Apm nomad fixes (#11)

* Removed redundant writing of the NeXus definition and its version * Removed obsolete version writing --------- Co-authored-by: mkuehbach <[email protected]>
FAIRmat-NFDI · May 15, 2024 · 2366b6f · 2366b6f
1 parent 3387238
commit 2366b6f
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Showing 3 changed files with 11 additions and 26 deletions.
diff --git a/pynxtools_apm/config/oasis_cfg.py b/pynxtools_apm/config/oasis_cfg.py
@@ -40,13 +40,9 @@
 
 import datetime as dt
 
-from pynxtools_apm.utils.versioning import NX_APM_ADEF_NAME
-
-
 APM_OASISCONFIG_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]",
     "use": [
-        ("definition", f"{NX_APM_ADEF_NAME}"),
         (
             "start_time",
             f"{dt.datetime.now(dt.timezone.utc).isoformat().replace('+00:00', 'Z')}",

diff --git a/pynxtools_apm/utils/generate_synthetic_data.py b/pynxtools_apm/utils/generate_synthetic_data.py
@@ -20,41 +20,34 @@
 # MK::2023/05/04 the code in this file can currently not be used when
 # developers have an environment which uses ase==3.19.0 and numpy>=1.2x
 
-import hashlib
-
 import datetime
-
+import hashlib
 from typing import List
 
-import numpy as np
-
 import ase
+import numpy as np
+from ase.data import atomic_masses, atomic_numbers, chemical_symbols
 from ase.lattice.cubic import FaceCenteredCubic
-from ase.data import atomic_numbers, atomic_masses, chemical_symbols
-
 from ifes_apt_tc_data_modeling.utils.utils import (
-    create_nuclide_hash,
-    nuclide_hash_to_nuclide_list,
-    nuclide_hash_to_human_readable_name,
     MAX_NUMBER_OF_ATOMS_PER_ION,
     MQ_EPSILON,
+    create_nuclide_hash,
+    nuclide_hash_to_human_readable_name,
+    nuclide_hash_to_nuclide_list,
+)
+
+from pynxtools_apm.utils.load_ranging import (
+    add_unknown_iontype,
 )
 
 # do not use ase directly any longer for NIST isotopes, instead this syntatic equivalent
 # from ifes_apt_tc_data_modeling.utils.nist_isotope_data \
 #     import isotopes
-
 from pynxtools_apm.utils.versioning import (
-    NX_APM_ADEF_NAME,
     NX_APM_EXEC_NAME,
     NX_APM_EXEC_VERSION,
 )
 
-from pynxtools_apm.utils.load_ranging import (
-    add_unknown_iontype,
-)
-
-
 # parameter affecting reconstructed positions and size
 CRYSTAL_ORIENTATION = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
 # MK::add analysis how large aggregate has to be
@@ -313,7 +306,6 @@ def emulate_entry(self, template: dict) -> dict:
         # check if required fields exists and are valid
         # print("Parsing entry...")
         trg = f"/ENTRY[entry{self.entry_id}]/"
-        template[f"{trg}definition"] = NX_APM_ADEF_NAME
         template[f"{trg}programID[program1]/program"] = NX_APM_EXEC_NAME
         template[f"{trg}programID[program1]/program/@version"] = NX_APM_EXEC_VERSION
         template[f"{trg}start_time"] = datetime.datetime.now().astimezone().isoformat()

diff --git a/pynxtools_apm/utils/versioning.py b/pynxtools_apm/utils/versioning.py
@@ -20,10 +20,6 @@
 from pynxtools_apm.utils.get_gitrepo_commit import get_repo_last_commit
 
 
-NX_APM_ADEF_NAME = "NXapm"
-NX_APM_EXEC_NAME = "pynxtools-apm/reader.py"
-
-
 def get_apm_exec_version() -> str:
     tag = get_repo_last_commit()
     if tag is not None:
@@ -34,6 +30,7 @@ def get_apm_exec_version() -> str:
         )
 
 
+NX_APM_EXEC_NAME = "pynxtools-apm/reader.py"
 NX_APM_EXEC_VERSION = get_apm_exec_version()
 
 # numerics