Fixes detected while preparing the run-through

FAIRmat-NFDI · Apr 24, 2024 · b19df3c · b19df3c
1 parent 09562cb
commit b19df3c
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Showing 4 changed files with 6 additions and 4 deletions.
diff --git a/pynxtools_apm/concepts/mapping_functors.py b/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(

diff --git a/pynxtools_apm/reader.py b/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 !")

diff --git a/pynxtools_apm/utils/oasis_config_reader.py b/pynxtools_apm/utils/oasis_config_reader.py
@@ -37,7 +37,7 @@ def __init__(self, file_path: str, entry_id: int, verbose: bool = False):
         )
         if (
             file_path.rsplit("/", 1)[-1].endswith(".oasis.specific.yaml")
-            or file_path.endswith(".oasis.specific.yml")
+            or file_path.rsplit("/", 1)[-1].endswith(".oasis.specific.yml")
         ) and entry_id > 0:
             self.entry_id = entry_id
             self.file_path = file_path

diff --git a/pynxtools_apm/utils/oasis_eln_reader.py b/pynxtools_apm/utils/oasis_eln_reader.py
@@ -59,8 +59,8 @@ 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")
+            file_path.rsplit("/", 1)[-1].endswith("eln_data.yaml")
+            or file_path.rsplit("/", 1)[-1].endswith("eln_data.yml")
         ) and entry_id > 0:
             self.entry_id = entry_id
             self.file_path = file_path