Add tests for new eln data formalism

FAIRmat-NFDI · Aug 12, 2024 · c92d0c1 · c92d0c1
1 parent 1ab0d64
commit c92d0c1
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Showing 5 changed files with 24 additions and 15 deletions.
diff --git a/scripts/regenerate_examples.sh b/scripts/regenerate_examples.sh
@@ -7,7 +7,13 @@ function update_mpes_example {
   dataconverter xarray_saved_small_calibration.h5 config_file.json --reader $READER --nxdl $NXDL --output example.nxs
 }
 
+function update_mpes_eln_example {
+  echo "Update mpes example with eln file"
+  dataconverter xarray_saved_small_calibration.h5 config_file.json eln_data.yaml --reader $READER --nxdl $NXDL --output example_eln.nxs
+}
+
 project_dir=$(dirname $(dirname $(realpath $0)))
 cd $project_dir/tests/data
 
-update_mpes_example
+update_mpes_example
+update_mpes_eln_example
diff --git a/tests/data/config_file.json b/tests/data/config_file.json
@@ -2,7 +2,7 @@
   "/@default": "entry",
   "/ENTRY/@default": "data",
   "/ENTRY/definition": "NXmpes",
-  "/ENTRY/title": "@attrs:metadata/entry_title",
+  "/ENTRY/title": "['@eln:/ENTRY/title', '@attrs:metadata/entry_title']",
   "/ENTRY/start_time": "@attrs:metadata/timing/acquisition_start",
   "/ENTRY/experiment_institution": "Fritz Haber Institute - Max Planck Society",
   "/ENTRY/experiment_facility": "Time Resolved ARPES",

diff --git a/tests/data/eln_data.yaml b/tests/data/eln_data.yaml
@@ -1,4 +1,4 @@
-title: Valence Band Dynamics - 1030 nm linear p-polarized pump, 0.6 mJ/cm2 absorbed fluence
+title: Title from ELN file
 Instrument:
   energy_resolution:
     unit: meV

diff --git a/tests/data/example_eln.nxs b/tests/data/example_eln.nxs
diff --git a/tests/test_reader.py b/tests/test_reader.py
@@ -2,10 +2,8 @@
 Basic example based test for the stm reader
 """
 
-import os
 from pathlib import Path
 
-import pynxtools.dataconverter.convert as dataconverter
 from pynxtools.testing.nexus_conversion import ReaderTest
 
 
@@ -30,18 +28,23 @@ def test_nexus_conversion(caplog, tmp_path):
     test.check_reproducibility_of_nexus()
 
 
-def test_eln_data(tmp_path):
-    """Check if the subsections in the eln_data.yml file work."""
+def test_conversion_w_eln_data(caplog, tmp_path):
+    """
+    Tests the conversion with additional ELN data
+    """
+    caplog.clear()
     dir_path = Path(__file__).parent / "data"
-    dataconverter.convert(
-        input_file=(
+    test = ReaderTest(
+        nxdl="NXmpes",
+        reader_name="mpes",
+        files_or_dir=[
             str(dir_path / "xarray_saved_small_calibration.h5"),
             str(dir_path / "config_file.json"),
             str(dir_path / "eln_data.yaml"),
-        ),
-        reader="mpes",
-        nxdl="NXmpes",
-        output=os.path.join(tmp_path, "mpes.small_test.nxs"),
-        skip_verify=False,
-        ignore_undocumented=False,
+            str(dir_path / "example_eln.nxs"),
+        ],
+        tmp_path=tmp_path,
+        caplog=caplog,
     )
+    test.convert_to_nexus(caplog_level="WARNING", ignore_undocumented=False)
+    test.check_reproducibility_of_nexus()