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Hardens Dataverse file ID parsing for nested PIDs

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Handles Dataverse file-level persistent identifiers that themselves contain URI schemes and slashes, ensuring correct resolution of files with independent persistent IDs. Enhances parsing logic to support more complex Dataverse path structures and improves robustness when extracting dataset and file identifiers.
This commit is contained in:
davelopez
2026-01-20 12:55:36 +01:00
parent 15319d1006
commit e201d590d2
1 changed files with 38 additions and 3 deletions
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lib/galaxy/files/sources/dataverse.py
+38 -3
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@@ -106,6 +106,7 @@ class DataverseRDMFilesSource(RDMFilesSource):
- doi:10.70122/FK2/AVNCLL (persistent ID)
- doi:10.70122/FK2/DIG2DG/AVNCLL (persistent ID)
- doi:10.70122/FK2/DIG2DG/id:12345 (database ID)
- doi:10.5072/FK2/doi:10.70122/AVNCLL (persistent ID)
- perma:BSC/3ST00L/id:9056 (database ID)
"""
if not source_path.startswith("/"):
@@ -126,8 +127,7 @@ class DataverseRDMFilesSource(RDMFilesSource):
f"Invalid source path: '{source_path}'. Expected format: '/<dataset_id>/<file_identifier>'."
)
file_id_part = parts[-1]
dataset_id = "/".join(parts[:-1])
dataset_id, file_id_part = self._split_dataset_and_file_pid(parts)
# The file identifier can be either:
# - A persistent ID suffix (e.g., 'AVNCLL' -> full ID is 'doi:10.70122/FK2/DIG2DG/AVNCLL')
@@ -135,11 +135,46 @@ class DataverseRDMFilesSource(RDMFilesSource):
if file_id_part.startswith("id:"):
# Database ID format - keep the 'id:' prefix as the file identifier
file_id = file_id_part
elif re.match(r"^[a-zA-Z][a-zA-Z0-9+.-]*:.*", file_id_part):
# Full persistent identifier (e.g. doi:, hdl:, ark:, or custom PID providers).
# Files in Dataverse may have their own independent persistent IDs that are
# not hierarchically related to the dataset persistent ID.
file_id = file_id_part
else:
# Persistent ID format - construct full persistent ID
# Dataset-scoped persistent ID suffix - construct full persistent ID
file_id = f"{dataset_id}/{file_id_part}"
return ContainerAndFileIdentifier(container_id=dataset_id, file_identifier=file_id)
@staticmethod
def _split_dataset_and_file_pid(parts: list[str]) -> tuple[str, str]:
"""
Split a Dataverse source path into dataset ID and file identifier parts.
Dataverse file-level persistent IDs may themselves contain slashes and are not
necessarily hierarchically related to the dataset persistent ID. For example:
/doi:10.57745/I8EUTL/doi:10.57745/L7SOAJ
In this case:
dataset_id = doi:10.57745/I8EUTL
file_id = doi:10.57745/L7SOAJ
This helper detects such cases by recognizing URI-scheme prefixes in path segments
and grouping them accordingly.
"""
# Default: last segment is the file identifier
file_id_part = parts[-1]
dataset_id = "/".join(parts[:-1])
# Heuristic: if the penultimate segment starts a URI scheme (e.g. doi:, hdl:, ark:),
# then the file persistent ID spans the last two segments.
pid_scheme_re = re.compile(r"^[a-zA-Z][a-zA-Z0-9+.-]*:")
if len(parts) >= 3 and pid_scheme_re.match(parts[-2]):
file_id_part = f"{parts[-2]}/{parts[-1]}"
dataset_id = "/".join(parts[:-2])
return dataset_id, file_id_part
def get_container_id_from_path(self, source_path: str) -> str:
return self.parse_path(source_path, container_id_only=True).container_id