Merge pull request #9 from FAIRmat-NFDI/runthrough

Fixes detected while preparing the run-through

pynxtools_apm/concepts/mapping_functors.py

@@ -326,6 +326,8 @@ def add_specific_metadata(
                 if len(entry) == 2:
                     if not all(isinstance(elem, str) for elem in entry):
                         continue
+                    if f"{prefix_src}{entry[1]}" not in orgmeta:
+                        continue
                     if orgmeta[f"{prefix_src}{entry[1]}"] == "":
                         continue
                     trg = variadic_path_to_specific_path(

pynxtools_apm/reader.py

@@ -114,7 +114,7 @@ def read(
 
             if len(case.eln) == 1:
                 print("Parse (meta)data coming from an ELN...")
-                nx_apm_eln = NxApmNomadOasisElnSchemaParser(case.eln[0], entry_id, True)
+                nx_apm_eln = NxApmNomadOasisElnSchemaParser(case.eln[0], entry_id)
                 nx_apm_eln.parse(template)
             else:
                 print("No input file defined for eln data !")

pynxtools_apm/utils/load_ranging.py

@@ -233,7 +233,7 @@ def extract_data_from_rng_file(file_path: str, template: dict, entry_id: int) ->
 def extract_data_from_rrng_file(file_path: str, template: dict, entry_id) -> dict:
     """Add those required information which an RRNG file has."""
     print(f"Extracting data from RRNG file: {file_path}")
-    rangefile = ReadRrngFileFormat(file_path)
+    rangefile = ReadRrngFileFormat(file_path, unique=False)
     if len(rangefile.rrng["molecular_ions"]) > np.iinfo(np.uint8).max + 1:
         print(WARNING_TOO_MANY_DEFINITIONS)
 

pynxtools_apm/utils/oasis_config_reader.py

@@ -19,6 +19,7 @@
 
 import flatdict as fd
 import yaml
+import pathlib
 
 from pynxtools_apm.concepts.mapping_functors import add_specific_metadata
 from pynxtools_apm.config.oasis_cfg import (
@@ -36,8 +37,8 @@ def __init__(self, file_path: str, entry_id: int, verbose: bool = False):
             f"Extracting data from deployment-specific configuration file: {file_path}"
         )
         if (
-            file_path.rsplit("/", 1)[-1].endswith(".oasis.specific.yaml")
-            or file_path.endswith(".oasis.specific.yml")
+            pathlib.Path(file_path).name.endswith(".oasis.specific.yaml")
+            or pathlib.Path(file_path).name.endswith(".oasis.specific.yml")
         ) and entry_id > 0:
             self.entry_id = entry_id
             self.file_path = file_path

pynxtools_apm/utils/oasis_eln_reader.py

@@ -19,6 +19,7 @@
 
 import flatdict as fd
 import yaml
+import pathlib
 
 from ase.data import chemical_symbols
 from pynxtools_apm.config.eln_cfg import (
@@ -59,8 +60,8 @@ class NxApmNomadOasisElnSchemaParser:
     def __init__(self, file_path: str, entry_id: int, verbose: bool = False):
         print(f"Extracting data from ELN file: {file_path}")
         if (
-            file_path.rsplit("/", 1)[-1].startswith("eln_data")
-            or file_path.startswith("eln_data")
+            pathlib.Path(file_path).name.endswith("eln_data.yaml")
+            or pathlib.Path(file_path).name.endswith("eln_data.yml")
         ) and entry_id > 0:
             self.entry_id = entry_id
             self.file_path = file_path

pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
 ]
 dependencies = [
     "pynxtools>=0.2.1",
-    "ifes_apt_tc_data_modeling>=0.2.1",
+    "ifes_apt_tc_data_modeling>=0.2.2",
 ]
 
 [project.urls]