollection = "");
+                    const std::string& dataCollection = "",
+                    const std::string& sessionStartTime = "",
+                    const std::string& timestampsReferenceTime = "");
 
   /**
    * @brief Check if the NWB file is initialized.
@@ -155,11 +161,17 @@ class NWBFile : public Container
    * @param identifierText The identifier text for the NWBFile.
    * @param description A description of the NWBFile session.
    * @param dataCollection Information about the data collection methods.
+   * @param sessionStartTime ISO formatted time string with the session start
+   * time
+   * @param timestampsReferenceTime ISO formatted time string with the timestamp
+   * reference time
    * @return Status The status of the file structure creation.
    */
   Status createFileStructure(const std::string& identifierText,
                              const std::string& description,
-                             const std::string& dataCollection);
+                             const std::string& dataCollection,
+                             const std::string& sessionStartTime,
+                             const std::string& timestampsReferenceTime);
 
 private:
   /**

diff --git a/tests/testNWBFile.cpp b/tests/testNWBFile.cpp
@@ -26,6 +26,39 @@ TEST_CASE("saveNWBFile", "[nwb]")
   nwbfile.finalize();
 }
 
+TEST_CASE("initialize", "[nwb]")
+{
+  std::string filename = getTestFilePath("testInitializeNWBFile.nwb");
+
+  // initialize nwbfile object and create base structure
+  auto io = std::make_shared<IO::HDF5::HDF5IO>(filename);
+  io->open();
+  NWB::NWBFile nwbfile(io);
+
+  // bad session start time
+  Status initStatus = nwbfile.initialize(generateUuid(),
+                                         "test file",
+                                         "no collection",
+                                         "bad time",
+                                         AQNWB::getCurrentTime());
+  REQUIRE(initStatus == Status::Failure);
+
+  // bad timestamp reference time
+  initStatus = nwbfile.initialize(generateUuid(),
+                                  "test file",
+                                  "no collection",
+                                  AQNWB::getCurrentTime(),
+                                  "bad time");
+  REQUIRE(initStatus == Status::Failure);
+
+  // check that regular init with current times works
+  initStatus = nwbfile.initialize(generateUuid());
+  REQUIRE(initStatus == Status::Success);
+  REQUIRE(nwbfile.isInitialized());
+  nwbfile.finalize();
+  io->close();
+}
+
 TEST_CASE("createElectricalSeries", "[nwb]")
 {
   std::string filename = getTestFilePath("createElectricalSeries.nwb");

diff --git a/tests/testUtilsFunctions.cpp b/tests/testUtilsFunctions.cpp
@@ -4,6 +4,37 @@
 
 #include "Utils.hpp"
 
+TEST_CASE("isISO8601Date function tests", "[utils]")
+{
+  SECTION("Valid ISO 8601 date strings")
+  {
+    REQUIRE(AQNWB::isISO8601Date("2018-09-28T14:43:54.123+02:00"));
+    REQUIRE(AQNWB::isISO8601Date("2025-01-19T00:40:03.214144-08:00"));
+    REQUIRE(AQNWB::isISO8601Date("2021-12-31T23:59:59.999999+00:00"));
+    REQUIRE(AQNWB::isISO8601Date("2000-01-01T00:00:00.0+01:00"));
+    REQUIRE(AQNWB::isISO8601Date(
+        "2018-09-28T14:43:54.12345+02:00"));  // Allow for too many fractional
+                                              // seconds
+  }
+
+  SECTION("Invalid ISO 8601 date strings")
+  {
+    REQUIRE_FALSE(AQNWB::isISO8601Date(
+        "2018-09-28 14:43:54.123+02:00"));  // Space instead of 'T'
+    REQUIRE_FALSE(AQNWB::isISO8601Date(
+        "2018-09-28T14:43:54+02:00"));  // Missing fractional seconds
+    REQUIRE_FALSE(AQNWB::isISO8601Date(
+        "2018-09-28T14:43:54.123+0200"));  // Missing colon in timezone
+    REQUIRE_FALSE(AQNWB::isISO8601Date(
+        "2018-09-28T14:43:54.123Z"));  // Missing timezone offset
+    REQUIRE_FALSE(AQNWB::isISO8601Date(
+        "2018-09-28T14:43:54.123-0800"));  // Incorrect timezone format
+    REQUIRE_FALSE(
+        AQNWB::isISO8601Date("2018-09-28T14:43:54.123"));  // Missing timezone
+    REQUIRE_FALSE(AQNWB::isISO8601Date("Random text 1213"));
+  }
+}
+
 TEST_CASE("Test UUID generation", "[utils]")
 {
   // Test that generated UUIDs are valid