pylint and pytest.

Author: RubelMozumder

src/pynxtools_spm/nomad_uploader/uploader.py

@@ -23,9 +23,7 @@
 )
 
 # from pynxtools_spm.nomad_uploader.files_movers import copy_directory_structure
-from pynxtools_spm.nomad_uploader.helper import (
-    setup_logger,
-)
+
 from multiprocessing import Process, Lock, Queue
 
 
@@ -257,9 +255,10 @@ def run_uploader_with(
     #     )
 
     file_list = get_unprocessed_files(data_proc_settings.src_dir, data_proc_settings)
+    separator = "\n\t\t"
     upload_logger.info(
         f"Total '{len(file_list)}' files to process in in {data_proc_settings.src_dir}:\n"
-        f"{'\n\t\t'.join([str(file) for file in file_list])}"
+        f"{separator.join([str(file) for file in file_list])}"
     )
     # Prepare the input parameters for the SPM reader for each file
     _ = [
@@ -369,8 +368,9 @@ def queue_results(input_params, lock, results_q):
                     nomad_settings.url, nomad_settings.token, zip_to_upload
                 )
 
+                separator = "\n"
                 upload_logger.info(
-                    f"Upload request with Upload ID ({upload_id}) corresponding to files \n{'\n'.join(map(str, complete_param_obj.input_file))}."
+                    f"Upload request with Upload ID ({upload_id}) corresponding to files {separator}{separator.join(map(str, complete_param_obj.input_file))}."
                 )
                 # trigger_reprocess_upload(
                 #     nomad_settings.url, nomad_settings.token, upload_id

src/pynxtools_spm/nxformatters/base_formatter.py

@@ -377,7 +377,7 @@ def _resolve_link_in_config(self, val: str, path: str = "/"):
         """
 
         if val.startswith("@default_link:"):
-            val = val.split("@default_link:")[-1]
+            val = val.rsplit("@default_link:", maxsplit=1)[-1]
 
             classes = val.split("/")[1:]
             pattern = ""

src/pynxtools_spm/nxformatters/helpers.py

@@ -267,7 +267,7 @@ def get_actual_from_variadic_name(name: str) -> str:
     str
         The actual name.
     """
-    return name.split("[")[-1].split("]")[0]
+    return name.rsplit("[", maxsplit=1)[-1].split("]", maxsplit=1)[0]
 
 
 def flatten_nested_list(list_dt: Union[list, tuple, Any]):

tests/nomad_upload/data/src_dir_tree/stm/STM_nanonis_generic_4_5.sxm

@@ -1,15 +1,21 @@
 from pynxtools_spm.nomad_uploader.files_movers import copy_directory_structure
+from pynxtools_spm.nomad_uploader.helper import setup_logger
 from pynxtools_spm.nomad_uploader.reader_config_setup import (
     SPMConvertInputParameters,
     convert_spm_experiments,
 )
+from pynxtools_spm.nomad_uploader.helper import (
+    setup_logger,
+)
 import pytest
 from pathlib import Path
 import os
 import shutil
 
-nomad_upload_data_dir = Path(__file__).parent / "data"
-src_dir_tree = nomad_upload_data_dir / "src_dir_tree"
+data_dir = Path(__file__).parent / "data"
+
+
+# data_dir = data_dir / "data_dir"
 
 
 def test_directory_structure(tmp_path):
@@ -22,28 +28,44 @@ def run_action_on_files(file):
         copy_file_ls.append(file)
 
     copy_directory_structure(
-        src_dir_tree,
+        data_dir,
         dst_dir_tree,
         extension=".sxm",
         run_action_on_files=run_action_on_files,
     )
-    assert len(copy_file_ls) == 1, "File no properly copied over."
+    assert len(copy_file_ls) == 5, "File no properly copied over."
 
+    copy_file_ls = []
     copy_directory_structure(
-        src_dir_tree,
+        data_dir,
         dst_dir_tree,
         extension=".dat",
         run_action_on_files=run_action_on_files,
     )
-    assert len(copy_file_ls) == 2, "File no properly copied over."
+    assert len(copy_file_ls) == 3, "File no properly copied over."
 
 
 @pytest.fixture
 def spm_reader_input_params(tmp_path):
-    stm_file_name = "STM_nanonis_generic_4_5.sxm"
+    upload_logger, upload_handler = setup_logger(
+        name="uploader", log_file=tmp_path / "upload.log"
+    )
+    stm_file_name = "Au_mica_2023_Y_A_diPAMY_195.sxm"
     eln_file_name = "eln_data.yaml"
-    stm_raw = src_dir_tree / "stm" / stm_file_name
-    stm_eln = src_dir_tree / "stm" / eln_file_name
+    stm_raw = (
+        data_dir
+        / "nanonis"
+        / "stm"
+        / "version_gen_5_with_default_config"
+        / stm_file_name
+    )
+    stm_eln = (
+        data_dir
+        / "nanonis"
+        / "stm"
+        / "version_gen_5_with_default_config"
+        / eln_file_name
+    )
 
     stm_raw_tmp_path = tmp_path / stm_file_name
     stm_eln_tmp_path = tmp_path / eln_file_name
@@ -61,7 +83,7 @@ def spm_reader_input_params(tmp_path):
         create_zip=True,
         skip_verify=True,
     )
-    _ = convert_spm_experiments(input_params)
+    _ = convert_spm_experiments(input_params, upload_logger, upload_handler)
     return input_params