Fix Zero Pattern Issue

include/openPMD/Iteration.hpp

@@ -102,6 +102,14 @@ namespace internal
          * Otherwise empty.
          */
         std::optional<DeferredParseAccess> m_deferredParseAccess{};
+
+        /**
+         * Upon reading a file, set this field to the used file name.
+         * In inconsistent iteration paddings, we must remember the name of the
+         * file since it cannot be reconstructed from the filename pattern
+         * alone.
+         */
+        std::optional<std::string> m_overrideFilebasedFilename{};
     };
 } // namespace internal
 /** @brief  Logical compilation of data from one snapshot (e.g. a single

src/IO/JSON/JSONIOHandlerImpl.cpp

@@ -916,7 +916,7 @@ JSONIOHandlerImpl::getFilehandle(File fileName, Access access)
         fs->open(path, std::ios_base::in);
         break;
     }
-    VERIFY(fs->good(), "[JSON] Failed opening a file");
+    VERIFY(fs->good(), "[JSON] Failed opening a file '" + path + "'");
     return fs;
 }
 

src/Iteration.cpp

@@ -364,6 +364,7 @@ void Iteration::readFileBased(
     auto series = retrieveSeries();
 
     series.readOneIterationFileBased(filePath);
+    get().m_overrideFilebasedFilename = filePath;
 
     read_impl(groupPath);
 }

src/Series.cpp

@@ -1191,14 +1191,34 @@ void Series::readBase()
 
 std::string Series::iterationFilename(uint64_t i)
 {
+    /*
+     * The filename might have been overridden at the Series level or at the
+     * Iteration level. See the struct members' documentation for the reasons.
+     */
     auto &series = get();
     if (series.m_overrideFilebasedFilename.has_value())
     {
         return series.m_overrideFilebasedFilename.value();
     }
-    std::stringstream iteration("");
-    iteration << std::setw(series.m_filenamePadding) << std::setfill('0') << i;
-    return series.m_filenamePrefix + iteration.str() + series.m_filenamePostfix;
+    else if (auto iteration = iterations.find(i); //
+             iteration != iterations.end() &&
+             iteration->second.get().m_overrideFilebasedFilename.has_value())
+    {
+        return iteration->second.get().m_overrideFilebasedFilename.value();
+    }
+    else
+    {
+
+        /*
+         * If no filename has been explicitly stored, we use the filename
+         * pattern to compute it.
+         */
+        std::stringstream iterationNr("");
+        iterationNr << std::setw(series.m_filenamePadding) << std::setfill('0')
+                    << i;
+        return series.m_filenamePrefix + iterationNr.str() +
+            series.m_filenamePostfix;
+    }
 }
 
 Series::iterations_iterator Series::indexOf(Iteration const &iteration)

test/SerialIOTest.cpp

@@ -5659,3 +5659,47 @@ TEST_CASE("late_setting_of_iterationencoding", "[serial]")
     REQUIRE(
         auxiliary::file_exists("../samples/change_name_and_encoding_10.json"));
 }
+
+void varying_pattern(std::string const file_ending)
+{
+    {
+        std::string filename = "../samples/varying_pattern_%06T." + file_ending;
+        ::openPMD::Series series =
+            ::openPMD::Series(filename, ::openPMD::Access::CREATE);
+
+        for (auto i : {0, 8000, 10000, 100000, 2000000})
+        {
+            auto it = series.iterations[i];
+            it.setAttribute("my_step", i);
+        }
+        series.flush();
+    }
+    {
+        std::string filename = "../samples/varying_pattern_%T." + file_ending;
+        ::openPMD::Series series =
+            ::openPMD::Series(filename, ::openPMD::Access::READ_ONLY);
+
+        REQUIRE(series.iterations.size() == 5);
+        for (auto const &[step, it] : series.iterations)
+        {
+            std::cout << "Iteration: " << step << "\n";
+            REQUIRE(it.getAttribute("my_step").get<int>() == int(step));
+        }
+
+        helper::listSeries(series, true, std::cout);
+
+        for (auto i : {0, 8000, 10000, 100000, 2000000})
+        {
+            auto it = series.iterations[i];
+            REQUIRE(it.getAttribute("my_step").get<int>() == i);
+        }
+    }
+}
+
+TEST_CASE("varying_zero_pattern", "[serial]")
+{
+    for (auto const &t : testedFileExtensions())
+    {
+        varying_pattern(t);
+    }
+}