Add testing files

pynxtools_mpes/reader.py

@@ -179,7 +179,7 @@ def iterate_dictionary(dic, key_string):
     "source_TYPE[source]/Pump": "source_TYPE[source_pump]",
     "beam_TYPE[beam]/Probe": "beam_TYPE[beam_probe]",
     "beam_TYPE[beam]/Pump": "beam_TYPE[beam_pump]",
-    "sample_history": "sample_history/notes/description",
+    "sample_history": "sample_history/notes",
     "ELECTRONANALYSER[electronanalyser]/RESOLUTION[momentum_resolution]": (
         "ELECTRONANALYSER[electronanalyser]/momentum_resolution"
     ),

tests/data/config_file.json

@@ -37,7 +37,7 @@
       "type": "estimated"
     },
     "RESOLUTION[momentum_resolution]": {
-      "resolution": "@attrs:metadata/instrument/analyzer/momentum_resolution",
+      "resolution": "@link:/entry/instrument/electronanalyser/momentum_resolution",
       "resolution/@units": "1/angstrom",
       "physical_quantity": "momentum",
       "type": "estimated"
@@ -167,7 +167,7 @@
     "mode": "Single Bunch",
     "frequency": "@attrs:metadata/instrument/beam/probe/frequency",
     "frequency/@units": "kHz",
-    "associated_beam": "@link:/entry/instrument/beam_probe"
+    "associated_beam": "/entry/instrument/beam_probe"
   },
   "/ENTRY[entry]/INSTRUMENT[instrument]/beam_TYPE[beam_probe]": {
     "distance": 0.0,
@@ -182,7 +182,7 @@
     "incident_polarization/@units": "V^2/mm^2",
     "extent": "@attrs:metadata/instrument/beam/probe/extent",
     "extent/@units": "µm",
-    "associated_source": "@link:/entry/instrument/source_probe"
+    "associated_source": "/entry/instrument/source_probe"
   },
   "/ENTRY[entry]/INSTRUMENT[instrument]/source_TYPE[source_pump]": {
     "name": "OPCPA @ TR-ARPES @ FHI",
@@ -191,7 +191,7 @@
     "mode": "Single Bunch",
     "frequency": "@attrs:metadata/instrument/beam/pump/frequency",
     "frequency/@units": "kHz",
-    "associated_beam": "@link:/entry/instrument/beam_pump"
+    "associated_beam": "/entry/instrument/beam_pump"
   },
   "/ENTRY[entry]/INSTRUMENT[instrument]/beam_TYPE[beam_pump]": {
     "distance": 0.0,
@@ -214,7 +214,7 @@
     "extent/@units": "µm",
     "fluence": "@attrs:metadata/instrument/beam/pump/fluence",
     "fluence/@units": "mJ/cm^2",
-    "associated_source": "@link:/entry/instrument/source_pump"
+    "associated_source": "/entry/instrument/source_pump"
   },
   "/ENTRY[entry]/INSTRUMENT[instrument]/MANIPULATOR[manipulator]": {
     "temperature_sensor": {
@@ -262,8 +262,7 @@
   },
   "/ENTRY[entry]/SAMPLE[sample]": {
     "preparation_date": "@attrs:metadata/sample/preparation_date",
-    "sample_history/notes/type": "text/plain",
-    "sample_history/notes/description": "@attrs:metadata/sample/sample_history",
+    "sample_history/notes": "@attrs:metadata/sample/sample_history",
     "description": "@attrs:metadata/sample/chemical_formula",
     "name": "@attrs:metadata/sample/chemical_formula",
     "situation": "vacuum",

tests/data/eln_data.yaml

@@ -27,14 +27,14 @@ Instrument:
   Source:
     Probe:
       frequency:
-        unit: kHz
+        unit: KHz
         value: 500.0
       photon_energy:
         unit: eV
         value: 21.7
     Pump:
       frequency:
-        unit: kHz
+        unit: KHz
         value: 500.0
       photon_energy:
         unit: eV

tests/test_reader.py

@@ -1,15 +1,19 @@
 """
 Basic example based test for the stm reader
 """
+import logging
 import os
 import xml.etree.ElementTree as ET
-from glob import glob
+from pathlib import Path
 
+import pynxtools.dataconverter.convert as dataconverter
+from pynxtools.dataconverter.convert import get_reader
 from pynxtools.dataconverter.helpers import (
     generate_template_from_nxdl,
     validate_data_dict,
 )
 from pynxtools.dataconverter.template import Template
+from pynxtools.nexus import nexus  # noqa: E402 # noqa: E402
 from pynxtools.nexus.nxdl_utils import get_nexus_definitions_path
 
 from pynxtools_mpes.reader import MPESReader
@@ -24,8 +28,11 @@ def test_example_data():
 
     def_dir = get_nexus_definitions_path()
 
-    data_dir = os.path.join(os.path.dirname(__file__), "data")
-    input_files = sorted(glob(os.path.join(data_dir, "*")))
+    data_dir = Path(__file__).parent / "data"
+    input_files = (
+        str(data_dir / "config_file.json"),
+        str(data_dir / "xarray_saved_small_calibration.h5"),
+    )
 
     for supported_nxdl in reader.supported_nxdls:
         nxdl_file = os.path.join(
@@ -36,9 +43,84 @@ def test_example_data():
         template = Template()
         generate_template_from_nxdl(root, template)
 
-        read_data = reader().read(
-            template=Template(template), file_paths=tuple(input_files)
-        )
+        read_data = reader().read(template=Template(template), file_paths=input_files)
 
         assert isinstance(read_data, Template)
         assert validate_data_dict(template, read_data, root)
+
+
+def test_mpes_writing(tmp_path):
+    """Check if mpes example can be reproduced"""
+    # dataconverter
+    dir_path = Path(__file__).parent / "data"
+    dataconverter.convert(
+        (
+            str(dir_path / "xarray_saved_small_calibration.h5"),
+            str(dir_path / "config_file.json"),
+        ),
+        "mpes",
+        "NXmpes",
+        os.path.join(tmp_path, "mpes.small_test.nxs"),
+        False,
+        False,
+    )
+    # check generated nexus file
+    test_data = os.path.join(tmp_path, "mpes.small_test.nxs")
+    logger = logging.getLogger(__name__)
+    logger.setLevel(logging.DEBUG)
+    handler = logging.FileHandler(os.path.join(tmp_path, "mpes_test.log"), "w")
+    formatter = logging.Formatter("%(levelname)s - %(message)s")
+    handler.setLevel(logging.DEBUG)
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
+    nexus_helper = nexus.HandleNexus(logger, test_data, None, None)
+    nexus_helper.process_nexus_master_file(None)
+    with open(
+        os.path.join(tmp_path, "mpes_test.log"), "r", encoding="utf-8"
+    ) as logfile:
+        log = logfile.readlines()
+    with open(dir_path / "Ref_nexus_mpes.log", "r", encoding="utf-8") as logfile:
+        ref_log = logfile.readlines()
+    assert log == ref_log
+
+
+def test_shows_correct_warnings():
+    """
+    Checks whether the read function generates the correct warnings.
+    """
+    def_dir = get_nexus_definitions_path()
+
+    data_dir = Path(__file__).parent / "data"
+    input_files = (
+        str(data_dir / "config_file.json"),
+        str(data_dir / "xarray_saved_small_calibration.h5"),
+    )
+    nxdl_file = os.path.join(def_dir, "contributed_definitions", "NXmpes.nxdl.xml")
+
+    root = ET.parse(nxdl_file).getroot()
+    template = Template()
+    generate_template_from_nxdl(root, template)
+
+    read_data = get_reader("mpes")().read(
+        template=Template(template), file_paths=tuple(input_files)
+    )
+
+    assert validate_data_dict(template, read_data, root)
+    assert not list(read_data.undocumented.keys())
+
+
+def test_eln_data(tmp_path):
+    """Check if the subsections in the eln_data.yml file work."""
+    dir_path = Path(__file__).parent / "data"
+    dataconverter.convert(
+        (
+            str(dir_path / "xarray_saved_small_calibration.h5"),
+            str(dir_path / "config_file.json"),
+            str(dir_path / "eln_data.yaml"),
+        ),
+        "mpes",
+        "NXmpes",
+        os.path.join(tmp_path, "mpes.small_test.nxs"),
+        False,
+        False,
+    )