hook nexus definition to SPM_domain_app_def (#396)

* rebase.

* Fix bug in find plotable plot.

* Update nexus definition submodule.

* New Nexus file has been generated because:
space difference in root doc from
'        A generic positioner such as a motor or piezo-electric transducer.  \n'
to
'         A generic positioner such as a motor or piezo-electric transducer.\n

in NXpositioner.

* deactivate spm and raman for the time being.

.github/workflows/plugin_test.yaml

@@ -32,12 +32,12 @@ jobs:
           - plugin: pynxtools-mpes
             branch: main
             tests_to_run: tests/.
-          - plugin: pynxtools-raman
-            branch: main
-            tests_to_run: tests/.
-          - plugin: pynxtools-stm
-            branch: main
-            tests_to_run: tests/.
+          # - plugin: pynxtools-raman
+          #   branch: main
+          #   tests_to_run: tests/.
+          # - plugin: pynxtools-spm
+          #   branch: main
+          #   tests_to_run: tests/.
           - plugin: pynxtools-xps
             branch: main
             tests_to_run: tests/.

src/pynxtools/nexus-version.txt

@@ -1 +1 @@
-v2022.07-1518-g4931f392
+v2022.07-1520-g6e313456

src/pynxtools/nexus/nexus.py

@@ -526,7 +526,10 @@ def get_default_plotable(root, logger):
             nxgroup = nxgroup[default_group_name]
             default_group_name = decode_if_string(nxgroup.attrs.get("default"))
         except KeyError:
-            pass
+            logger.debug(f"""No default group with a name
+                         {default_group_name} for {nxgroup} has been found.""")
+            break
+
     if nxgroup == nxentry:
         nxdata = nxdata_helper(nxentry)
     else:
@@ -833,7 +836,7 @@ def process_nexus_master_file(self, parser):
 
             self.full_visit(self.in_file, self.in_file, "", self.visit_node)
 
-            if self.d_inq_nd is None and self.c_inq_nd is None:
+            if self.d_inq_nd is None and self.c_inq_nd is None and parser is None:
                 get_default_plotable(self.in_file, self.logger)
             # To log the provided concept and concepts founded
             if self.c_inq_nd is not None:

src/pynxtools/testing/nexus_conversion.py

@@ -20,7 +20,7 @@
 import logging
 import os
 from glob import glob
-from typing import List, Literal, Tuple, Dict
+from typing import Dict, List, Literal, Tuple
 
 try:
     from nomad.client import parse

tests/data/nexus/Ref_nexus_test.log

@@ -1170,7 +1170,7 @@ DEBUG - documentation (NXinstrument.nxdl.xml:/POSITIONER):
 DEBUG - 
 DEBUG - documentation (NXpositioner.nxdl.xml:):
 DEBUG - 
-        A generic positioner such as a motor or piezo-electric transducer.  
+         A generic positioner such as a motor or piezo-electric transducer.
 
 DEBUG - ===== ATTRS (//entry/instrument/manipulator@NX_class)
 DEBUG - value: NXpositioner