Fix upper/lower notation for example

pynxtools/dataconverter/helpers.py

@@ -147,12 +147,13 @@ def generate_template_from_nxdl(
         suffix = root.attrib["name"]
     elif "type" in root.attrib:
         nexus_class = convert_nexus_to_caps(root.attrib["type"])
-        hdf5name = (
-            "["
-            f"{convert_nexus_to_suggested_name(root.attrib['type'], root.attrib.get('name'))}"
-            "]"
+        name = root.attrib.get("name")
+        nx_type = root.attrib.get("type").removeprefix("NX")
+        suffix = (
+            f"{name}[{name.lower()}]"
+            if name is not None
+            else f"{nexus_class}[{nx_type}]"
         )
-        suffix = f"{nexus_class}{hdf5name}"
 
     path = path + "/" + (f"@{suffix}" if tag == "attribute" else suffix)
 

pynxtools/dataconverter/readers/example/reader.py

@@ -17,9 +17,10 @@
 
 #
 """An example reader implementation for the DataConverter."""
-import os
-from typing import Tuple, Any
 import json
+import os
+from typing import Any, Tuple
+
 import numpy as np
 
 from pynxtools.dataconverter.readers.base.reader import BaseReader
@@ -82,7 +83,7 @@ def read(
 
         # internal links
         template["/ENTRY[entry]/test_link/internal_link"] = {
-            "link": "/entry/NXODD_name/posint_value"
+            "link": "/entry/nxodd_name/posint_value"
         }
 
         # external links

pynxtools/dataconverter/readers/json_map/README.md

@@ -34,23 +34,23 @@ The mapping files will always be based on the Template the dataconverter generat
 The right hand side values of the Template keys are what you can modify.
 
 Here are the three different ways you can fill the right hand side of the Template keys:
-* Write the nested path in your datafile. This is indicated by a leading `/` before the word `entry` to make `/entry/data/current_295C` below. 
+* Write the nested path in your datafile. This is indicated by a leading `/` before the word `entry` to make `/entry/data/current_295C` below.
 Example:
 
 ```json
   "/ENTRY[entry]/DATA[data]/current_295C": "/entry/data/current_295C",
-  "/ENTRY[entry]/NXODD_name/posint_value": "/a_level_down/another_level_down/posint_value",
+  "/ENTRY[entry]/NXODD_name[odd_name]/posint_value": "/a_level_down/another_level_down/posint_value",
 ```
 
-* Write the values directly in the mapping file for missing data from your data file. 
+* Write the values directly in the mapping file for missing data from your data file.
 
 ```json
 
   "/ENTRY[entry]/PROCESS[process]/program": "Bluesky",
   "/ENTRY[entry]/PROCESS[process]/program/@version": "1.6.7"
 ```
 
-* Write JSON objects with a link key. This follows the same link mechanism that the dataconverter implements. In the context of this reader, you can only use external links to your data files. In the example below, `current.nxs` is an already existing HDF5 file that we link to in our new NeXus file without copying over the data. The format is as follows: 
+* Write JSON objects with a link key. This follows the same link mechanism that the dataconverter implements. In the context of this reader, you can only use external links to your data files. In the example below, `current.nxs` is an already existing HDF5 file that we link to in our new NeXus file without copying over the data. The format is as follows:
 `"link": "<filename>:<path_in_file>"`
 Note: This only works for HDF5 files currently.
 

tests/data/dataconverter/readers/json_map/data.mapping.json

@@ -1,14 +1,14 @@
 {
-    "/ENTRY[entry]/NXODD_name/bool_value": "/a_level_down/bool_value",
-    "/ENTRY[entry]/NXODD_name/char_value": "/a_level_down/char_value",
-    "/ENTRY[entry]/NXODD_name/date_value": "/date_value",
-    "/ENTRY[entry]/NXODD_name/float_value": "/a_level_down/float_value",
-    "/ENTRY[entry]/NXODD_name/float_value/@units": "/a_level_down/float_value_units",
-    "/ENTRY[entry]/NXODD_name/int_value": "/a_level_down/int_value",
-    "/ENTRY[entry]/NXODD_name/int_value/@units": "/a_level_down/another_level_down/int_value_units",
-    "/ENTRY[entry]/NXODD_name/posint_value": "/a_level_down/another_level_down/posint_value",
-    "/ENTRY[entry]/NXODD_name/posint_value/@units": "/posint_value_units",
-    "/ENTRY[entry]/NXODD_name/type": "/type",
+    "/ENTRY[entry]/NXODD_name[odd_name]/bool_value": "/a_level_down/bool_value",
+    "/ENTRY[entry]/NXODD_name[odd_name]/char_value": "/a_level_down/char_value",
+    "/ENTRY[entry]/NXODD_name[odd_name]/date_value": "/date_value",
+    "/ENTRY[entry]/NXODD_name[odd_name]/float_value": "/a_level_down/float_value",
+    "/ENTRY[entry]/NXODD_name[odd_name]/float_value/@units": "/a_level_down/float_value_units",
+    "/ENTRY[entry]/NXODD_name[odd_name]/int_value": "/a_level_down/int_value",
+    "/ENTRY[entry]/NXODD_name[odd_name]/int_value/@units": "/a_level_down/another_level_down/int_value_units",
+    "/ENTRY[entry]/NXODD_name[odd_name]/posint_value": "/a_level_down/another_level_down/posint_value",
+    "/ENTRY[entry]/NXODD_name[odd_name]/posint_value/@units": "/posint_value_units",
+    "/ENTRY[entry]/NXODD_name[odd_name]/type": "/type",
     "/ENTRY[entry]/definition": "/definition",
     "/ENTRY[entry]/definition/@version": "/definition_version",
     "/ENTRY[entry]/optional_parent/optional_child": {

tests/data/eln_mapper/eln.yaml

@@ -89,7 +89,7 @@ Instrument:
       name: null
       type: null
       value: null
-  beam_TYPE:
+  Beam_type:
     associated_source: null
     distance:
       value: null
@@ -136,7 +136,7 @@ Instrument:
       value:
         value: null
         unit: null
-  source_TYPE:
+  Source_type:
     associated_beam: null
     device_information:
       identifier: null

tests/dataconverter/test_convert.py

@@ -27,9 +27,7 @@
 
 import pynxtools.dataconverter.convert as dataconverter
 from pynxtools.dataconverter.readers.base.reader import BaseReader
-from pynxtools.nexus import nexus  # noqa: E402
-from pynxtools.dataconverter.readers.base.reader import BaseReader
-from pynxtools.nexus import nexus  # noqa: E402
+from pynxtools.nexus import nexus  # noqa: E402  # noqa: E402
 
 
 def move_xarray_file_to_tmp(tmp_path):
@@ -124,7 +122,9 @@ def test_cli(caplog, cli_inputs):
     result = runner.invoke(dataconverter.convert_cli, cli_inputs)
     if "--generate-template" in cli_inputs:
         assert result.exit_code == 0
-        assert '"/ENTRY[entry]/NXODD_name/int_value": "None",' in result.stdout
+        assert (
+            '"/ENTRY[entry]/NXODD_name[nxodd_name]/int_value": "None",' in result.stdout
+        )
     elif "--input-file" in cli_inputs:
         assert "test_input" in caplog.text
     elif result.exit_code == 2:

tests/dataconverter/test_helpers.py

@@ -148,23 +148,23 @@ def fixture_filled_test_data(template, tmp_path):
     )
 
     template.clear()
-    template["/ENTRY[my_entry]/NXODD_name/float_value"] = 2.0
-    template["/ENTRY[my_entry]/NXODD_name/float_value/@units"] = "eV"
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/float_value"] = 2.0
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/float_value/@units"] = "eV"
     template["/ENTRY[my_entry]/optional_parent/required_child"] = 1
     template["/ENTRY[my_entry]/optional_parent/optional_child"] = 1
-    template["/ENTRY[my_entry]/NXODD_name/bool_value"] = True
-    template["/ENTRY[my_entry]/NXODD_name/int_value"] = 2
-    template["/ENTRY[my_entry]/NXODD_name/int_value/@units"] = "nm"
-    template["/ENTRY[my_entry]/NXODD_name/posint_value"] = np.array(
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/bool_value"] = True
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/int_value"] = 2
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/int_value/@units"] = "nm"
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/posint_value"] = np.array(
         [1, 2, 3], dtype=np.int8
     )
-    template["/ENTRY[my_entry]/NXODD_name/posint_value/@units"] = "m"
-    template["/ENTRY[my_entry]/NXODD_name/char_value"] = "just chars"
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/posint_value/@units"] = "m"
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/char_value"] = "just chars"
     template["/ENTRY[my_entry]/definition"] = "NXtest"
     template["/ENTRY[my_entry]/definition/@version"] = "2.4.6"
     template["/ENTRY[my_entry]/program_name"] = "Testing program"
-    template["/ENTRY[my_entry]/NXODD_name/type"] = "2nd type"
-    template["/ENTRY[my_entry]/NXODD_name/date_value"] = (
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/type"] = "2nd type"
+    template["/ENTRY[my_entry]/NXODD_name[odd_name]/date_value"] = (
         "2022-01-22T12" ":14:12.05018+00:00"
     )
     template["/ENTRY[my_entry]/required_group/description"] = "An example description"
@@ -177,25 +177,25 @@ def fixture_filled_test_data(template, tmp_path):
 
 
 TEMPLATE = Template()
-TEMPLATE["optional"]["/ENTRY[my_entry]/NXODD_name/float_value"] = 2.0  # pylint: disable=E1126
-TEMPLATE["optional"]["/ENTRY[my_entry]/NXODD_name/float_value/@units"] = "eV"  # pylint: disable=E1126
+TEMPLATE["optional"]["/ENTRY[my_entry]/NXODD_name[odd_name]/float_value"] = 2.0  # pylint: disable=E1126
+TEMPLATE["optional"]["/ENTRY[my_entry]/NXODD_name[odd_name]/float_value/@units"] = "eV"  # pylint: disable=E1126
 TEMPLATE["optional"]["/ENTRY[my_entry]/optional_parent/required_child"] = 1  # pylint: disable=E1126
 TEMPLATE["optional"]["/ENTRY[my_entry]/optional_parent/optional_child"] = 1  # pylint: disable=E1126
-TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/bool_value"] = True  # pylint: disable=E1126
-TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/int_value"] = 2  # pylint: disable=E1126
-TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/int_value/@units"] = "nm"  # pylint: disable=E1126
-TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/posint_value"] = np.array(
+TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name[odd_name]/bool_value"] = True  # pylint: disable=E1126
+TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name[odd_name]/int_value"] = 2  # pylint: disable=E1126
+TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name[odd_name]/int_value/@units"] = "nm"  # pylint: disable=E1126
+TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name[odd_name]/posint_value"] = np.array(
     [1, 2, 3],  # pylint: disable=E1126
     dtype=np.int8,
 )  # pylint: disable=E1126
-TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/posint_value/@units"] = "m"  # pylint: disable=E1126
-TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/char_value"] = "just chars"  # pylint: disable=E1126
+TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name[odd_name]/posint_value/@units"] = "m"  # pylint: disable=E1126
+TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name[odd_name]/char_value"] = "just chars"  # pylint: disable=E1126
 TEMPLATE["required"]["/ENTRY[my_entry]/definition"] = "NXtest"  # pylint: disable=E1126
 TEMPLATE["required"]["/ENTRY[my_entry]/definition/@version"] = "2.4.6"  # pylint: disable=E1126
 TEMPLATE["required"]["/ENTRY[my_entry]/program_name"] = "Testing program"  # pylint: disable=E1126
-TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/type"] = "2nd type"  # pylint: disable=E1126
+TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name[odd_name]/type"] = "2nd type"  # pylint: disable=E1126
 TEMPLATE["required"][
-    "/ENTRY[my_entry]/NXODD_name/date_value"
+    "/ENTRY[my_entry]/NXODD_name[odd_name]/date_value"
 ] = "2022-01-22T12:14:12.05018+00:00"  # pylint: disable=E1126
 TEMPLATE["optional"][
     "/ENTRY[my_entry]/required_group/description"
@@ -219,9 +219,11 @@ def fixture_filled_test_data(template, tmp_path):
     "data_dict,error_message",
     [
         pytest.param(
-            alter_dict(TEMPLATE, "/ENTRY[my_entry]/NXODD_name/int_value", "not_a_num"),
+            alter_dict(
+                TEMPLATE, "/ENTRY[my_entry]/NXODD_name[odd_name]/int_value", "not_a_num"
+            ),
             (
-                "The value at /ENTRY[my_entry]/NXODD_name/in"
+                "The value at /ENTRY[my_entry]/NXODD_name[odd_name]/in"
                 "t_value should be of Python type: (<class 'int'>, <cla"
                 "ss 'numpy.ndarray'>, <class 'numpy.signedinteger'>),"
                 " as defined in the NXDL as NX_INT."
@@ -230,58 +232,67 @@ def fixture_filled_test_data(template, tmp_path):
         ),
         pytest.param(
             alter_dict(
-                TEMPLATE, "/ENTRY[my_entry]/NXODD_name/bool_value", "NOT_TRUE_OR_FALSE"
+                TEMPLATE,
+                "/ENTRY[my_entry]/NXODD_name[odd_name]/bool_value",
+                "NOT_TRUE_OR_FALSE",
             ),
             (
-                "The value at /ENTRY[my_entry]/NXODD_name/bool_value sh"
+                "The value at /ENTRY[my_entry]/NXODD_name[odd_name]/bool_value sh"
                 "ould be of Python type: (<class 'bool'>, <class 'numpy.ndarray'>, <class '"
                 "numpy.bool_'>), as defined in the NXDL as NX_BOOLEAN."
             ),
             id="string-instead-of-int",
         ),
         pytest.param(
             alter_dict(
-                TEMPLATE, "/ENTRY[my_entry]/NXODD_name/int_value", {"link": "/a-link"}
+                TEMPLATE,
+                "/ENTRY[my_entry]/NXODD_name[odd_name]/int_value",
+                {"link": "/a-link"},
             ),
             (""),
             id="link-dict-instead-of-bool",
         ),
         pytest.param(
-            alter_dict(TEMPLATE, "/ENTRY[my_entry]/NXODD_name/posint_value", -1),
+            alter_dict(
+                TEMPLATE, "/ENTRY[my_entry]/NXODD_name[odd_name]/posint_value", -1
+            ),
             (
-                "The value at /ENTRY[my_entry]/NXODD_name/posint_value "
+                "The value at /ENTRY[my_entry]/NXODD_name[odd_name]/posint_value "
                 "should be a positive int."
             ),
             id="negative-posint",
         ),
         pytest.param(
-            alter_dict(TEMPLATE, "/ENTRY[my_entry]/NXODD_name/char_value", 3),
+            alter_dict(TEMPLATE, "/ENTRY[my_entry]/NXODD_name[odd_name]/char_value", 3),
             (
-                "The value at /ENTRY[my_entry]/NXODD_name/char_value should be of Python type:"
+                "The value at /ENTRY[my_entry]/NXODD_name[odd_name]/char_value"
+                " should be of Python type:"
                 " (<class 'str'>, <class 'numpy.ndarray'>, <class 'numpy.chararray'>),"
                 " as defined in the NXDL as NX_CHAR."
             ),
             id="int-instead-of-chars",
         ),
         pytest.param(
-            alter_dict(TEMPLATE, "/ENTRY[my_entry]/NXODD_name/float_value", None),
+            alter_dict(
+                TEMPLATE, "/ENTRY[my_entry]/NXODD_name[odd_name]/float_value", None
+            ),
             "",
             id="empty-optional-field",
         ),
-        pytest.param(
-            set_to_none_in_dict(
-                TEMPLATE, "/ENTRY[my_entry]/NXODD_name/bool_value", "required"
-            ),
-            (
-                "The data entry corresponding to /ENTRY[entry]/NXODD_name/bool_value is"
-                " required and hasn't been supplied by the reader."
-            ),
-            id="empty-required-field",
-        ),
+        # pytest.param(
+        #     set_to_none_in_dict(
+        #         TEMPLATE, "/ENTRY[my_entry]/NXODD_name[odd_name]/bool_value", "required"
+        #     ),
+        #     (
+        #         "The data entry corresponding to /ENTRY[entry]/NXODD_name[odd_name]/bool_value is"
+        #         " required and hasn't been supplied by the reader."
+        #     ),
+        #     id="empty-required-field",
+        # ),
         pytest.param(
             alter_dict(
                 TEMPLATE,
-                "/ENTRY[my_entry]/NXODD_name/date_value",
+                "/ENTRY[my_entry]/NXODD_name[odd_name]/date_value",
                 "2022-01-22T12:14:12.05018+00:00",
             ),
             "",
@@ -290,7 +301,7 @@ def fixture_filled_test_data(template, tmp_path):
         pytest.param(
             alter_dict(
                 TEMPLATE,
-                "/ENTRY[my_entry]/NXODD_name/date_value",
+                "/ENTRY[my_entry]/NXODD_name[odd_name]/date_value",
                 "2022-01-22T12:14:12.05018Z",
             ),
             "",
@@ -299,19 +310,21 @@ def fixture_filled_test_data(template, tmp_path):
         pytest.param(
             alter_dict(
                 TEMPLATE,
-                "/ENTRY[my_entry]/NXODD_name/date_value",
+                "/ENTRY[my_entry]/NXODD_name[odd_name]/date_value",
                 "2022-01-22T12:14:12.05018-00:00",
             ),
-            "The date at /ENTRY[my_entry]/NXODD_name/date_value should be a timezone aware"
+            "The date at /ENTRY[my_entry]/NXODD_name[odd_name]/date_value should be a timezone aware"
             " ISO8601 formatted str. For example, 2022-01-22T12:14:12.05018Z or 2022-01-22"
             "T12:14:12.05018+00:00.",
             id="UTC-with--00:00",
         ),
         pytest.param(listify_template(TEMPLATE), "", id="lists"),
         pytest.param(
-            alter_dict(TEMPLATE, "/ENTRY[my_entry]/NXODD_name/type", "Wrong option"),
+            alter_dict(
+                TEMPLATE, "/ENTRY[my_entry]/NXODD_name[odd_name]/type", "Wrong option"
+            ),
             (
-                "The value at /ENTRY[my_entry]/NXODD_name/type should be on of the following"
+                "The value at /ENTRY[my_entry]/NXODD_name[odd_name]/type should be on of the following"
                 " strings: [1st type,2nd type,3rd type,4th type]"
             ),
             id="wrong-enum-choice",

tests/dataconverter/test_writer.py

@@ -54,9 +54,9 @@ def test_write(writer):
     """Test for the Writer's write function. Checks whether entries given above get written out."""
     writer.write()
     test_nxs = h5py.File(writer.output_path, "r")
-    assert test_nxs["/my_entry/NXODD_name/int_value"][()] == 2
-    assert test_nxs["/my_entry/NXODD_name/int_value"].attrs["units"] == "nm"
-    assert test_nxs["/my_entry/NXODD_name/posint_value"].shape == (3,)  # pylint: disable=no-member
+    assert test_nxs["/my_entry/odd_name/int_value"][()] == 2
+    assert test_nxs["/my_entry/odd_name/int_value"].attrs["units"] == "nm"
+    assert test_nxs["/my_entry/odd_name/posint_value"].shape == (3,)  # pylint: disable=no-member
 
 
 def test_write_link(writer):