cleaning up the paths

ingestion_tools/scripts/importers/alignment.py

@@ -50,10 +50,10 @@ class AlignmentImporter(BaseFileImporter):
 
     type_key = "alignment"
     plural_key = "alignments"
-
     finder_factory = MultiSourceFileFinder
     has_metadata = True
     dir_path = "{dataset_name}/{run_name}/Alignments"
+    metadata_path = "{dataset_name}/{run_name}/Alignments/{alignment_id}-alignment_metadata.json"
 
     def __init__(self, *args, file_paths: dict[str, str], **kwargs):
         super().__init__(*args, **kwargs)
@@ -69,7 +69,7 @@ def __init__(self, *args, file_paths: dict[str, str], **kwargs):
 
     def import_metadata(self) -> None:
         if not self.is_import_allowed():
-            print(f"Skipping import of {self.name}")
+            print(f"Skipping import of {self.name} metadata")
             return
         metadata_path = self.get_metadata_path()
         try:
@@ -103,9 +103,6 @@ def get_dest_filename(self, path: str) -> str | None:
         output_dir = self.get_output_path()
         return f"{output_dir}{os.path.basename(path)}"
 
-    def get_metadata_path(self) -> str:
-        return self.get_output_path() + "alignment_metadata.json"
-
     def get_extra_metadata(self) -> dict:
         extra_metadata = {
             "per_section_alignment_parameters": self.converter.get_per_section_alignment_parameters(),
@@ -150,11 +147,6 @@ def get_tiltseries_path(self) -> str | None:
             return ts.get_metadata_path()
         return None
 
-    def get_tiltseries_path(self) -> str | None:
-        for ts in TiltSeriesImporter.finder(self.config, **self.parents):
-            return ts.get_metadata_path()
-        return None
-
     @classmethod
     def get_default_config(cls) -> list[dict]:
         return [{"metadata": cls.get_default_metadata(), "sources": [{"literal": {"value": ["default"]}}]}]

ingestion_tools/scripts/importers/annotation.py

@@ -160,7 +160,7 @@ def get_output_path(self):
 
     def import_metadata(self):
         if not self.is_import_allowed():
-            print(f"Skipping import of {self.name}")
+            print(f"Skipping import of {self.name} metadata")
             return
         dest_prefix = self.get_output_path()
         filename = f"{dest_prefix}.json"

ingestion_tools/scripts/importers/base_importer.py

@@ -64,6 +64,8 @@ def get_glob_vars(self) -> dict[str, Any]:
         glob_vars = {}
         glob_vars[f"{self.type_key}_path"] = self.path
         glob_vars[f"{self.type_key}_name"] = self.name
+        if hasattr(self, "identifier") and self.identifier:
+            glob_vars[f"{self.type_key}_id"] = self.identifier
         with contextlib.suppress(ValueError, TypeError):
             glob_vars[f"int_{self.type_key}_name"] = int(self.name)
 

ingestion_tools/scripts/importers/dataset.py

@@ -17,7 +17,7 @@ def import_item(self) -> None:
 
     def import_metadata(self) -> None:
         if not self.is_import_allowed():
-            print(f"Skipping import of {self.name}")
+            print(f"Skipping import of {self.name} metadata")
             return
         meta = DatasetMetadata(self.config.fs, self.get_deposition().name, self.get_base_metadata())
         extra_data = self.load_extra_metadata()

ingestion_tools/scripts/importers/deposition.py

@@ -19,7 +19,7 @@ def import_item(self) -> None:
 
     def import_metadata(self) -> None:
         if not self.is_import_allowed():
-            print(f"Skipping import of {self.name}")
+            print(f"Skipping import of {self.name} metadata")
             return
         meta = DepositionMetadata(self.config.fs, self.name, self.get_base_metadata())
         extra_data = self.load_extra_metadata()

ingestion_tools/scripts/importers/run.py

@@ -29,7 +29,7 @@ def import_item(self) -> None:
 
     def import_metadata(self) -> None:
         if not self.is_import_allowed():
-            print(f"Skipping import of {self.name}")
+            print(f"Skipping import of {self.name} metadata")
             return
         dest_run_metadata = self.get_metadata_path()
         print(dest_run_metadata)

ingestion_tools/scripts/importers/tiltseries.py

@@ -42,8 +42,8 @@ class TiltSeriesImporter(VolumeImporter):
     plural_key = "tiltseries"
     finder_factory = DefaultImporterFactory
     has_metadata = True
-    dir_path = "{dataset_name}/{run_name}/TiltSeries"
-    metadata_path = "{dataset_name}/{run_name}/TiltSeries/{{identifier}}-tiltseries_metadata.json"
+    dir_path = "{dataset_name}/{run_name}/TiltSeries/"
+    metadata_path = os.path.join(dir_path, "{tiltseries_id}-tiltseries_metadata.json")
 
     def __init__(
         self,
@@ -55,13 +55,15 @@ def __init__(
         parents: dict[str, Any],
     ):
         super().__init__(
-            config=config, metadata=metadata, name=name, path=path, parents=parents, allow_imports=allow_imports,
+            config=config,
+            metadata=metadata,
+            name=name,
+            path=path,
+            parents=parents,
+            allow_imports=allow_imports,
         )
         self.identifier = TiltSeriesIdentifierHelper.get_identifier(config, self.get_base_metadata(), self.parents)
 
-    def get_metadata_path(self) -> str:
-        return super().get_metadata_path().format(identifier=self.identifier)
-
     def import_item(self) -> None:
         if not self.is_import_allowed():
             print(f"Skipping import of {self.name}")
@@ -83,7 +85,7 @@ def get_frames_count(self) -> int:
 
     def import_metadata(self) -> None:
         if not self.is_import_allowed():
-            print(f"Skipping import of {self.name}")
+            print(f"Skipping import of {self.name} metadata")
             return
         dest_ts_metadata = self.get_metadata_path()
         merge_data = self.load_extra_metadata()

ingestion_tools/scripts/importers/tomogram.py

@@ -48,8 +48,8 @@ class TomogramImporter(VolumeImporter):
     finder_factory = DefaultImporterFactory
     cached_find_results: dict[str, Any] = {}
     has_metadata = True
-    dir_path = "{dataset_name}/{run_name}/Reconstructions/VoxelSpacing{voxel_spacing_name}/Tomograms"
-    metadata_path = "{dataset_name}/{run_name}/Reconstructions/VoxelSpacing{voxel_spacing_name}/Tomograms/{{identifier}}-tomogram_metadata.json"
+    dir_path = "{dataset_name}/{run_name}/Reconstructions/VoxelSpacing{voxel_spacing_name}/Tomograms/"
+    metadata_path = os.path.join(dir_path, "{tomogram_id}-tomogram_metadata.json")
 
     def __init__(
         self,
@@ -61,7 +61,12 @@ def __init__(
         parents: dict[str, Any],
     ):
         super().__init__(
-            config=config, metadata=metadata, name=name, path=path, parents=parents, allow_imports=allow_imports,
+            config=config,
+            metadata=metadata,
+            name=name,
+            path=path,
+            parents=parents,
+            allow_imports=allow_imports,
         )
         self.alignment_metadata_path = self.get_alignment_metadata_path()
         self.identifier = TomogramIdentifierHelper.get_identifier(
@@ -84,12 +89,9 @@ def import_item(self) -> None:
     def get_identifier(self) -> int:
         return self.identifier
 
-    def get_metadata_path(self) -> str:
-        return super().get_metadata_path().format(identifier=self.identifier)
-
     def import_metadata(self) -> None:
         if not self.is_import_allowed():
-            print(f"Skipping import of {self.name}")
+            print(f"Skipping import of {self.name} metadata")
             return
         dest_tomo_metadata = self.get_metadata_path()
         merge_data = self.load_extra_metadata()