Adding fixing ci.

pynxtools/dataconverter/helpers.py

@@ -684,9 +684,9 @@ def transform_to_intended_dt(str_value: Any) -> Optional[Any]:
         except ValueError:
             pass
 
-    if isinstance(str_value, np.ndarray):
+    elif isinstance(str_value, np.ndarray):
         return str_value
-    if isinstance(str_value, str):
+    elif isinstance(str_value, str):
         try:
             transformed = int(str_value)
         except ValueError:
@@ -695,7 +695,7 @@ def transform_to_intended_dt(str_value: Any) -> Optional[Any]:
             except ValueError:
                 if '[' in str_value and ']' in str_value:
                     transformed = json.loads(str_value)
-        if transformed:
+        if transformed is not None:
             return transformed
         for sym in symbol_list_for_data_seperation:
             if sym in str_value:

pynxtools/dataconverter/readers/sts/reader.py

@@ -168,8 +168,7 @@ def get_appropriate_parser(self, eln_dict: Dict) -> Callable:
 
 # pylint: disable=invalid-name, too-few-public-methods
 class STMReader(BaseReader):
-    """ Reader for XPS.
-    """
+    """Reader for STM/STS."""
 
     supported_nxdls = ["NXsts"]
 

pynxtools/dataconverter/readers/xrd/reader.py

@@ -30,13 +30,22 @@
 from pynxtools.dataconverter.readers.utils import flatten_and_replace, FlattenSettings
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 
-CONVERT_DICT: Dict[str, str] = {}
+CONVERT_DICT: Dict[str, str] = {
+    'unit': '@units',
+    'Instrument': 'INSTRUMENT[instrument]',
+    'Source': 'SOURCE[source]',
+    'Detector': 'DETECTOR[detector]',
+    'Collection': 'COLLECTION[collection]',
+    'Sample': 'SAMPLE[sample]',
+    'version': '@version',
+    'User': 'USER[user]',
+}
 
 
 # Global var to collect the root from get_template_from_nxdl_name()
 # and use it in the the the varidate_data_dict()
 ROOT: ET.Element = None
-REPLACE_NESTED: Dict[str, str] = {}
+REPLACE_NESTED: Dict[str, Any] = {}
 XRD_FILE_EXTENSIONS = [".xrdml", "xrdml", ".udf", ".raw", ".xye"]
 
 

pynxtools/dataconverter/readers/xrd/xrd_helper.py

@@ -100,9 +100,6 @@ def fill_template_from_config_data(config_dict: dict, template: Template,
             if not isinstance(val, dict) and isinstance(val, str):
                 template[nx_key] = val
 
-    fill_template_from_config_data(config_dict, template,
-                                   xrd_dict, file_term)
-
     def two_theta_plot():
         two_theta_gr = "/ENTRY[entry]/2theta_plot"
         template[two_theta_gr + "/" + "@axes"] = ["two_theta"]
@@ -128,6 +125,8 @@ def q_plot():
             template[q_plot_gr + "/" + "@q_vec_indicies"] = 0
             template[q_plot_gr + "/" + "@axes"] = ["q_vec"]
 
+        template[q_plot_gr + "/" + "@signal"] = "intensity"
+
     def handle_special_fields():
         """Some fields need special treatment."""
 
@@ -155,6 +154,8 @@ def handle_special_fields():
         template[key] = count_time[0] if (isinstance(count_time, np.ndarray)
                                           and count_time.shape == (1,)) else count_time
 
+    fill_template_from_config_data(config_dict, template,
+                                   xrd_dict, file_term)
     two_theta_plot()
     q_plot()
     handle_special_fields()

pynxtools/dataconverter/writer.py

@@ -192,7 +192,8 @@ class Writer:
 
     def __init__(self, data: dict = None,
                  nxdl_path: str = None,
-                 output_path: str = None, write_in_memory: bool = False):
+                 output_path: str = None,
+                 write_in_memory: bool = False):
         """Constructs the necessary objects required by the Writer class."""
         self.data = data
         self.nxdl_path = nxdl_path
@@ -248,7 +249,7 @@ def ensure_and_get_parent_node(self, path: str, undocumented_paths) -> h5py.Grou
             return grp
         return self.output_nexus[parent_path_hdf5]
 
-    def _process_data_into_hdf5(self):
+    def _put_data_into_hdf5(self):
         """Store data in hdf5 in in-memory file or file."""
 
         hdf5_links_for_later = []
@@ -321,7 +322,7 @@ def write(self):
             if self.write_in_memory:
                 raise ValueError("To write in memory and get the file obhect please use  "
                                  "the method get_in_memory_obj()")
-            self._process_data_into_hdf5()
+            self._put_data_into_hdf5()
         finally:
             self.output_nexus.close()
 
@@ -332,7 +333,7 @@ def get_in_memory_obj(self):
         """
         try:
             if self.write_in_memory:
-                self._process_data_into_hdf5()
+                self._put_data_into_hdf5()
             else:
                 raise ValueError("The write_in_memory variable is False Writer"
                                  "class initialization.")