Use log files in testing

.github/workflows/plugin_test.yaml

@@ -34,7 +34,7 @@ jobs:
             branch: main
             tests_to_run: tests/.
           - plugin: pynxtools-xps
-            branch: main
+            branch: adapt-testing
             tests_to_run: tests/.
           # - plugin: pynxtools-apm
           #   branch: main

src/pynxtools/testing/nexus_conversion.py

@@ -5,6 +5,8 @@
 from glob import glob
 from typing import Literal
 
+# from click.testing import CliRunner
+
 try:
     from nomad.client import parse
 
@@ -39,7 +41,9 @@ def get_log_file(nxs_file, log_file, tmp_path):
 class ReaderTest:
     """Generic test for reader plugins."""
 
-    def __init__(self, nxdl, reader_name, files_or_dir, tmp_path, caplog) -> None:
+    def __init__(
+        self, nxdl, reader_name, files_or_dir, tmp_path, caplog, ref_log_file=None
+    ) -> None:
         """Initialize the test object.
 
         Parameters
@@ -51,22 +55,24 @@ def __init__(self, nxdl, reader_name, files_or_dir, tmp_path, caplog) -> None:
         files_or_dir : str
             List of input files or full path string to the example data directory that contains all the files
             required for running the data conversion through the reader.
-        ref_nexus_file : str
-            Full path string to the reference NeXus file generated from the same
-            set of input files.
         tmp_path : pathlib.PosixPath
             Pytest fixture variable, used to clean up the files generated during the test.
         caplog : _pytest.logging.LogCaptureFixture
             Pytest fixture variable, used to capture the log messages during the test.
+        ref_log_file : str
+            Full path string to the reference log file generated from the same
+            set of input files in files_or_dir. This can also be parsed automatically if files_or_dir
+            is the full path string to the example data directory and there is only one reference
+            log file.
         """
 
         self.nxdl = nxdl
         self.reader_name = reader_name
         self.reader = get_reader(self.reader_name)
         self.files_or_dir = files_or_dir
-        self.ref_nexus_file = ""
         self.tmp_path = tmp_path
         self.caplog = caplog
+        self.ref_log_file = ref_log_file
         self.created_nexus = f"{tmp_path}/{os.sep}/output.nxs"
 
     def convert_to_nexus(
@@ -86,11 +92,17 @@ def convert_to_nexus(
             example_files = self.files_or_dir
         else:
             example_files = sorted(glob(os.path.join(self.files_or_dir, "*")))
-        self.ref_nexus_file = [file for file in example_files if file.endswith(".nxs")][
-            0
+
+        if not self.ref_log_file:
+            self.ref_log_file = [
+                file for file in example_files if file.endswith(".log")
+            ][0]
+        assert self.ref_log_file, "Reference nexus .log file not found"
+
+        input_files = [
+            file for file in example_files if not file.endswith((".nxs", ".log"))
         ]
-        input_files = [file for file in example_files if not file.endswith(".nxs")]
-        assert self.ref_nexus_file, "Reference nexus (.nxs) file not found"
+
         assert (
             self.nxdl in self.reader.supported_nxdls
         ), f"Reader does not support {self.nxdl} NXDL."
@@ -117,27 +129,23 @@ def convert_to_nexus(
 
         Writer(read_data, nxdl_file, self.created_nexus).write()
 
-        if NOMAD_AVAILABLE:
-            kwargs = dict(
-                strict=True,
-                parser_name=None,
-                server_context=False,
-                username=None,
-                password=None,
-            )
-
-            parse(self.created_nexus, **kwargs)
+    # This shall be reactivated once verify_nexus works!
+    # # def test_verify_nexus(
+    #     self,
+    #     caplog_level: Literal["ERROR", "WARNING"] = "ERROR",
+    # ):
+    #     with self.caplog.at_level(caplog_level):
+    #         _ = CliRunner().invoke(verify, [str(self.created_nexus)])
 
     def check_reproducibility_of_nexus(self):
         """Reproducibility test for the generated nexus file."""
         IGNORE_LINES = [
             "DEBUG - value: v",
             "DEBUG - value: https://github.com/FAIRmat-NFDI/nexus_definitions/blob/",
         ]
-        ref_log = get_log_file(self.ref_nexus_file, "ref_nexus.log", self.tmp_path)
-        gen_log = get_log_file(self.created_nexus, "gen_nexus.log", self.tmp_path)
-        with open(gen_log, "r", encoding="utf-8") as gen, open(
-            ref_log, "r", encoding="utf-8"
+        gen_log_file = get_log_file(self.created_nexus, "gen_nexus.log", self.tmp_path)
+        with open(gen_log_file, "r", encoding="utf-8") as gen, open(
+            self.ref_log_file, "r", encoding="utf-8"
         ) as ref:
             gen_lines = gen.readlines()
             ref_lines = ref.readlines()
@@ -154,3 +162,16 @@ def check_reproducibility_of_nexus(self):
                         f"Log files are different at line {ind}"
                         f" generated: {gen_l} \n referenced : {ref_l}"
                     )
+
+    def test_parse_nomad(self):
+        """Check if the generated nexus file can be parse by NOMAD."""
+        if NOMAD_AVAILABLE:
+            kwargs = dict(
+                strict=True,
+                parser_name=None,
+                server_context=False,
+                username=None,
+                password=None,
+            )
+
+            parse(self.created_nexus, **kwargs)