Map to basesections reorganized 2

.gitignore

@@ -202,6 +202,7 @@ cython_debug/
 !dev-requirements.txt
 !mkdocs-requirements.txt
 !src/pynxtools/nexus-version.txt
+!src/pynxtools/remote_definitions_url.txt
 build/
 nexusparser.egg-info/PKG-INFO
 .python-version

MANIFEST.in

@@ -9,5 +9,5 @@ recursive-include src/pynxtools/definitions/applications/ *.xml
 recursive-include src/pynxtools/definitions/contributed_definitions/ *.xml
 include src/pynxtools/definitions/*.xsd
 include src/pynxtools/nexus-version.txt
-include src/pynxtools/definitions/NXDL_VERSION
-
+include src/pynxtools/remote_definitions_url.txt
+include src/pynxtools/definitions/NXDL_VERSION

src/pynxtools/__init__.py

@@ -105,3 +105,10 @@ def get_nexus_version_hash() -> str:
         return MAIN_BRANCH_NAME
 
     return version.group(1)
+
+
+def get_definitions_url() -> str:
+    """Get the URL of the NeXus definitions that are submoduled in pynxtools."""
+    url_file = os.path.join(os.path.dirname(__file__), "remote_definitions_url.txt")
+    with open(url_file, encoding="utf-8") as file:
+        return file.read().strip()

src/pynxtools/_build_wrapper.py

@@ -56,21 +56,71 @@ def _write_version_to_metadata():
         file.write(version)
 
 
+def get_definitions_submodule_url():
+    """
+    The URL of the definitions submodule in pynxtools.
+    """
+    submodule_path = "src/pynxtools/definitions"
+
+    try:
+        # Define the command to run
+        url_line = run(
+            [
+                "git",
+                "config",
+                "--file",
+                ".git/config",
+                "--get-regexp",
+                f"^submodule\\.{submodule_path}\\.url",
+            ],
+            text=True,
+            capture_output=True,
+            check=True,
+        ).stdout.strip()
+
+        if url_line:
+            url = url_line.split(" ")[1]
+            return url
+        else:
+            return None
+
+    except (FileNotFoundError, CalledProcessError):
+        return None
+
+
+def _write_definitions_remote_url():
+    """Write the URL of the definitions remote to file."""
+    remote_repo_url = get_definitions_submodule_url()
+    if remote_repo_url is None or not remote_repo_url:
+        return
+
+    with open(
+        os.path.join(os.path.dirname(__file__), "remote_definitions_url.txt"),
+        "w+",
+        encoding="utf-8",
+    ) as file:
+        file.write(remote_repo_url)
+
+
 # pylint: disable=function-redefined
 def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
     """
     PEP 517 compliant build wheel hook.
-    This is a wrapper for setuptools and adds a nexus version file.
+    This is a wrapper for setuptools and adds a nexus version file and a
+    file with the remote of the definitions submodule.
     """
     _write_version_to_metadata()
+    _write_definitions_remote_url()
     return _orig.build_wheel(wheel_directory, config_settings, metadata_directory)
 
 
 # pylint: disable=function-redefined
 def build_sdist(sdist_directory, config_settings=None):
     """
     PEP 517 compliant build sdist hook.
-    This is a wrapper for setuptools and adds a nexus version file.
+    This is a wrapper for setuptools and adds a nexus version file and a
+    file with the remote of the definitions submodule.
     """
     _write_version_to_metadata()
+    _write_definitions_remote_url()
     return _orig.build_sdist(sdist_directory, config_settings)

src/pynxtools/nomad/parser.py

@@ -40,13 +40,34 @@
 import pynxtools.nomad.schema as nexus_schema
 from pynxtools.nexus.nexus import HandleNexus
 
+__REPLACEMENT_FOR_NX = "BS"
+__REPLACEMENT_LEN = len(__REPLACEMENT_FOR_NX)
+
+
+def _rename_nx_to_nomad(name: str) -> Optional[str]:
+    """
+    Rename the NXDL name to NOMAD.
+    For example: NXdata -> BSdata,
+    except NXobject -> NXobject
+    """
+    if name == "NXobject":
+        return name
+    if name is not None:
+        if name.startswith("NX"):
+            return name.replace("NX", __REPLACEMENT_FOR_NX)
+    return name
+
 
 def _to_group_name(nx_node: ET.Element):
     """
     Normalise the given group name
     """
     # assuming always upper() is incorrect, e.g. NXem_msr is a specific one not EM_MSR!
-    return nx_node.attrib.get("name", nx_node.attrib["type"][2:].upper())
+    grp_nm = nx_node.attrib.get(
+        "name", nx_node.attrib["type"][__REPLACEMENT_LEN:].upper()
+    )
+
+    return grp_nm
 
 
 # noinspection SpellCheckingInspection
@@ -203,7 +224,6 @@ def _populate_data(
                                 target_name=attr_name,
                                 exc_info=exc,
                             )
-
                         if parent_field_name in current.__dict__:
                             quantity = current.__dict__[parent_field_name]
                             if isinstance(quantity, dict):
@@ -328,7 +348,8 @@ def __nexus_populate(self, params: dict, attr=None):  # pylint: disable=W0613
 
         hdf_path: str = hdf_info["hdf_path"]
         hdf_node = hdf_info["hdf_node"]
-
+        if nx_def is not None:
+            nx_def = _rename_nx_to_nomad(nx_def)
         if nx_path is None:
             return