Fix bugs detected by this verifier

Both of the form "data not found in places where data was expected"

Author: franzpoeschel

src/Series.cpp

@@ -742,8 +742,13 @@ void Series::flushFileBased(
     bool flushIOHandler)
 {
     auto &series = get();
-    if (end == begin)
-        throw std::runtime_error(
+    if (end == begin &&
+        /*
+         * At parsing time, this might happen since iterations might contain
+         * errors and be deleted.
+         */
+        IOHandler()->m_seriesStatus != internal::SeriesStatus::Parsing)
+        throw error::WrongAPIUsage(
             "fileBased output can not be written with no iterations.");
 
     switch (IOHandler()->m_frontendAccess)
@@ -859,6 +864,26 @@ void Series::flushGorVBased(
     bool flushIOHandler)
 {
     auto &series = get();
+    if (iterationEncoding() == IterationEncoding::variableBased &&
+        /*
+         * At parsing time, this might happen since iterations might contain
+         * errors and be deleted.
+         */
+        IOHandler()->m_seriesStatus != internal::SeriesStatus::Parsing &&
+        iterations.empty())
+        /*
+         * Note: Unlike flushFileBased, it's ok if `begin == end` since this
+         * method may be called without an explicit iteration.
+         * But since in variable-based encoding the base path is the same as the
+         * path to the (currently active) iteration, there must be at least one
+         * iteration present since the openPMD standard requires mandatory
+         * attributes.
+         * In group-based encoding, any number of iterations might be included
+         * in the base path, in variable-based encoding there must be exactly
+         * one iteration currently active.
+         */
+        throw error::WrongAPIUsage(
+            "variableBased output can not be written with no iterations.");
     if (access::readOnly(IOHandler()->m_frontendAccess))
     {
         for (auto it = begin; it != end; ++it)

test/CoreTest.cpp

@@ -190,7 +190,8 @@ TEST_CASE("myPath", "[core]")
     REQUIRE(
         pathOf(scalarMesh) ==
         vec_t{"iterations", "1234", "meshes", "e_chargeDensity"});
-    auto scalarMeshComponent = scalarMesh[RecordComponent::SCALAR];
+    auto scalarMeshComponent = scalarMesh[RecordComponent::SCALAR].resetDataset(
+        {Datatype::FLOAT, {10}});
     REQUIRE(
         pathOf(scalarMeshComponent) ==
         vec_t{
@@ -203,7 +204,8 @@ TEST_CASE("myPath", "[core]")
 
     auto vectorMesh = iteration.meshes["E"];
     REQUIRE(pathOf(vectorMesh) == vec_t{"iterations", "1234", "meshes", "E"});
-    auto vectorMeshComponent = vectorMesh["x"];
+    auto vectorMeshComponent =
+        vectorMesh["x"].resetDataset({Datatype::FLOAT, {10}});
     REQUIRE(
         pathOf(vectorMeshComponent) ==
         vec_t{"iterations", "1234", "meshes", "E", "x"});
@@ -220,7 +222,8 @@ TEST_CASE("myPath", "[core]")
         pathOf(speciesPosition) ==
         vec_t{"iterations", "1234", "particles", "e", "position"});
 
-    auto speciesPositionX = speciesPosition["x"];
+    auto speciesPositionX =
+        speciesPosition["x"].resetDataset({Datatype::FLOAT, {10}});
     REQUIRE(
         pathOf(speciesPositionX) ==
         vec_t{"iterations", "1234", "particles", "e", "position", "x"});
@@ -231,7 +234,9 @@ TEST_CASE("myPath", "[core]")
         pathOf(speciesWeighting) ==
         vec_t{"iterations", "1234", "particles", "e", "weighting"});
 
-    auto speciesWeightingX = speciesWeighting[RecordComponent::SCALAR];
+    auto speciesWeightingX =
+        speciesWeighting[RecordComponent::SCALAR].resetDataset(
+            {Datatype::FLOAT, {10}});
     REQUIRE(
         pathOf(speciesWeightingX) ==
         vec_t{
@@ -258,7 +263,7 @@ TEST_CASE("myPath", "[core]")
             "particlePatches",
             "extent"});
 
-    auto patchExtentX = patchExtent["x"];
+    auto patchExtentX = patchExtent["x"].resetDataset({Datatype::INT, {10}});
     REQUIRE(
         pathOf(patchExtentX) ==
         vec_t{
@@ -282,7 +287,8 @@ TEST_CASE("myPath", "[core]")
             "numParticles"});
 
     auto patchNumParticlesComponent =
-        patchNumParticles[RecordComponent::SCALAR];
+        patchNumParticles[RecordComponent::SCALAR].resetDataset(
+            {Datatype::INT, {10}});
     REQUIRE(
         pathOf(patchNumParticlesComponent) ==
         vec_t{
@@ -293,6 +299,10 @@ TEST_CASE("myPath", "[core]")
             "particlePatches",
             "numParticles",
             RecordComponent::SCALAR});
+
+    speciesE.particlePatches["offset"]["x"].resetDataset({Datatype::INT, {10}});
+    speciesE.particlePatches["numParticlesOffset"][RecordComponent::SCALAR]
+        .resetDataset({Datatype::INT, {10}});
 #endif
 }
 
@@ -1058,6 +1068,7 @@ TEST_CASE("backend_via_json", "[core]")
     {
         Series series(
             "../samples/optionsViaJson", Access::CREATE, encodingVariableBased);
+        series.iterations[0]; // v-based encoding requires at least 1 iteration
         REQUIRE(series.backend() == "JSON");
         REQUIRE(series.iterationEncoding() == IterationEncoding::variableBased);
     }
@@ -1071,6 +1082,7 @@ TEST_CASE("backend_via_json", "[core]")
             "../samples/optionsViaJson.bp",
             Access::CREATE,
             encodingVariableBased);
+        series.iterations[0]; // v-based encoding requires at least 1 iteration
         REQUIRE(series.backend() == "JSON");
         REQUIRE(series.iterationEncoding() == IterationEncoding::variableBased);
     }