Add JSON schema

.github/workflows/linux.yml

@@ -257,7 +257,7 @@ jobs:
     - name: Install
       run: |
         sudo apt-get update
-        sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev python3 python3-numpy python3-mpi4py python3-pandas
+        sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev python3 python3-numpy python3-mpi4py python3-pandas python3-pip
 #       TODO ADIOS2
     - name: Build
       env: {CXXFLAGS: -Werror, PKG_CONFIG_PATH: /usr/lib/x86_64-linux-gnu/pkgconfig}
@@ -272,6 +272,22 @@ jobs:
         cd build
         ctest --output-on-failure
 
+        python3 -m pip install jsonschema
+        cd ../share/openPMD/json_schema
+        PATH="../../../build/bin:$PATH" make -j 2
+        # We need to exclude the thetaMode example since that has a different
+        # meshesPath and the JSON schema needs to hardcode that.
+        find ../../../build/samples/      \
+            ! -path '*thetaMode*'         \
+            ! -path '/*many_iterations/*' \
+            ! -name 'profiling.json'      \
+            ! -name '*config.json'        \
+            -iname '*.json'               \
+          | while read i; do
+            echo "Checking $i"
+            ./check.py "$i"
+        done
+
   musllinux_py10:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false

CMakeLists.txt

@@ -747,11 +747,12 @@ set(openPMD_TEST_NAMES
 # command line tools
 set(openPMD_CLI_TOOL_NAMES
     ls
+    convert-json-toml
 )
 set(openPMD_PYTHON_CLI_TOOL_NAMES
     pipe
 )
-set(openPMD_PYTHON_CLI_MODULE_NAMES ${openPMD_CLI_TOOL_NAMES})
+set(openPMD_PYTHON_CLI_MODULE_NAMES ls)
 # examples
 set(openPMD_EXAMPLE_NAMES
     1_structure
@@ -920,6 +921,9 @@ if(openPMD_BUILD_CLI_TOOLS)
         endif()
 
         target_link_libraries(openpmd-${toolname} PRIVATE openPMD)
+        target_include_directories(openpmd-${toolname} SYSTEM PRIVATE
+            $<TARGET_PROPERTY:openPMD::thirdparty::nlohmann_json,INTERFACE_INCLUDE_DIRECTORIES>
+            $<TARGET_PROPERTY:openPMD::thirdparty::toml11,INTERFACE_INCLUDE_DIRECTORIES>)
     endforeach()
 endif()
 

include/openPMD/auxiliary/JSON_internal.hpp

@@ -190,16 +190,25 @@ namespace json
      * @param options as a parsed JSON object.
      * @param considerFiles If yes, check if `options` refers to a file and read
      *        from there.
+     * @param convertLowercase If yes, lowercase conversion is applied
+     *        recursively to keys and values, except for some hardcoded places
+     *        that should be left untouched.
      */
-    ParsedConfig parseOptions(std::string const &options, bool considerFiles);
+    ParsedConfig parseOptions(
+        std::string const &options,
+        bool considerFiles,
+        bool convertLowercase = true);
 
 #if openPMD_HAVE_MPI
 
     /**
      * Parallel version of parseOptions(). MPI-collective.
      */
-    ParsedConfig
-    parseOptions(std::string const &options, MPI_Comm comm, bool considerFiles);
+    ParsedConfig parseOptions(
+        std::string const &options,
+        MPI_Comm comm,
+        bool considerFiles,
+        bool convertLowercase = true);
 
 #endif
 

share/openPMD/json_schema/Makefile

@@ -0,0 +1,13 @@
+convert := openpmd-convert-json-toml
+
+json_files = attribute_defs.json attributes.json dataset_defs.json iteration.json mesh.json mesh_record_component.json particle_patches.json particle_species.json patch_record.json record.json record_component.json series.json
+
+.PHONY: all
+all: $(json_files)
+
+$(json_files): %.json: %.toml
+	$(convert) @$^ > $@
+
+.PHONY: clean
+clean:
+	-rm $(json_files)

share/openPMD/json_schema/README.md

@@ -0,0 +1,47 @@
+# JSON Validation
+
+This folder contains a JSON schema for validation of openPMD files written as `.json` files.
+
+## Usage
+
+### Generating the JSON schema
+
+For improved readability, maintainability and documentation purposes, the JSON schema is written in `.toml` format and needs to be "compiled" to `.json` files first before usage.
+To do this, the openPMD-api installs a tool named `openpmd-convert-json-toml` which can be used to convert between JSON and TOML files in both directions, e.g.:
+
+```bash
+openpmd_convert-json-toml @series.toml > series.json
+```
+
+A `Makefile` is provided in this folder to simplify the application of this conversion tool.
+
+### Verifying a file against the JSON schema
+
+In theory, the JSON schema should be applicable by any JSON validator. This JSON schema is written in terms of multiple files however, and most validators require special care to properly set up the links between the single files. A Python script `check.py` is provided in this folder which sets up the [Python jsonschema](https://python-jsonschema.readthedocs.io) library and verifies a file against it, e.g.:
+
+```bash
+./check.py path/to/my/dataset.json
+```
+
+For further usage notes check the documentation of the script itself `./check.py --help`.
+
+## Caveats
+
+The openPMD standard is not entirely expressible in terms of a JSON schema:
+
+* Many semantic dependencies, e.g. that the `position/x` and `position/y` vector of a particle species be of the same size, or that the `axisLabels` have the same dimensionality as the dataset itself, will go unchecked.
+* The `meshesPath` is assumed to be `meshes/` and the `particlesPath` is assumed to be `particles/`. This dependency cannot be expressed.
+
+While a large part of the openPMD standard can indeed be verified by checking against a JSON schema, the standard is generally large enough to make this approach come to its limits. Verification of a JSON schema is similar to the use of a naive recursive-descent parser. Error messages will often be unexpectedly verbose and not very informative.
+A challenge for the JSON validator are disjunctive statements such as "A Record is either a scalar Record Component or a vector of non-scalar Record Components". If there is even a tiny mistake somewhere down in the hierarchy, the entire disjunctive branch will fail evaluating.
+
+The layout of attributes is assumed to be that which is created by the JSON backend of the openPMD-api, e.g.:
+
+```json
+"meshesPath": {
+  "datatype": "STRING",
+  "value": "meshes/"
+}
+```
+
+Support for an abbreviated notation such as `"meshesPath": "meshes/"` is currently not (yet) available.

share/openPMD/json_schema/attribute_defs.toml

@@ -0,0 +1,236 @@
+
+["$defs"]
+
+######################
+# Vectors of strings #
+######################
+
+[["$defs".vec_string_attribute.oneOf]]
+title = "Shorthand notation"
+anyOf = [
+    { type = "string" },
+    { type = "array", items = { "type" = "string" } },
+]
+
+[["$defs".vec_string_attribute.oneOf]]
+title = "Long notation"
+type = "object"
+required = ["value", "datatype"]
+
+["$defs".vec_string_attribute.oneOf.properties]
+
+value.anyOf = [
+    { type = "string" },
+    { type = "array", items = { "type" = "string" } },
+]
+
+datatype.enum = [
+    "STRING",
+    "CHAR",
+    "SCHAR",
+    "UCHAR",
+    "VEC_STRING",
+    "VEC_CHAR",
+    "VEC_SCHAR",
+    "VEC_UCHAR",
+]
+
+##################
+# Vectors of int #
+##################
+
+[["$defs".vec_int_attribute.oneOf]]
+title = "Shorthand notation"
+anyOf = [
+    { type = "integer" },
+    { type = "array", items = { "type" = "integer" } },
+]
+
+[["$defs".vec_int_attribute.oneOf]]
+title = "Long notation"
+type = "object"
+required = ["value", "datatype"]
+
+["$defs".vec_int_attribute.oneOf.properties]
+
+value.anyOf = [
+    { type = "integer" },
+    { type = "array", items = { "type" = "integer" } },
+]
+
+datatype.enum = [
+    "SHORT",
+    "INT",
+    "LONG",
+    "LONGLONG",
+    "USHORT",
+    "UINT",
+    "ULONG",
+    "ULONGLONG",
+    "VEC_SHORT",
+    "VEC_INT",
+    "VEC_LONG",
+    "VEC_LONGLONG",
+    "VEC_USHORT",
+    "VEC_UINT",
+    "VEC_ULONG",
+    "VEC_ULONGLONG",
+]
+
+####################
+# Vectors of float #
+####################
+
+[["$defs".vec_float_attribute.oneOf]]
+title = "Shorthand notation"
+anyOf = [
+    { type = "number" },
+    { type = "array", items = { "type" = "number" } },
+]
+
+[["$defs".vec_float_attribute.oneOf]]
+title = "Long notation"
+type = "object"
+required = ["value", "datatype"]
+
+["$defs".vec_float_attribute.oneOf.properties]
+
+value.anyOf = [
+    { type = "number" },
+    { type = "array", items = { "type" = "number" } },
+]
+
+datatype.enum = [
+    "CHAR",
+    "UCHAR",
+    "SCHAR",
+    "SHORT",
+    "INT",
+    "LONG",
+    "LONGLONG",
+    "USHORT",
+    "UINT",
+    "ULONG",
+    "ULONGLONG",
+    "FLOAT",
+    "DOUBLE",
+    "LONG_DOUBLE",
+    "CFLOAT",
+    "CDOUBLE",
+    "CLONG_DOUBLE",
+    "VEC_SHORT",
+    "VEC_INT",
+    "VEC_LONG",
+    "VEC_LONGLONG",
+    "VEC_USHORT",
+    "VEC_UINT",
+    "VEC_ULONG",
+    "VEC_ULONGLONG",
+    "VEC_FLOAT",
+    "VEC_DOUBLE",
+    "VEC_LONG_DOUBLE",
+    "VEC_CFLOAT",
+    "VEC_CDOUBLE",
+    "VEC_CLONG_DOUBLE",
+]
+
+###########################
+# Special case:           #
+# unitDimension attribute #
+###########################
+
+[["$defs".unitDimension.oneOf]]
+title = "Shorthand notation"
+type = "array"
+items.type = "number"
+
+[["$defs".unitDimension.oneOf]]
+title = "Long notation"
+type = "object"
+required = ["value", "datatype"]
+
+["$defs".unitDimension.oneOf.properties]
+
+value = { type = "array", items = { type = "number" } }
+datatype.const = "ARR_DBL_7"
+
+#####################
+# string attributes #
+#####################
+
+[["$defs".string_attribute.oneOf]]
+title = "Shorthand notation"
+type = "string"
+
+[["$defs".string_attribute.oneOf]]
+title = "Long notation"
+type = "object"
+required = ["value", "datatype"]
+
+["$defs".string_attribute.oneOf.properties]
+
+value.type = "string"
+datatype.enum = ["STRING", "CHAR", "SCHAR", "UCHAR"]
+
+##################
+# int attributes #
+##################
+
+[["$defs".int_attribute.oneOf]]
+title = "Shorthand notation"
+type = "integer"
+
+[["$defs".int_attribute.oneOf]]
+title = "Long notation"
+type = "object"
+required = ["value", "datatype"]
+
+["$defs".int_attribute.oneOf.properties]
+
+value.type = "integer"
+datatype.enum = [
+    "SHORT",
+    "INT",
+    "LONG",
+    "LONGLONG",
+    "USHORT",
+    "UINT",
+    "ULONG",
+    "ULONGLONG",
+]
+
+####################
+# float attributes #
+####################
+
+[["$defs".float_attribute.oneOf]]
+title = "Shorthand notation"
+type = "number"
+
+[["$defs".float_attribute.oneOf]]
+title = "Long notation"
+type = "object"
+required = ["value", "datatype"]
+
+["$defs".float_attribute.oneOf.properties]
+
+value.type = "number"
+datatype.enum = [
+    "CHAR",
+    "UCHAR",
+    "SCHAR",
+    "SHORT",
+    "INT",
+    "LONG",
+    "LONGLONG",
+    "USHORT",
+    "UINT",
+    "ULONG",
+    "ULONGLONG",
+    "FLOAT",
+    "DOUBLE",
+    "LONG_DOUBLE",
+    "CFLOAT",
+    "CDOUBLE",
+    "CLONG_DOUBLE",
+]